Dear all, I'm wondering when I extract a alignments with coorfinates (for refseqs) from Multiz from genome-wide alignments I can make fasta MAFs with info-line with coordinates but never looking like this:
NM_017821.0.1 hg17.chr1 206501580 206501621 - 245522847 mm5.chr4
122200029 122200071 + 154141344 rn3.chr5 143135020 143135060 + 173106704 canFam1.chr15 6850518 6850559 + 67237905 CCTGCCCCTATTGTAAGTCAATTAATA-AAAAGAGCCATCTGG CTTGCCTCTATGATAAACCAGTTAATATAAAAGTGTCACATGG CTTGCCTCTGTTATAAGCCACTTAATA--AAAGTGTCACATGG CCTGCCTCTCATAGGAAGCAAGTAATG-AAAAGAGCCATCTGG
NM_004070.0.0 hg17.chr1 16105460 16105489 + 245522847 mm5.chr4
14280459 14280491 - 154141344 rn3.chr5 12802003 12802032 - 173106704 canFam1.chr2 5413700 5413729 - 87725193 GCCGGCCCAGCAAGATGAAACAG---GGCACCC GTCAGCCTGGGGGGGGTCGGCAGCCTGGCACCC GTCAGCCTGG---GAGTCGGCAGCCTGGCGCCC GCCAGCCCAGCAAGATGAAACAG---GGTGGCC
How to make this? I have failed trying do this...
Vesko