CLUSTAL O(1.0.3) multiple sequence alignment 435590.150003364 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 226186.29348112 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 295405.53715441 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 272559.60683413 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 411901.149130658 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 411476.156111512 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 411479.156862051 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 449673.167697753 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 470145.189432667 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 483215.260624635 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 483218.217990640 -------MTKKRVKKNVEHGQAHIQSSFNNTIVTLTDAEGNALSWASAGGLGFRGSKKST 483216.217986519 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 484018.198273057 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIIAWSSAGKMGFRGSKKNT 483217.212662191 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 511680.292809380 MAKVTKKVTKKRVKKNVERGQAHIQSSFNNTIVTITDTEGNALSWASAGGLGFRGSRKST 537012.224520527 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 547042.224016865 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 469586.251841635 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 469590.229451850 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 457392.251944867 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 457394.254834140 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 457395.229454394 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 556258.229443407 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 556260.229435668 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 469587.263252878 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 469588.262357064 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 457391.263236304 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 585543.270273974 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 702446.294448298 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 702443.292632887 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 702444.292640606 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 702447.294446237 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 657309.locus_tag:BXY_18280 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 457424.EQ973217.G291 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 556259.GG663458.G80 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT 471870.DS562360.G288 MAKKTV-AAKKRNVKVDANGQLHVHSSFNNIIVSLANSEGQIISWSSAGKMGFRGSKKNT :*** * .** *::***** **:::::**: ::*:*** :*****:*.* 435590.150003364 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 226186.29348112 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 295405.53715441 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 272559.60683413 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 411901.149130658 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 411476.156111512 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 411479.156862051 PYAAQMAAQDCAKIAYDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 449673.167697753 PYAAQMAAQDCAKVAYDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 470145.189432667 PYAAQMAAQDCAKVAYDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 483215.260624635 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 483218.217990640 PYAAQMAAETATKAALIHGLKSVDVMVKGPGSGREAAIRALSAAGLTVTSIKDVTPVPHN 483216.217986519 PYAAQMAAQDCAKIAYDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 484018.198273057 PYAAQMAAQDCAKVAYDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 483217.212662191 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 511680.292809380 PYAAQMAAETATKAALIHGLKSVDVMVKGPGSGREAAIRALQACGLEVTSIKDVTPVPHN 537012.224520527 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIVDVTPLPHN 547042.224016865 PYAAQMAAQDCAKVAYDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 469586.251841635 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 469590.229451850 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 457392.251944867 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 457394.254834140 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 457395.229454394 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 556258.229443407 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 556260.229435668 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 469587.263252878 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 469588.262357064 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 457391.263236304 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 585543.270273974 PYAAQMAAQDCAKIAYDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 702446.294448298 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTVHGAGIEVTEIIDVTPLPHN 702443.292632887 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 702444.292640606 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 702447.294446237 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 657309.locus_tag:BXY_18280 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 457424.EQ973217.G291 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 556259.GG663458.G80 PYAAQMAAQDCAKIAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN 471870.DS562360.G288 PYAAQMAAQDCAKVAFDLGLRKVKAYVKGPGNGRESAIRTIHGAGIEVTEIIDVTPLPHN ********: .:* * **:.*.. *****.***:***:: ..*: **.* ****:*** 435590.150003364 GCRPPKRRRV 226186.29348112 GCRPPKRRRV 295405.53715441 GCRPPKRRRV 272559.60683413 GCRPPKRRRV 411901.149130658 GCRPPKRRRV 411476.156111512 GCRPPKRRRV 411479.156862051 GCRPPKRRRV 449673.167697753 GCRPPKRRRV 470145.189432667 GCRPPKRRRV 483215.260624635 GCRPPKRRRV 483218.217990640 GCRPPKRRRV 483216.217986519 GCRPPKRRRV 484018.198273057 GCRPPKRRRV 483217.212662191 GCRPPKRRRV 511680.292809380 GCRPPKRRRV 537012.224520527 GCRPPKRRRV 547042.224016865 GCRPPKRRRV 469586.251841635 GCRPPKRRRV 469590.229451850 GCRPPKRRRV 457392.251944867 GCRPPKRRRV 457394.254834140 GCRPPKRRRV 457395.229454394 GCRPPKRRRV 556258.229443407 GCRPPKRRRV 556260.229435668 GCRPPKRRRV 469587.263252878 GCRPPKRRRV 469588.262357064 GCRPPKRRRV 457391.263236304 GCRPPKRRRV 585543.270273974 GCRPPKRRRV 702446.294448298 GCRPPKRRRV 702443.292632887 GCRPPKRRRV 702444.292640606 GCRPPKRRRV 702447.294446237 GCRPPKRRRV 657309.locus_tag:BXY_18280 GCRPPKRRRV 457424.EQ973217.G291 GCRPPKRRRV 556259.GG663458.G80 GCRPPKRRRV 471870.DS562360.G288 GCRPPKRRRV ********** #### use strict; use warnings; my $clu_align=$ARGV[0]; open(IN,">",$clu_align) or die "can't open file $clu_align"; my @consensus; while(my $line=){ chomp($line); next if ($line =~ /^CLUSTAL/); # header row next if ($line=~ /^$/); # a few blank rows if ($line =~ /\*/){ push (@consensus,$line); } } close(IN); chomp(@consensus); #foreach my $c (@consensus){ just for debugging # print "consensus\n"; # print "$c\t"; # print "\n"; #} my( @index )= grep { $consensus[$_] eq "*" } 0..$#consensus; my $outfile="$clu_align.VarPositions"; open (OUT,">",$outfile); foreach my $i (@index) { print OUT "$i\tis not conserved\n"; }