[galaxy-commits] commit/galaxy-central: greg: Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed.

21 Mar 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/4dd1e50e78ef/
changeset:   4dd1e50e78ef
user:        greg
date:        2012-03-21 21:41:45
summary:     Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed.
affected #:  78 files

diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_antigenic_out.tabular

--- a/test-data/emboss_antigenic_out.tabular
+++ /dev/null
@@ -1,23 +0,0 @@
-SeqName	Start	End	Score	Strand	Max_score_pos
-Sequence	196	225	1.340	+	221
-Sequence	253	283	1.263	+	266
-Sequence	27	45	1.241	+	32
-Sequence	60	72	1.236	+	66
-Sequence	357	368	1.214	+	360
-Sequence	130	159	1.191	+	148
-Sequence	83	93	1.186	+	87
-Sequence	165	175	1.147	+	173
-Sequence	6	22	1.147	+	20
-Sequence	293	301	1.147	+	299
-Sequence	324	343	1.147	+	330
-Sequence	473	481	1.142	+	479
-Sequence	540	551	1.119	+	545
-Sequence	501	510	1.114	+	504
-Sequence	409	415	1.097	+	412
-Sequence	48	56	1.097	+	51
-Sequence	553	558	1.092	+	558
-Sequence	106	112	1.087	+	110
-Sequence	488	494	1.075	+	490
-Sequence	423	429	1.075	+	426
-Sequence	118	123	1.070	+	118
-Sequence	239	247	1.042	+	245


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_backtranseq_out.fasta
--- a/test-data/emboss_backtranseq_out.fasta
+++ /dev/null
@@ -1,30 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-GGCACCACCTGCGGCGCCACCGGCTGCTGCACCGCCGCCGCCGCCACCGCCTGCTGCACC
-ACCTGCACCACCACCACCGGCACCTGCTGCTGCACCGCCTGCGCCTGCGCCGGCGCCTGC
-TGCGCCTGCGCCGGCACCACCACCACCTGCTGCACCGCCGCCACCGGCGGCTGCACCACC
-ACCGCCTGCGCCTGCTGCGGCGCCTGCACCGCCGGCGCCGCCGCCACCACCTGCACCACC
-GGCACCGGCTGCGCCGCCGGCTGCGCCTGCACCGCCGCCACCACCGGCGCCGCCGCCGGC
-TGCGGCGGCACCACCGGCGGCTGCTGCACCGCCGGCGCCGGCACCGGCACCACCGCCTGC
-TGCGGCGGCACCACCACCGGCACCGCCACCGCCGGCTGCACCGGCGCCGGCTGCGGCTGC
-GGCACCTGCACCTGCACCACCGGCTGCTGCTGCACCGGCGCCACCTGCGCCGCCGCCGGC
-GGCACCACCTGCGCCACCACCACCACCTGCACCTGCACCGCCTGCACCACCACCGGCGGC
-GCCGCCGGCGCCTGCGGCACCACCGGCACCGGCGGCGCCGCCGGCGCCGCCACCGCCTGC
-GCCGCCTGCGCCGCCGGCACCGCCTGCGGCGCCGGCACCTGCACCTGCACCTGCTGCTGC
-TGCTGCTGCACCGGCGGCACCACCACCGGCTGCACCGGCGCCACCACCGCCTGCACCGGC
-GGCGCCACCGCCTGCGCCGGCACCACCGGCACCGCCGCCACCGCCTGCTGCTGCACCACC
-TGCGGCTGCGCCGCCTGCGCCTGCTGCGGCTGCGGCACCGCCGCCTGCACCGCCACCTGC
-ACCGCCACCGCCACCGGCGCCGCCACCACCGCCACCACCACCACCTGCTGCTGCACCACC
-ACCGCCACCACCGCCACCGCCACCGGCACCGCCGGCACCGCCGGCGGCACCACCTGCGGC
-ACCTGCACCACCACCGCCGCCACCTGCACCACCTGCTGCACCACCACCGCCGGCTGCGCC
-GCCGGCACCTGCACCACCACCACCGCCTGCACCGGCACCACCACCACCTGCGGCGCCTGC
-TGCACCTGCGCCGCCACCGGCACCACCTGCGCCACCGGCACCACCTGCACCACCGCCGGC
-GGCACCACCGGCACCACCACCACCGGCGGCGCCACCGCCGCCACCGCCACCGGCTGCGGC
-GGCACCTGCGCCGGCACCACCACCGCCGCCACCTGCACCACCTGCGGCACCACCGGCACC
-ACCACCTGCACCACCTGCACCACCGCCGCCGCCGCCACCGCCACCACCACCGCCACCACC
-TGCGCCACCGGCGGCACCACCACCGCCGCCACCACCACCACCACCGGCGGCACCACCACC
-GGCACCGCCTGCACCACCGGCACCACCTGCGCCGGCGGCGGCGGCTGCTGCGCCGGCACC
-ACCTGCGCCACCACCGCCACCACCACCGCCTGCACCTGCACCGGCACCACCACCGGCACC
-GCCACCGCCTGCGCCGGCTGCGCCGGCACCACCTGCACCACCACCACCGCCACCACCACC
-ACCACCGCCGGCACCGCCACCGGCGCCACCACCACCACCGCCGCCACCACCACCGCCGCC
-GCCGCCTGCGCCGCCACCACCTGCACCGCCGCCACCGGCGGCACCTGCGCCGCCGCCGCC
-GCC


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_banana_out.txt
--- a/test-data/emboss_banana_out.txt
+++ /dev/null
@@ -1,562 +0,0 @@
-Base   Bend      Curve
-g       0.0      0.0
-t      10.8      0.0
-t      18.5      0.0
-c      26.9      0.0
-g      22.1      0.0
-a      19.5      0.0
-t      20.7      0.0
-g      26.2      0.0
-c      25.2      0.0
-c      12.5      0.0
-t       6.8      0.0
-a       3.4      0.0
-a       0.0      0.0
-a       1.3      0.0
-a       5.9      0.0
-t      10.6      0.0
-a      14.9      0.0
-c      17.7      0.0
-c      17.3      0.0
-t      13.3      0.0
-t      10.2     23.2
-c      13.9     22.5
-t       8.8     21.7
-t       0.0     20.6
-t       5.7     19.2
-t      13.9     17.7
-g      17.3     16.5
-t      15.1     15.5
-c      16.1     14.7
-c      18.7     13.9
-c      12.5     13.2
-t       9.7     12.5
-a      14.5     11.8
-c      19.1     11.1
-a      19.1     10.6
-c      15.3     10.0
-a      12.2      9.2
-g      14.3      7.9
-a      17.7      6.4
-c      17.7      5.0
-c      19.5      3.5
-a      19.1      2.9
-c      15.3      3.9
-a      16.3      5.5
-g      15.5      6.8
-t       6.3      7.8
-t       0.0      8.5
-t       5.0      9.3
-t      11.0     10.0
-c      15.1     10.8
-c      12.5     11.6
-t       6.8     12.5
-a       4.5     13.4
-a      12.4     14.3
-t      19.7     15.1
-g      25.2     15.7
-g      28.5     16.2
-c      20.7     16.6
-t       8.8     17.0
-t       3.4     17.5
-t       9.3     18.1
-a      14.5     18.5
-c      19.1     18.6
-a      19.5     18.5
-c      16.5     18.3
-c      21.1     18.0
-g      22.3     17.4
-a      18.3     16.3
-c      13.2     15.1
-t       7.2     13.8
-a       9.0     12.6
-g      10.2     11.4
-a       5.0     10.9
-a       1.3     11.0
-a       2.4     11.4
-t       6.1     11.9
-t      10.2     12.3
-c      13.9     12.5
-t      13.9     12.4
-t      13.9     12.4
-g      19.1     12.6
-t      20.5     12.9
-g      19.7     13.2
-c      15.3     13.1
-a      13.9     12.7
-a      20.7     12.2
-g      22.1     11.8
-c      20.5     11.5
-a      20.1     11.3
-c      13.2     10.9
-t       6.8     10.2
-a       4.5      9.6
-a       2.4      9.9
-t       6.7     10.9
-t      14.3     12.1
-g      13.7     13.2
-a       5.0     13.8
-a       8.8     13.6
-a      20.7     12.9
-g      24.5     12.1
-c      19.9     11.3
-g      16.5     10.3
-g      14.9      9.0
-t      11.4      7.5
-t      14.3      6.2
-g      25.2      5.2
-g      32.5      4.4
-c      25.2      4.0
-c      12.5      3.8
-t       7.2      3.4
-a       9.0      2.8
-g      14.3      2.4
-a      18.3      2.5
-g      20.1      2.8
-t      19.1      3.1
-g      14.5      3.2
-t       9.3      3.1
-t       9.3      2.6
-a      14.9      2.5
-c      16.5      2.7
-c      15.3      2.7
-g      16.5      2.6
-g      14.9      2.8
-t       6.3      2.9
-t       5.7      2.8
-t      13.9      2.3
-g      14.5      1.6
-t      10.6      0.6
-a       9.2      0.7
-t       8.2      1.8
-a      16.1      2.7
-g      24.5      3.7
-c      19.1      4.6
-t      15.7      5.6
-g      17.7      6.4
-a      21.1      7.1
-g      24.5      7.7
-c      24.5      8.1
-g      24.5      8.2
-c      21.1      8.0
-g      17.7      7.8
-t      14.3      7.7
-c      14.3      7.7
-t      14.3      7.9
-c      13.9      8.4
-t      13.9      9.1
-t      15.3     10.2
-g      26.2     11.3
-c      26.2     12.2
-c      18.7     12.7
-c      15.7     12.9
-t      15.7     12.9
-g      17.5     12.9
-a      17.3     13.0
-t      17.5     13.2
-c      14.3     13.3
-a       5.7     13.3
-a       8.8     13.2
-a      17.3     13.0
-g      17.7     12.9
-g      14.9     12.7
-t      10.8     12.6
-t      13.7     12.6
-c      19.7     12.6
-a      12.4     12.7
-t       1.3     12.9
-t       0.0     13.1
-t       5.0     13.1
-t      10.2     12.9
-c      14.3     12.6
-t      14.3     12.3
-c       9.0     11.9
-t       9.7     11.6
-a      15.5     11.2
-c      17.9     10.6
-t       8.8      9.9
-t       5.7      9.0
-t      14.3      8.1
-g      15.1      7.4
-g      11.0      6.8
-a      13.3      6.3
-a      13.9      5.9
-g      14.3      5.6
-a      17.7      5.3
-c      17.7      5.1
-g      14.9      5.0
-t      11.4      5.1
-t      13.9      5.2
-g      19.1      5.2
-t      19.5      5.0
-g      15.1      4.9
-g      11.0      4.9
-a      13.3      4.9
-a      13.9      4.9
-g      10.2      5.1
-a       6.1      5.5
-a       5.9      6.3
-t      10.6      7.0
-a      14.5      7.8
-c      13.9      8.4
-a      11.4      8.6
-a      14.5      8.7
-c      13.9      8.8
-a      13.9      8.9
-a      17.9      9.0
-g      15.5      9.0
-t      12.0      8.8
-a      14.9      8.9
-c      22.3      9.1
-g      22.3      9.3
-a      18.3      9.6
-g      18.3      9.9
-t      14.3     10.1
-c      14.3     10.2
-t      14.3     10.5
-c      14.3     11.2
-t      15.1     12.3
-c      16.1     13.4
-c      19.7     14.2
-c      19.7     14.9
-c      19.7     15.1
-c      18.7     15.0
-c      15.7     14.8
-t      15.7     14.4
-g      17.7     14.1
-g      14.9     13.5
-t       6.3     12.9
-t       5.7     12.4
-t      15.3     11.9
-g      22.1     11.5
-c      19.1     11.1
-t      15.7     10.4
-g      17.5      9.4
-a      10.1      8.3
-t       4.5      7.2
-t       9.3      6.2
-a      15.5      5.2
-c      16.3      4.2
-t      15.7      3.2
-g      15.1      2.5
-g      14.9      2.3
-a      13.3      2.9
-t      10.6      3.7
-a      14.5      4.5
-c      15.3      5.3
-a      16.3      6.1
-g      15.5      7.0
-t      11.4      7.5
-t      13.9      7.7
-g      14.5      7.9
-t       9.3      8.3
-a       4.5      8.6
-a       5.9      9.1
-t      10.6      9.7
-a      14.9     10.4
-c      18.7     11.1
-c      18.7     11.7
-c      17.3     12.1
-t      13.3     12.6
-t      18.5     12.9
-c      25.7     12.9
-g      22.1     12.6
-c      15.3     12.2
-a      11.4     11.7
-a      14.5     11.0
-c      19.1     10.3
-a      19.5      9.7
-c      16.5      9.0
-c      19.9      8.1
-g      24.5      7.2
-c      21.1      6.4
-g      14.9      5.5
-t       9.3      4.5
-a       9.3      3.5
-a      15.5      2.5
-c      13.2      1.7
-t       8.2      1.0
-a      13.3      0.8
-t      14.1      1.6
-c       9.0      2.9
-t       8.2      4.5
-a       9.2      6.0
-t       9.2      7.4
-a      15.6      8.8
-t      19.7     10.3
-g      13.7     11.7
-a       6.1     12.9
-a       2.4     14.1
-t       4.5     15.4
-t       7.8     16.6
-a       5.9     17.4
-t       1.3     17.8
-t       0.0     18.0
-t       5.0     18.0
-t      11.0     18.0
-c      16.1     17.9
-c      18.7     17.9
-c      17.3     17.6
-t       8.8     17.4
-t       3.4     17.4
-t       7.8     17.4
-a       5.9     17.5
-t       4.5     17.6
-t       7.8     17.6
-a       9.2     17.8
-t       9.2     18.3
-a      15.6     18.7
-t      19.3     18.8
-g      14.5     18.5
-t       9.7     17.9
-a      13.2     17.3
-g      15.5     16.7
-t       9.7     16.4
-a      12.5     16.0
-g      17.7     15.7
-g      14.9     15.6
-t      10.8     15.7
-t      18.5     15.7
-c      22.3     15.8
-g      17.7     15.6
-t      14.3     15.3
-c      13.9     15.2
-t       8.8     15.3
-t       3.4     15.6
-t       6.4     15.9
-a       4.5     16.4
-a      10.1     17.0
-t      14.1     18.0
-c      13.9     18.9
-t      13.3     19.6
-t      11.0     20.1
-c      15.1     20.5
-c      17.3     20.8
-t       8.8     21.1
-t       3.4     21.3
-t       6.8     21.4
-a      16.1     20.9
-g      22.1     19.9
-c      15.3     18.9
-a      13.9     18.1
-a      17.9     17.4
-g      18.3     16.9
-t      14.3     16.5
-c      13.9     16.5
-t       8.8     16.6
-t       0.0     16.6
-t       3.4     16.6
-t       9.3     16.7
-a      15.5     16.6
-c      16.3     16.4
-t      15.3     16.1
-g      14.5     15.8
-t       6.3     15.5
-t       0.0     15.3
-t       5.0     15.1
-t      18.5     15.2
-c      26.9     15.3
-g      22.3     15.6
-a      17.7     16.2
-c      17.7     16.7
-c      17.7     16.9
-t      17.7     17.1
-c      14.3     17.0
-a       6.7     16.9
-a      12.4     16.5
-t      19.3     16.1
-g      14.5     16.1
-t      10.8     16.2
-t      13.7     16.1
-c      19.7     16.0
-a      21.7     15.7
-t      19.3     15.3
-g      14.5     14.7
-t      10.8     14.3
-t      10.2     14.0
-c      13.9     13.8
-t      11.7     13.5
-t       6.8     12.9
-a      12.5     12.3
-g      17.7     11.7
-g      14.9     11.2
-t      11.4     10.6
-t      13.9     10.3
-g      14.5     10.2
-t       6.3     10.2
-t       0.0     10.2
-t       5.7     10.4
-t      14.3     11.0
-g      15.1     11.5
-g      14.9     11.9
-a      13.3     12.0
-t       7.8     12.0
-a       4.5     12.0
-a       5.9     12.0
-t       9.2     12.1
-a      15.6     12.2
-t      20.7     11.8
-g      22.1     11.3
-c      19.9     10.5
-g      16.5      9.8
-g      17.7      8.9
-t      17.7      7.9
-c      15.7      6.9
-a      16.3      5.8
-g      15.5      5.0
-t       6.3      4.5
-t       3.4      4.5
-t       6.4      5.1
-a       4.5      6.2
-a      10.1      7.8
-t      14.1      9.7
-c      13.9     11.7
-t      13.3     13.4
-t      18.5     14.9
-c      22.3     15.9
-g      14.9     16.5
-t      11.4     16.9
-t      13.9     17.0
-g      14.5     16.8
-t       6.3     16.2
-t       5.0     15.3
-t      10.2     14.0
-c      13.9     12.6
-t      13.3     11.1
-t      10.2      9.7
-c      13.9      8.5
-t      11.7      7.2
-t       6.4      6.1
-a       3.4      5.5
-a       0.0      5.7
-a       1.3      6.7
-a       5.9      7.9
-t       9.2      9.1
-a       5.9      9.8
-t       1.3     10.1
-t       3.4     10.3
-t       7.8     10.7
-a       5.9     11.0
-t       6.1     11.3
-t      13.7     11.4
-c      19.7     11.2
-a      21.7     10.8
-t      19.7     10.4
-g      17.7     10.4
-g      14.9     10.8
-t       6.3     11.3
-t       3.4     11.8
-t       6.4     12.2
-a       4.5     12.6
-a       2.4     12.9
-t       1.3     13.2
-t       0.0     13.3
-t       0.0     13.2
-t       5.7     12.8
-t      14.3     12.3
-g      17.7     12.1
-g      14.9     12.0
-t       6.3     12.0
-t       5.7     12.1
-t      13.9     12.2
-g      14.5     12.3
-t      12.0     12.4
-a      15.5     12.5
-c      17.9     12.9
-t      13.9     13.2
-t      13.9     12.8
-g      14.5     11.9
-t      10.8     10.9
-t      13.7     10.1
-c      15.7      9.7
-a      15.7      9.7
-g      18.7      9.8
-g      19.7      9.7
-g      26.2      9.2
-g      32.5      8.8
-c      25.2      8.6
-c      15.7      8.5
-a      16.3      8.4
-g      15.5      8.4
-t      10.8      8.4
-t      13.7      8.6
-c      19.7      8.8
-a      12.4      8.7
-t       4.5      8.5
-t       7.8      8.1
-a       5.9      7.9
-t       1.3      7.8
-t       3.4      7.8
-t       9.3      7.9
-a      15.5      8.2
-c      18.3      8.5
-t      14.3      8.8
-c      12.2      9.1
-t      15.3      9.2
-g      14.5      9.0
-t       6.3      8.4
-t       5.7      7.5
-t      13.9      6.4
-g      14.5      5.5
-t      10.6      4.9
-a       9.2      4.5
-t      10.6      4.1
-a      14.5      3.8
-c      15.3      3.7
-a      19.1      3.8
-g      22.1      3.9
-c      16.7      4.2
-a      16.3      4.8
-g      15.5      5.6
-t      10.8      6.6
-t      10.2      7.6
-c      13.9      8.6
-t       8.8      9.7
-t       0.0     10.8
-t       3.4     11.8
-t       7.8     12.6
-a       5.9     12.8
-t       1.3     12.4
-t       0.0     11.8
-t       0.0     11.2
-t       3.4     10.6
-t       6.8      9.8
-a      13.2      9.0
-g      15.5      8.2
-t      10.6      7.8
-a      15.6      7.8
-t      19.7      8.2
-g      17.5      8.8
-a      10.1      9.2
-t       1.3      9.3
-t       0.0      9.0
-t       3.4      8.5
-t       6.4      7.9
-a       4.5      7.1
-a       2.4      6.1
-t       1.3      5.0
-t       3.4      3.8
-t       6.4      2.6
-a       3.4      2.4
-a       0.0     90.8
-a       6.3      0.0
-a      14.5      0.0
-c      13.9      0.0
-a       6.7      0.0
-a       2.4      0.0
-t       6.1      0.0
-t      10.2      0.0
-c       9.0      0.0
-t       6.8      0.0
-a       4.5      0.0
-a      12.4      0.0
-t      19.7      0.0
-g      17.7      0.0
-g      17.7      0.0
-t      17.7      0.0
-c      14.3      0.0
-a       5.7      0.0
-a       0.0      0.0
-a       0.0      0.0
-a       0.0      0.0
-a       0.0      0.0


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_biosed_out.fasta
--- a/test-data/emboss_biosed_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-GTTCGAGTCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAAGTGCTT
-TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC
-CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG
-AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG
-GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATAGTAATTATTTTCCCTT
-TATTATAGTTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC
-CTCAAGTTTCAGTTTCTTAGGTTGTTTTGGATAATAGTCGGTCAGTTTAATCTTCGTTGT
-TTCTTCTTAAAATATTTATTCAGTGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT
-TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTAGTATTTTAATTTAA
-AACAATTCTAAGTGTCAAAAA


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_btwisted_out.btwisted
--- a/test-data/emboss_btwisted_out.btwisted
+++ /dev/null
@@ -1,7 +0,0 @@
-# Output from BTWISTED
-# Twisting calculated from 1 to 561 of Sequence
-Total twist (degrees): 19085.5
-Total turns : 53.02
-Average bases per turn: 10.58
-Total stacking energy : -4107.68
-Average stacking energy per dinucleotide: -7.34


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cai_out.cai
--- a/test-data/emboss_cai_out.cai
+++ /dev/null
@@ -1,1 +0,0 @@
-Sequence: Sequence CAI: 0.188
\ No newline at end of file


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_charge_out.charge
--- a/test-data/emboss_charge_out.charge
+++ /dev/null
@@ -1,560 +0,0 @@
-CHARGE of Sequence from 1 to 561: window 5
-
-Position	Residue	Charge
-1		G	0.000
-2		T	0.000
-3		T	0.000
-4		C	0.000
-5		G	0.000
-6		A	0.000
-7		T	0.000
-8		G	0.000
-9		C	0.000
-10		C	0.000
-11		T	0.000
-12		A	0.000
-13		A	0.000
-14		A	0.000
-15		A	0.000
-16		T	0.000
-17		A	0.000
-18		C	0.000
-19		C	0.000
-20		T	0.000
-21		T	0.000
-22		C	0.000
-23		T	0.000
-24		T	0.000
-25		T	0.000
-26		T	0.000
-27		G	0.000
-28		T	0.000
-29		C	0.000
-30		C	0.000
-31		C	0.000
-32		T	0.000
-33		A	0.000
-34		C	0.000
-35		A	0.000
-36		C	0.000
-37		A	0.000
-38		G	0.000
-39		A	0.000
-40		C	0.000
-41		C	0.000
-42		A	0.000
-43		C	0.000
-44		A	0.000
-45		G	0.000
-46		T	0.000
-47		T	0.000
-48		T	0.000
-49		T	0.000
-50		C	0.000
-51		C	0.000
-52		T	0.000
-53		A	0.000
-54		A	0.000
-55		T	0.000
-56		G	0.000
-57		G	0.000
-58		C	0.000
-59		T	0.000
-60		T	0.000
-61		T	0.000
-62		A	0.000
-63		C	0.000
-64		A	0.000
-65		C	0.000
-66		C	0.000
-67		G	0.000
-68		A	0.000
-69		C	0.000
-70		T	0.000
-71		A	0.000
-72		G	0.000
-73		A	0.000
-74		A	0.000
-75		A	0.000
-76		T	0.000
-77		T	0.000
-78		C	0.000
-79		T	0.000
-80		T	0.000
-81		G	0.000
-82		T	0.000
-83		G	0.000
-84		C	0.000
-85		A	0.000
-86		A	0.000
-87		G	0.000
-88		C	0.000
-89		A	0.000
-90		C	0.000
-91		T	0.000
-92		A	0.000
-93		A	0.000
-94		T	0.000
-95		T	0.000
-96		G	0.000
-97		A	0.000
-98		A	0.000
-99		A	0.000
-100		G	0.000
-101		C	0.000
-102		G	0.000
-103		G	0.000
-104		T	0.000
-105		T	0.000
-106		G	0.000
-107		G	0.000
-108		C	0.000
-109		C	0.000
-110		T	0.000
-111		A	0.000
-112		G	0.000
-113		A	0.000
-114		G	0.000
-115		T	0.000
-116		G	0.000
-117		T	0.000
-118		T	0.000
-119		A	0.000
-120		C	0.000
-121		C	0.000
-122		G	0.000
-123		G	0.000
-124		T	0.000
-125		T	0.000
-126		T	0.000
-127		G	0.000
-128		T	0.000
-129		A	0.000
-130		T	0.000
-131		A	0.000
-132		G	0.000
-133		C	0.000
-134		T	0.000
-135		G	0.000
-136		A	0.000
-137		G	0.000
-138		C	0.000
-139		G	0.000
-140		C	0.000
-141		G	0.000
-142		T	0.000
-143		C	0.000
-144		T	0.000
-145		C	0.000
-146		T	0.000
-147		T	0.000
-148		G	0.000
-149		C	0.000
-150		C	0.000
-151		C	0.000
-152		T	0.000
-153		G	0.000
-154		A	0.000
-155		T	0.000
-156		C	0.000
-157		A	0.000
-158		A	0.000
-159		A	0.000
-160		G	0.000
-161		G	0.000
-162		T	0.000
-163		T	0.000
-164		C	0.000
-165		A	0.000
-166		T	0.000
-167		T	0.000
-168		T	0.000
-169		T	0.000
-170		C	0.000
-171		T	0.000
-172		C	0.000
-173		T	0.000
-174		A	0.000
-175		C	0.000
-176		T	0.000
-177		T	0.000
-178		T	0.000
-179		G	0.000
-180		G	0.000
-181		A	0.000
-182		A	0.000
-183		G	0.000
-184		A	0.000
-185		C	0.000
-186		G	0.000
-187		T	0.000
-188		T	0.000
-189		G	0.000
-190		T	0.000
-191		G	0.000
-192		G	0.000
-193		A	0.000
-194		A	0.000
-195		G	0.000
-196		A	0.000
-197		A	0.000
-198		T	0.000
-199		A	0.000
-200		C	0.000
-201		A	0.000
-202		A	0.000
-203		C	0.000
-204		A	0.000
-205		A	0.000
-206		G	0.000
-207		T	0.000
-208		A	0.000
-209		C	0.000
-210		G	0.000
-211		A	0.000
-212		G	0.000
-213		T	0.000
-214		C	0.000
-215		T	0.000
-216		C	0.000
-217		T	0.000
-218		C	0.000
-219		C	0.000
-220		C	0.000
-221		C	0.000
-222		C	0.000
-223		C	0.000
-224		T	0.000
-225		G	0.000
-226		G	0.000
-227		T	0.000
-228		T	0.000
-229		T	0.000
-230		G	0.000
-231		C	0.000
-232		T	0.000
-233		G	0.000
-234		A	0.000
-235		T	0.000
-236		T	0.000
-237		A	0.000
-238		C	0.000
-239		T	0.000
-240		G	0.000
-241		G	0.000
-242		A	0.000
-243		T	0.000
-244		A	0.000
-245		C	0.000
-246		A	0.000
-247		G	0.000
-248		T	0.000
-249		T	0.000
-250		G	0.000
-251		T	0.000
-252		A	0.000
-253		A	0.000
-254		T	0.000
-255		A	0.000
-256		C	0.000
-257		C	0.000
-258		C	0.000
-259		T	0.000
-260		T	0.000
-261		C	0.000
-262		G	0.000
-263		C	0.000
-264		A	0.000
-265		A	0.000
-266		C	0.000
-267		A	0.000
-268		C	0.000
-269		C	0.000
-270		G	0.000
-271		C	0.000
-272		G	0.000
-273		T	0.000
-274		A	0.000
-275		A	0.000
-276		C	0.000
-277		T	0.000
-278		A	0.000
-279		T	0.000
-280		C	0.000
-281		T	0.000
-282		A	0.000
-283		T	0.000
-284		A	0.000
-285		T	0.000
-286		G	0.000
-287		A	0.000
-288		A	0.000
-289		T	0.000
-290		T	0.000
-291		A	0.000
-292		T	0.000
-293		T	0.000
-294		T	0.000
-295		T	0.000
-296		C	0.000
-297		C	0.000
-298		C	0.000
-299		T	0.000
-300		T	0.000
-301		T	0.000
-302		A	0.000
-303		T	0.000
-304		T	0.000
-305		A	0.000
-306		T	0.000
-307		A	0.000
-308		T	0.000
-309		G	0.000
-310		T	0.000
-311		A	0.000
-312		G	0.000
-313		T	0.000
-314		A	0.000
-315		G	0.000
-316		G	0.000
-317		T	0.000
-318		T	0.000
-319		C	0.000
-320		G	0.000
-321		T	0.000
-322		C	0.000
-323		T	0.000
-324		T	0.000
-325		T	0.000
-326		A	0.000
-327		A	0.000
-328		T	0.000
-329		C	0.000
-330		T	0.000
-331		T	0.000
-332		C	0.000
-333		C	0.000
-334		T	0.000
-335		T	0.000
-336		T	0.000
-337		A	0.000
-338		G	0.000
-339		C	0.000
-340		A	0.000
-341		A	0.000
-342		G	0.000
-343		T	0.000
-344		C	0.000
-345		T	0.000
-346		T	0.000
-347		T	0.000
-348		T	0.000
-349		A	0.000
-350		C	0.000
-351		T	0.000
-352		G	0.000
-353		T	0.000
-354		T	0.000
-355		T	0.000
-356		T	0.000
-357		C	0.000
-358		G	0.000
-359		A	0.000
-360		C	0.000
-361		C	0.000
-362		T	0.000
-363		C	0.000
-364		A	0.000
-365		A	0.000
-366		T	0.000
-367		G	0.000
-368		T	0.000
-369		T	0.000
-370		C	0.000
-371		A	0.000
-372		T	0.000
-373		G	0.000
-374		T	0.000
-375		T	0.000
-376		C	0.000
-377		T	0.000
-378		T	0.000
-379		A	0.000
-380		G	0.000
-381		G	0.000
-382		T	0.000
-383		T	0.000
-384		G	0.000
-385		T	0.000
-386		T	0.000
-387		T	0.000
-388		T	0.000
-389		G	0.000
-390		G	0.000
-391		A	0.000
-392		T	0.000
-393		A	0.000
-394		A	0.000
-395		T	0.000
-396		A	0.000
-397		T	0.000
-398		G	0.000
-399		C	0.000
-400		G	0.000
-401		G	0.000
-402		T	0.000
-403		C	0.000
-404		A	0.000
-405		G	0.000
-406		T	0.000
-407		T	0.000
-408		T	0.000
-409		A	0.000
-410		A	0.000
-411		T	0.000
-412		C	0.000
-413		T	0.000
-414		T	0.000
-415		C	0.000
-416		G	0.000
-417		T	0.000
-418		T	0.000
-419		G	0.000
-420		T	0.000
-421		T	0.000
-422		T	0.000
-423		C	0.000
-424		T	0.000
-425		T	0.000
-426		C	0.000
-427		T	0.000
-428		T	0.000
-429		A	0.000
-430		A	0.000
-431		A	0.000
-432		A	0.000
-433		T	0.000
-434		A	0.000
-435		T	0.000
-436		T	0.000
-437		T	0.000
-438		A	0.000
-439		T	0.000
-440		T	0.000
-441		C	0.000
-442		A	0.000
-443		T	0.000
-444		G	0.000
-445		G	0.000
-446		T	0.000
-447		T	0.000
-448		T	0.000
-449		A	0.000
-450		A	0.000
-451		T	0.000
-452		T	0.000
-453		T	0.000
-454		T	0.000
-455		T	0.000
-456		G	0.000
-457		G	0.000
-458		T	0.000
-459		T	0.000
-460		T	0.000
-461		G	0.000
-462		T	0.000
-463		A	0.000
-464		C	0.000
-465		T	0.000
-466		T	0.000
-467		G	0.000
-468		T	0.000
-469		T	0.000
-470		C	0.000
-471		A	0.000
-472		G	0.000
-473		G	0.000
-474		G	0.000
-475		G	0.000
-476		C	0.000
-477		C	0.000
-478		A	0.000
-479		G	0.000
-480		T	0.000
-481		T	0.000
-482		C	0.000
-483		A	0.000
-484		T	0.000
-485		T	0.000
-486		A	0.000
-487		T	0.000
-488		T	0.000
-489		T	0.000
-490		A	0.000
-491		C	0.000
-492		T	0.000
-493		C	0.000
-494		T	0.000
-495		G	0.000
-496		T	0.000
-497		T	0.000
-498		T	0.000
-499		G	0.000
-500		T	0.000
-501		A	0.000
-502		T	0.000
-503		A	0.000
-504		C	0.000
-505		A	0.000
-506		G	0.000
-507		C	0.000
-508		A	0.000
-509		G	0.000
-510		T	0.000
-511		T	0.000
-512		C	0.000
-513		T	0.000
-514		T	0.000
-515		T	0.000
-516		T	0.000
-517		A	0.000
-518		T	0.000
-519		T	0.000
-520		T	0.000
-521		T	0.000
-522		T	0.000
-523		A	0.000
-524		G	0.000
-525		T	0.000
-526		A	0.000
-527		T	0.000
-528		G	0.000
-529		A	0.000
-530		T	0.000
-531		T	0.000
-532		T	0.000
-533		T	0.000
-534		A	0.000
-535		A	0.000
-536		T	0.000
-537		T	0.000
-538		T	0.000
-539		A	0.000
-540		A	0.000
-541		A	0.000
-542		A	0.000
-543		C	0.000
-544		A	0.000
-545		A	0.000
-546		T	0.000
-547		T	0.000
-548		C	0.000
-549		T	0.000
-550		A	0.000
-551		A	0.000
-552		T	0.000
-553		G	0.000
-554		G	0.000
-555		T	0.000
-556		C	0.000
-557		A	0.000


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_chips_out.chips
--- a/test-data/emboss_chips_out.chips
+++ /dev/null
@@ -1,3 +0,0 @@
-# CHIPS codon usage statistics
-
-Nc = 61.000


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_codcmp_out.codcmp
--- a/test-data/emboss_codcmp_out.codcmp
+++ /dev/null
@@ -1,9 +0,0 @@
-# CODCMP codon usage table comparison
-# Ehum.cut vs Eacc.cut
-
-Sum Squared Difference = 3.044
-Mean Squared Difference = 0.048
-Root Mean Squared Difference = 0.218
-Sum Difference         = 11.470
-Mean Difference         = 0.179
-Codons not appearing   = 0


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_coderet_out.coderet
--- a/test-data/emboss_coderet_out.coderet
+++ /dev/null
@@ -1,3 +0,0 @@
-   CDS  mRNA non-c Trans Total Sequence
- ===== ===== ===== ===== ===== ========
-     0     0     0     0     0 Sequence


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_compseq_out.compseq
--- a/test-data/emboss_compseq_out.compseq
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# Output from 'compseq'
-#
-# The Expected frequencies are calculated on the (false) assumption that every
-# word has equal frequency.
-#
-# The input sequences are:
-#	Sequence
-
-
-Word size	2
-Total count	560
-
-#
-# Word	Obs Count	Obs Frequency	Exp Frequency	Obs/Exp Frequency
-#
-AA	40		0.0714286	0.0625000	1.1428571
-AC	27		0.0482143	0.0625000	0.7714286
-AG	26		0.0464286	0.0625000	0.7428571
-AT	41		0.0732143	0.0625000	1.1714286
-CA	26		0.0464286	0.0625000	0.7428571
-CC	24		0.0428571	0.0625000	0.6857143
-CG	15		0.0267857	0.0625000	0.4285714
-CT	41		0.0732143	0.0625000	1.1714286
-GA	19		0.0339286	0.0625000	0.5428571
-GC	17		0.0303571	0.0625000	0.4857143
-GG	19		0.0339286	0.0625000	0.5428571
-GT	43		0.0767857	0.0625000	1.2285714
-TA	50		0.0892857	0.0625000	1.4285714
-TC	38		0.0678571	0.0625000	1.0857143
-TG	37		0.0660714	0.0625000	1.0571429
-TT	97		0.1732143	0.0625000	2.7714286
-
-Other	0		0.0000000	0.0000000	10000000000.0000000


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cpgreport_out1.gff
--- a/test-data/emboss_cpgreport_out1.gff
+++ /dev/null
@@ -1,13 +0,0 @@
-##gff-version 2.0
-##date 2007-10-15
-##Type DNA Sequence
-Sequence	cpgreport	misc_feature	4	5	17.000	+	.	Sequence "Sequence.1"
-Sequence	cpgreport	misc_feature	66	67	17.000	+	.	Sequence "Sequence.2"
-Sequence	cpgreport	misc_feature	101	102	17.000	+	.	Sequence "Sequence.3"
-Sequence	cpgreport	misc_feature	121	141	34.000	+	.	Sequence "Sequence.4"
-Sequence	cpgreport	misc_feature	185	186	17.000	+	.	Sequence "Sequence.5"
-Sequence	cpgreport	misc_feature	209	210	17.000	+	.	Sequence "Sequence.6"
-Sequence	cpgreport	misc_feature	261	272	43.000	+	.	Sequence "Sequence.7"
-Sequence	cpgreport	misc_feature	319	320	17.000	+	.	Sequence "Sequence.8"
-Sequence	cpgreport	misc_feature	357	358	17.000	+	.	Sequence "Sequence.9"
-Sequence	cpgreport	misc_feature	399	416	19.000	+	.	Sequence "Sequence.10"


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cpgreport_out2.cpgreport
--- a/test-data/emboss_cpgreport_out2.cpgreport
+++ /dev/null
@@ -1,15 +0,0 @@
-
-
-CPGREPORT of Sequence from 1 to 561
-
-Sequence              Begin    End Score        CpG   %CG  CG/GC
-Sequence                  4      5    17          1 100.0    -
-Sequence                 66     67    17          1 100.0    -
-Sequence                101    102    17          1 100.0    -
-Sequence                121    141    34          3  57.1   1.00
-Sequence                185    186    17          1 100.0    -
-Sequence                209    210    17          1 100.0    -
-Sequence                261    272    43          3  75.0   1.00
-Sequence                319    320    17          1 100.0    -
-Sequence                357    358    17          1 100.0    -
-Sequence                399    416    19          2  44.4    -


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cusp_out.cusp
--- a/test-data/emboss_cusp_out.cusp
+++ /dev/null
@@ -1,72 +0,0 @@
-#CdsCount: 10
-
-#Coding GC 36.36%
-#1st letter GC 34.22%
-#2nd letter GC 35.29%
-#3rd letter GC 39.57%
-
-#Codon AA Fraction Frequency Number
-GCA    A     0.200     5.348      1
-GCC    A     0.400    10.695      2
-GCG    A     0.400    10.695      2
-GCT    A     0.000     0.000      0
-TGC    C     0.500    21.390      4
-TGT    C     0.500    21.390      4
-GAC    D     0.667    10.695      2
-GAT    D     0.333     5.348      1
-GAA    E     0.500     5.348      1
-GAG    E     0.500     5.348      1
-TTC    F     0.316    32.086      6
-TTT    F     0.684    69.519     13
-GGA    G     0.000     0.000      0
-GGC    G     0.200     5.348      1
-GGG    G     0.200     5.348      1
-GGT    G     0.600    16.043      3
-CAC    H     0.667    10.695      2
-CAT    H     0.333     5.348      1
-ATA    I     0.429    16.043      3
-ATC    I     0.143     5.348      1
-ATT    I     0.429    16.043      3
-AAA    K     0.600    32.086      6
-AAG    K     0.400    21.390      4
-CTA    L     0.152    26.738      5
-CTC    L     0.061    10.695      2
-CTG    L     0.152    26.738      5
-CTT    L     0.273    48.128      9
-TTA    L     0.182    32.086      6
-TTG    L     0.182    32.086      6
-ATG    M     1.000    16.043      3
-AAC    N     0.286    10.695      2
-AAT    N     0.714    26.738      5
-CCA    P     0.250     5.348      1
-CCC    P     0.500    10.695      2
-CCG    P     0.250     5.348      1
-CCT    P     0.000     0.000      0
-CAA    Q     0.333     5.348      1
-CAG    Q     0.667    10.695      2
-AGA    R     0.143     5.348      1
-AGG    R     0.143     5.348      1
-CGA    R     0.143     5.348      1
-CGC    R     0.000     0.000      0
-CGG    R     0.143     5.348      1
-CGT    R     0.429    16.043      3
-AGC    S     0.136    16.043      3
-AGT    S     0.227    26.738      5
-TCA    S     0.136    16.043      3
-TCC    S     0.227    26.738      5
-TCG    S     0.000     0.000      0
-TCT    S     0.273    32.086      6
-ACA    T     0.400    21.390      4
-ACC    T     0.100     5.348      1
-ACG    T     0.200    10.695      2
-ACT    T     0.300    16.043      3
-GTA    V     0.231    16.043      3
-GTC    V     0.000     0.000      0
-GTG    V     0.000     0.000      0
-GTT    V     0.769    53.476     10
-TGG    W     1.000    21.390      4
-TAC    Y     0.444    21.390      4
-TAT    Y     0.556    26.738      5
-TAA    *     0.500    26.738      5
-TAG    *     0.400    21.390      4
-TGA    *     0.100     5.348      1


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cutseq_out.fasta
--- a/test-data/emboss_cutseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-ttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggcttt
-acaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttacc
-ggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgga
-agacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactgg
-atacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttcccttt
-attatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgacc
-tcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgtt
-tcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagtt
-cattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaaa
-acaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_dan_out.png
Binary file test-data/emboss_dan_out.png has changed


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_degapseq_out.fasta
--- a/test-data/emboss_degapseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_descseq_out.fasta
--- a/test-data/emboss_descseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequencetest 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;test
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_einverted_out.einverted
--- a/test-data/emboss_einverted_out.einverted
+++ /dev/null
@@ -1,20 +0,0 @@
-
-hg17: Score 97: 63/77 ( 81%) matches, 3 gaps
-    2684 gtggcaggctcggttcaccaacgtcatttgcagttccccgctttatgttatggg-t--tttgttttgttttgtttttttt 2760    
-         |||| ||||  | ||||||    || |||| ||||||||||||||  | ||||| |  |||||||||||||||||| |||
-    3298 caccatccgtacaaagtggacatagcaaacatcaaggggcgaaatgtactacccaaccaaacaaaacaaaacaaaacaaa 3219    
-
-hg17: Score 94: 34/36 ( 94%) matches, 0 gaps
-    7058 gacacacacacacacacacacacacacacacacaca 7093    
-         |||||||| ||||||||||| |||||||||||||||
-    7888 ctgtgtgtatgtgtgtgtgtctgtgtgtgtgtgtgt 7853    
-
-hg17: Score 139: 213/305 ( 69%) matches, 11 gaps
-    8604 ggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcac--gaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaa-aattagccaggt-gcggtg-gtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaa 8914    
-         ||||||||| |||| |||||||||   ||||||||||| |||| || ||||| |  |||  ||||||||  |||||||||||| | | |  |  |  || | ||||||  ||||||| ||| ||  |   |  | || | | ||||  ||      ||   | | |||  |   ||  ||||||  |||  ||||  | || ||| ||| ||| |  |||| |||||||||    | ||||  || ||||||| |||||| |  ||| |||||||| || ||     ||||| ||||    ||||| ||||  |||
-    9563 ccaccgagt-cggatattagggtcccgaaaccctccggttccgtcctcctagcgaactcgggtcctcaagttctggtcggacccgctgtgtcgttctggggtagagattttttttatttttatttttatttttatcgactcacaccaccgtttgcgaa-cacca-ggg-tcgatgaaccctccggttccaccctccaaacggactcgggtcctacagctccgacgtcactccatactagtg-tgtcacgtgaggtcggacacactgtgtcgttctggggtag-agaatttttgttttcggttttttctattacttt 9254    
-
-hg17: Score 202: 70/72 ( 97%) matches, 0 gaps
-   18075 tgcattttattctggatggatttgaagcaaagcaccagcttctccaggctctttggggtcagccagggccag 18146   
-         ||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
-   18677 acgcaaaataagacctacctaaacttcgtttcgtagtcgaagaggtccgagaaaccccagtcggtcccggtc 18606   


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_epestfind_out.epestfind
--- a/test-data/emboss_epestfind_out.epestfind
+++ /dev/null
@@ -1,41 +0,0 @@
-PEST-find: Finds PEST motifs as potential proteolytic cleavage sites.
-
-    No PEST motif was identified in Sequence from 1 to 561.
-
-
-       ---------+---------+---------+---------+---------+---------+
-
-     1 GTTCGATGCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAATGGCTT 60
-                                                                   
-
-    61 TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC 120
-                                                                   
-
-   121 CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG 180
-                                                                   
-
-   181 AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG 240
-                                                                   
-
-   241 GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATATGAATTATTTTCCCTT 300
-                                                                   
-
-   301 TATTATATGTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC 360
-                                                                   
-
-   361 CTCAATGTTCATGTTCTTAGGTTGTTTTGGATAATATGCGGTCAGTTTAATCTTCGTTGT 420
-                                                                   
-
-   421 TTCTTCTTAAAATATTTATTCATGGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT 480
-                                                                   
-
-   481 TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTATGATTTTAATTTAA 540
-                                                                   
-
-   541 AACAATTCTAATGGTCAAAAA 561
-                            
-
-       Symbols   PEST motifs
-       +++++++   potential
-       OOOOOOO   poor     
-


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_equicktandem_out.equicktandem
--- a/test-data/emboss_equicktandem_out.equicktandem
+++ /dev/null
@@ -1,16 +0,0 @@
-    22       8881       8915  1  35
-    33       7059       7093  2  17
-    29       7847       7891  2  22
-    27       3213       3248  5   7
-    20       9430       9457  6   4
-    39      19631      19709 36   2
-    39      19851      19927 36   2
-    37      20067      20141 36   2
-    21      19550      19630 60   1
-    21      19770      19850 60   1
-    79      19928      20066 60   2
-    24       8595       8793 133   1
-    26       2844       3045 134   1
-    35      10945      11179 136   1
-    22      15264      15435 138   1
-    29      11181      11429 168   1


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_est2genome_out.est2genome
--- a/test-data/emboss_est2genome_out.est2genome
+++ /dev/null
@@ -1,1 +0,0 @@
-Note Best alignment is between reversed est and forward genome, and splice sites imply forward gene


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_etandem_out.table
--- a/test-data/emboss_etandem_out.table
+++ /dev/null
@@ -1,2 +0,0 @@
-    24       7847       7886 10   4  92.5 tgtgtgtgtg
-    22       7059       7098 10   4  90.0 acacacacac


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_extractseq_out.fasta
--- a/test-data/emboss_extractseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_freak_out.freak
--- a/test-data/emboss_freak_out.freak
+++ /dev/null
@@ -1,534 +0,0 @@
-FREAK of Sequence from 1 to 561 Window 30 Step 1
-
-1          0.400000
-2          0.400000
-3          0.400000
-4          0.400000
-5          0.400000
-6          0.366667
-7          0.400000
-8          0.400000
-9          0.400000
-10         0.366667
-11         0.366667
-12         0.400000
-13         0.400000
-14         0.433333
-15         0.433333
-16         0.466667
-17         0.466667
-18         0.466667
-19         0.433333
-20         0.400000
-21         0.433333
-22         0.466667
-23         0.433333
-24         0.433333
-25         0.433333
-26         0.433333
-27         0.466667
-28         0.466667
-29         0.500000
-30         0.466667
-31         0.433333
-32         0.400000
-33         0.400000
-34         0.433333
-35         0.400000
-36         0.433333
-37         0.433333
-38         0.466667
-39         0.433333
-40         0.466667
-41         0.433333
-42         0.400000
-43         0.433333
-44         0.400000
-45         0.400000
-46         0.366667
-47         0.366667
-48         0.366667
-49         0.400000
-50         0.400000
-51         0.366667
-52         0.366667
-53         0.366667
-54         0.400000
-55         0.433333
-56         0.433333
-57         0.400000
-58         0.400000
-59         0.400000
-60         0.400000
-61         0.433333
-62         0.433333
-63         0.433333
-64         0.400000
-65         0.400000
-66         0.366667
-67         0.366667
-68         0.333333
-69         0.333333
-70         0.300000
-71         0.333333
-72         0.366667
-73         0.366667
-74         0.400000
-75         0.400000
-76         0.400000
-77         0.433333
-78         0.466667
-79         0.466667
-80         0.500000
-81         0.500000
-82         0.466667
-83         0.500000
-84         0.466667
-85         0.466667
-86         0.466667
-87         0.500000
-88         0.466667
-89         0.433333
-90         0.433333
-91         0.433333
-92         0.466667
-93         0.500000
-94         0.533333
-95         0.533333
-96         0.533333
-97         0.500000
-98         0.533333
-99         0.533333
-100        0.533333
-101        0.500000
-102        0.466667
-103        0.466667
-104        0.466667
-105        0.466667
-106        0.500000
-107        0.466667
-108        0.466667
-109        0.466667
-110        0.466667
-111        0.500000
-112        0.533333
-113        0.500000
-114        0.533333
-115        0.500000
-116        0.533333
-117        0.500000
-118        0.500000
-119        0.533333
-120        0.566667
-121        0.566667
-122        0.566667
-123        0.533333
-124        0.533333
-125        0.533333
-126        0.533333
-127        0.566667
-128        0.533333
-129        0.533333
-130        0.533333
-131        0.566667
-132        0.600000
-133        0.566667
-134        0.533333
-135        0.566667
-136        0.533333
-137        0.533333
-138        0.500000
-139        0.466667
-140        0.433333
-141        0.433333
-142        0.400000
-143        0.433333
-144        0.400000
-145        0.400000
-146        0.400000
-147        0.400000
-148        0.400000
-149        0.366667
-150        0.366667
-151        0.366667
-152        0.333333
-153        0.333333
-154        0.333333
-155        0.333333
-156        0.366667
-157        0.366667
-158        0.366667
-159        0.366667
-160        0.400000
-161        0.366667
-162        0.366667
-163        0.400000
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-341        0.366667
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-345        0.333333
-346        0.333333
-347        0.366667
-348        0.366667
-349        0.366667
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-353        0.366667
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-392        0.333333
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-436        0.233333
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-514        0.100000
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diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_fuzznuc_out.tabular
--- a/test-data/emboss_fuzznuc_out.tabular
+++ /dev/null
@@ -1,41 +0,0 @@
-SeqName	Start	End	Score	Strand	Pattern_name	Mismatch
-Sequence	12	13	2	+	pattern1	.
-Sequence	13	14	2	+	pattern1	.
-Sequence	14	15	2	+	pattern1	.
-Sequence	53	54	2	+	pattern1	.
-Sequence	73	74	2	+	pattern1	.
-Sequence	74	75	2	+	pattern1	.
-Sequence	85	86	2	+	pattern1	.
-Sequence	92	93	2	+	pattern1	.
-Sequence	97	98	2	+	pattern1	.
-Sequence	98	99	2	+	pattern1	.
-Sequence	157	158	2	+	pattern1	.
-Sequence	158	159	2	+	pattern1	.
-Sequence	181	182	2	+	pattern1	.
-Sequence	193	194	2	+	pattern1	.
-Sequence	196	197	2	+	pattern1	.
-Sequence	201	202	2	+	pattern1	.
-Sequence	204	205	2	+	pattern1	.
-Sequence	252	253	2	+	pattern1	.
-Sequence	264	265	2	+	pattern1	.
-Sequence	274	275	2	+	pattern1	.
-Sequence	287	288	2	+	pattern1	.
-Sequence	326	327	2	+	pattern1	.
-Sequence	340	341	2	+	pattern1	.
-Sequence	364	365	2	+	pattern1	.
-Sequence	393	394	2	+	pattern1	.
-Sequence	409	410	2	+	pattern1	.
-Sequence	429	430	2	+	pattern1	.
-Sequence	430	431	2	+	pattern1	.
-Sequence	431	432	2	+	pattern1	.
-Sequence	449	450	2	+	pattern1	.
-Sequence	534	535	2	+	pattern1	.
-Sequence	539	540	2	+	pattern1	.
-Sequence	540	541	2	+	pattern1	.
-Sequence	541	542	2	+	pattern1	.
-Sequence	544	545	2	+	pattern1	.
-Sequence	550	551	2	+	pattern1	.
-Sequence	557	558	2	+	pattern1	.
-Sequence	558	559	2	+	pattern1	.
-Sequence	559	560	2	+	pattern1	.
-Sequence	560	561	2	+	pattern1	.


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_fuzzpro_out.tabular
--- a/test-data/emboss_fuzzpro_out.tabular
+++ /dev/null
@@ -1,41 +0,0 @@
-SeqName	Start	End	Score	Strand	Pattern_name	Mismatch
-Sequence	12	13	2	+	pattern1	.
-Sequence	13	14	2	+	pattern1	.
-Sequence	14	15	2	+	pattern1	.
-Sequence	53	54	2	+	pattern1	.
-Sequence	73	74	2	+	pattern1	.
-Sequence	74	75	2	+	pattern1	.
-Sequence	85	86	2	+	pattern1	.
-Sequence	92	93	2	+	pattern1	.
-Sequence	97	98	2	+	pattern1	.
-Sequence	98	99	2	+	pattern1	.
-Sequence	157	158	2	+	pattern1	.
-Sequence	158	159	2	+	pattern1	.
-Sequence	181	182	2	+	pattern1	.
-Sequence	193	194	2	+	pattern1	.
-Sequence	196	197	2	+	pattern1	.
-Sequence	201	202	2	+	pattern1	.
-Sequence	204	205	2	+	pattern1	.
-Sequence	252	253	2	+	pattern1	.
-Sequence	264	265	2	+	pattern1	.
-Sequence	274	275	2	+	pattern1	.
-Sequence	287	288	2	+	pattern1	.
-Sequence	326	327	2	+	pattern1	.
-Sequence	340	341	2	+	pattern1	.
-Sequence	364	365	2	+	pattern1	.
-Sequence	393	394	2	+	pattern1	.
-Sequence	409	410	2	+	pattern1	.
-Sequence	429	430	2	+	pattern1	.
-Sequence	430	431	2	+	pattern1	.
-Sequence	431	432	2	+	pattern1	.
-Sequence	449	450	2	+	pattern1	.
-Sequence	534	535	2	+	pattern1	.
-Sequence	539	540	2	+	pattern1	.
-Sequence	540	541	2	+	pattern1	.
-Sequence	541	542	2	+	pattern1	.
-Sequence	544	545	2	+	pattern1	.
-Sequence	550	551	2	+	pattern1	.
-Sequence	557	558	2	+	pattern1	.
-Sequence	558	559	2	+	pattern1	.
-Sequence	559	560	2	+	pattern1	.
-Sequence	560	561	2	+	pattern1	.


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_fuzztran_out.tabular
--- a/test-data/emboss_fuzztran_out.tabular
+++ /dev/null
@@ -1,133 +0,0 @@
-SeqName	Start	End	Score	Strand	Pattern_name	Mismatch	Frame	PStart	PEnd	Translation
-hg17	3958	3963	2	+	pattern1	.	1	1320	1321	AA
-hg17	3961	3966	2	+	pattern1	.	1	1321	1322	AA
-hg17	4099	4104	2	+	pattern1	.	1	1367	1368	AA
-hg17	4315	4320	2	+	pattern1	.	1	1439	1440	AA
-hg17	5194	5199	2	+	pattern1	.	1	1732	1733	AA
-hg17	8584	8589	2	+	pattern1	.	1	2862	2863	AA
-hg17	9232	9237	2	+	pattern1	.	1	3078	3079	AA
-hg17	9343	9348	2	+	pattern1	.	1	3115	3116	AA
-hg17	9715	9720	2	+	pattern1	.	1	3239	3240	AA
-hg17	9769	9774	2	+	pattern1	.	1	3257	3258	AA
-hg17	9841	9846	2	+	pattern1	.	1	3281	3282	AA
-hg17	9994	9999	2	+	pattern1	.	1	3332	3333	AA
-hg17	10045	10050	2	+	pattern1	.	1	3349	3350	AA
-hg17	10048	10053	2	+	pattern1	.	1	3350	3351	AA
-hg17	12157	12162	2	+	pattern1	.	1	4053	4054	AA
-hg17	12487	12492	2	+	pattern1	.	1	4163	4164	AA
-hg17	12688	12693	2	+	pattern1	.	1	4230	4231	AA
-hg17	12691	12696	2	+	pattern1	.	1	4231	4232	AA
-hg17	15010	15015	2	+	pattern1	.	1	5004	5005	AA
-hg17	17521	17526	2	+	pattern1	.	1	5841	5842	AA
-hg17	17551	17556	2	+	pattern1	.	1	5851	5852	AA
-hg17	1148	1153	2	+	pattern1	.	2	383	384	AA
-hg17	2078	2083	2	+	pattern1	.	2	693	694	AA
-hg17	2432	2437	2	+	pattern1	.	2	811	812	AA
-hg17	3080	3085	2	+	pattern1	.	2	1027	1028	AA
-hg17	3593	3598	2	+	pattern1	.	2	1198	1199	AA
-hg17	3692	3697	2	+	pattern1	.	2	1231	1232	AA
-hg17	4055	4060	2	+	pattern1	.	2	1352	1353	AA
-hg17	5018	5023	2	+	pattern1	.	2	1673	1674	AA
-hg17	5147	5152	2	+	pattern1	.	2	1716	1717	AA
-hg17	8276	8281	2	+	pattern1	.	2	2759	2760	AA
-hg17	9587	9592	2	+	pattern1	.	2	3196	3197	AA
-hg17	9668	9673	2	+	pattern1	.	2	3223	3224	AA
-hg17	9920	9925	2	+	pattern1	.	2	3307	3308	AA
-hg17	9971	9976	2	+	pattern1	.	2	3324	3325	AA
-hg17	10112	10117	2	+	pattern1	.	2	3371	3372	AA
-hg17	10115	10120	2	+	pattern1	.	2	3372	3373	AA
-hg17	11837	11842	2	+	pattern1	.	2	3946	3947	AA
-hg17	12026	12031	2	+	pattern1	.	2	4009	4010	AA
-hg17	12944	12949	2	+	pattern1	.	2	4315	4316	AA
-hg17	12953	12958	2	+	pattern1	.	2	4318	4319	AA
-hg17	13229	13234	2	+	pattern1	.	2	4410	4411	AA
-hg17	13232	13237	2	+	pattern1	.	2	4411	4412	AA
-hg17	15356	15361	2	+	pattern1	.	2	5119	5120	AA
-hg17	15482	15487	2	+	pattern1	.	2	5161	5162	AA
-hg17	16061	16066	2	+	pattern1	.	2	5354	5355	AA
-hg17	17822	17827	2	+	pattern1	.	2	5941	5942	AA
-hg17	15	20	2	+	pattern1	.	3	5	6	AA
-hg17	33	38	2	+	pattern1	.	3	11	12	AA
-hg17	3669	3674	2	+	pattern1	.	3	1223	1224	AA
-hg17	3759	3764	2	+	pattern1	.	3	1253	1254	AA
-hg17	5646	5651	2	+	pattern1	.	3	1882	1883	AA
-hg17	5847	5852	2	+	pattern1	.	3	1949	1950	AA
-hg17	5850	5855	2	+	pattern1	.	3	1950	1951	AA
-hg17	5853	5858	2	+	pattern1	.	3	1951	1952	AA
-hg17	7674	7679	2	+	pattern1	.	3	2558	2559	AA
-hg17	9699	9704	2	+	pattern1	.	3	3233	3234	AA
-hg17	9891	9896	2	+	pattern1	.	3	3297	3298	AA
-hg17	10074	10079	2	+	pattern1	.	3	3358	3359	AA
-hg17	10407	10412	2	+	pattern1	.	3	3469	3470	AA
-hg17	12675	12680	2	+	pattern1	.	3	4225	4226	AA
-hg17	13746	13751	2	+	pattern1	.	3	4582	4583	AA
-hg17	17115	17120	2	+	pattern1	.	3	5705	5706	AA
-hg17	17421	17426	2	+	pattern1	.	3	5807	5808	AA
-hg17	19122	19127	2	+	pattern1	.	3	6374	6375	AA
-hg17	19353	19358	2	+	pattern1	.	3	6451	6452	AA
-hg17	-2312	-2317	2	-	pattern1	.	1	772	773	AA
-hg17	-4073	-4078	2	-	pattern1	.	1	1359	1360	AA
-hg17	-4652	-4657	2	-	pattern1	.	1	1552	1553	AA
-hg17	-4778	-4783	2	-	pattern1	.	1	1594	1595	AA
-hg17	-6902	-6907	2	-	pattern1	.	1	2302	2303	AA
-hg17	-6905	-6910	2	-	pattern1	.	1	2303	2304	AA
-hg17	-7181	-7186	2	-	pattern1	.	1	2395	2396	AA
-hg17	-7190	-7195	2	-	pattern1	.	1	2398	2399	AA
-hg17	-8108	-8113	2	-	pattern1	.	1	2704	2705	AA
-hg17	-8297	-8302	2	-	pattern1	.	1	2767	2768	AA
-hg17	-10019	-10024	2	-	pattern1	.	1	3341	3342	AA
-hg17	-10022	-10027	2	-	pattern1	.	1	3342	3343	AA
-hg17	-10163	-10168	2	-	pattern1	.	1	3389	3390	AA
-hg17	-10214	-10219	2	-	pattern1	.	1	3406	3407	AA
-hg17	-10466	-10471	2	-	pattern1	.	1	3490	3491	AA
-hg17	-10547	-10552	2	-	pattern1	.	1	3517	3518	AA
-hg17	-11858	-11863	2	-	pattern1	.	1	3954	3955	AA
-hg17	-14987	-14992	2	-	pattern1	.	1	4997	4998	AA
-hg17	-15116	-15121	2	-	pattern1	.	1	5040	5041	AA
-hg17	-16079	-16084	2	-	pattern1	.	1	5361	5362	AA
-hg17	-16442	-16447	2	-	pattern1	.	1	5482	5483	AA
-hg17	-16541	-16546	2	-	pattern1	.	1	5515	5516	AA
-hg17	-17054	-17059	2	-	pattern1	.	1	5686	5687	AA
-hg17	-17702	-17707	2	-	pattern1	.	1	5902	5903	AA
-hg17	-18056	-18061	2	-	pattern1	.	1	6020	6021	AA
-hg17	-18986	-18991	2	-	pattern1	.	1	6330	6331	AA
-hg17	-783	-788	2	-	pattern1	.	2	262	263	AA
-hg17	-1014	-1019	2	-	pattern1	.	2	339	340	AA
-hg17	-2715	-2720	2	-	pattern1	.	2	906	907	AA
-hg17	-3021	-3026	2	-	pattern1	.	2	1008	1009	AA
-hg17	-6390	-6395	2	-	pattern1	.	2	2131	2132	AA
-hg17	-7461	-7466	2	-	pattern1	.	2	2488	2489	AA
-hg17	-9729	-9734	2	-	pattern1	.	2	3244	3245	AA
-hg17	-10062	-10067	2	-	pattern1	.	2	3355	3356	AA
-hg17	-10245	-10250	2	-	pattern1	.	2	3416	3417	AA
-hg17	-10437	-10442	2	-	pattern1	.	2	3480	3481	AA
-hg17	-12462	-12467	2	-	pattern1	.	2	4155	4156	AA
-hg17	-14283	-14288	2	-	pattern1	.	2	4762	4763	AA
-hg17	-14286	-14291	2	-	pattern1	.	2	4763	4764	AA
-hg17	-14289	-14294	2	-	pattern1	.	2	4764	4765	AA
-hg17	-14490	-14495	2	-	pattern1	.	2	4831	4832	AA
-hg17	-16377	-16382	2	-	pattern1	.	2	5460	5461	AA
-hg17	-16467	-16472	2	-	pattern1	.	2	5490	5491	AA
-hg17	-20103	-20108	2	-	pattern1	.	2	6702	6703	AA
-hg17	-20121	-20126	2	-	pattern1	.	2	6708	6709	AA
-hg17	17553	17548	2	-	pattern1	.	3	863	864	AA
-hg17	17523	17518	2	-	pattern1	.	3	873	874	AA
-hg17	15012	15007	2	-	pattern1	.	3	1710	1711	AA
-hg17	12693	12688	2	-	pattern1	.	3	2483	2484	AA
-hg17	12690	12685	2	-	pattern1	.	3	2484	2485	AA
-hg17	12489	12484	2	-	pattern1	.	3	2551	2552	AA
-hg17	12159	12154	2	-	pattern1	.	3	2661	2662	AA
-hg17	10050	10045	2	-	pattern1	.	3	3364	3365	AA
-hg17	10047	10042	2	-	pattern1	.	3	3365	3366	AA
-hg17	9996	9991	2	-	pattern1	.	3	3382	3383	AA
-hg17	9843	9838	2	-	pattern1	.	3	3433	3434	AA
-hg17	9771	9766	2	-	pattern1	.	3	3457	3458	AA
-hg17	9717	9712	2	-	pattern1	.	3	3475	3476	AA
-hg17	9345	9340	2	-	pattern1	.	3	3599	3600	AA
-hg17	9234	9229	2	-	pattern1	.	3	3636	3637	AA
-hg17	8586	8581	2	-	pattern1	.	3	3852	3853	AA
-hg17	5196	5191	2	-	pattern1	.	3	4982	4983	AA
-hg17	4317	4312	2	-	pattern1	.	3	5275	5276	AA
-hg17	4101	4096	2	-	pattern1	.	3	5347	5348	AA
-hg17	3963	3958	2	-	pattern1	.	3	5393	5394	AA
-hg17	3960	3955	2	-	pattern1	.	3	5394	5395	AA


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_garnier_out.tabular
--- a/test-data/emboss_garnier_out.tabular
+++ /dev/null
@@ -1,102 +0,0 @@
-SeqName	Start	End	Score	Strand	helix	sheet	turns	coil
-Sequence	1	9	0.000	+	.	.	T	.
-Sequence	10	10	0.000	+	.	E	.	.
-Sequence	11	16	0.000	+	H	.	.	.
-Sequence	17	39	0.000	+	.	.	T	.
-Sequence	40	40	0.000	+	H	.	.	.
-Sequence	41	42	0.000	+	.	E	.	.
-Sequence	43	48	0.000	+	.	.	T	.
-Sequence	49	52	0.000	+	.	E	.	.
-Sequence	53	68	0.000	+	.	.	T	.
-Sequence	69	75	0.000	+	H	.	.	.
-Sequence	76	78	0.000	+	.	E	.	.
-Sequence	79	87	0.000	+	.	.	T	.
-Sequence	88	90	0.000	+	.	E	.	.
-Sequence	91	96	0.000	+	H	.	.	.
-Sequence	97	98	0.000	+	.	E	.	.
-Sequence	99	99	0.000	+	.	.	.	C
-Sequence	100	107	0.000	+	.	.	T	.
-Sequence	108	111	0.000	+	.	E	.	.
-Sequence	112	116	0.000	+	.	.	T	.
-Sequence	117	120	0.000	+	.	E	.	.
-Sequence	121	123	0.000	+	.	.	T	.
-Sequence	124	126	0.000	+	.	.	.	C
-Sequence	127	131	0.000	+	.	E	.	.
-Sequence	132	153	0.000	+	.	.	T	.
-Sequence	154	157	0.000	+	.	E	.	.
-Sequence	158	161	0.000	+	.	.	T	.
-Sequence	162	162	0.000	+	.	.	.	C
-Sequence	163	164	0.000	+	.	E	.	.
-Sequence	165	172	0.000	+	.	.	T	.
-Sequence	173	176	0.000	+	.	E	.	.
-Sequence	177	180	0.000	+	.	.	T	.
-Sequence	181	183	0.000	+	.	.	.	C
-Sequence	184	187	0.000	+	.	E	.	.
-Sequence	188	194	0.000	+	.	.	.	C
-Sequence	195	206	0.000	+	H	.	.	.
-Sequence	207	234	0.000	+	.	.	T	.
-Sequence	235	237	0.000	+	.	E	.	.
-Sequence	238	241	0.000	+	.	.	T	.
-Sequence	242	242	0.000	+	.	.	.	C
-Sequence	243	246	0.000	+	.	E	.	.
-Sequence	247	247	0.000	+	.	.	T	.
-Sequence	248	249	0.000	+	.	.	.	C
-Sequence	250	275	0.000	+	.	.	T	.
-Sequence	276	282	0.000	+	.	E	.	.
-Sequence	283	283	0.000	+	H	.	.	.
-Sequence	284	289	0.000	+	.	.	.	C
-Sequence	290	301	0.000	+	.	.	T	.
-Sequence	302	307	0.000	+	.	E	.	.
-Sequence	308	313	0.000	+	.	.	.	C
-Sequence	314	321	0.000	+	.	.	T	.
-Sequence	322	322	0.000	+	.	E	.	.
-Sequence	323	344	0.000	+	.	.	T	.
-Sequence	345	348	0.000	+	.	E	.	.
-Sequence	349	360	0.000	+	.	.	T	.
-Sequence	361	363	0.000	+	.	E	.	.
-Sequence	364	374	0.000	+	.	.	T	.
-Sequence	375	378	0.000	+	.	E	.	.
-Sequence	379	381	0.000	+	.	.	T	.
-Sequence	382	384	0.000	+	.	.	.	C
-Sequence	385	386	0.000	+	.	E	.	.
-Sequence	387	392	0.000	+	.	.	.	C
-Sequence	393	396	0.000	+	.	E	.	.
-Sequence	397	401	0.000	+	.	.	T	.
-Sequence	402	402	0.000	+	.	.	.	C
-Sequence	403	403	0.000	+	.	E	.	.
-Sequence	404	406	0.000	+	.	.	T	.
-Sequence	407	407	0.000	+	.	.	.	C
-Sequence	408	409	0.000	+	.	.	T	.
-Sequence	410	412	0.000	+	.	E	.	.
-Sequence	413	422	0.000	+	.	.	T	.
-Sequence	423	427	0.000	+	.	E	.	.
-Sequence	428	436	0.000	+	H	.	.	.
-Sequence	437	441	0.000	+	.	E	.	.
-Sequence	442	444	0.000	+	.	.	T	.
-Sequence	445	447	0.000	+	.	.	.	C
-Sequence	448	452	0.000	+	.	E	.	.
-Sequence	453	455	0.000	+	.	.	.	C
-Sequence	456	457	0.000	+	.	.	T	.
-Sequence	458	460	0.000	+	.	.	.	C
-Sequence	461	463	0.000	+	.	E	.	.
-Sequence	464	467	0.000	+	.	.	T	.
-Sequence	468	469	0.000	+	.	E	.	.
-Sequence	470	480	0.000	+	.	.	T	.
-Sequence	481	484	0.000	+	.	E	.	.
-Sequence	485	490	0.000	+	.	.	T	.
-Sequence	491	491	0.000	+	.	E	.	.
-Sequence	492	496	0.000	+	.	.	T	.
-Sequence	497	497	0.000	+	.	.	.	C
-Sequence	498	500	0.000	+	.	.	T	.
-Sequence	501	504	0.000	+	.	E	.	.
-Sequence	505	510	0.000	+	.	.	T	.
-Sequence	511	514	0.000	+	.	E	.	.
-Sequence	515	517	0.000	+	.	.	.	C
-Sequence	518	520	0.000	+	.	E	.	.
-Sequence	521	532	0.000	+	.	.	.	C
-Sequence	533	534	0.000	+	.	E	.	.
-Sequence	535	547	0.000	+	H	.	.	.
-Sequence	548	549	0.000	+	.	E	.	.
-Sequence	550	554	0.000	+	.	.	T	.
-Sequence	555	555	0.000	+	.	.	.	C
-Sequence	556	561	0.000	+	H	.	.	.


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_geecee_out.geecee
--- a/test-data/emboss_geecee_out.geecee
+++ /dev/null
@@ -1,2 +0,0 @@
-#Sequence   GC content
-Sequence      0.36


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_getorf_out.fasta
--- a/test-data/emboss_getorf_out.fasta
+++ /dev/null
@@ -1,65 +0,0 @@
->Sequence_1 [1 - 51] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-VRCLKYLLLSLHRPQFS
->Sequence_2 [14 - 94] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-NTFFCPYTDHSFPNGFTPTRNSCASTN
->Sequence_3 [94 - 129] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-LKAVGLECYRFV
->Sequence_4 [133 - 231] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-LSASLALIKGSFSLLWKTLWKNTTSTSLSPLVC
->Sequence_5 [155 - 250] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-SKVHFLYFGRRCGRIQQVRVSPPWFADYWIQL
->Sequence_6 [3 - 272] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAERVSCPDQRFIFSTLE
-DVVEEYNKYESLPPGLLITGYSCNTLRNTA
->Sequence_7 [235 - 309] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-LLDTVVIPFATPRNYLYELFSLYYM
->Sequence_8 [288 - 335] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-IIFPLLYVVGSSLIFL
->Sequence_9 [339 - 377] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-QVFYCFRPQCSCS
->Sequence_10 [254 - 391] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-YPSQHRVTIYMNYFPFIICSRFVFNLPLASLLLFSTSMFMFLGCFG
->Sequence_11 [395 - 427] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-YAVSLIFVVSS
->Sequence_12 [328 - 447] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-SSFSKSFTVFDLNVHVLRLFWIICGQFNLRCFFLKYLFMV
->Sequence_13 [411 - 521] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-SSLFLLKIFIHGLIFGLYLFRGQFIIYSVCIQQFFYF
->Sequence_14 [431 - 526] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-NIYSWFNFWFVLVQGPVHYLLCLYTAVLLFLV
->Sequence_15 [451 - 537] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-FLVCTCSGASSLFTLFVYSSSFIFSMILI
->Sequence_16 [531 - 487] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-NHTKNKRTAVYKQSK
->Sequence_17 [536 - 450] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-IKIILKIKELLYTNRVNNELAPEQVQTKN
->Sequence_18 [487 - 443] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-IMNWPLNKYKPKIKP
->Sequence_19 [468 - 439] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-TSTNQKLNHE
->Sequence_20 [439 - 410] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-INILRRNNED
->Sequence_21 [446 - 405] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-TMNKYFKKKQRRLN
->Sequence_22 [401 - 372] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-PHIIQNNLRT
->Sequence_23 [368 - 327] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-TLRSKTVKDLLKED
->Sequence_24 [426 - 292] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-EETTKIKLTAYYPKQPKNMNIEVENSKRLAKGRLKTNLLHIIKGK
->Sequence_25 [279 - 238] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-IVTRCCEGYYNCIQ
->Sequence_26 [234 - 175] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-SANQGGETRTCCILPQRLPK
->Sequence_27 [334 - 158] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-RKIKDEPTTYNKGKIIHIDSYAVLRRVLQLYPVISKPGGRDSYLLYSSTTSSKVEKMNL
->Sequence_28 [275 - 120] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-LRGVAKGITTVSSNQQTRGERLVLVVFFHNVFQSRENEPLIRARDALSYTNR
->Sequence_29 [162 - 112] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-TFDQGKRRAQLYKPVTL
->Sequence_30 [108 - 34] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-ANRFQLVLAQEFLVGVKPLGKLWSV
->Sequence_31 [50 - 3] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-ENCGLCRDKRRYFRHR
->Sequence_32 [154 - 2] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-SGQETRSAIQTGNTLGQPLSISACTRISSRCKAIRKTVVCVGTKEGILGIE


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_helixturnhelix_out.tabular
--- a/test-data/emboss_helixturnhelix_out.tabular
+++ /dev/null
@@ -1,1 +0,0 @@
-SeqName	Start	End	Score	Strand	Maximum_score_at	Standard_deviations


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_hmoment_out.hmoment
--- a/test-data/emboss_hmoment_out.hmoment
+++ /dev/null
@@ -1,556 +0,0 @@
-HMOMENT of Sequence from 1 to 561
-
-Window: 10 Angle: 100 Max uH: 0.205
-Position	uH
-1		0.100
-2		0.071
-3		0.127
-4		0.152
-5		0.127
-6		0.056
-7		0.049
-8		0.032
-9		0.066
-10		0.041
-11		0.019
-12		0.020
-13		0.081
-14		0.125
-15		0.092
-16		0.044
-17		0.040
-18		0.051
-19		0.063
-20		0.038
-21		0.063
-22		0.052
-23		0.065
-24		0.086
-25		0.106
-26		0.073
-27		0.048
-28		0.088
-29		0.082
-30		0.044
-31		0.007
-32		0.035
-33		0.041
-34		0.094
-35		0.035
-36		0.045
-37		0.073
-38		0.069
-39		0.024
-40		0.055
-41		0.040
-42		0.007
-43		0.066
-44		0.009
-45		0.071
-46		0.111
-47		0.095
-48		0.144
-49		0.138
-50		0.143
-51		0.113
-52		0.120
-53		0.078
-54		0.051
-55		0.042
-56		0.035
-57		0.055
-58		0.027
-59		0.037
-60		0.029
-61		0.032
-62		0.077
-63		0.148
-64		0.108
-65		0.035
-66		0.098
-67		0.128
-68		0.118
-69		0.083
-70		0.108
-71		0.112
-72		0.076
-73		0.116
-74		0.102
-75		0.043
-76		0.090
-77		0.073
-78		0.025
-79		0.031
-80		0.058
-81		0.043
-82		0.066
-83		0.075
-84		0.146
-85		0.173
-86		0.140
-87		0.142
-88		0.200
-89		0.154
-90		0.089
-91		0.140
-92		0.121
-93		0.063
-94		0.055
-95		0.051
-96		0.057
-97		0.075
-98		0.136
-99		0.132
-100		0.068
-101		0.067
-102		0.076
-103		0.055
-104		0.019
-105		0.043
-106		0.041
-107		0.022
-108		0.064
-109		0.060
-110		0.085
-111		0.090
-112		0.111
-113		0.049
-114		0.083
-115		0.131
-116		0.137
-117		0.099
-118		0.119
-119		0.120
-120		0.054
-121		0.064
-122		0.059
-123		0.042
-124		0.026
-125		0.032
-126		0.078
-127		0.104
-128		0.117
-129		0.096
-130		0.116
-131		0.108
-132		0.084
-133		0.056
-134		0.063
-135		0.058
-136		0.050
-137		0.048
-138		0.025
-139		0.047
-140		0.093
-141		0.072
-142		0.027
-143		0.021
-144		0.053
-145		0.022
-146		0.049
-147		0.040
-148		0.103
-149		0.154
-150		0.105
-151		0.076
-152		0.127
-153		0.126
-154		0.105
-155		0.088
-156		0.107
-157		0.131
-158		0.095
-159		0.052
-160		0.114
-161		0.088
-162		0.041
-163		0.071
-164		0.067
-165		0.008
-166		0.056
-167		0.060
-168		0.064
-169		0.059
-170		0.055
-171		0.046
-172		0.030
-173		0.092
-174		0.062
-175		0.036
-176		0.019
-177		0.038
-178		0.032
-179		0.037
-180		0.051
-181		0.100
-182		0.051
-183		0.036
-184		0.088
-185		0.090
-186		0.039
-187		0.080
-188		0.076
-189		0.079
-190		0.061
-191		0.074
-192		0.090
-193		0.042
-194		0.024
-195		0.063
-196		0.065
-197		0.050
-198		0.061
-199		0.077
-200		0.136
-201		0.116
-202		0.037
-203		0.092
-204		0.120
-205		0.066
-206		0.026
-207		0.070
-208		0.075
-209		0.041
-210		0.075
-211		0.082
-212		0.034
-213		0.031
-214		0.023
-215		0.048
-216		0.047
-217		0.098
-218		0.098
-219		0.083
-220		0.059
-221		0.103
-222		0.099
-223		0.085
-224		0.110
-225		0.127
-226		0.163
-227		0.132
-228		0.190
-229		0.194
-230		0.197
-231		0.154
-232		0.205
-233		0.171
-234		0.166
-235		0.148
-236		0.161
-237		0.106
-238		0.035
-239		0.026
-240		0.026
-241		0.038
-242		0.084
-243		0.016
-244		0.060
-245		0.121
-246		0.061
-247		0.028
-248		0.076
-249		0.046
-250		0.050
-251		0.072
-252		0.042
-253		0.033
-254		0.083
-255		0.031
-256		0.093
-257		0.106
-258		0.042
-259		0.055
-260		0.053
-261		0.008
-262		0.030
-263		0.062
-264		0.078
-265		0.037
-266		0.114
-267		0.108
-268		0.078
-269		0.107
-270		0.134
-271		0.117
-272		0.091
-273		0.150
-274		0.147
-275		0.071
-276		0.025
-277		0.064
-278		0.022
-279		0.069
-280		0.072
-281		0.044
-282		0.107
-283		0.170
-284		0.176
-285		0.116
-286		0.110
-287		0.128
-288		0.078
-289		0.059
-290		0.055
-291		0.061
-292		0.020
-293		0.051
-294		0.048
-295		0.055
-296		0.112
-297		0.139
-298		0.083
-299		0.055
-300		0.105
-301		0.100
-302		0.049
-303		0.087
-304		0.086
-305		0.069
-306		0.131
-307		0.096
-308		0.090
-309		0.095
-310		0.134
-311		0.102
-312		0.098
-313		0.062
-314		0.055
-315		0.111
-316		0.098
-317		0.106
-318		0.131
-319		0.132
-320		0.098
-321		0.097
-322		0.096
-323		0.059
-324		0.089
-325		0.083
-326		0.088
-327		0.025
-328		0.103
-329		0.065
-330		0.028
-331		0.086
-332		0.109
-333		0.100
-334		0.094
-335		0.116
-336		0.109
-337		0.111
-338		0.063
-339		0.043
-340		0.074
-341		0.099
-342		0.090
-343		0.073
-344		0.067
-345		0.086
-346		0.092
-347		0.089
-348		0.092
-349		0.044
-350		0.045
-351		0.066
-352		0.039
-353		0.019
-354		0.013
-355		0.059
-356		0.069
-357		0.070
-358		0.045
-359		0.079
-360		0.117
-361		0.081
-362		0.138
-363		0.135
-364		0.083
-365		0.034
-366		0.096
-367		0.071
-368		0.034
-369		0.029
-370		0.038
-371		0.083
-372		0.105
-373		0.112
-374		0.070
-375		0.096
-376		0.096
-377		0.079
-378		0.078
-379		0.072
-380		0.088
-381		0.036
-382		0.059
-383		0.056
-384		0.043
-385		0.114
-386		0.114
-387		0.107
-388		0.101
-389		0.089
-390		0.079
-391		0.029
-392		0.098
-393		0.100
-394		0.036
-395		0.106
-396		0.075
-397		0.085
-398		0.090
-399		0.091
-400		0.096
-401		0.048
-402		0.032
-403		0.049
-404		0.070
-405		0.110
-406		0.059
-407		0.107
-408		0.102
-409		0.106
-410		0.081
-411		0.138
-412		0.143
-413		0.112
-414		0.138
-415		0.136
-416		0.127
-417		0.113
-418		0.107
-419		0.111
-420		0.092
-421		0.134
-422		0.098
-423		0.055
-424		0.044
-425		0.055
-426		0.056
-427		0.040
-428		0.041
-429		0.095
-430		0.158
-431		0.153
-432		0.106
-433		0.186
-434		0.187
-435		0.118
-436		0.167
-437		0.162
-438		0.168
-439		0.108
-440		0.155
-441		0.121
-442		0.121
-443		0.059
-444		0.053
-445		0.098
-446		0.087
-447		0.119
-448		0.149
-449		0.149
-450		0.113
-451		0.069
-452		0.083
-453		0.084
-454		0.095
-455		0.119
-456		0.117
-457		0.100
-458		0.102
-459		0.096
-460		0.100
-461		0.116
-462		0.187
-463		0.150
-464		0.080
-465		0.106
-466		0.115
-467		0.085
-468		0.036
-469		0.098
-470		0.095
-471		0.112
-472		0.061
-473		0.077
-474		0.119
-475		0.141
-476		0.099
-477		0.154
-478		0.184
-479		0.185
-480		0.136
-481		0.194
-482		0.178
-483		0.177
-484		0.138
-485		0.132
-486		0.087
-487		0.055
-488		0.057
-489		0.051
-490		0.037
-491		0.087
-492		0.035
-493		0.031
-494		0.080
-495		0.053
-496		0.023
-497		0.045
-498		0.033
-499		0.030
-500		0.087
-501		0.089
-502		0.035
-503		0.064
-504		0.125
-505		0.132
-506		0.069
-507		0.085
-508		0.072
-509		0.088
-510		0.050
-511		0.049
-512		0.043
-513		0.064
-514		0.071
-515		0.111
-516		0.109
-517		0.082
-518		0.089
-519		0.054
-520		0.038
-521		0.032
-522		0.032
-523		0.038
-524		0.054
-525		0.059
-526		0.015
-527		0.068
-528		0.073
-529		0.026
-530		0.106
-531		0.055
-532		0.047
-533		0.103
-534		0.091
-535		0.049
-536		0.031
-537		0.032
-538		0.038
-539		0.068
-540		0.130
-541		0.077
-542		0.043
-543		0.104
-544		0.058
-545		0.045
-546		0.108
-547		0.084
-548		0.139
-549		0.189
-550		0.130
-551		0.062
-552		0.136


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_iep_out.iep
--- a/test-data/emboss_iep_out.iep
+++ /dev/null
@@ -1,31 +0,0 @@
-IEP of Sequence from 1 to 561
-Isoelectric Point = 5.0278
-
-   pH     Bound    Charge
-  1.00   108.00     1.00
-  1.50   107.99     0.99
-  2.00   107.98     0.98
-  2.50   107.93     0.93
-  3.00   107.80     0.80
-  3.50   107.56     0.56
-  4.00   107.28     0.28
-  4.50   107.10     0.10
-  5.00   107.00     0.00
-  5.50   106.91    -0.09
-  6.00   106.67    -0.33
-  6.50   105.94    -1.06
-  7.00   103.73    -3.27
-  7.50    97.29    -9.71
-  8.00    81.33   -25.67
-  8.50    53.56   -53.44
-  9.00    25.75   -81.25
-  9.50     9.75   -97.25
- 10.00     3.29   -103.71
- 10.50     1.06   -105.94
- 11.00     0.34   -106.66
- 11.50     0.11   -106.89
- 12.00     0.03   -106.97
- 12.50     0.01   -106.99
- 13.00     0.00   -107.00
- 13.50     0.00   -107.00
- 14.00     0.00   -107.00


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_isochore_out.isochore
--- a/test-data/emboss_isochore_out.isochore
+++ /dev/null
@@ -1,7 +0,0 @@
-Position	Percent G+C 1 .. 561
-140	0.446
-196	0.414
-252	0.396
-308	0.357
-364	0.332
-420	0.282


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_marscan_out.tabular
--- a/test-data/emboss_marscan_out.tabular
+++ /dev/null
@@ -1,4 +0,0 @@
-SeqName	Start	End	Score	Strand	type	start8bp	end8bp	start16bp	end16bp
-hg17	440	492	0.000	+	MAR/SAR recognition site (MRS)	440	447	477	492
-hg17	13640	13750	0.000	+	MAR/SAR recognition site (MRS)	13640	13647	13735	13750
-hg17	15229	15392	0.000	+	MAR/SAR recognition site (MRS)	15385	15392	15229	15244


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_maskfeat_out.fasta
--- a/test-data/emboss_maskfeat_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_maskseq_out.fasta
--- a/test-data/emboss_maskseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-NNNcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_matcher_out.fasta
--- a/test-data/emboss_matcher_out.fasta
+++ /dev/null
@@ -1,6 +0,0 @@
->Sequence
-CTTTAGCAAGTCTTTTACTGTTTTCGACCTCAATGTTCATGTTCTTAGGTTGTTTTGGAT
-A
->hg17
-CTTCAGCAAGTTCCTTACTGTCTTTAAGCCTTGTTTTCATCATCT--GGATAATGGGGAT
-A


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_msbar_out.fasta
--- a/test-data/emboss_msbar_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_needle_out.score
--- a/test-data/emboss_needle_out.score
+++ /dev/null
@@ -1,4 +0,0 @@
-Sequence hg17 20190 (604.5)
-
-#---------------------------------------
-#---------------------------------------


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_newcpgreport_out.newcpgreport
--- a/test-data/emboss_newcpgreport_out.newcpgreport
+++ /dev/null
@@ -1,11 +0,0 @@
-ID   Sequence  561 BP.
-XX
-DE   CpG Island report.
-XX
-CC   Obs/Exp ratio > 0.60.
-CC   % C + % G > 50.00.
-CC   Length > 200.
-XX
-FH   Key              Location/Qualifiers
-FT   no islands detected
-//


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_newcpgseek_out.newcpgseek
--- a/test-data/emboss_newcpgseek_out.newcpgseek
+++ /dev/null
@@ -1,9 +0,0 @@
-
-
-NEWCPGSEEK of Sequence from 1 to 561
-with score > 17 
-
- Begin    End  Score        CpG  %CG  CG/GC
-   121    141    34          3  57.1   1.00
-   261    272    43          3  75.0   1.00
--------------------------------------------
\ No newline at end of file


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_newseq_out.fasta
--- a/test-data/emboss_newseq_out.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->cytoc fragment of cytochrome c
-KKKEERADLIAY


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_noreturn_out.noreturn
--- a/test-data/emboss_noreturn_out.noreturn
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt
-tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac
-cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg
-aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg
-gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt
-tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac
-ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt
-ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt
-tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa
-aacaattcta atggtcaaaa a


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_notseq_out.fasta
--- a/test-data/emboss_notseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_nthseq_out.fasta
--- a/test-data/emboss_nthseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_palindrome_out.palindrome
--- a/test-data/emboss_palindrome_out.palindrome
+++ /dev/null
@@ -1,15 +0,0 @@
-Palindromes of:  Sequence 
-Sequence length is: 561 
-Start at position: 1
-End at position: 561
-Minimum length of Palindromes is: 10 
-Maximum length of Palindromes is: 100 
-Maximum gap between elements is: 100 
-Number of mismatches allowed in Palindrome: 0
-
-
-
-Palindromes:
-
-
-


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_pasteseq_out.fasta
--- a/test-data/emboss_pasteseq_out.fasta
+++ /dev/null
@@ -1,371 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccag
-gctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagt
-caggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagcca
-ctaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTG
-ACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC----------------
----------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------T
-GAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATT
-ATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtata
-gactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-c
-agaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtc
-atgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt-----------
------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatat
-tgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaa
-actttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa------
-------------------------------------------------------------
-----------------------------atagactcctaccaa-----------------
----------------------------------ctc-aaagaatgcacattctCTGGGAA
-ACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTG
-ATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTT
-TAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT
--ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTC
-Aattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggac
-tgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAA
-AGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGC
-TTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGA
-TGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATC
-AATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-
-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatatt
-acatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaat
-tcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaact
-attcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctcc
-ctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccg
-tggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaa
-ataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatctt
-cataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacaga
-ttgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcag
-aataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcgggg
-tcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagta
-ggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaa
-ggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgca
-atggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggt
-ggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactg
-ttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagaccctta
-tcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccct
-caccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacag
-tactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtact
-ctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaa
-atattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagc
-atgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgta
-gaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcacca
-acgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-at
-tgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcac
-tgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctggg
-attacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttc
-accatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcct
-cccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGG
-AGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg--------
------------ggttcctagcccattgctattcctt----accagctgtggattctaagg
-aaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaac
-aaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATA
-CAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACA
-TCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGA
-CCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGA
-GCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTC
-TCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGG
-AGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAG
-GGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAG
-GACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAccc
-ccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC---
--------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTA
-CCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCC
-GAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAG
-CAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGC
-CGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGG
-CATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTC
-CTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATC
-CCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAG
-CTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGA
-TTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCA
-GGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATT
-GGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA-
---TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGAC
-ATTGCCTTGCTCTGCGGGTAGGAATTCAGGATTCATTTTCCAGGGAAG--------TTCC
-TGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAG
-TAGAGGTGGGGGGAAACAAGTGTCAGGAAGA-----------------------------
----------------CTCAAA---------ATCTTC------------------------
---------------------------------------CAGAGAAATTGT-----GCAGG
-GTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATG
-AGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAAC
-TTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTAT
-AGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACAC
-TCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACA
-GTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAG
-G----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAG
-AGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GT
-GCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGG
-TGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGAT
-TGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAA
-TGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAGACAAGG
-CAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCC
-CAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCC
-TCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAA
-TATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGAC
-AGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGT
-CTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC-
-TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAG
-GAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGC
-ACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCA
-TCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCC
-TTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGC
-TTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTG
-ACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTG
-TTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATT
-TCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGG
-G-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---G
-GGAGGGCAGGGCAGGGGTCTCTGAGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCC
-AGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGA
-TGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCAC
-ATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCA
-TTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCA
-AAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTT
-ACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagat
-atttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga-
----------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttct
-gagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaa
-ttgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaag
-gcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaacccc
-atctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagct
-acttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgag
-ccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacaca
-cacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-t
-atctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATGTAACCCCT
-GTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTG
-GTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTG
-TGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTG
-AATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGA
-AAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCC
-TGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCT
-CACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTC
-TGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAA
-TGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCC
-ACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAG
-GAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGT
-AGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgt
-gtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCC
-TACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTC
-TACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttg
-gcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagt
-tcacacactgcctcccttgcaaagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTT
-TGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGT
-TGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAAC
-TTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGA
-GTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG-
-AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCA
-AATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT---
-----CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTG
-GG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAA
-GAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggcc
-gaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcct
-cgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagc
-tacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggtt
-gcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtca
-aaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCA
-TCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTT
-GTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACCAGCTTCTTAG
-GGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAA
-CTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGC
-AGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTAT
-ATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatctttttt
-ggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtg
-atcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcc
-caagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta
---ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggct
-caagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacac
-ccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTT
-CTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GC
-CAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AG
-GGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC
----CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCT
-CCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC----
-----TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAA
-TGTTCAA--AACTGCTTTGGAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACA
-GCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACA
-GCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGA
-CTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGG
-ACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAG
-TTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TG
-CTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGA
-TTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCC
-ACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctc
-tcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatct
-cctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gca
-ttggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcag
-ccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaa
-aactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATA
-GCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACC
-CAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaat
-gcggtggctcacgcctgtaatctcaacactttgggaggccgaggtgggcagataatctga
-ggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatac
-aaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaa
-ggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcc
-tatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccag
-ctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgag
-ccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaag
-aaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggagg
-atgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaa
-cactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaat
-aaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGC
-ACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAAT
-CAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATC
-CCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTG
-GCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATT
-ATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtg
-gtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGA
-ATTATTCCTCCTCTC-CTCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTT
-CTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTA
-ATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtt
-tggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtct
-ctcacacacacccagcacaagtccaag-------------------------accagcat
-ggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagt
-tgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccata
-tctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacg
-acaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttag
-tcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatg
-gccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaaga
-tattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgt
-gtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GAT
-TCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATA
-GGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAG
-CTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTG
-GTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGAGGGTGGCCATTATT
-TGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGG
-GGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTG
-GAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCA
-CTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTA
-ACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGG
-AAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAA
-ATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAG
-CTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGAC
-TGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGG
-A---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc-------
--------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctg
-agccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAA
-CATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCC
-TACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACG
-AGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAAT
-ATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATT
-GGCCACAGACTCGCATACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAA
-TTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGA
-CTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtc
-tttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccat
-atttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgcctt
-ccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcc
-cattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgt
-tgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcag
-taagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAG
-TGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATG
-GGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACA
-CCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagataga
-tatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatg
-cagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AG
-CATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAG
-CTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCT
-AAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTCTTTGACTTTGAGGGGA
-TGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTG
-GTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCT
-GTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTG
-TGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAA
-GTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCA
-CACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCAC
-TGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctg
-aatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTC
-TGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG----------
-----------------------------------------------TTCTAATTCTAAAC
-CACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggct
-gggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcat
-tcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaa
-taataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggct
-gagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgcca
-ccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaat
-aaaAGTCATAGGATTTgatcaggcatgatgggtcacatctgtaagcccattgctttagga
-ggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggca
-agacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGA
-TTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCG
-ATTAGCTGAGC----------CACATGCAGGCACAG------------------------
-CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCC
-TCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCT
-TG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------C
-TCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tg
-tagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccct
-ttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtctttt
-ctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaa
-ttaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaa
-gttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacaca
-cta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCC
-CCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA
--GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGAT
-AGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaa
-aaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCC
-CACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGT
-CAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACT
-GGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTAC
-GGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCG
-GCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGA
-GGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGT
-TCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAG
-GGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTG
-GCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAG
-GAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCG
-A--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGT
-CTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGAC
-CTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTC
-CAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCT
-GGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCT
-GGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCA
-GGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGA
-AGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCC
-AGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGAC
-TCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAA
-GATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGG
-CTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCC
-TCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCA
-GGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGG
-TTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTC
-CC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATG
-GATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCT
-CCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTT
-GAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCA
-GTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTG
-CAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTT
-TTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGG
-GAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAG
-TGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA--------
-----TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTT
-CTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCA
-GAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTC
-CGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGA
-TCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCT
-GGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTC
-TTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTT
-TACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACT
-GCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGG
-TCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTT
-TTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-
-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagct
-cacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCA
-AACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCA
-AATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCA
-GGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggca
-tcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaa
-tttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC
-TTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC
-TTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACG
-CAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAA
-ACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA
-AACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA
-AACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA
-GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA
-GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA
-GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATC
-CATCCAGAATAAAACGCAgttcgatgcctaaaataccttcttttgtccctacacagacca
-cagttttcctaatggctttacaccgactagaaattcttgtgcaagcactaattgaaagcg
-gttggcctagagtgttaccggtttgtatagctgagcgcgtctcttgccctgatcaaaggt
-tcattttctctactttggaagacgttgtggaagaatacaacaagtacgagtctctccccc
-ctggtttgctgattactggatacagttgtaatacccttcgcaacaccgcgtaactatcta
-tatgaattattttccctttattatatgtagtaggttcgtctttaatcttcctttagcaag
-tcttttactgttttcgacctcaatgttcatgttcttaggttgttttggataatatgcggt
-cagtttaatcttcgttgtttcttcttaaaatatttattcatggtttaatttttggtttgt
-acttgttcaggggccagttcattatttactctgtttgtatacagcagttcttttattttt
-agtatgattttaatttaaaacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_patmatdb_out.tabular
--- a/test-data/emboss_patmatdb_out.tabular
+++ /dev/null
@@ -1,41 +0,0 @@
-SeqName	Start	End	Score	Strand
-Sequence	560	561	2	+
-Sequence	559	560	2	+
-Sequence	558	559	2	+
-Sequence	557	558	2	+
-Sequence	550	551	2	+
-Sequence	544	545	2	+
-Sequence	541	542	2	+
-Sequence	540	541	2	+
-Sequence	539	540	2	+
-Sequence	534	535	2	+
-Sequence	449	450	2	+
-Sequence	431	432	2	+
-Sequence	430	431	2	+
-Sequence	429	430	2	+
-Sequence	409	410	2	+
-Sequence	393	394	2	+
-Sequence	364	365	2	+
-Sequence	340	341	2	+
-Sequence	326	327	2	+
-Sequence	287	288	2	+
-Sequence	274	275	2	+
-Sequence	264	265	2	+
-Sequence	252	253	2	+
-Sequence	204	205	2	+
-Sequence	201	202	2	+
-Sequence	196	197	2	+
-Sequence	193	194	2	+
-Sequence	181	182	2	+
-Sequence	158	159	2	+
-Sequence	157	158	2	+
-Sequence	98	99	2	+
-Sequence	97	98	2	+
-Sequence	92	93	2	+
-Sequence	85	86	2	+
-Sequence	74	75	2	+
-Sequence	73	74	2	+
-Sequence	53	54	2	+
-Sequence	14	15	2	+
-Sequence	13	14	2	+
-Sequence	12	13	2	+


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_pepcoil_out.pepcoil
--- a/test-data/emboss_pepcoil_out.pepcoil
+++ /dev/null
@@ -1,6 +0,0 @@
-PEPCOIL of Sequence
-   using a window of 28 residues
-
-
-Other structures from 1 to 561 (561 residues)
-   Max score: 0.827 (probability 0.00)


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_pepstats_out.pepstats
--- a/test-data/emboss_pepstats_out.pepstats
+++ /dev/null
@@ -1,48 +0,0 @@
-PEPSTATS of Sequence from 1 to 561
-
-Molecular weight = 48582.66  		Residues = 561   
-Average Residue Weight  = 86.600  	Charge   = 0.0   
-Isoelectric Point = 5.0278
-A280 Molar Extinction Coefficient  = 0       
-A280 Extinction Coefficient 1mg/ml = 0.00      
-Improbability of expression in inclusion bodies = 0.520
-
-Residue		Number		Mole%		DayhoffStat
-A = Ala		135		24.064 		2.798  	
-B = Asx		0		0.000  		0.000  	
-C = Cys		106		18.895 		6.515  	
-D = Asp		0		0.000  		0.000  	
-E = Glu		0		0.000  		0.000  	
-F = Phe		0		0.000  		0.000  	
-G = Gly		98		17.469 		2.080  	
-H = His		0		0.000  		0.000  	
-I = Ile		0		0.000  		0.000  	
-J = ---		0		0.000  		0.000  	
-K = Lys		0		0.000  		0.000  	
-L = Leu		0		0.000  		0.000  	
-M = Met		0		0.000  		0.000  	
-N = Asn		0		0.000  		0.000  	
-O = ---		0		0.000  		0.000  	
-P = Pro		0		0.000  		0.000  	
-Q = Gln		0		0.000  		0.000  	
-R = Arg		0		0.000  		0.000  	
-S = Ser		0		0.000  		0.000  	
-T = Thr		222		39.572 		6.487  	
-U = ---		0		0.000  		0.000  	
-V = Val		0		0.000  		0.000  	
-W = Trp		0		0.000  		0.000  	
-X = Xaa		0		0.000  		0.000  	
-Y = Tyr		0		0.000  		0.000  	
-Z = Glx		0		0.000  		0.000  	
-
-Property	Residues		Number		Mole%
-Tiny		(A+C+G+S+T)		561		100.000
-Small		(A+B+C+D+G+N+P+S+T+V)	561		100.000
-Aliphatic	(A+I+L+V)		135		24.064
-Aromatic	(F+H+W+Y)		0		 0.000
-Non-polar	(A+C+F+G+I+L+M+P+V+W+Y)	339		60.428
-Polar		(D+E+H+K+N+Q+R+S+T+Z)	222		39.572
-Charged		(B+D+E+H+K+R+Z)		0		 0.000
-Basic		(H+K+R)			0		 0.000
-Acidic		(B+D+E+Z)		0		 0.000
-


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_plotorf_out.png
Binary file test-data/emboss_plotorf_out.png has changed


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_plotorf_out1.png
Binary file test-data/emboss_plotorf_out1.png has changed


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_polydot_out.png
Binary file test-data/emboss_polydot_out.png has changed


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_prettyseq_out.prettyseq
--- a/test-data/emboss_prettyseq_out.prettyseq
+++ /dev/null
@@ -1,42 +0,0 @@
-PRETTYSEQ of Sequence from 1 to 561
-
-           ---------|---------|---------|---------|---------|---------|
-         1 gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt 60
-         1 V  R  C  L  K  Y  L  L  L  S  L  H  R  P  Q  F  S  *  W  L   2
-
-           ---------|---------|---------|---------|---------|---------|
-        61 tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac 120
-         3 Y  T  D  *  K  F  L  C  K  H  *  L  K  A  V  G  L  E  C  Y   9
-
-           ---------|---------|---------|---------|---------|---------|
-       121 cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg 180
-        10 R  F  V  *  L  S  A  S  L  A  L  I  K  G  S  F  S  L  L  W   16
-
-           ---------|---------|---------|---------|---------|---------|
-       181 aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg 240
-        17 K  T  L  W  K  N  T  T  S  T  S  L  S  P  L  V  C  *  L  L   2
-
-           ---------|---------|---------|---------|---------|---------|
-       241 gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt 300
-         3 D  T  V  V  I  P  F  A  T  P  R  N  Y  L  Y  E  L  F  S  L   22
-
-           ---------|---------|---------|---------|---------|---------|
-       301 tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac 360
-        23 Y  Y  M  *  *  V  R  L  *  S  S  F  S  K  S  F  T  V  F  D   11
-
-           ---------|---------|---------|---------|---------|---------|
-       361 ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt 420
-        12 L  N  V  H  V  L  R  L  F  W  I  I  C  G  Q  F  N  L  R  C   31
-
-           ---------|---------|---------|---------|---------|---------|
-       421 ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt 480
-        32 F  F  L  K  Y  L  F  M  V  *  F  L  V  C  T  C  S  G  A  S   10
-
-           ---------|---------|---------|---------|---------|---------|
-       481 tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa 540
-        11 S  L  F  T  L  F  V  Y  S  S  S  F  I  F  S  M  I  L  I  *   29
-
-           ---------|---------|-
-       541 aacaattctaatggtcaaaaa 561
-         1 N  N  S  N  G  Q  K   7
-


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_primersearch.fasta
--- a/test-data/emboss_primersearch.fasta
+++ /dev/null
@@ -1,7 +0,0 @@
-# This is my primer file
-D1S243  cacacaggctcacatgcc      gctccagcgtcatggact
-D1S468 aattaaccgttttggtcct     gcgacacacacttccc 
-D1S2845 ccaaagggtgcttctc        gtggcattccaacctc
-D1S1608 gatggcttttggggactatt    cactgagccaagtgacacag
-D1S2893 aaaacatcaactctcccctg    ctcaaaccccaataagcctt
-D1S2660 cacacatgcacatgcac       agtgacaccagcaggg


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_primersearch_out.primersearch
--- a/test-data/emboss_primersearch_out.primersearch
+++ /dev/null
@@ -1,12 +0,0 @@
-
-Primer name D1S243
-
-Primer name D1S468
-
-Primer name D1S2845
-
-Primer name D1S1608
-
-Primer name D1S2893
-
-Primer name D1S2660


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_revseq_out.fasta
--- a/test-data/emboss_revseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tttttgaccattagaattgttttaaattaaaatcatactaaaaataaaagaactgctgta
-tacaaacagagtaaataatgaactggcccctgaacaagtacaaaccaaaaattaaaccat
-gaataaatattttaagaagaaacaacgaagattaaactgaccgcatattatccaaaacaa
-cctaagaacatgaacattgaggtcgaaaacagtaaaagacttgctaaaggaagattaaag
-acgaacctactacatataataaagggaaaataattcatatagatagttacgcggtgttgc
-gaagggtattacaactgtatccagtaatcagcaaaccaggggggagagactcgtacttgt
-tgtattcttccacaacgtcttccaaagtagagaaaatgaacctttgatcagggcaagaga
-cgcgctcagctatacaaaccggtaacactctaggccaaccgctttcaattagtgcttgca
-caagaatttctagtcggtgtaaagccattaggaaaactgtggtctgtgtagggacaaaag
-aaggtattttaggcatcgaac


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_seqmatchall_out.fasta
--- a/test-data/emboss_seqmatchall_out.fasta
+++ /dev/null
@@ -1,3 +0,0 @@
-
-#---------------------------------------
-#---------------------------------------


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_seqret_out.fasta
--- a/test-data/emboss_seqret_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_sigcleave_out.tabular
--- a/test-data/emboss_sigcleave_out.tabular
+++ /dev/null
@@ -1,6 +0,0 @@
-SeqName	Start	End	Score	Strand	mature_peptide
-Sequence	27	39	5.175	+	CCACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCA
-Sequence	253	265	4.809	+	CACCGCGTAACTATCTATATGAATTATTTTCCCTTTATTATATGTAGTAG
-Sequence	29	41	4.790	+	ACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACT
-Sequence	541	553	3.820	+	GTCAAAAA
-Sequence	30	42	3.530	+	CAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACTA


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_sirna_out.fasta
--- a/test-data/emboss_sirna_out.fasta
+++ /dev/null
@@ -1,158 +0,0 @@
->Sequence_92 %GC 50.0 Score 9 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aattgaaagcggttggcctagag
->Sequence_53 %GC 45.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aatggctttacaccgactagaaa
->Sequence_97 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aaagcggttggcctagagtgtta
->Sequence_98 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aagcggttggcctagagtgttac
->Sequence_201 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aacaagtacgagtctctcccccc
->Sequence_14 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aataccttcttttgtccctacac
->Sequence_85 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aagcactaattgaaagcggttgg
->Sequence_181 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aagacgttgtggaagaatacaac
->Sequence_196 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aatacaacaagtacgagtctctc
->Sequence_204 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aagtacgagtctctcccccctgg
->Sequence_252 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aatacccttcgcaacaccgcgta
->Sequence_264 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aacaccgcgtaactatctatatg
->Sequence_38 %GC 45.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gaccacagttttcctaatggctt
->Sequence_73 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aaattcttgtgcaagcactaatt
->Sequence_96 %GC 55.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gaaagcggttggcctagagtgtt
->Sequence_118 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taccggtttgtatagctgagcgc
->Sequence_200 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-caacaagtacgagtctctccccc
->Sequence_326 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aatcttcctttagcaagtctttt
->Sequence_364 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aatgttcatgttcttaggttgtt
->Sequence_12 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aaaataccttcttttgtccctac
->Sequence_13 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aaataccttcttttgtccctaca
->Sequence_16 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taccttcttttgtccctacacag
->Sequence_32 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tacacagaccacagttttcctaa
->Sequence_52 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taatggctttacaccgactagaa
->Sequence_74 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aattcttgtgcaagcactaattg
->Sequence_88 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-cactaattgaaagcggttggcct
->Sequence_91 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taattgaaagcggttggcctaga
->Sequence_128 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tatagctgagcgcgtctcttgcc
->Sequence_173 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tactttggaagacgttgtggaag
->Sequence_193 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aagaatacaacaagtacgagtct
->Sequence_198 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tacaacaagtacgagtctctccc
->Sequence_243 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tacagttgtaatacccttcgcaa
->Sequence_251 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taatacccttcgcaacaccgcgt
->Sequence_313 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taggttcgtctttaatcttcctt
->Sequence_340 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aagtcttttactgttttcgacct
->Sequence_393 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aatatgcggtcagtttaatcttc
->Sequence_489 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tactctgtttgtatacagcagtt
->Sequence_34 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-cacagaccacagttttcctaatg
->Sequence_36 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-cagaccacagttttcctaatggc
->Sequence_61 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tacaccgactagaaattcttgtg
->Sequence_63 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-caccgactagaaattcttgtgca
->Sequence_70 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tagaaattcttgtgcaagcacta
->Sequence_84 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-caagcactaattgaaagcggttg
->Sequence_110 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tagagtgttaccggtttgtatag
->Sequence_112 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gagtgttaccggtttgtatagct
->Sequence_135 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gagcgcgtctcttgccctgatca
->Sequence_180 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gaagacgttgtggaagaatacaa
->Sequence_183 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gacgttgtggaagaatacaacaa
->Sequence_203 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-caagtacgagtctctcccccctg
->Sequence_210 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gagtctctcccccctggtttgct
->Sequence_245 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-cagttgtaatacccttcgcaaca
->Sequence_254 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tacccttcgcaacaccgcgtaac
->Sequence_263 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-caacaccgcgtaactatctatat
->Sequence_266 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-caccgcgtaactatctatatgaa
->Sequence_348 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tactgttttcgacctcaatgttc
->Sequence_395 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tatgcggtcagtttaatcttcgt
->Sequence_157 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aaaggttcattttctctactttg
->Sequence_158 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aaggttcattttctctactttgg
->Sequence_207 %GC 65.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tacgagtctctcccccctggttt
->Sequence_325 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taatcttcctttagcaagtcttt
->Sequence_392 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taatatgcggtcagtttaatctt
->Sequence_409 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-aatcttcgttgtttcttcttaaa
->Sequence_11 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-taaaataccttcttttgtcccta
->Sequence_41 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-cacagttttcctaatggctttac
->Sequence_43 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-cagttttcctaatggctttacac
->Sequence_67 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gactagaaattcttgtgcaagca
->Sequence_72 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gaaattcttgtgcaagcactaat
->Sequence_130 %GC 65.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tagctgagcgcgtctcttgccct
->Sequence_192 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gaagaatacaacaagtacgagtc
->Sequence_195 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gaatacaacaagtacgagtctct
->Sequence_236 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tactggatacagttgtaataccc
->Sequence_241 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gatacagttgtaatacccttcgc
->Sequence_304 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tatatgtagtaggttcgtcttta
->Sequence_306 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tatgtagtaggttcgtctttaat
->Sequence_310 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-tagtaggttcgtctttaatcttc
->Sequence_358 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gacctcaatgttcatgttcttag
->Sequence_370 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-catgttcttaggttgttttggat
->Sequence_156 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-caaaggttcattttctctacttt
->Sequence_403 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-cagtttaatcttcgttgtttctt


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_sixpack_out2.sixpack
--- a/test-data/emboss_sixpack_out2.sixpack
+++ /dev/null
@@ -1,134 +0,0 @@
-
-
-          V  R  C  L  K  Y  L  L  L  S  L  H  R  P  Q  F  S  *  W  L     F1
-           F  D  A  *  N  T  F  F  C  P  Y  T  D  H  S  F  P  N  G  F    F2
-            S  M  P  K  I  P  S  F  V  P  T  Q  T  T  V  F  L  M  A  L   F3
-          gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-                   10        20        30        40        50        60        
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          caagctacggattttatggaagaaaacagggatgtgtctggtgtcaaaaggattaccgaa
-           T  R  H  R  F  Y  R  R  K  D  R  C  L  G  C  N  E  *  H  S    F6
-          X  E  I  G  L  I  G  E  K  T  G  V  C  V  V  T  K  R  I  A     F5
-            N  S  A  *  F  V  K  K  Q  G  *  V  S  W  L  K  G  L  P  K   F4
-
-
-          Y  T  D  *  K  F  L  C  K  H  *  L  K  A  V  G  L  E  C  Y     F1
-           T  P  T  R  N  S  C  A  S  T  N  *  K  R  L  A  *  S  V  T    F2
-            H  R  L  E  I  L  V  Q  A  L  I  E  S  G  W  P  R  V  L  P   F3
-          tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-                   70        80        90        100       110       120       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          atgtggctgatctttaagaacacgttcgtgattaactttcgccaaccggatctcacaatg
-           *  V  S  *  F  N  K  H  L  C  *  N  F  A  T  P  R  S  H  *    F6
-          K  C  R  S  S  I  R  T  C  A  S  I  S  L  P  Q  G  L  T  N     F5
-            V  G  V  L  F  E  Q  A  L  V  L  Q  F  R  N  A  *  L  T  V   F4
-
-
-          R  F  V  *  L  S  A  S  L  A  L  I  K  G  S  F  S  L  L  W     F1
-           G  L  Y  S  *  A  R  L  L  P  *  S  K  V  H  F  L  Y  F  G    F2
-            V  C  I  A  E  R  V  S  C  P  D  Q  R  F  I  F  S  T  L  E   F3
-          cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-                   130       140       150       160       170       180       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          gccaaacatatcgactcgcgcagagaacgggactagtttccaagtaaaagagatgaaacc
-           R  N  T  Y  S  L  A  D  R  A  R  I  L  P  E  N  E  R  S  Q    F6
-          G  T  Q  I  A  S  R  T  E  Q  G  S  *  L  N  M  K  E  V  K     F5
-            P  K  Y  L  Q  A  R  R  K  G  Q  D  F  T  *  K  R  *  K  P   F4
-
-
-          K  T  L  W  K  N  T  T  S  T  S  L  S  P  L  V  C  *  L  L     F1
-           R  R  C  G  R  I  Q  Q  V  R  V  S  P  P  W  F  A  D  Y  W    F2
-            D  V  V  E  E  Y  N  K  Y  E  S  L  P  P  G  L  L  I  T  G   F3
-          aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-                   190       200       210       220       230       240       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          ttctgcaacaccttcttatgttgttcatgctcagagaggggggaccaaacgactaatgac
-           F  V  N  H  F  F  V  V  L  V  L  R  E  G  R  T  Q  Q  N  S    F6
-          S  S  T  T  S  S  Y  L  L  Y  S  D  R  G  G  P  K  S  I  V     F5
-            L  R  Q  P  L  I  C  C  T  R  T  E  G  G  Q  N  A  S  *  Q   F4
-
-
-          D  T  V  V  I  P  F  A  T  P  R  N  Y  L  Y  E  L  F  S  L     F1
-           I  Q  L  *  Y  P  S  Q  H  R  V  T  I  Y  M  N  Y  F  P  F    F2
-            Y  S  C  N  T  L  R  N  T  A  *  L  S  I  *  I  I  F  P  L   F3
-          gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-                   250       260       270       280       290       300       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          ctatgtcaacattatgggaagcgttgtggcgcattgatagatatacttaataaaagggaa
-           S  V  T  T  I  G  K  A  V  G  R  L  *  R  Y  S  N  N  E  R    F6
-          P  Y  L  Q  L  V  R  R  L  V  A  Y  S  D  I  H  I  I  K  G     F5
-            I  C  N  Y  Y  G  E  C  C  R  T  V  I  *  I  F  *  K  G  K   F4
-
-
-          Y  Y  M  *  *  V  R  L  *  S  S  F  S  K  S  F  T  V  F  D     F1
-           I  I  C  S  R  F  V  F  N  L  P  L  A  S  L  L  L  F  S  T    F2
-            L  Y  V  V  G  S  S  L  I  F  L  *  Q  V  F  Y  C  F  R  P   F3
-          tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-                   310       320       330       340       350       360       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          ataatatacatcatccaagcagaaattagaaggaaatcgttcagaaaatgacaaaagctg
-           *  *  I  Y  Y  T  R  R  *  D  E  K  L  L  D  K  V  T  K  S    F6
-          K  N  Y  T  T  P  E  D  K  I  K  R  *  C  T  K  *  Q  K  R     F5
-            I  I  H  L  L  N  T  K  L  R  G  K  A  L  R  K  S  N  E  V   F4
-
-
-          L  N  V  H  V  L  R  L  F  W  I  I  C  G  Q  F  N  L  R  C     F1
-           S  M  F  M  F  L  G  C  F  G  *  Y  A  V  S  L  I  F  V  V    F2
-            Q  C  S  C  S  *  V  V  L  D  N  M  R  S  V  *  S  S  L  F   F3
-          ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-                   370       380       390       400       410       420       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          gagttacaagtacaagaatccaacaaaacctattatacgccagtcaaattagaagcaaca
-           R  L  T  *  T  R  L  N  N  Q  I  I  H  P  *  N  L  R  R  Q    F6
-          G  *  H  E  H  E  *  T  T  K  S  L  I  R  D  T  *  D  E  N     F5
-            E  I  N  M  N  K  P  Q  K  P  Y  Y  A  T  L  K  I  K  T  T   F4
-
-
-          F  F  L  K  Y  L  F  M  V  *  F  L  V  C  T  C  S  G  A  S     F1
-           S  S  *  N  I  Y  S  W  F  N  F  W  F  V  L  V  Q  G  P  V    F2
-            L  L  K  I  F  I  H  G  L  I  F  G  L  Y  L  F  R  G  Q  F   F3
-          ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-                   430       440       450       460       470       480       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          aagaagaattttataaataagtaccaaattaaaaaccaaacatgaacaagtccccggtca
-           K  K  K  F  Y  K  N  M  T  *  N  K  T  Q  V  Q  E  P  A  L    F6
-          N  R  R  L  I  N  I  *  P  K  I  K  P  K  Y  K  N  L  P  W     F5
-            E  E  *  F  I  *  E  H  N  L  K  Q  N  T  S  T  *  P  G  T   F4
-
-
-          S  L  F  T  L  F  V  Y  S  S  S  F  I  F  S  M  I  L  I  *     F1
-           H  Y  L  L  C  L  Y  T  A  V  L  L  F  L  V  *  F  *  F  K    F2
-            I  I  Y  S  V  C  I  Q  Q  F  F  Y  F  *  Y  D  F  N  L  K   F3
-          tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-                   490       500       510       520       530       540       
-          ----:----|----:----|----:----|----:----|----:----|----:----|
-          agtaataaatgagacaaacatatgtcgtcaagaaaataaaaatcatactaaaattaaatt
-           E  N  N  V  R  N  T  Y  L  L  E  K  I  K  L  I  I  K  I  *    F6
-          N  M  I  *  E  T  Q  I  C  C  N  K  *  K  *  Y  S  K  L  K     F5
-            *  *  K  S  Q  K  Y  V  A  T  R  K  N  K  T  H  N  *  N  L   F4
-
-
-          N  N  S  N  G  Q  K                                            F1
-           T  I  L  M  V  K  X                                           F2
-            Q  F  *  W  S  K  X                                          F3
-          aacaattctaatggtcaaaaa
-                   550       560       
-          ----:----|----:----|-
-          ttgttaagattaccagttttt
-           F  L  E  L  P  *  F                                           F6
-          F  C  N  *  H  D  F                                            F5
-            V  I  R  I  T  L  F                                          F4
-
-##############################
-Minimum size of ORFs : 1
-
-Total ORFs in frame 1 :    10
-Total ORFs in frame 2 :    11
-Total ORFs in frame 3 :     8
-Total ORFs in frame 4 :    14
-Total ORFs in frame 5 :    12
-Total ORFs in frame 6 :    14
-
-Total ORFs :    69
-##############################
-


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_skipseq_out.fasta
--- a/test-data/emboss_skipseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_splitter_out.fasta
--- a/test-data/emboss_splitter_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence_1-561 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_supermatcher_out.fasta
--- a/test-data/emboss_supermatcher_out.fasta
+++ /dev/null
@@ -1,24 +0,0 @@
->hg17
-CCCTAGAGCTTCTGAGCCCTCAACAG--------AGATGAACTGGACTCTCTGCAGCCCC
-ACTCTAAATTC-----------CTAAGAGAGAAGTTGATTGACCCAATCAG-------GG
-TCAGGAGAAGGAAGGGAGGAGGAAAGGGAG---------GAGAGAAGAGCCTCTTCGTCT
-CTTGCCTACCAC--TGGCCAGGCAATTGTAG---------CCAAGGGGGCT-GGAGTGTA
-AATGCAAACATAGCC----------ATCAAGGGTt---gtgtatgtgtgtgtgt------
-----gtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGATCTCCC---------
----AGGAGGTCCCTAC--TAAACAGACTTAAGCCCGCAAAA---TTTTA--GCTCTCCAG
-CCTCACACACTCCACCCCTCTAC-----CATA-------TTGAATCTTCCCAAACCAACT
-ATG-GCT---TTCCCTAA-CTCCGGAGcttggcctggaa--------tgccctgcttccc
-ct--ctttcccctgg---ggaacgcctgtccttcaggcctcagttca-----cacactgc
-ctcccttgca-----aagctct
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-ccctaca----caga-----ccacagttttcctaa-------tgg---ctttaca--ccg
-actagaaattcttgtgcaagcactaattga-aag-cggttggccta--gagtgttaccgg
-tttgta------------tagctgagcgcgtctcttgccctgatcaaaggttcattttct
-ct--------actttgg--aagacgttgtggaagaatacaacaag-----tacgagtctc
-tcccc--------cctggtttgctgattactggatacagt-----------tgtaatacc
-cttcgcaacaccgcgtaactatctatat-------gaa--tta-ttttccctttattata
-tgtagtaggttcgt-ctttaatcttcctttagc------aagtcttttactgttttcga-
-cctca------------atgttcatgttcttaggttgttttggat------------aat
-atgcggtcagtt---taatcttcgttgtttcttcttaaaatatttatt--catggtt---
--taatttt----tggtttgta---cttg---ttcaggggccagttcattatttactctg-
-----tttgtatacagcagttct


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_syco_out.syco
--- a/test-data/emboss_syco_out.syco
+++ /dev/null
@@ -1,484 +0,0 @@
-SYCO of Sequence from 1 to 561
-
-
-Frame 1
-Mid base	Gribskov value
-46      	1.007
-49      	1.014
-52      	1.012
-55      	1.002
-58      	1.003
-61      	0.997
-64      	0.998
-67      	0.996
-70      	1.005
-73      	1.006
-76      	1.007
-79      	1.020
-82      	1.008
-85      	1.000
-88      	0.995
-91      	1.005
-94      	1.023
-97      	1.011
-100     	1.008
-103     	1.003
-106     	1.017
-109     	1.028
-112     	1.029
-115     	1.019
-118     	1.013
-121     	1.014
-124     	1.003
-127     	1.003
-130     	0.990
-133     	0.981
-136     	0.975
-139     	0.981
-142     	0.983
-145     	0.981
-148     	0.987
-151     	1.000
-154     	0.989
-157     	0.997
-160     	0.995
-163     	0.998
-166     	0.988
-169     	0.981
-172     	0.993
-175     	1.007
-178     	1.016
-181     	1.016
-184     	0.994
-187     	1.006
-190     	1.017
-193     	1.008
-196     	1.016
-199     	0.995
-202     	0.987
-205     	0.982
-208     	0.983
-211     	0.978
-214     	0.989
-217     	1.000
-220     	1.006
-223     	1.013
-226     	1.008
-229     	0.992
-232     	1.002
-235     	1.002
-238     	0.996
-241     	0.987
-244     	0.988
-247     	0.972
-250     	0.966
-253     	0.973
-256     	0.972
-259     	0.968
-262     	0.956
-265     	0.951
-268     	0.942
-271     	0.923
-274     	0.923
-277     	0.907
-280     	0.897
-283     	0.908
-286     	0.888
-289     	0.896
-292     	0.891
-295     	0.911
-298     	0.923
-301     	0.924
-304     	0.914
-307     	0.904
-310     	0.896
-313     	0.901
-316     	0.910
-319     	0.928
-322     	0.918
-325     	0.914
-328     	0.915
-331     	0.911
-334     	0.910
-337     	0.927
-340     	0.926
-343     	0.917
-346     	0.922
-349     	0.920
-352     	0.917
-355     	0.923
-358     	0.917
-361     	0.926
-364     	0.931
-367     	0.937
-370     	0.937
-373     	0.929
-376     	0.930
-379     	0.931
-382     	0.940
-385     	0.915
-388     	0.908
-391     	0.908
-394     	0.899
-397     	0.909
-400     	0.918
-403     	0.904
-406     	0.896
-409     	0.885
-412     	0.884
-415     	0.884
-418     	0.885
-421     	0.889
-424     	0.889
-427     	0.884
-430     	0.892
-433     	0.903
-436     	0.902
-439     	0.906
-442     	0.900
-445     	0.890
-448     	0.893
-451     	0.903
-454     	0.903
-457     	0.899
-460     	0.910
-463     	0.932
-466     	0.935
-469     	0.925
-472     	0.915
-475     	0.926
-478     	0.925
-481     	0.929
-484     	0.943
-487     	0.934
-490     	0.920
-493     	0.925
-496     	0.925
-499     	0.935
-502     	0.936
-505     	0.939
-508     	0.940
-511     	0.936
-514     	0.932
-
-
-Frame 2
-Mid base	Gribskov value
-47      	1.003
-50      	0.992
-53      	1.002
-56      	0.997
-59      	1.006
-62      	1.005
-65      	1.007
-68      	0.997
-71      	1.001
-74      	0.996
-77      	0.997
-80      	0.982
-83      	0.975
-86      	0.965
-89      	0.971
-92      	0.977
-95      	0.975
-98      	0.968
-101     	0.979
-104     	0.968
-107     	0.978
-110     	0.982
-113     	0.984
-116     	0.994
-119     	0.984
-122     	0.983
-125     	0.984
-128     	0.996
-131     	1.004
-134     	0.986
-137     	0.992
-140     	0.997
-143     	0.980
-146     	0.972
-149     	0.966
-152     	0.971
-155     	0.956
-158     	0.950
-161     	0.943
-164     	0.944
-167     	0.933
-170     	0.944
-173     	0.944
-176     	0.955
-179     	0.949
-182     	0.944
-185     	0.945
-188     	0.952
-191     	0.941
-194     	0.952
-197     	0.946
-200     	0.934
-203     	0.943
-206     	0.935
-209     	0.940
-212     	0.952
-215     	0.953
-218     	0.937
-221     	0.923
-224     	0.934
-227     	0.938
-230     	0.930
-233     	0.936
-236     	0.949
-239     	0.943
-242     	0.944
-245     	0.946
-248     	0.950
-251     	0.954
-254     	0.968
-257     	0.968
-260     	0.962
-263     	0.960
-266     	0.949
-269     	0.943
-272     	0.946
-275     	0.956
-278     	0.963
-281     	0.963
-284     	0.952
-287     	0.947
-290     	0.950
-293     	0.930
-296     	0.934
-299     	0.936
-302     	0.925
-305     	0.915
-308     	0.939
-311     	0.943
-314     	0.928
-317     	0.930
-320     	0.936
-323     	0.941
-326     	0.938
-329     	0.943
-332     	0.949
-335     	0.939
-338     	0.935
-341     	0.934
-344     	0.924
-347     	0.929
-350     	0.929
-353     	0.932
-356     	0.930
-359     	0.934
-362     	0.930
-365     	0.911
-368     	0.916
-371     	0.925
-374     	0.921
-377     	0.917
-380     	0.916
-383     	0.924
-386     	0.922
-389     	0.919
-392     	0.921
-395     	0.930
-398     	0.912
-401     	0.916
-404     	0.920
-407     	0.909
-410     	0.908
-413     	0.908
-416     	0.898
-419     	0.890
-422     	0.880
-425     	0.885
-428     	0.899
-431     	0.907
-434     	0.912
-437     	0.904
-440     	0.901
-443     	0.901
-446     	0.893
-449     	0.897
-452     	0.894
-455     	0.903
-458     	0.890
-461     	0.886
-464     	0.894
-467     	0.894
-470     	0.894
-473     	0.885
-476     	0.884
-479     	0.875
-482     	0.870
-485     	0.879
-488     	0.878
-491     	0.875
-494     	0.875
-497     	0.876
-500     	0.881
-503     	0.878
-506     	0.876
-509     	0.883
-512     	0.891
-515     	0.896
-
-
-Frame 3
-Mid base	Gribskov value
-48      	0.929
-51      	0.933
-54      	0.930
-57      	0.946
-60      	0.940
-63      	0.947
-66      	0.947
-69      	0.953
-72      	0.968
-75      	0.950
-78      	0.949
-81      	0.939
-84      	0.929
-87      	0.915
-90      	0.910
-93      	0.922
-96      	0.921
-99      	0.931
-102     	0.925
-105     	0.935
-108     	0.945
-111     	0.935
-114     	0.930
-117     	0.940
-120     	0.949
-123     	0.949
-126     	0.960
-129     	0.944
-132     	0.947
-135     	0.943
-138     	0.946
-141     	0.955
-144     	0.949
-147     	0.948
-150     	0.953
-153     	0.950
-156     	0.960
-159     	0.965
-162     	0.958
-165     	0.979
-168     	0.987
-171     	0.991
-174     	1.003
-177     	1.017
-180     	1.018
-183     	1.004
-186     	0.994
-189     	1.008
-192     	1.010
-195     	0.998
-198     	1.002
-201     	1.013
-204     	1.021
-207     	1.012
-210     	1.002
-213     	1.013
-216     	1.001
-219     	1.012
-222     	1.024
-225     	1.037
-228     	1.035
-231     	1.025
-234     	1.028
-237     	1.011
-240     	1.007
-243     	1.016
-246     	1.006
-249     	0.997
-252     	0.999
-255     	0.989
-258     	0.971
-261     	0.962
-264     	0.950
-267     	0.936
-270     	0.931
-273     	0.931
-276     	0.928
-279     	0.907
-282     	0.897
-285     	0.910
-288     	0.915
-291     	0.904
-294     	0.902
-297     	0.899
-300     	0.905
-303     	0.895
-306     	0.905
-309     	0.896
-312     	0.887
-315     	0.877
-318     	0.879
-321     	0.874
-324     	0.875
-327     	0.878
-330     	0.880
-333     	0.871
-336     	0.871
-339     	0.866
-342     	0.853
-345     	0.851
-348     	0.861
-351     	0.870
-354     	0.874
-357     	0.887
-360     	0.892
-363     	0.892
-366     	0.897
-369     	0.897
-372     	0.903
-375     	0.891
-378     	0.881
-381     	0.881
-384     	0.879
-387     	0.884
-390     	0.875
-393     	0.875
-396     	0.866
-399     	0.865
-402     	0.861
-405     	0.852
-408     	0.852
-411     	0.856
-414     	0.852
-417     	0.850
-420     	0.859
-423     	0.859
-426     	0.867
-429     	0.879
-432     	0.893
-435     	0.903
-438     	0.912
-441     	0.913
-444     	0.910
-447     	0.910
-450     	0.908
-453     	0.908
-456     	0.906
-459     	0.905
-462     	0.918
-465     	0.929
-468     	0.939
-471     	0.940
-474     	0.940
-477     	0.939
-480     	0.943
-483     	0.943
-486     	0.942
-489     	0.943
-492     	0.948
-495     	0.948
-498     	0.948
-501     	0.943
-504     	0.958
-507     	0.960
-510     	0.954
-513     	0.956
-516     	0.947


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_tranalign_out.fasta
--- a/test-data/emboss_tranalign_out.fasta
+++ /dev/null
@@ -1,45 +0,0 @@
->HSFAU1
-cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
-ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
-cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
-ctcctggcaggc---cccctggaggatgaggccactctgggccagtgcggggtggaggcc
-ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
-gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
-aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
-cccacctttggcaagaagaagggccccaatgccaactct
->HSFAU2
-cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
-ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
-cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
-ctcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc---
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
----------------------------------------
->HSFAU3
-cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
-ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
-cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
-ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
-ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
-gcccgtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaag
-aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
-cccacctttggcaagaagaagggccccaatgccaactct
->HSFAU4
-cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
-ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
-cagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtg
-ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
-ctgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctg
-gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
-aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
-cccacctttggcaagaagaagggccccaatgccaactct
->HSFAU5
-cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
-ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
-cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
-ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
-ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg
-gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
-aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
-cccacctttggcaagaagaagggccccaatgccaactct
\ No newline at end of file


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_transeq_out.fasta
--- a/test-data/emboss_transeq_out.fasta
+++ /dev/null
@@ -1,5 +0,0 @@
->Sequence_1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-VRCLKYLLLSLHRPQFS*WLYTD*KFLCKH*LKAVGLECYRFV*LSASLALIKGSFSLLW
-KTLWKNTTSTSLSPLVC*LLDTVVIPFATPRNYLYELFSLYYM**VRL*SSFSKSFTVFD
-LNVHVLRLFWIICGQFNLRCFFLKYLFMV*FLVCTCSGASSLFTLFVYSSSFIFSMILI*
-NNSNGQK


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_trimest_out.fasta
--- a/test-data/emboss_trimest_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; [poly-A tail removed]
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtc


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_trimseq_out.fasta
--- a/test-data/emboss_trimseq_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_union_out.fasta
--- a/test-data/emboss_union_out.fasta
+++ /dev/null
@@ -1,11 +0,0 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
-tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
-cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
-aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
-gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
-tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
-ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
-ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
-tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
-aacaattctaatggtcaaaaa


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_water_out.fasta
--- a/test-data/emboss_water_out.fasta
+++ /dev/null
@@ -1,32 +0,0 @@
->hg17
-GTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTC------CAGAGCAGGGTAT
-TTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTGTGATTTG
-GGCTTTT-----CCTTAAATCCTTGAGGAGCTGGAGGGGTGGGTGGCTCGCACTCCTGCT
-TTctggatctgaatcctgactctgtcatggacctgtttgactttgggcaagttgactcct
-attcctgagccccatatttttctcttctgtgaaattcagattaaaaAAACATGGCTTTGA
-TCAAA----CATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAGAA
-ATGAATCCTACTAATA-------------------TTGC-CATCTA-TGG--ACAGAAAA
-TGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGA--------
----GATTAATTTTACTGCC-------ATCTCCAGAA---CCGTCATCCTAATATTTACTT
-A-CA----TTTTATTATTATTTCAGGCTC-ATGCACATATACTTAG-----CATGGATCA
-T-TGGCCACAGACTCGCATACATTTAA-CTTTATTACCTTTTGCCTCATGTATCTCATTA
-AAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCA
-AGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgctctctcccgcca--ccat
-gtctttataccccctgatttct---cagccactatggcaaccactttctactcttagta-
-gcccat----atttagtccaatccccagctcaggagacacttct
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-gttcga----------tgcctaaaatacctt--cttttgtccctacacagaccacagt--
----tttcctaatggc---tttacacc----------gactagaaatt-------------
---cttgtgcaagcactaa----ttga-aagc---------ggttggc-------------
---ctaga--------------gtgt----taccggtttg--------------------t
-atagctgagcgc-------gtctctt---------------------------gccctga
-tcaaaggttcattttctctact---ttggaagac-----------gttgt-------gga
-a-gaatacaacaagtacgagtctctcccccctggtttgctgat-tactggatacag---t
-tgtaatacc---cttc-gcaacacc----------------------gcgtaactatcta
-tatgaattatttt----ccctttattatatgtagtaggttcgtctt--taatcttccttt
-agcaagtcttttactgt--tttcgacctcaatgttcatgttcttaggttgttttggataa
-tatgcggtcag-----------tttaatcttcgt--------------tgtttcttctta
-aaatat------ttattcatgg-------------tttaatttttggttt----gt----
---actt--------------gttcaggg----------------------gccagttcat
--tattta----ctctg-tttgtatacagc----------agttcttt-tatttttagtat
-g---attttaattta-------------------aaacaattct


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_water_out.score
--- a/test-data/emboss_water_out.score
+++ /dev/null
@@ -1,4 +0,0 @@
-Sequence hg17 884 (610.5)
-
-#---------------------------------------
-#---------------------------------------


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_wobble_out.png
Binary file test-data/emboss_wobble_out.png has changed


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_wobble_out.wobble
--- a/test-data/emboss_wobble_out.wobble
+++ /dev/null
@@ -1,1 +0,0 @@
-Expected GC content in third position = 36.36


diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_wordcount_out.wordcount
--- a/test-data/emboss_wordcount_out.wordcount
+++ /dev/null
@@ -1,202 +0,0 @@
-ttta	13
-tttt	13
-tctt	11
-gttt	10
-ttgt	10
-taat	9
-ttct	8
-attt	8
-tttg	8
-gttc	8
-tgtt	8
-ggtt	8
-cttt	8
-aatt	6
-tatt	6
-ttaa	6
-ttat	6
-ttca	5
-ttcg	5
-tttc	5
-cagt	5
-gttg	5
-taca	5
-aata	5
-ccct	5
-agtt	5
-tgta	5
-tact	5
-cttc	5
-atac	5
-ttac	5
-aaaa	5
-atta	4
-tctc	4
-ctaa	4
-gtct	4
-ccta	4
-tata	4
-ctct	4
-cctt	4
-tatg	4
-ttgg	4
-acag	4
-tgga	4
-atat	4
-tcat	4
-tggt	4
-atct	3
-aaat	3
-ttcc	3
-taaa	3
-tcta	3
-attc	3
-tgat	3
-cggt	3
-agca	3
-aaca	3
-cccc	3
-agta	3
-tacc	3
-aatg	3
-caag	3
-cttg	3
-atgg	3
-atgt	3
-acaa	3
-acac	3
-tcaa	3
-aggt	3
-gcaa	3
-ttag	3
-ctga	3
-accg	3
-gtat	3
-acta	3
-tccc	3
-tgaa	2
-tcct	2
-actt	2
-ggaa	2
-gcct	2
-gtca	2
-ctac	2
-gaaa	2
-ctag	2
-gaag	2
-gctg	2
-ggat	2
-ctat	2
-gaat	2
-agcg	2
-tgcc	2
-agtc	2
-aatc	2
-cgac	2
-ggcc	2
-caaa	2
-caac	2
-gacc	2
-cctg	2
-tgtg	2
-caat	2
-ggtc	2
-ctta	2
-gata	2
-atga	2
-atgc	2
-tcga	2
-gatt	2
-gcgg	2
-tcgt	2
-ttgc	2
-gcgt	2
-cgcg	2
-caca	2
-cacc	2
-cgtc	2
-aaga	2
-catg	2
-aagc	2
-cgtt	2
-tcag	2
-catt	2
-aagt	2
-tggc	2
-taga	2
-tagc	2
-tagg	2
-gtaa	2
-ctgg	2
-gtac	2
-gtag	2
-tagt	2
-ctgt	2
-gagt	2
-agaa	2
-agac	2
-acct	2
-aaag	2
-actg	2
-gccc	1
-ccag	1
-tgag	1
-taac	1
-attg	1
-caga	1
-tctg	1
-cagc	1
-gtcc	1
-cagg	1
-gctt	1
-gtta	1
-agct	1
-tgca	1
-aact	1
-tgcg	1
-agtg	1
-tacg	1
-ctca	1
-cgag	1
-ctcc	1
-cctc	1
-tgct	1
-acga	1
-gacg	1
-tgtc	1
-cgat	1
-ggct	1
-tatc	1
-gact	1
-acgt	1
-gatc	1
-tcgc	1
-gatg	1
-gcgc	1
-ttga	1
-cgca	1
-gtgc	1
-gtgg	1
-cgta	1
-gtgt	1
-cact	1
-aggg	1
-ataa	1
-aagg	1
-atag	1
-ccga	1
-ccgc	1
-ccgg	1
-gcac	1
-gcag	1
-gggc	1
-gggg	1
-gagc	1
-acca	1
-accc	1
-atca	1
-agag	1
-aaac	1
-actc	1
-gcca	1
-ccac	1

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: greg: Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed.

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