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 -164 0.400000 -165 0.366667 -166 0.400000 -167 0.400000 -168 0.400000 -169 0.400000 -170 0.400000 -171 0.400000 -172 0.400000 -173 0.366667 -174 0.400000 -175 0.400000 -176 0.366667 -177 0.400000 -178 0.400000 -179 0.400000 -180 0.400000 -181 0.400000 -182 0.400000 -183 0.433333 -184 0.400000 -185 0.433333 -186 0.400000 -187 0.400000 -188 0.400000 -189 0.433333 -190 0.433333 -191 0.466667 -192 0.466667 -193 0.466667 -194 0.500000 -195 0.500000 -196 0.500000 -197 0.533333 -198 0.533333 -199 0.533333 -200 0.533333 -201 0.533333 -202 0.566667 -203 0.566667 -204 0.566667 -205 0.566667 -206 0.566667 -207 0.533333 -208 0.533333 -209 0.566667 -210 0.533333 -211 0.533333 -212 0.566667 -213 0.533333 -214 0.533333 -215 0.500000 -216 0.533333 -217 0.500000 -218 0.533333 -219 0.500000 -220 0.466667 -221 0.466667 -222 0.433333 -223 0.400000 -224 0.366667 -225 0.366667 -226 0.333333 -227 0.333333 -228 0.366667 -229 0.400000 -230 0.400000 -231 0.366667 -232 0.366667 -233 0.400000 -234 0.400000 -235 0.400000 -236 0.400000 -237 0.433333 -238 0.433333 -239 0.433333 -240 0.466667 -241 0.466667 -242 0.466667 -243 0.500000 -244 0.500000 -245 0.500000 -246 0.466667 -247 0.500000 -248 0.466667 -249 0.466667 -250 0.466667 -251 0.466667 -252 0.466667 -253 0.466667 -254 0.466667 -255 0.466667 -256 0.466667 -257 0.466667 -258 0.433333 -259 0.400000 -260 0.400000 -261 0.400000 -262 0.366667 -263 0.333333 -264 0.300000 -265 0.300000 -266 0.300000 -267 0.300000 -268 0.333333 -269 0.333333 -270 0.300000 -271 0.266667 -272 0.233333 -273 0.200000 -274 0.200000 -275 0.200000 -276 0.200000 -277 0.166667 -278 0.166667 -279 0.166667 -280 0.200000 -281 0.166667 -282 0.166667 -283 0.200000 -284 0.200000 -285 0.200000 -286 0.233333 -287 0.233333 -288 0.233333 -289 0.233333 -290 0.266667 -291 0.300000 -292 0.300000 -293 0.333333 -294 0.333333 -295 0.333333 -296 0.333333 -297 0.300000 -298 0.266667 -299 0.233333 -300 0.266667 -301 0.266667 -302 0.266667 -303 0.300000 -304 0.333333 -305 0.333333 -306 0.333333 -307 0.333333 -308 0.333333 -309 0.366667 -310 0.366667 -311 0.366667 -312 0.366667 -313 0.366667 -314 0.366667 -315 0.400000 -316 0.366667 -317 0.333333 -318 0.333333 -319 0.333333 -320 0.300000 -321 0.300000 -322 0.300000 -323 0.300000 -324 0.300000 -325 0.300000 -326 0.300000 -327 0.300000 -328 0.333333 -329 0.366667 -330 0.333333 -331 0.366667 -332 0.400000 -333 0.366667 -334 0.366667 -335 0.366667 -336 0.366667 -337 0.366667 -338 0.400000 -339 0.366667 -340 0.333333 -341 0.366667 -342 0.366667 -343 0.333333 -344 0.366667 -345 0.333333 -346 0.333333 -347 0.366667 -348 0.366667 -349 0.366667 -350 0.366667 -351 0.366667 -352 0.400000 -353 0.366667 -354 0.366667 -355 0.400000 -356 0.400000 -357 0.400000 -358 0.366667 -359 0.333333 -360 0.366667 -361 0.366667 -362 0.333333 -363 0.333333 -364 0.300000 -365 0.300000 -366 0.300000 -367 0.300000 -368 0.266667 -369 0.300000 -370 0.333333 -371 0.333333 -372 0.366667 -373 0.366667 -374 0.366667 -375 0.366667 -376 0.400000 -377 0.366667 -378 0.366667 -379 0.366667 -380 0.366667 -381 0.333333 -382 0.300000 -383 0.333333 -384 0.333333 -385 0.300000 -386 0.333333 -387 0.366667 -388 0.366667 -389 0.366667 -390 0.366667 -391 0.333333 -392 0.333333 -393 0.333333 -394 0.366667 -395 0.366667 -396 0.366667 -397 0.400000 -398 0.400000 -399 0.366667 -400 0.333333 -401 0.300000 -402 0.266667 -403 0.266667 -404 0.233333 -405 0.233333 -406 0.200000 -407 0.200000 -408 0.200000 -409 0.200000 -410 0.200000 -411 0.200000 -412 0.233333 -413 0.200000 -414 0.200000 -415 0.233333 -416 0.233333 -417 0.200000 -418 0.200000 -419 0.200000 -420 0.166667 -421 0.166667 -422 0.166667 -423 0.166667 -424 0.133333 -425 0.133333 -426 0.133333 -427 0.133333 -428 0.166667 -429 0.166667 -430 0.166667 -431 0.166667 -432 0.200000 -433 0.200000 -434 0.200000 -435 0.233333 -436 0.233333 -437 0.233333 -438 0.266667 -439 0.266667 -440 0.266667 -441 0.300000 -442 0.266667 -443 0.300000 -444 0.333333 -445 0.333333 -446 0.333333 -447 0.366667 -448 0.400000 -449 0.400000 -450 0.433333 -451 0.433333 -452 0.433333 -453 0.466667 -454 0.466667 -455 0.466667 -456 0.466667 -457 0.433333 -458 0.400000 -459 0.400000 -460 0.400000 -461 0.400000 -462 0.400000 -463 0.400000 -464 0.433333 -465 0.400000 -466 0.433333 -467 0.433333 -468 0.400000 -469 0.400000 -470 0.433333 -471 0.400000 -472 0.400000 -473 0.366667 -474 0.333333 -475 0.333333 -476 0.300000 -477 0.300000 -478 0.300000 -479 0.300000 -480 0.300000 -481 0.300000 -482 0.300000 -483 0.300000 -484 0.300000 -485 0.300000 -486 0.300000 -487 0.300000 -488 0.300000 -489 0.300000 -490 0.300000 -491 0.300000 -492 0.266667 -493 0.266667 -494 0.233333 -495 0.266667 -496 0.233333 -497 0.233333 -498 0.233333 -499 0.266667 -500 0.233333 -501 0.233333 -502 0.233333 -503 0.233333 -504 0.233333 -505 0.200000 -506 0.200000 -507 0.166667 -508 0.133333 -509 0.133333 -510 0.100000 -511 0.100000 -512 0.100000 -513 0.066667 -514 0.100000 -515 0.100000 -516 0.100000 -517 0.100000 -518 0.100000 -519 0.133333 -520 0.133333 -521 0.133333 -522 0.133333 -523 0.133333 -524 0.166667 -525 0.166667 -526 0.166667 -527 0.200000 -528 0.200000 -529 0.166667 -530 0.166667 -531 0.166667 -532 0.166667 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/ -- This is a commit notification from bitbucket.org. 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