Mercurial > repos > devteam > indels_3way
changeset 0:5ad24b81dd10 draft default tip
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 11:24:53 -0400 |
| parents | |
| children | |
| files | getIndels_3way.xml parseMAF_smallIndels.pl test-data/3way.maf test-data/indels_3way.tabular |
| diffstat | 4 files changed, 976 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getIndels_3way.xml Wed Sep 25 11:24:53 2013 -0400 @@ -0,0 +1,53 @@ +<tool id="indels_3way" name="Fetch Indels" version="1.0.3"> + <description> from 3-way alignments</description> + <command interpreter="perl"> + parseMAF_smallIndels.pl $input1 $out_file1 $outgroup + </command> + <inputs> + <page> + <param format="maf" name="input1" type="data" label="Select data"/> + <param name="outgroup" type="select" label="Select outgroup species"> + <options> + <filter type="data_meta" ref="input1" key="species" /> + </options> + </param> + </page> + </inputs> + <outputs> + <data format="tabular" name="out_file1" metadata_source="input1"/> + <!--<data format="tabular" name="out_file2" metadata_source="input1"/>--> + </outputs> + <tests> + <test> + <param name="input1" value="3way.maf"/> + <param name="outgroup" value="canFam2"/> + <output name="out_file1" file="indels_3way.tabular"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +This tool consists of the first module from the computational pipeline to identify indels as described in Kvikstad et al., 2007. Note that the generated output does not include subsequent filtering steps. + +Deletions in a particular species are identified as one or more consecutive gap columns within an alignment block, given that the orthologous positions in the other two species contain nucleotides of +equal length. +Similarly, insertions in a particular species are identified as one or more consecutive nucleotide columns within an alignment block, given that the orthologous positions in the other two +species contain gaps. + +*Kvikstad E. M. et al. (2007). A Macaques-Eye View of Human Insertions and Deletions: Differences in Mechanisms. PLoS Computational Biology 3(9):e176* + +----- + +.. class:: warningmark + +**Note** + +Any block/s not containing exactly 3 sequences will be omitted. + + </help> + + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parseMAF_smallIndels.pl Wed Sep 25 11:24:53 2013 -0400 @@ -0,0 +1,698 @@ +#!/usr/bin/perl -w +# a program to get indels +# input is a MAF format 3-way alignment file +# from 3-way blocks only at this time +# translate seq2, seq3, etc coordinates to + if align orient is reverse complement + +use strict; +use warnings; + +# declare and initialize variables +my $fh; # variable to store filehandle +my $record; +my $offset; +my $library = $ARGV[0]; +my $count = 0; +my $count2 = 0; +my $count3 = 0; +my $count4 = 0; +my $start1 = my $start2 = my $start3 = my $start4 = my $start5 = my $start6 = 0; +my $orient = ""; +my $outgroup = $ARGV[2]; +my $ingroup1 = my $ingroup2 = ""; +my $count_seq1insert = my $count_seq1delete = 0; +my $count_seq2insert = my $count_seq2delete = 0; +my $count_seq3insert = my $count_seq3delete = 0; +my @seq1_insert_lengths = my @seq1_delete_lengths = (); +my @seq2_insert_lengths = my @seq2_delete_lengths = (); +my @seq3_insert_lengths = my @seq3_delete_lengths = (); +my @seq1_insert = my @seq1_delete = my @seq2_insert = my @seq2_delete = my @seq3_insert = my @seq3_delete = (); +my @seq1_insert_startOnly = my @seq1_delete_startOnly = my @seq2_insert_startOnly = my @seq2_delete_startOnly = (); +my @seq3_insert_startOnly = my @seq3_delete_startOnly = (); +my @indels = (); + +# check to make sure correct files +my $usage = "usage: parseMAF_smallIndels.pl [MAF.in] [small_Indels_summary.out] [outgroup]\n"; +die $usage unless @ARGV == 3; + +# perform some standard subroutines +$fh = open_file($library); + +$offset = tell($fh); + +#my $ofile = $ARGV[2]; +#unless (open(OFILE, ">$ofile")){ +# print "Cannot open output file \"$ofile\"\n\n"; +# exit; +#} + +my $ofile2 = $ARGV[1]; +unless (open(OFILE2, ">$ofile2")){ + print "Cannot open output file \"$ofile2\"\n\n"; + exit; +} + + +# header line for output files +#print OFILE "# small indel events, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n"; +#print OFILE "#align\tingroup1\tingroup1_coord\tingroup1_orient\tingroup2\tingroup2_coord\tingroup2_orient\toutgroup\toutgroup_coord\toutgroup_orient\tindel_type\n"; + +#print OFILE2 "# small indels summary, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n"; +print OFILE2 "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_alignSize\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_alignSize\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_alignSize\toutgroup_orient\n"; + +# main body of program +while ($record = get_next_record($fh) ){ + if ($record=~ m/\s*##maf(.*)\s*# maf/s){ + next; + } + + my @sequences = get_sequences_within_block($record); + my @seq_info = get_indels_within_block(@sequences); + get_indels_lengths(@seq_info); + + $offset = tell($fh); + $count++; + +} + +get_starts_only(@seq1_insert); +get_starts_only(@seq1_delete); +get_starts_only(@seq2_insert); +get_starts_only(@seq2_delete); +get_starts_only(@seq3_insert); +get_starts_only(@seq3_delete); + +# print some things to keep track of progress +#print "# $library\n"; +#print "# number of records = $count\n"; +#print "# number of sequence \"s\" lines = $count2\n"; +if ($count3 != 0){ + print "Skipped $count3 blocks with only 2 seqs;\n"; +} +#print "# number of records with only h-m = $count4\n\n"; + +print "Ingroup1 = $ingroup1; Ingroup2 = $ingroup2; Outgroup = $outgroup;\n"; +print "# of ingroup1 inserts = $count_seq1insert;\n"; +print "# of ingroup1 deletes = $count_seq1delete;\n"; +print "# of ingroup2 inserts = $count_seq2insert;\n"; +print "# of ingroup2 deletes = $count_seq2delete;\n"; +print "# of outgroup3 inserts = $count_seq3insert;\n"; +print "# of outgroup3 deletes = $count_seq3delete\n"; + + +#close OFILE; + +if ($count == $count3){ + print STDERR "Skipped all blocks since none of them contain 3-way alignments.\n"; + exit -1; +} + +###################SUBROUTINES##################################### + +# subroutine to open file +sub open_file { + my($filename) = @_; + my $fh; + + unless (open($fh, $filename)){ + print "Cannot open file $filename\n"; + exit; + } + return $fh; +} + +# get next record +sub get_next_record { + my ($fh) = @_; + my ($offset); + my ($record) = ""; + my ($save_input_separator) = $/; + + $/ = "a score"; + + $record = <$fh>; + + $/ = $save_input_separator; + return $record; +} + +# get header info +sub get_sequences_within_block{ + my (@alignment) = @_; + my @lines = (); + + my @sequences = (); + + @lines = split ("\n", $record); + foreach (@lines){ + chomp($_); + if (m/^\s*$/){ + next; + } + elsif (m/^\s*=(\d+\.*\d*)/){ + + }elsif (m/^\s*s(.*)$/){ + $count2++; + + push (@sequences,$_); + } + } + return @sequences; +} + +sub get_indels_within_block{ + my (@sequences) = @_; + my $line1 = my $line2 = my $line3 = ""; + my @line1 = my @line2 = my @line3 = (); + my $score = 0; + my $start1 = my $align_length1 = my $end1 = my $seq_length1 = 0; + my $start2 = my $align_length2 = my $end2 = my $seq_length2 = 0; + my $start3 = my $align_length3 = my $end3 = my $seq_length3 = 0; + my $seq1 = my $orient1 = ""; + my $seq2 = my $orient2 = ""; + my $seq3 = my $orient3 = ""; + my $start1_plus = my $end1_plus = 0; + my $start2_plus = my $end2_plus = 0; + my $start3_plus = my $end3_plus = 0; + my @test = (); + my $test = ""; + my $header = ""; + my @header = (); + my $sequence1 = my $sequence2 = my $sequence3 =""; + my @array_return = (); + my $test1 = 0; + my $line1_stat = my $line2_stat = my $line3_stat = ""; + + # process 3-way blocks only + if (scalar(@sequences) == 3){ + $line1 = $sequences[0]; + chomp ($line1); + $line2 = $sequences[1]; + chomp ($line2); + $line3 = $sequences[2]; + chomp ($line3); + # check order of sequences and assign uniformly seq1= human, seq2 = chimp, seq3 = macaque + if ($line1 =~ m/$outgroup/){ + $line1_stat = "out"; + $line2=~ s/^\s*//; + $line2 =~ s/\s+/\t/g; + @line2 = split(/\t/, $line2); + if (($ingroup1 eq "") || ($line2[1] =~ m/$ingroup1/)){ + $line2_stat = "in1"; + $line3_stat = "in2"; + } + else{ + $line3_stat = "in1"; + $line2_stat = "in2"; } + } + elsif ($line2 =~ m/$outgroup/){ + $line2_stat = "out"; + $line1=~ s/^\s*//; + $line1 =~ s/\s+/\t/g; + @line1 = split(/\t/, $line1); + if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){ + $line1_stat = "in1"; + $line3_stat = "in2"; + } + else{ + $line3_stat = "in1"; + $line1_stat = "in2"; } + } + elsif ($line3 =~ m/$outgroup/){ + $line3_stat = "out"; + $line1=~ s/^\s*//; + $line1 =~ s/\s+/\t/g; + @line1 = split(/\t/, $line1); + if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){ + $line1_stat = "in1"; + $line2_stat = "in2"; + } + else{ + $line2_stat = "in1"; + $line1_stat = "in2"; } + } + + #print "# l1 = $line1_stat\n"; + #print "# l2 = $line2_stat\n"; + #print "# l3 = $line3_stat\n"; + my $linei1 = my $linei2 = my $lineo = ""; + my @linei1 = my @linei2 = my @lineo = (); + + if ($line1_stat eq "out"){ + $lineo = $line1; + } + elsif ($line1_stat eq "in1"){ + $linei1 = $line1; + } + else{ + $linei2 = $line1; + } + + if ($line2_stat eq "out"){ + $lineo = $line2; + } + elsif ($line2_stat eq "in1"){ + $linei1 = $line2; + } + else{ + $linei2 = $line2; + } + + if ($line3_stat eq "out"){ + $lineo = $line3; + } + elsif ($line3_stat eq "in1"){ + $linei1 = $line3; + } + else{ + $linei2 = $line3; + } + + $linei1=~ s/^\s*//; + $linei1 =~ s/\s+/\t/g; + @linei1 = split(/\t/, $linei1); + $end1 =($linei1[2]+$linei1[3]-1); + $seq1 = $linei1[1].":".$linei1[3]; + $ingroup1 = (split(/\./, $seq1))[0]; + $start1 = $linei1[2]; + $align_length1 = $linei1[3]; + $orient1 = $linei1[4]; + $seq_length1 = $linei1[5]; + $sequence1 = $linei1[6]; + $test1 = length($sequence1); + my $total_length1 = $test1+$start1; + my @array1 = ($start1,$end1,$orient1,$seq_length1); + ($start1_plus, $end1_plus) = convert_coords(@array1); + + $linei2=~ s/^\s*//; + $linei2 =~ s/\s+/\t/g; + @linei2 = split(/\t/, $linei2); + $end2 =($linei2[2]+$linei2[3]-1); + $seq2 = $linei2[1].":".$linei2[3]; + $ingroup2 = (split(/\./, $seq2))[0]; + $start2 = $linei2[2]; + $align_length2 = $linei2[3]; + $orient2 = $linei2[4]; + $seq_length2 = $linei2[5]; + $sequence2 = $linei2[6]; + my $test2 = length($sequence2); + my $total_length2 = $test2+$start2; + my @array2 = ($start2,$end2,$orient2,$seq_length2); + ($start2_plus, $end2_plus) = convert_coords(@array2); + + $lineo=~ s/^\s*//; + $lineo =~ s/\s+/\t/g; + @lineo = split(/\t/, $lineo); + $end3 =($lineo[2]+$lineo[3]-1); + $seq3 = $lineo[1].":".$lineo[3]; + $start3 = $lineo[2]; + $align_length3 = $lineo[3]; + $orient3 = $lineo[4]; + $seq_length3 = $lineo[5]; + $sequence3 = $lineo[6]; + my $test3 = length($sequence3); + my $total_length3 = $test3+$start3; + my @array3 = ($start3,$end3,$orient3,$seq_length3); + ($start3_plus, $end3_plus) = convert_coords(@array3); + + #print "# l1 = $ingroup1\n"; + #print "# l2 = $ingroup2\n"; + #print "# l3 = $outgroup\n"; + + my $ABC = ""; + my $coord1 = my $coord2 = my $coord3 = 0; + $coord1 = $start1_plus; + $coord2 = $start2_plus; + $coord3 = $start3_plus; + + for (my $position = 0; $position < $test1; $position++) { + my $indelType = ""; + my $indel_line = ""; + # seq1 deletes + if ((substr($sequence1,$position,1) eq "-") + && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) + && (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){ + $ABC = join("",($ABC,"X")); + my @s = split(/:/, $seq1); + $indelType = $s[0]."_delete"; + + #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; + $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); + push (@indels,$indel_line); + push (@seq1_delete,$indel_line); + $coord2++; $coord3++; + } + # seq2 deletes + elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/) + && (substr($sequence2,$position,1) eq "-") + && (substr($sequence3,$position,1) !~ m/[-*\$?^]/)){ + $ABC = join("",($ABC,"Y")); + my @s = split(/:/, $seq2); + $indelType = $s[0]."_delete"; + #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; + $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); + push (@indels,$indel_line); + push (@seq2_delete,$indel_line); + $coord1++; + $coord3++; + + } + # seq1 inserts + elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/) + && (substr($sequence2,$position,1) eq "-") + && (substr($sequence3,$position,1) eq "-")){ + $ABC = join("",($ABC,"Z")); + my @s = split(/:/, $seq1); + $indelType = $s[0]."_insert"; + #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; + $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); + push (@indels,$indel_line); + push (@seq1_insert,$indel_line); + $coord1++; + } + # seq2 inserts + elsif ((substr($sequence1,$position,1) eq "-") + && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) + && (substr($sequence3,$position,1) eq "-")){ + $ABC = join("",($ABC,"W")); + my @s = split(/:/, $seq2); + $indelType = $s[0]."_insert"; + #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; + $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); + push (@indels,$indel_line); + push (@seq2_insert,$indel_line); + $coord2++; + } + # seq3 deletes + elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/) + && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) + && (substr($sequence3,$position,1) eq "-")){ + $ABC = join("",($ABC,"S")); + my @s = split(/:/, $seq3); + $indelType = $s[0]."_delete"; + #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; + $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); + push (@indels,$indel_line); + push (@seq3_delete,$indel_line); + $coord1++; $coord2++; + } + # seq3 inserts + elsif ((substr($sequence1,$position,1) eq "-") + && (substr($sequence2,$position,1) eq "-") + && (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){ + $ABC = join("",($ABC,"T")); + my @s = split(/:/, $seq3); + $indelType = $s[0]."_insert"; + #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; + $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); + push (@indels,$indel_line); + push (@seq3_insert,$indel_line); + $coord3++; + }else{ + $ABC = join("",($ABC,"N")); + $coord1++; $coord2++; $coord3++; + } + + } + @array_return=($seq1,$seq2,$seq3,$ABC); + return (@array_return); + + } + # ignore pairwise cases for now, just count the number of blocks + elsif (scalar(@sequences) == 2){ + my $ABC = ""; + my $coord1 = my $coord2 = my $coord3 = 0; + $count3++; + + $line1 = $sequences[0]; + $line2 = $sequences[1]; + chomp ($line1); + chomp ($line2); + + if ($line2 !~ m/$ingroup2/){ + $count4++; + } + } +} + + +sub get_indels_lengths{ + my (@array) = @_; + if (scalar(@array) == 4){ + my $seq1 = $array[0]; my $seq2 = $array[1]; my $seq3 = $array[2]; my $ABC = $array[3]; + + while ($ABC =~ m/(X+)/g) { + push (@seq1_delete_lengths,length($1)); + $count_seq1delete++; + } + + while ($ABC =~ m/(Y+)/g) { + push (@seq2_delete_lengths,length($1)); + $count_seq2delete++; + } + while ($ABC =~ m/(S+)/g) { + push (@seq3_delete_lengths,length($1)); + $count_seq3delete++; + } + while ($ABC =~ m/(Z+)/g) { + push (@seq1_insert_lengths,length($1)); + $count_seq1insert++; + } + while ($ABC =~ m/(W+)/g) { + push(@seq2_insert_lengths,length($1)); + $count_seq2insert++; + } + while ($ABC =~ m/(T+)/g) { + push (@seq3_insert_lengths,length($1)); + $count_seq3insert++; + } + } + elsif (scalar(@array) == 0){ + next; + } + +} +# convert to coordinates to + strand if align orient = - +sub convert_coords{ + my (@array) = @_; + my $s = $array[0]; + my $e = $array[1]; + my $o = $array[2]; + my $l = $array[3]; + my $start_plus = my $end_plus = 0; + + if ($o eq "-"){ + $start_plus = ($l - $e); + $end_plus = ($l - $s); + }elsif ($o eq "+"){ + $start_plus = $s; + $end_plus = $e; + } + + return ($start_plus, $end_plus); +} + +# get first line only for each event +sub get_starts_only{ + my (@test) = @_; + my $seq1 = my $seq2 = my $seq3 = my $indelType = my $old_seq1 = my $old_seq2 = my $old_seq3 = my $old_indelType = my $old_line = ""; + my $coord1 = my $coord2 = my $coord3 = my $old_coord1 = my $old_coord2 = my $old_coord3 = 0; + + my @matches = (); + my @seq1_insert = my @seq1_delete = my @seq2_insert = my @seq2_delete = my @seq3_insert = my @seq3_delete = (); + + + foreach my $line (@test){ + chomp($line); + $line =~ s/^\s*//; + $line =~ s/\s+/\t/g; + my @line1 = split(/\t/, $line); + $seq1 = $line1[1]; + $coord1 = $line1[2]; + $seq2 = $line1[4]; + $coord2 = $line1[5]; + $seq3 = $line1[7]; + $coord3 = $line1[8]; + $indelType = $line1[10]; + if ($indelType =~ m/$ingroup1/ && $indelType =~ m/insert/){ + if ($coord1 != $old_coord1+1 || ($coord2 != $old_coord2 || $coord3 != $old_coord3)){ + $start1++; + push (@seq1_insert_startOnly,$line); + } + } + elsif ($indelType =~ m/$ingroup1/ && $indelType =~ m/delete/){ + if ($coord1 != $old_coord1 || ($coord2 != $old_coord2+1 || $coord3 != $old_coord3+1)){ + $start2++; + push(@seq1_delete_startOnly,$line); + } + } + elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/insert/){ + if ($coord2 != $old_coord2+1 || ($coord1 != $old_coord1 || $coord3 != $old_coord3)){ + $start3++; + push(@seq2_insert_startOnly,$line); + } + } + elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/delete/){ + if ($coord2 != $old_coord2 || ($coord1 != $old_coord1+1 || $coord3 != $old_coord3+1)){ + $start4++; + push(@seq2_delete_startOnly,$line); + } + } + elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/insert/){ + if ($coord3 != $old_coord3+1 || ($coord1 != $old_coord1 || $coord2 != $old_coord2)){ + $start5++; + push(@seq3_insert_startOnly,$line); + } + } + elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/delete/){ + if ($coord3 != $old_coord3 || ($coord1 != $old_coord1+1 ||$coord2 != $old_coord2+1)){ + $start6++; + push(@seq3_delete_startOnly,$line); + } + } + $old_indelType = $indelType; + $old_seq1 = $seq1; + $old_coord1 = $coord1; + $old_seq2 = $seq2; + $old_coord2 = $coord2; + $old_seq3 = $seq3; + $old_coord3 = $coord3; + $old_line = $line; + } +} +# append lengths to each event start line +my $counter1; my $counter2; my $counter3; my $counter4; my $counter5; my $counter6; +my @final1 = my @final2 = my @final3 = my @final4 = my @final5 = my @final6 = (); +my $final_line1 = my $final_line2 = my $final_line3 = my $final_line4 = my $final_line5 = my $final_line6 = ""; + + +for ($counter1 = 0; $counter1 < @seq3_insert_startOnly; $counter1++){ + $final_line1 = join("\t",($seq3_insert_startOnly[$counter1],$seq3_insert_lengths[$counter1])); + push (@final1,$final_line1); +} + +for ($counter2 = 0; $counter2 < @seq3_delete_startOnly; $counter2++){ + $final_line2 = join("\t",($seq3_delete_startOnly[$counter2],$seq3_delete_lengths[$counter2])); + push(@final2,$final_line2); +} + +for ($counter3 = 0; $counter3 < @seq2_insert_startOnly; $counter3++){ + $final_line3 = join("\t",($seq2_insert_startOnly[$counter3],$seq2_insert_lengths[$counter3])); + push(@final3,$final_line3); +} + +for ($counter4 = 0; $counter4 < @seq2_delete_startOnly; $counter4++){ + $final_line4 = join("\t",($seq2_delete_startOnly[$counter4],$seq2_delete_lengths[$counter4])); + push(@final4,$final_line4); +} + +for ($counter5 = 0; $counter5 < @seq1_insert_startOnly; $counter5++){ + $final_line5 = join("\t",($seq1_insert_startOnly[$counter5],$seq1_insert_lengths[$counter5])); + push(@final5,$final_line5); +} + +for ($counter6 = 0; $counter6 < @seq1_delete_startOnly; $counter6++){ + $final_line6 = join("\t",($seq1_delete_startOnly[$counter6],$seq1_delete_lengths[$counter6])); + push(@final6,$final_line6); +} + +# format final output +# # if inserts, increase coords for the sequence inserted, other sequences give coords for 5' and 3' bases flanking the gap +# # for deletes, increase coords for other 2 sequences and the one deleted give coords for 5' and 3' bases flanking the gap + +get_final_format(@final5); +get_final_format(@final6); +get_final_format(@final3); +get_final_format(@final4); +get_final_format(@final1); +get_final_format(@final2); + +sub get_final_format{ + my (@final) = @_; + foreach (@final){ + my $event_line = $_; + my @events = split(/\t/, $event_line); + my $event_type = $events[10]; + my @name_align1 = split(/:/, $events[1]); + my @name_align2 = split(/:/, $events[4]); + my @name_align3 = split(/:/, $events[7]); + my $seq1_event_start = my $seq1_event_end = my $seq2_event_start = my $seq2_event_end = my $seq3_event_start = my $seq3_event_end = 0; + my $final_event_line = ""; + # seq1_insert + if ($event_type =~ m/$ingroup1/ && $event_type =~ m/insert/){ + # only increase coord for human + # remember that other two sequnences, the gap spans (coord - 1) --> coord + $seq1_event_start = ($events[2]); + $seq1_event_end = ($events[2]+$events[11]-1); + $seq2_event_start = ($events[5]-1); + $seq2_event_end = ($events[5]); + $seq3_event_start = ($events[8]-1); + $seq3_event_end = ($events[8]); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); + } + # seq1_delete + elsif ($event_type =~ m/$ingroup1/ && $event_type =~ m/delete/){ + # only increase coords for seq2 and seq3 + # remember for seq1, the gap spans (coord - 1) --> coord + $seq1_event_start = ($events[2]-1); + $seq1_event_end = ($events[2]); + $seq2_event_start = ($events[5]); + $seq2_event_end = ($events[5]+$events[11]-1); + $seq3_event_start = ($events[8]); + $seq3_event_end = ($events[8]+$events[11]-1); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); + } + # seq2_insert + elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/insert/){ + # only increase coords for seq2 + # remember that other two sequnences, the gap spans (coord - 1) --> coord + $seq1_event_start = ($events[2]-1); + $seq1_event_end = ($events[2]); + $seq2_event_start = ($events[5]); + $seq2_event_end = ($events[5]+$events[11]-1); + $seq3_event_start = ($events[8]-1); + $seq3_event_end = ($events[8]); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); + } + # seq2_delete + elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/delete/){ + # only increase coords for seq1 and seq3 + # remember for seq2, the gap spans (coord - 1) --> coord + $seq1_event_start = ($events[2]); + $seq1_event_end = ($events[2]+$events[11]-1); + $seq2_event_start = ($events[5]-1); + $seq2_event_end = ($events[5]); + $seq3_event_start = ($events[8]); + $seq3_event_end = ($events[8]+$events[11]-1); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); + } + # start testing w/seq3_insert + elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/insert/){ + # only increase coord for rheMac + # remember that other two sequnences, the gap spans (coord - 1) --> coord + $seq1_event_start = ($events[2]-1); + $seq1_event_end = ($events[2]); + $seq2_event_start = ($events[5]-1); + $seq2_event_end = ($events[5]); + $seq3_event_start = ($events[8]); + $seq3_event_end = ($events[8]+$events[11]-1); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); + } + # seq3_delete + elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/delete/){ + # only increase coords for seq1 and seq2 + # remember for seq3, the gap spans (coord - 1) --> coord + $seq1_event_start = ($events[2]); + $seq1_event_end = ($events[2]+$events[11]-1); + $seq2_event_start = ($events[5]); + $seq2_event_end = ($events[5]+$events[11]-1); + $seq3_event_start = ($events[8]-1); + $seq3_event_end = ($events[8]); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); + + } + + print OFILE2 "$final_event_line\n"; + } +} +close OFILE2;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3way.maf Wed Sep 25 11:24:53 2013 -0400 @@ -0,0 +1,76 @@ +##maf version=1 +a score=56674.0 +s hg18.chr1 46772 143 + 247249719 TTACAGAAACTCAGAATGATTCTAT----TTTTTCTTTTATATTTGTATATGTTTTTCCAATACCTCTGAAAAAACTGATCCAAAAAAAA--TACAAATTTTAATTGTAGCCAGTCAATTCAGGAAGGATAAAGGTCAAAAACTTTCAA +s panTro2.chrUn 9712379 145 + 58616431 TTACAGAAACTCAGAATGATTCTAT----TTTTTCTTTTATATTTGTATATGTTTTTCCAATACCTCTGAAAAAACTGATCCAAAAAAAAAATACAAATTTTAATTGTAGCCAGTCAATTCAGGAAGGATAAAGGTCAAAAACTTTCAA +s canFam2.chr30 39837824 145 - 43206070 TTACAAACACTCAAAATAACTCCCTATATTTTTCCTCTTTTGTGTTTGTATGTTTTCCACTGATCTCTTAAGAAATTGATCCAATAATG---TACAAATTTTACTTTTAGTCAGTTAACTCAGAAAAAATAAAG-TTAAAAGCACTCAA + +a score=597116.0 +s hg18.chr1 46915 1380 + 247249719 AGAAACCTTCAGCCCCAACACACTAAACTTTGGGAGCACAGGTTGGCATCCAGAGGTAAACATTTGCTATAACTGATAACAGGAGAAGGATCCATTTATTCACCTGTTATCAATTACAGGCATTGTATTTAAAGATCAGATGTTTTATATTTATTTCTTCAAATTTCATTCATGGTGCCATAAGTGAAGGTATCTCTGTCCACCCTGAATATATTTTCACTCCC--------TCATCTCAGTCATTCCGAACAATTCACACACTAAGATTACCCATGCTAAATGGGGATTCTTTTTTACTAGCCAATGTAGTACCTCAAATCCTTCCTTCCCTCCCCCTATTTCATCAGCAGGCAAT---TCTTTTGATACTTTTGTCAAGGGGAAATTG-TGTGACTCAGAGATCTAGT-CCCCAAGAGAAACTAATAATGGGCTGGGTATTGTCTGTCTCAGCAGCATCAGTGGGTCCCTCTCCTGTGCAGCTAATTAGCTTCCTTTCCAATATGAAGAATCTTATATATAGCTTTGTCTTTGGGGT-------ATTACATAAATGAAGATTAAGCTATCTGAATTTCTCCTTCTCCTAAAAATGCACATCCTATGACTGAAAAGACAGGTAAAAGAGATGC-TTTTAATTACAAAACTTT----------CCCTGTCGTGGTTGCT----TCTCTCTATCCTTCTAAACTCCCTTTCAATTTCTTCTCTTCTGTAACATATTTGTGCCCAAAATCTTCTGCTTTCTGAAATATTTT-ATCTTTTTCTTCCACACTATCTCT---TATTTTCCAATTTTAATCATTAAATTATATTATGTCTTATAAAACTAATCCCACATATAAAC-----CCCTATGATAATTTCAGTTTGTCCC--TAGTATGAAGTTCTTTAAAGATGTGTAGTTTTCTAACTTTCATGCTCTCCAATTAATTATAAACTTCATTTTCCAC--TCTGAAAAGGAGATGTCTGATCTCAGCTATTTCCATCCTATTTGAAAACCAGATTTAGTTTTAAACCAGAGGAAGGGAATCTCAAGTCTTTACCTCCCACAGTCTGGTGTGATTCTCTCTCTTTTGGTATTACCTTCCTCCACATTGGAACACTCCAGCCAATGCATAGGCTGAGAGGCTAT-CTCAGATTCAGAAAGATT-TGGCCTCATCCCAGGGGAGGGTACAGAGGAGCTGATGACTATGAATTCTGAAATGG----AACTGTTCCAGG--------------TTGAAGAAATAAGAAAGGGAATTGGGAAGAGCAATGCCCAGTGAAAAAGAAGAAATAATATTTTAGGAAGTGAATGCTAATTTTATTTTAAACAAAATAAGAACTCAAGGAATAAGAGGGTTCTTCCAA-TAGGTTAGAGTGATCCTGTCAAACATATATGCTTCTAGATTTTTTTAAAGACTGTTTCTACT +s panTro2.chrUn 9712524 1384 + 58616431 AGAAACCTTCAGCCCCAACACGCTAAACTTTGGGAGCACAGGTTGGCATCCAGAGGTAAACATTTGCTATAACTGATAACAGGAGAAGGATCCATTTATTCACCTGTTATCAATTACAGGCATTGTATTTAAAGATCAGATGTTTTATATTTATTTCTTCAAATTTCATTCATGGTGCCATAAGTGAAGGTATGTCTGTCCACCCTGAATATATTTTCACTCCC--------TCATCTCGGTCATTCCGAACAATTCACACACTAAGATTACCCATGCTAAATGGGGATTCTTTTTTACTAGCCAATGTAGTACCTCACATCCTTCCTTCCTTCCCCCTATTTCATCAGCAGGCAAT---TCTTTCGATACTTTTGTCAAGGGGAAATTG-TGTGACTCAGAGATTTAGT-CCCCAAGAGAAACTAATAATGGGCTGGGTATTGTCTGTCTCAGCAGCATCAGTGGGTCCCTCTCCTGTGCAGCTAATTAGCTTCCTTTCCAATATGAAGAATCTTATATATAGCTTTGTCTTTGGGGT-------ATTACATAAATGAAGATTAAGCTATCTGAATTTCTCCTTCTCCTAAAAATGCACATCCTATGACTGAAAAGACAGGTAAAAGAGATGC-TTTTAATTACAAAACTTT----------CCCTGTCGTGGTTGCT----TCTCTCTATCCTTCTAAACTCCCTTTCAATTTCTTCTCTTCTGTAACATATTTGTGCCCAAAATCTTCTGCTTTCTGAAATATTTT-ATCTTTTTCTTCCACACTATCTCT---TATTTTCAAATTTTAATCATTAAATTATATTATGTCTTATAAAACTAATCCCACATATAAAC-----CCCTATGATAATTTCAGTTTGTCCC--TAGTATGAAGTTCTTTAAAGATGTGTAGTTTTCTAACTTTCATGCTCTCCAATTCATTATAAACTTCATTTTCCAC--TCTGAAAAGGAGATGTCTGATCTCAGCTATTTCCATCCTATTTGAAAACCGGATTTAGTTTTAAACCAGAGGAAGGGAATCTCAAGTCTTTACCTCCCACAGTCTGGTGTGATTCTCTCTCTTTTGGTATTACCTTCCTCCACATTGGAACACTCCAGCCAATGCATAGGCTGAGAGGCTAT-CTCAGATTCAGAAAGATT-TGGCCTCATCCCAGGGGAGGGTACAGAGGAGCTGATGGCTATGAATTCTGAAATGG----AACTGTTCCAGG----------TTGTTTGAAGAAATACGAAAGGGAATTGGGAAGAGCAATGCCCAGTGAAAAAGAAGAAATAATATTTTAGGAAGTGAATGCTAATTTTATTTTAAACAAAATAAGAACTCAAGGAAAAAGAGGGTTCTTCCCA-TAGGTTAGAGTGATCCTGTCAAACATATATGCTTCTAGATTTTTTTAAAGACTGTTTCTACT +s canFam2.chr30 39838143 1415 - 43206070 AGAAGACTTTATCTTCAACACTCCAAAGTTTGGGACTGCAGGTAAATCTACAAAGGTAAACACTGGCTATAATTGATAACAGAAAAGTGATCTATTTATTCCCCTACTGTCAGTTGTAAGAATTATCTTTACATATCAGAGCTTTTATATCTATCTCTTCAAGTT-------TGGTACTACAAGTGAAGATATATCTGTCCATTTAGGTTATGTTTTCACACCCTCATCCCATCATCTCAGTACTTTCAAACAATTCATGC-CAAATATCATGTAACCTATACAGGGATATTTTTACACAAACCAATATATTGCCTCAAAATCTTCCCTCTTCCTCTTGGTTTCATAACCAGGCAATTTCTCTTTCACTATTTCTCTCATGGGAAAACCAATGTGATTCAAGGATTTAGTCCCCCAAGAGGAACAAATAATGGGCTCAGTATTGGCCTTCTCTGAGACAACAGTAGGTCACTCTCCTGTGTGCCTAATTAACTTATTTTCCATTTAGAAGAATATTATATATAGCTTTGTCTTTGAAGGAAGATTATATACAGATATTAAGACTAAGCTCTCTGAACTACTATTTTT-CCAAAAATGTAAATCCTGTGGCTGAACAGGCAGGTAGGAAAACTGCTTTTTAATTATAAAACTACAAGGGATGCAACCGGTCATGGTTGCATCCCTTGCTCTATCCCCCTTAACACTGCTTCAGTGTTTGCTCTTCTGTAAAATATCTGCATCAGAAATTTTCTCCTTTTGAAAATAGTTTCATCCTTTTATTCTACACCATCACTCTCTATTCTCAAATTGCAATCACTGAATTGCAT--TGTCTTATCAAATCGATTCCACACACACACACACATCTTTTGATATGTTTAATTTATCTCCTTGATGTGAAAATTTTTCAAGATTCATGTGCTTCTGATTTTTGTGCTCTCCAACTCATTTTAAAATTTTCCCCCCGCTGTATAAAAAAGAGACATTTGGCCTTAATTATTTCTACCTTATTTGAGAACCAAATTTTGTTTTAAACCAGAGGGAGGAAATCTCAATCCTCAACTTCCAGGATTCTGGTGTGATTCCCTCCCCTTCAGTATTAATTTCCTCTGCATTGGAAGGAACCAGCCAATGCCTAGTCTGAGAGGCTGTGCTCAGAGTCAAAGAGCTTCTGGTCCTGTGCCAGGGGATGGTAGAGGGGAACTGGTGGTTATAAATTCTGAGATGGAAGTAAGTGTTCAAGGACTGACTAGTTTGTGTGAAGAAACAGGAAAGCGGGTTAGGAAGAGCAAG---------------ATAAAT-GTCTTTCAGGAAG-GAAGGCCAATTTTATTTTAAAT-GAATAAAAACTCATGGTTGAATAGGATACTTTCAGTTAGGTTAGAGTGATCCTTTGAAATATAAATAATTCTAGCTTTTTTCA-----TGACTCTATT + +a score=213480.0 +s hg18.chr1 48332 455 + 247249719 CTGGAATTTAGGAGGTCTGCCTTCTGATTCTGACTTCTTGAATGTATT---------------GTTAGCCATTTAACCACACTGTGTTGTTTCTCATTCTACCTGTAGAA---------------------TCTCAAAGTTCTTTCCCACTTCTATACAAAACTATAATTCTGAACATCCTTTTTGTTTAATATAAGTCTGCATTTCCTGTTTGAAGATATGTGTCCC-AGACCCTAAATGACTGACAAATTTTAAATCTCCAATAGGAAAGATGACAAACTCTATGGAAACTTGGCTTCTGAAGAACTCCTAGAAGCTTTCCAAAGTCATCAGTGTTTCCTAAGAAGGCAGAGAAATCAAACACATGGTCTTTTCCTCCAGACAAGCTCCTTTGGGTCATCAGGATTTCTTCAACAATAAAATGTAATAATTCCAAATGTTTGTAACAGAATGGGTAGGACTTTCTTCACTTATTTAAATACTCCCTTTTT +s panTro2.chrUn 9714242 455 + 58616431 CTGGAATTTAGGAGGTCTGCCTTCTGATTCTGACTTCTTGAATGTATT---------------GTTAGCCATTTAACCACACTGTGTTGTTTCTCATTCTACCTGTAGAA---------------------TCTCAAAGTTCTTTCCCACTTCTATACAAAACTATAATTCTGAACATCCTTTTTGTTTAATATAAGTCTGCATTTCCTGTTTGAAGATATGTGTCCC-AGACCCTAAATGACTGACAAATTTTAAATCTCCAATAGGAAAGATGACAAACTCTATGGAAATTTGGCTTCTGAAGAACTCCTAGAAGCTTTCCAAAGTCATCAGTGTTTCCTAAGAAGGCAGAGAAATCAAACACATGGTCTTTTCCTCCAGACAAGCTCCTTTGGGTCATCAGGATTTCTTCAACAATAAAATGTAATAATTCCAAATGTTTGTAACAGAATGGGTAGGACTTTCTTCACTTATTTAAATACTCCCTTTTT +s canFam2.chr30 39839594 483 - 43206070 ctagaagttagg----ctgacttctagttctggatctgtgaacatactgctgtgaacacactggctagccatttaccctcatggggttggctc----tctacacgtacaaggaagtaactgaaaaagattctctcaaagttctttcccacttctatacacgtctataattctGA-TATCCTTTTTGTTCAATATGTATCTATATTTCCTGTTTAATGATGGGTCTTCCTAGACCCTGAATAACTGAAAAAGTTTACATCTCCAAGAGGAAGGATACCAAACTGTATGGGAACTTGGCCTCTGAGAAATTCTTGAGAGCTTCACAAAGTCATCAGAGTTTTCTAAAAAGGCAGAGAAACCAAGTGCATGGTCTTTTTCTCCCAGCAAGCTCTCTCTGGTCATAAGGATTTCCTCATCAATGATACATGCTAATTCCAGACATCTGGAAGAAGGGGGGTAGAAATTTCTTCACTCAGTTAAATACTCATTTTTT + +a score=83239.0 +s hg18.chr1 52524 183 + 247249719 TTTTATGCATTC--------TTTTCCAGTTTCTTAAGATG-CTAATAAGTTCATGTATTTGAGCAATTGAGAAC-ATTTAAAGCAATAGACTGCCTCTGAGCACAGCTTTGTCCATATTACATTAACCTTTTATACCCTGGGTTCCCACTAGTTTTTAAATAATCTACTATCAAATAA----AAGATTTGTTAATAA +s panTro2.chrUn 9718427 183 + 58616431 TTTTATGCATTC--------TTTTCCAATTTCTTAAGATG-CTAATAAGTTCATGTATTTGAGCAATTGAGAAC-ATTTAAAACAATAGACTGCCTCTGAGCACAGCTTTGTCCATATTACATTAACCTTTTATACCCTGGGTTCCCACTAGTTTTTAAATAATCTACTATCAAATAA----AAGATTTGTTAATAA +s canFam2.chr30 39841235 193 - 43206070 TTTTATACATCCTTTTCTAGTTTTCTAGTTTCTTAAATTGCCTGCTTACTCCATGTACATGAACAAATAAGAGCAATTTAAAGCAATAGACTGCCTCTGAGTGCAGCTTTGGTCATACTACCAAA----CTCATATCCCGGGTTCCCATTAATTTGTAAATAATTTACTATCAATTAAATACAAGATCTGTCAATAG + +a score=28580.0 +s hg18.chr1 52707 115 + 247249719 TAA---ATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAA-GTTGATTCC----TTCGTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAGTGGACCAAGT +s panTro2.chrUn 9718610 115 + 58616431 TAC---ATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAA-GTTGATTCC----TTCCTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAATGGACCAAGT +s canFam2.chr30 39841428 118 - 43206070 ---CTAGTATTAAATTATCAACATTCAAGACATTTTTTT--AGTACCTTAACATTGATTCCCTTTCTCATTTCTTTCAGATCACTTCAGAGTCTTCTCTTCCTTATGATTCAATGGACCAAGT + +a score=751514.0 +s hg18.chr1 52822 1040 + 247249719 AAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAAACTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGGTTGATCTACGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGCATGATACAAAAGTTCTTTATCCATGTTATGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGCATGTTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTATGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCGATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCAACGACATTCCTCAAATGATTTATCCAAAGCATTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTTGTCACCCCTGTCGTAAATCCTGCCATCTATACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAACACATTTGGTTGATGAGAGCACAGGATAAATGCCATGGACCATCAAGACTCCTGTGATCACCATGATCACTATGGAACGCGCACATTTTTAGTATTGCC-TGAAAAAACTGAA +s panTro2.chrUn 9718725 1040 + 58616431 AAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAACCTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGATTGATCTATGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGTATGATACAAATGTTCTTTATCCATGTTACGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGCATGCTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTACGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCTATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCGACGACATTCCTCAAATGATTTATCCAAAGCGTTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTGGTCACCCCTGTCTTAAATCCTGCCATCTACACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAACAGATTTGGTTGATGAGAGCACAGGATAAATGCCATGGACCATCAAGACTCCTGTGATCACCATGATCACTATGGAACGCGCACATTTTTAGTATTGCC-TGAAAAAACTGAA +s canFam2.chr30 39841546 1041 - 43206070 AAATGGCTCTTTGGTAACTGAATTTGTGTTACTGGGACTTGCACAATCCTTGGGAATGCAGATTTTCCTTTTTGTTTTTTTCTCTTTATTCTATGTTGGAATTATCTTAGGAAACCTCTTCATTATGTTAACAGTGATTTTTGATTCTCACTTACACTCCCCAATGTATATCCTGCTGGCCAACCTATCACTCATTGATGTGGGCCTTTCATCCACCACAGTTCCTAGAATGATCTCTGATCTTTTCAGTGGTTGTAAAATCATTTCCTTCCACAACTGCATGATACAAATGTTCTTTATTCATGTTATGGGAGGAGTTGAGATGGTGTTGCTCATAGCCATGGCATTTGACAGGTACACAGCGATCTGCAAGCCTCTCCACTATCTCACTACCATGAATACCAAAACGTGCATGCTTTTGGTAGTGGCTGCTTGGATCATTGGGGTGATTCATGCTGTATCTCAGTTTGTTTTTGTCATAAATTTACCTTTTTGTGGCCCTAATAATGTAGGGAGCTTTTATTGTGATTTTCCTAGGGTTATTAAACTTGCATGCATGGACACATACAGACTAGAATTTGTGGTCACTGCCAACAGTGGCTTCATATCTATGGGCACATTCTTTTTCTTAATTGTATCATACATCTTTATTCTGGCCACTGTTAGACAGCATTCTTCAAAAGACTTGTCCAAAGCATTTGTCACTCTGTCAGCTCACATCACTGTGTTGGTTTTGTTTTTCACTCCATGCATGTTTCTCTATGTGTGGCCTTTCCCTACCAAGTCAATGGATAAATTTTTTGCCATTGTGGATTTTGTTATCACTCCTGTATTAAATCCTGCCATCTATACTCTAAGGAACAGAGATATGAAGGTGGCAATGGGAAGGCTGAGTCGACAAGTTGTAAGTTCTAGAGACATACCATAACAGATTTTATTGGTAAGAGCACAAGATGAATGTTGTGGACCTTCAGGACCCTCGTGATCACCATGAACACTATGGATTATGTACAATTTCATTATTGCCTTTAAAAAACTGAG + +a score=139278.0 +s hg18.chr1 53862 335 + 247249719 AAATCTGC----AAAAAGGATGCATTAAATCTAAGAATTGTA-TTTCAGATAAAGTTGCAACATT-TTTTGTTAATCATAAAA--------AGTATATATTTCTATCTAATGTGTGTATCTAA-------TTAACAGCAATGACTACCTTTAATTTTGATGTAGTTATTTTATATCTGTATATAAGCACATACACATATATATGACCTAGGTTTATTTATCAGTATTTTTATGCTGATAATAAGCATCACTGGAAATTAAT-----TTTCTTATGGAAATTATGTGGATCCAATGGATAAAATATGAGTTTATATAAATTAGTAAATGC-CAAAATCAAGGAAGAAACAATTTTTATTTTAA +s panTro2.chrUn 9719765 335 + 58616431 AAATCTGC----AAAAAGGATGCATTAAATCTAAGAATTGTA-TTTCAGATAAAGTTGCAACATT-TTTTGTTAATCATAAAA--------AGTATGTATTTCTATCTAATGTGTGTATCTAA-------TTAACAGCAATGACTATCTTTAATTTTGATGTAGTTATTTTATATCTGTATATAAGCACATACACATATATATGACCTAGGTTTATTTATCAGTATTTTCATGCTGATAATAAGCATCACTGGAAATTAAT-----TTTCTTATGGAAATTATGGGGATCCAATGGATAAAATATGAGTTTATATAAATTAGTAAATGC-CAAAATCAAGGAAGAAACAATTTTTATTTTAA +s canFam2.chr30 39842587 356 - 43206070 ATATCTATGTAAAAAAAGGAT--ATTAAATCAAAGAACTATACTTTCAAATAGGGTTGCTGTAATAATCTGTTAAGTATGAAAAATAAAGTGTCATACATTCCTACCTAACCTATAAAACTAAGTTGCAATTATCATCAATGACCACATTCAATTTTCATGTAATTGTTTTATATCTCTATATAAATATATACATGTACATATGATTGAGC----TTTATCAGTATCTTCATACTGATCATAAGCATCACTGGAAATCAATTAATGTTTCTTATAGAAATTATGTGGATCCAATGGATAAAATATGAGTTTATACAAACCAGCAGCCATGAAAAATCAAGAAAGAAACAATTCTTATCCTAA + +a score=268726.0 +s hg18.chr1 54530 582 + 247249719 AGACTCTAGTACTCTGTATTATGCAAAATTTGTCTATGTTACACTTTTTT-AACAACACAATCCTATTGCCCTTGAAATCTTCTTCAAAGCATTTCTCGAGTCACTCTTAAAAAGCATCTACAACC-TAAAAGTATAGGAAGAGATTTATTTCCTGGAGAAGAG-ACCCCATTGAGATCTTAAAAGCACATTTAATGTGCCTGTGCTTAACTTAAGGT----GCTTAGGACAAAGAAGGCGATTGACATCTTT------------------CAGGTAAAACCTGGTAAGTTTGGT-GGTCAAGGAACACAACTGAGACATCACTTGGATGTATTCCTATGACTATTTTAAGAAACATAAATTGTGGTGACTCACTCAGCTCACTTTTAACTACTGCATGGTAATTAAAGATGCAAAATAAAATAAGTTACAAGAAGTGAGG----TTTTTTATTGGTTAAAGCAATTTTT-CTATATTTTCTCCGCAAGTTGGTCATAAAAGTTCTAAGCATTCCTCTTTTTATAAAATCGAAGCATTATTACTTACTCTCTTGTTAACCTATCTGGATTTTAATTTTGTAACTTTATTATATTTGTTTTGCTGTGATTCTTT +s panTro2.chrUn 9720721 585 + 58616431 aGACTCCAGTACTCTGTATTATGCAAAATTTGTCTATGTTACACTTTTTT-AACAACACAATCCTATTGCCCTTGAAATCTTCTTCAAAGCATTTCTCGAGTCACTCTTAAAAAGCATCTACAACC-TAAAAGTATAGGAAGAGATTTATTTCCTGGAGAAGAG-ACTCCATTGAGATCTTAAAAGCACATTTAATGTGCCCGTGCTTAACTTAAGGTAGGTGCTTAGGACAAAGAAGACGATTGACATCTTT------------------CAGGTAAAACCTGGTAAGTTTGGT-GGTCAAGGAACACAACTGAGACATCACTTGGATGTATTTCTATGACTATTTTAAGAAACATAAATTGTGGTGACTCACTCAGCTCACTTTTAACTACTGCATGGTAATTAAAGATGCAAAATAAAATAAGTTACAAGAAGTGAGG----TTTTTTATTGGTTAAAGCAATTTTT-CTATATTTT-TCCGCAAGTTGGTCCTAAAAGTTCTAAGCATTCCTCTTTTTATAAAATCGAAGCATTATTACTTACTCTCTTGTTAACCTATCTGGATTTTAATTTTGTAACTTTATTATATTTGTTTTGCTGTGATTCTTT +s canFam2.chr30 39843049 600 - 43206070 AGATTCTAGCATTTTGCATTATGCAAAATTTGTCTGTGTTCTATTTTTTTCAACAGCAAATTTCTGTTGTCCTTGCAGTCTTCTTCAAAGCATTTCTTGATTCAC-CCTAAAGAGTATCTACAATTATAAAAGTATTTTAAGGATCTTATTACCTAAAGAAAGGTACTCAACTCAGATCTCAA---CTTATTTAATGTACCTGTTCTTAAGCCAGGGT----GCTTAGGACAAAGAAGATGATTGACATCTTTACTTTTACTTTACTTTTCCAAATAAAACTTGGAAAGTCTGATGGGTCAAGGAGCACAATTGAGAAATCACTTGGGTATATTCCTGTGACTAATATAAGAAATGTAAATTGTAGTGACTA----AACTCGGTTGTAACTGCTGCATTGTAGTTAAAGCTGTTCAATAAAATGGCAAATAATGAATGAGACTTTCTTATTATTGGTCGAGGTATTTTTCCCTATATTTTATCCA-AAATTAGTCATAAGTGCTATAAGCTCTCCTCTTTTTATAATATCAAAGCATTATTATTTATTGTCTTCTTAATCCATCTGGATTTTAATTTCAGAACTTTATCTTATTGGTTTTACTATGATTCTTT + +a score=149740.0 +s hg18.chr1 55112 367 + 247249719 AAAAAGCACCTTTAGACTCAGTGAGATAGCAAAAATATCCAAATAGGCCAAAAAATTGTGGCAATGTCCTCTCACTCAGGAAAATTCTGTGTGTTTTCTCTAATGGCCAAGGGAAAACTTGTGAGACTATAAAAGTTAGTCTCAGTACACAAAGCTCAGACTGGCTATTCCCAGATCTCTTCAGGTACATCTAGTCCATTCATAAAGGGCTTTTAATTAACCAAGTGGTTTACTAAAAAGGACAATTCA-CTACATATTATTCTCTTA-CAGTTTTTATG-----------------------------------CCTCATT-CTGTGAAAATTGCTGTAGTCTCTTCCAGTTATGAAGAAGGTAGGTGGA--AACAAAGACAAAACACATATATTAGAAGAATGAA +s panTro2.chrUn 9721306 402 + 58616431 AAAAAGCACCTTTAGACTCAGTGAGATAGCAAAAATATCCAAATAGGCCAAAAAATTGTGGCAATGTCCTCTCACTCAGGAAAATTCTGTGTGTTTTCTCTAATGGCCAAGGGAAAACTTGTGAGACTATAAAAGTTAGTCTCAGTACACAAAGCTCAGACTGGCTATTCCCAGATCTCTTCAGGTACATCTAGTCCATTCATAAAGGGCTTTTAATTAACCAAGTGGTTTACTAAAAAGGACAATTCA-CTACATATTATTCTCTTA-CAGTTTTTATGCTTCAAGGCAGTGCAAATAAAGGGAAATTTGTACTCCTCATT-CTGTGAAAATTGCTGTAGTCTCTTCCAGTTATGAAGAAGGTAGGTGGA--AACAAAGATAAAACAAATATATTAGAAGAATGAA +s canFam2.chr30 39844287 382 - 43206070 AAAAATCATCTTTAGATTC-GTGAGGTAGTAGAAATACCTAAGTGAGCAAATAGCTTGAGATGACAGTCCCTAACTCAAGAAGATTTTGTGTGTATGTCCT------TAAGGGAAAACCAGTGACACTATATGACTTAGTCTCAGTACTCAAACTTCAGGCTGGATATTTCCAGATCTCCTCAACTGCCTCTGGTC-ATTCATAAATGGCTC----TTAACCAAGTGG-------AGGAGGATGATTCAGACAGACTTTATTCTCTTGGAAATTTT--TCCTTCAAGACAAAGTGCAAAATGGAAAATCTGTACTCTTCCTTGCTCTGAAAATTGCCGTAGCATCTTCCAGTTATGAAGGAGGTAGGTGGAATAATGATCATGAA----CTATATTAGCAGAACTAA + +a score=103163.0 +s hg18.chr1 55740 272 + 247249719 TCTTTCCCCAGGTCCGGTGTTTTCTTACCCACCTCCT-TCCCTCCTTTTTATAATACCAGTGAAACTTGGTTTGGAGCATTTCTTTCACATAAAGGTACAaatcatactgctagagttgtgaggat-----ttttacagcttttgaaagaataaactcattttaaaaacaggaaagctaaggcccagagatttttaaatgatattcccatgatcacactgtgaatttgtgccagaa--cccaaatgcct--actc-----------------------------------ccatctcactgaGACTTACTATAAGGA +s panTro2.chrUn 9721736 307 + 58616431 TCTTTCCTCAGGTCCGGTGTTTTCTTACCCACCTCCT-TCCCTCCTTTTTATAATACCAGTGAAACTTGGTTTGGAGCATTTCTTTCACATAAAGGTACAaatcatactgctagagttgtgaggat-----ttttagagcttttgaaagaataaactcattttaaaaacaggaaagctaaggcccagagatttttaaatgatattcccatgatcacactgtgaatttctgccagaa--cccaaatgcct--actcccaatatatattatataaatataacatatattttaCCATCTCACTGAGACTTACTATAAAAA +s canFam2.chr30 39844941 265 - 43206070 ATATACTTCAGATTCAGTGTTCTTTTACCCACCTTTTCCCCCTCTTTCCTGCAATCCCAATGAAGTCTGTTTTAGGATATTTCTTTCACATAAAGGTGCAAATCATACTCCTAACATTGTGGAATTTTGTCTTTAAGAGCTTTTGATCCAAAGAGCTCA-----------Ggaaaactaaggcttggaga-ttctaaatgacatg-tcaaaatcacacagtaaat-tgtactaatattcccaaatctcctgactt-----------------------------------caaTCTCAGTGAAATT---TATGAAGA + +a score=1417.0 +s hg18.chr1 56012 19 + 247249719 CATAAGGCatttatatata +s panTro2.chrUn 9722043 19 + 58616431 CATAATACATTTTtatata +s canFam2.chr30 39845206 19 - 43206070 CTTTAGGCATTTTTCTTTA + +a score=335729.0 +s hg18.chr1 56589 802 + 247249719 GATTCTGAAGGACTCCTTTAATAAGCCTAAACTTAATGTTCAACTTAGAATAAATACAATTCTTCTAATTTTTTTTGAATAATTTTTAAAAAGTCAGAAATGAGCTTTGAAAGAATTATGGTGGTGAAGGATCC---------------------------------CCTCAGCAGCACAAATTCAGGAGA-GAGATGTCTTAACTACGTTAGCAAGAAATTCCTTTTGCTAAAGAATAGCATTCCTGAATTCTTACTAACAGCCATGATAGAAAGTCTTTT-GCTACAGATGAGAACCCTCGGGTCAACC-TCATCCTTGGCATATTTCATGTGAAGATAT-AACTTCAAGATTGTCCTTGCCTATCAATGAAATGAATTAATTTTATGTCAATGCATATTTAAGGTCTATTCTAAATTGCACACTTTGATTCAAAAGAAACAGTCCAACCAACCAGTCAGGACAGAAATTATCTCACAATAAAAATCCTATCGTTTGTACTGTCAATGATTAGTATGATTATATTTATTACCGTGCTAAGCAGAAGAGAAATGAAGTGAATGTTCATGATTTATTCCACTATTAGACTTCTCTTTATTCTTAAAAATA--TTTAAGATCACTAAATTTTTATAGGACTTTAAAAACAGTAATGTGCTGCTTTGAGTGTGTAGGACTAAGAAATGGGATTCAGAGTAGTAAAGAGAAAAGTGGAATTTCCAAGCACTATGAATTACTGTTCTTTAAAAAACAGCAAAAATCAAATAACAGTATTCCTCCAAAAAAGATGGCAAGTGTAAACT-CTATACCTTCATGTCTCCCGTGGAATGTTAGTGATCAA +s panTro2.chrUn 9723768 801 + 58616431 GATTCTGAAGAACTCCTTTAATAAGCCTAAACTTAATGTTCAACTTAGAATAAATACAATTCTTCTAAATTTTTTTGAATAATTTTTGAAAAGTCAGAAATGAGCTTTGAAAGAATTATGGTGGTGAAGGATCC---------------------------------CCTCAGCAGCACAAATTCAGGAGA-GAGATGTCTTAACTACGTTAGCAAGAAATTCCTTTTGCTGAAGAATAGCATTCCTGAATTCTTACTAACAACCATGATAGAAAGTCTTTT-GCTACAGATGAGAACCCTCGGGTCAACC-TCATCCTTGGCATATTTCATGTGAAGATAT-AACTTCAAGATTGTCCTTGCCTATCAATGAAATGAATTAATTTTATGTCAATGCATATTTAAGGTCTATTCTAAATTGCACACTTTGATTCAAAAGAAACAGTCCAACCAACCAGTCAGGACAGAAATTATCTCACAATAAAAATCCTATCATTTGTACTGTCAATGATTAGTATGATTATATTTATTACCGTGCTAAGCAGAAGAGAACTGAAGTGAATGTTCATGATTTATTCCACTATTAGACTTCTCTTTATTCTTAAAAATA--TTTAAGATCACTAAATTTTTATAGGACTTTAAAAACAGTAATGTGCTGCTT-GAGTGTGTAGGACTAAGAAATGGGATTCAGAGTAGTAAAGAGAAAAGTGGAATTTCCAAGCACTATGAATTACTGTTCTTTAAAAAACAGCAAAAAACAAATAACAGTATTCCTCCAAAAAAGATGGCAAGTGTAAACT-CTATACCTTCATGTCTCCCGTGGAATGTTAGTGATCAA +s canFam2.chr30 39845358 805 - 43206070 GATTCTGGAGAACTTCTTCAGT------AAACTTAATATCTAACTTAGAATCAAAAGAATTCTTCTAAAACCCCTTGAACCGCTTTTGAAGAATCAGATATGAGCTT-GAAAGGATTACAGCAGTGAAGGATCCCCTGTAACTGAGAATCCCCTATCATCACTCACTCCTCAGTAGCATATACTCAGGAAATGAGATGTCTTAACTAAGTGAACAAGAAATTCTTTTTGCTGAAGTACAGCATATCTGAATTCTGACTTGTTACCATGGTATAAAGTCTTTTCACTGCAAAAGAGAAACCACTGGTCAGCTATCACCCTTGGTATATTTCTTATGGAGATATGAGCATCGAATTCATCC-------TCAGTGAAATGAGATGGTTGTACATAAGTAAATATTGAATTTCCATTCTAAGTTGCATACTTTGATTCTTAAC---CATCCTAACCAATCAGTCACATCAGAAATGATCTCACAATAAGAATACCATCCTCTTTATTGTCAGTGATTACAATGATTGTATTTACTACTGTGCTAAGCAGAAGGGAACAGAGG-----GTTTATTTCTTGTTTTACTCTTAGACTTCTCCTTATACTTGAAAATAAAATTAGAATTGTCAAATTCTTACAGGACTTTGAAAGCAGTAATAAGGAGCAT-TAG-GGATAGGGCTAAGGAATGGGATTTGGAAT-----AATGAAAAGTGTAACTTCCAAGGGTGTTGCAATAACCACAATCAGGCAGTGTTGAAAA--AAATAATACCACTCCTCCAAAAAATTTGGTAAGAGTAACCCACTATATTTTCACATGTCCCTAGGACC--TATTGA---- + +a score=65626.0 +s hg18.chr1 58409 176 + 247249719 ttctcacttcacttttgaattccctattcttttatcctctgttaatttttaagtattatatttgtgatattattttttctttttttctattttttatctttcatttcattttggcctattt--ttttctcttAAGAACTTTAATATCACCAAATAACATGTGTGCTACAAACTGTTTT +s panTro2.chrUn 9725587 176 + 58616431 ttctcacttcacttttgaattccctattcttttatcctctgttaatttttaagtattatatttgtgatattattttttctttttttctattttttatctttcatttcattttggcctattt--ttttctcttAAGAACTTTAATATCACCAAATAACATGTGTGCTACAAACTGTTTT +s canFam2.chr30 39846454 148 - 43206070 ---TCATTTCATTTCTAAATCACCT-TTCTTTAATCC--TATTATTTTCATGCTATTTTAT--------TTATTTTTTC-----TTCTATTTTTCATCTTT------ATTATGGGCTAACTCTTTTTCTTCTAAGCATTTCAATATCACTAAATGATA-----ACTACAAATTCTATT + +a score=986811.0 +s hg18.chr1 58585 1628 + 247249719 GTAGTTCAAAGAAAAAGGAGATAAACATAGAGTTATGGCATAGACTTAATCTGGCAGAGAGACAAGCATAAATAATGGTATTTTATATTAGGAATAAACCTAACATTAATGGAGAC-ACTGAGAAG-CCGAGATAACTGAATTATAAGGCATAGCCAGGGAAGTAGTGCGAGATAGAATTATGATCTT------GT-TGAATTCTGAATGTCTTTAAGTAATAGA---------------TTATAGAA---------AGTCACTGTAAGAGTGAGCAGAATGATATAAAATGAGGCTTTGAATTTGAATATAATAATTCTGACTTCCTTCTCCTTCTCTTCTTCAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAGCCCCTACACTACACTACAATTATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCACATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCGTTTGCCGTGCACTTACTCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACAGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAGATCTTATATAACTGTGAGATTAATCTCAGATAATGACACAAAATATAGTGAAGTTGGTAAGTTATTTAGTAAAGCTCATGAAAATTGTGCCCTCCATTCCCATATAATTTAGTAATTGTCTAGGAACTTCCACATACATTGCCTCAATTTATCTTTCAACAA-CTTGTGTGTTATATTTTGGAATACAGATACAAAGTTATTATGCTTTCAAAATATTCTTTTGCTAATTCTTAGAACAAAGAAAGGCATAAATATATTAGTATTTGTGTACACCTGTT----CCTTCCTGTGTGACCCTAAGTTTAGTAGAAGAAAGGAGAGAAAATATAGCCTAGCttataaatt +s panTro2.chrUn 9725763 1631 + 58616431 GTAGTTCAAAGAAAAAGGAGAAAAACATAGAGTTATGGCATAGACTTAATCTGGCAGAGAGACAAGCATAAATAATGGTATTTTATATTAGGAATAAACCTAACATTAATGGAGAC-ACTGAGAAG-CCGAGATAACTGAATTATAAGGCATAGCCAGGGAAGTAGTGCGAGATAAAATTATGATCTTT-GGTTGT-TGAATTCTGAATGTCTTTAAGTAATAGA---------------TTATAGAA---------AGTCACTGTAAGAGTGAGCAGAATGATATAAAATGAGGCTTTGAATTTGAATATAATAATTCTGACTTCCTTCTCCTTCTCTTCTTCAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATT-ATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCAGAATAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTGTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAACCCCTACACTACACTACAATTATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCGCATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCCTTTGCCGTGCACTTACCCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACGGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAGATCTTATATAACTGTGAGATTAATCTCAGATAATGACACAAAATATAGTGAAGTTGGTAAGTTATTTAGTAAAGCTCATGAAAATTGTGCCTTCCATTCCCATATAATTTAGTAATTGTCTAGGAACTTCCACATACATTGCCTCAATTTATCTTTCAACAA-CTTGTGTGTTATATTTTGGAATACAGATACAAAGTTATTATGCTTTCAAAATATTCTTTTGCTAATTCTTGGAACAAAGAAAGGCATAAATATATTAGTATTTGTGTACACCTGTT----CCTTCCTGTGTGATCCTAAGTTTAGTAGAAGAAAGGAGAGAAAATATAGCCTAGCttataaa-t +s canFam2.chr30 39847579 1623 - 43206070 GGAGTTCAAGGGAAAAGAAGTTAAATGTAGGATGGTGGTATAAACTTAATCTGGCAGACAAAGTAGCATGAAAAAAGGTACTTT-CATTAGGAATAAGCTTAGCATAAGTGGAAATAACTGAGCAGACTTGAGTAACTGGACTATAAAGCATAATCAAAGAACGAGTGTGATATAAAAATGGAGGGTTTAGATTGTGTACAATTTGAAAGCCTTTATGATATAAAGGCTTTTTCTGTGCTTTATAGCACTATATAATAGTCATTATATGAGTGAGCAGAATGACATAAAAGGAGACT---AACTGAAATATAATAATTTTGACTTCCTTCTTACTCTATTCTCCAAGGTAACTACACCGGCTGTTTCCTGGAATGAATCAATAAGTGACATGAATTACTCCATGGTGACTGAGTTCATTTTTCTGAGACTCTCTAATTCTCAGGAATTGCAGATTTTCCCTTTTGTGTTCTTTGTTGTATTCTATGTAGGAATTGTGTGTGGAAACCTTCCTATTGTCATAACTGTGGCCTCTGACTCCTACCTTCACTCCCCCTTGTACTTCCTGCTGGCTAACCTCTCACTCATTGACCTATGTCTGTCTTCAGTCACAGCCCCCAAGATGATTGCTGACATTTTTAGTAAACACAAAGTCATTTCTTTCAAGGGCTGCCTTGCTCAGCTATTTATCCTTTACTTTTTTGGTGGGAGCAAGCTGGTGATCCTTATAGCCATGGCCTTTGACAGATATGTAACAATCTGTAAACCACCTCGCTACACTACAGTTATGTG----------TGTGTTGGCCTTGTGGCTGCTGCATGGGGAACTGGCTTCCTCCATTCAGTCAGCCAGCTGGCCTTTGCAGTGAACTTACCTTTCTGTGGTCCCAATGAGGTTGACAGTTTTTATTGTGACCTCCCTAGGGTTATCAAACTTCCTTGTACAGATATCTATAGGTTGGATATCATGGTCATTGCTAACACTGGTGTGCTCACTGTGTGTTC-TTTATTTTCCTAATCATCTCCTATGCTATCATCCTAGTGACCATCCAGCAACACCCTTCAGACAAGTCATCCAAGGCACTGTCCACTTTGACTGCTCACGTCACAGTAGTTCTTTTGTTCTTTGGACCATGTATCTTCATTTATGCCTGGCCATTCCCCATGAAGTCATTAGATGAATTCCTTCCTGTGTTTTATTATGTGGTCACTCCTGTCTTGAACCCAATTATATATACACTGAGGAACAAGGACATGAAGACTGCACTGAAATGGCTGAGAAAATGGCATGTAAACTCTAGGGTAAAGTCTTAAATCTCTCATAATTGTA-----------AGATAATGAC-----ATATGGTAAAGTTGGTGAATTACTTAGGAAACCTCATGAAAATCTTACTTTCTATTTCCATATCCCTTAATAATTATCTAAGAGGTTTCACATACACTGCCTCAATTTATCCTTTGACACTTTTGCATTTTATATTTTTG------GATACAAAGTTGATATGTTTTTAAAATATTATTTCACTAATCCTCAGAACAGT----GGCATAAATCTGTCAATATCTGTATATTCCTCTGGCTACCTACCTGAGAGGTCCTGAGTGTAACTGATGGAA--ACACAGAAACTAGCCTGGTTTATAATTT + +a score=85144.0 +s hg18.chr1 60306 230 + 247249719 TATATGTCAACTTTTAAGAGG-TTGAAAAACAAACGCCTCCCATTATAA--GTTTATACTTCACCTCCCACCACTATAACAACCCAGAA-TCCATGAGGGCATTATCAGGAGTGAGTGGAAGAGTAAGTTTGCCAATGTGAAATGTGCCTTCTAGGTCCTAGACG-TCTGTGGTAT-----AACTGCTCATAAGCAGTAGAAAGAATTTAGAGGGATCCAGGCTCTCATCACGTTGGCAC +s panTro2.chrUn 9727487 230 + 58616431 TATATGTCAACTTTTAAGAGG-TTGAAAAACAAACGCCTCCTATTATAA--GTTTATACTTCACCTCCCACCACTATAACAACCCAGAA-TCCATGAGGGCATTATCAGGAGTGAGTGGAAGAGTAAGTTTGCCAATGTGAAATGTGCCTTCTAGGTCCTAGACA-TCTGTGGTAT-----AACTGCTCATAAGCAGTAGAAAGAATTTAGAGGGATCCAGGCTCTCATCATGTTGGCAC +s canFam2.chr30 39849231 218 - 43206070 TATAAGCTAACTTTTAAGAGGTTTAGAAAAGAAACTCCTCACATTGTTATGGTTCATAGTTCCTCTCCAATCACTATAGCAACTTAAAATTCCATGAG----TTATCAGGAATGACAAGAAGAGTGAGTCTGCCAACCCAAAAGTTGCCTTATAGACACTTGACATCCTGTTGCATACAAGAAGAGCCCATTTGTAGTAAAAAATACTTA--------CAAACT----------TGGCAC +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/indels_3way.tabular Wed Sep 25 11:24:53 2013 -0400 @@ -0,0 +1,149 @@ +#block indel_type indel_length ingroup1 ingroup1_start ingroup1_end ingroup1_alignSize ingroup1_orient ingroup2 ingroup2_start ingroup2_end ingroup2_alignSize ingroup2_orient outgroup outgroup_start outgroup_end outgroup_alignSize outgroup_orient +12 hg18.chr1_insert 1 hg18.chr1 57213 57213 802 + panTro2.chrUn 9724391 9724392 801 + canFam2.chr30 3360548 3360549 805 - +2 hg18.chr1_delete 4 hg18.chr1 48103 48104 1380 + panTro2.chrUn 9713713 9713716 1384 + canFam2.chr30 3367755 3367758 1415 - +9 hg18.chr1_delete 35 hg18.chr1 55389 55390 367 + panTro2.chrUn 9721584 9721618 402 + canFam2.chr30 3361661 3361695 382 - +14 hg18.chr1_delete 1 hg18.chr1 58770 58771 1628 + panTro2.chrUn 9725949 9725949 1631 + canFam2.chr30 3357056 3357056 1623 - +14 hg18.chr1_delete 4 hg18.chr1 58770 58771 1628 + panTro2.chrUn 9725950 9725953 1631 + canFam2.chr30 3357058 3357061 1623 - +1 panTro2.chrUn_insert 2 hg18.chr1 46857 46858 143 + panTro2.chrUn 9712465 9712466 145 + canFam2.chr30 3368190 3368191 145 - +8 panTro2.chrUn_insert 4 hg18.chr1 54744 54745 582 + panTro2.chrUn 9720936 9720939 585 + canFam2.chr30 3362635 3362636 600 - +10 panTro2.chrUn_insert 35 hg18.chr1 55984 55985 272 + panTro2.chrUn 9721981 9722015 307 + canFam2.chr30 3361105 3361106 265 - +8 panTro2.chrUn_delete 1 hg18.chr1 54979 54979 582 + panTro2.chrUn 9721173 9721174 585 + canFam2.chr30 3362890 3362890 600 - +14 panTro2.chrUn_delete 1 hg18.chr1 59015 59015 1628 + panTro2.chrUn 9726197 9726198 1631 + canFam2.chr30 3357328 3357328 1623 - +14 panTro2.chrUn_delete 1 hg18.chr1 60211 60211 1628 + panTro2.chrUn 9727392 9727393 1631 + canFam2.chr30 3358490 3358490 1623 - +1 canFam2.chr30_insert 4 hg18.chr1 46796 46797 143 + panTro2.chrUn 9712403 9712404 145 + canFam2.chr30 3368127 3368130 145 - +2 canFam2.chr30_insert 8 hg18.chr1 47138 47139 1380 + panTro2.chrUn 9712747 9712748 1384 + canFam2.chr30 3366730 3366737 1415 - +2 canFam2.chr30_insert 3 hg18.chr1 47263 47264 1380 + panTro2.chrUn 9712872 9712873 1384 + canFam2.chr30 3366862 3366864 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47293 47294 1380 + panTro2.chrUn 9712902 9712903 1384 + canFam2.chr30 3366895 3366895 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47312 47313 1380 + panTro2.chrUn 9712921 9712922 1384 + canFam2.chr30 3366915 3366915 1415 - +2 canFam2.chr30_insert 7 hg18.chr1 47440 47441 1380 + panTro2.chrUn 9713049 9713050 1384 + canFam2.chr30 3367044 3367050 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47528 47529 1380 + panTro2.chrUn 9713137 9713138 1384 + canFam2.chr30 3367138 3367138 1415 - +2 canFam2.chr30_insert 10 hg18.chr1 47546 47547 1380 + panTro2.chrUn 9713155 9713156 1384 + canFam2.chr30 3367157 3367166 1415 - +2 canFam2.chr30_insert 4 hg18.chr1 47562 47563 1380 + panTro2.chrUn 9713171 9713172 1384 + canFam2.chr30 3367183 3367186 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47648 47649 1380 + panTro2.chrUn 9713257 9713258 1384 + canFam2.chr30 3367273 3367273 1415 - +2 canFam2.chr30_insert 3 hg18.chr1 47672 47673 1380 + panTro2.chrUn 9713281 9713282 1384 + canFam2.chr30 3367298 3367300 1415 - +2 canFam2.chr30_insert 5 hg18.chr1 47734 47735 1380 + panTro2.chrUn 9713343 9713344 1384 + canFam2.chr30 3367361 3367365 1415 - +2 canFam2.chr30_insert 2 hg18.chr1 47759 47760 1380 + panTro2.chrUn 9713368 9713369 1384 + canFam2.chr30 3367391 3367392 1415 - +2 canFam2.chr30_insert 2 hg18.chr1 47835 47836 1380 + panTro2.chrUn 9713444 9713445 1384 + canFam2.chr30 3367469 3367470 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 48017 48018 1380 + panTro2.chrUn 9713626 9713627 1384 + canFam2.chr30 3367653 3367653 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 48035 48036 1380 + panTro2.chrUn 9713644 9713645 1384 + canFam2.chr30 3367672 3367672 1415 - +2 canFam2.chr30_insert 4 hg18.chr1 48091 48092 1380 + panTro2.chrUn 9713700 9713701 1384 + canFam2.chr30 3367729 3367732 1415 - +2 canFam2.chr30_insert 10 hg18.chr1 48103 48104 1380 + panTro2.chrUn 9713712 9713713 1384 + canFam2.chr30 3367745 3367754 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 48232 48233 1380 + panTro2.chrUn 9713845 9713846 1384 + canFam2.chr30 3367870 3367870 1415 - +3 canFam2.chr30_insert 15 hg18.chr1 48379 48380 455 + panTro2.chrUn 9714289 9714290 455 + canFam2.chr30 3366038 3366052 483 - +3 canFam2.chr30_insert 21 hg18.chr1 48426 48427 455 + panTro2.chrUn 9714336 9714337 455 + canFam2.chr30 3366096 3366116 483 - +3 canFam2.chr30_insert 1 hg18.chr1 48523 48524 455 + panTro2.chrUn 9714433 9714434 455 + canFam2.chr30 3366213 3366213 483 - +4 canFam2.chr30_insert 8 hg18.chr1 52535 52536 183 + panTro2.chrUn 9718438 9718439 183 + canFam2.chr30 3364655 3364662 193 - +4 canFam2.chr30_insert 1 hg18.chr1 52555 52556 183 + panTro2.chrUn 9718458 9718459 183 + canFam2.chr30 3364683 3364683 193 - +4 canFam2.chr30_insert 1 hg18.chr1 52588 52589 183 + panTro2.chrUn 9718491 9718492 183 + canFam2.chr30 3364717 3364717 193 - +4 canFam2.chr30_insert 4 hg18.chr1 52691 52692 183 + panTro2.chrUn 9718594 9718595 183 + canFam2.chr30 3364817 3364820 193 - +5 canFam2.chr30_insert 3 hg18.chr1 52709 52710 115 + panTro2.chrUn 9718612 9718613 115 + canFam2.chr30 3364525 3364527 118 - +5 canFam2.chr30_insert 1 hg18.chr1 52754 52755 115 + panTro2.chrUn 9718657 9718658 115 + canFam2.chr30 3364571 3364571 118 - +5 canFam2.chr30_insert 4 hg18.chr1 52763 52764 115 + panTro2.chrUn 9718666 9718667 115 + canFam2.chr30 3364581 3364584 118 - +6 canFam2.chr30_insert 1 hg18.chr1 53848 53849 1040 + panTro2.chrUn 9719751 9719752 1040 + canFam2.chr30 3364511 3364511 1041 - +7 canFam2.chr30_insert 4 hg18.chr1 53869 53870 335 + panTro2.chrUn 9719772 9719773 335 + canFam2.chr30 3363136 3363139 356 - +7 canFam2.chr30_insert 1 hg18.chr1 53899 53900 335 + panTro2.chrUn 9719802 9719803 335 + canFam2.chr30 3363168 3363168 356 - +7 canFam2.chr30_insert 1 hg18.chr1 53921 53922 335 + panTro2.chrUn 9719824 9719825 335 + canFam2.chr30 3363191 3363191 356 - +7 canFam2.chr30_insert 8 hg18.chr1 53938 53939 335 + panTro2.chrUn 9719841 9719842 335 + canFam2.chr30 3363209 3363216 356 - +7 canFam2.chr30_insert 7 hg18.chr1 53970 53971 335 + panTro2.chrUn 9719873 9719874 335 + canFam2.chr30 3363249 3363255 356 - +7 canFam2.chr30_insert 5 hg18.chr1 54101 54102 335 + panTro2.chrUn 9720004 9720005 335 + canFam2.chr30 3363383 3363387 356 - +7 canFam2.chr30_insert 1 hg18.chr1 54164 54165 335 + panTro2.chrUn 9720067 9720068 335 + canFam2.chr30 3363451 3363451 356 - +8 canFam2.chr30_insert 1 hg18.chr1 54579 54580 582 + panTro2.chrUn 9720770 9720771 585 + canFam2.chr30 3362472 3362472 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54654 54655 582 + panTro2.chrUn 9720845 9720846 585 + canFam2.chr30 3362547 3362547 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54691 54692 582 + panTro2.chrUn 9720882 9720883 585 + canFam2.chr30 3362585 3362585 600 - +8 canFam2.chr30_insert 18 hg18.chr1 54775 54776 582 + panTro2.chrUn 9720970 9720971 585 + canFam2.chr30 3362667 3362684 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54799 54800 582 + panTro2.chrUn 9720994 9720995 585 + canFam2.chr30 3362709 3362709 600 - +8 canFam2.chr30_insert 4 hg18.chr1 54944 54945 582 + panTro2.chrUn 9721139 9721140 585 + canFam2.chr30 3362851 3362854 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54969 54970 582 + panTro2.chrUn 9721164 9721165 585 + canFam2.chr30 3362880 3362880 600 - +9 canFam2.chr30_insert 1 hg18.chr1 55360 55361 367 + panTro2.chrUn 9721554 9721555 402 + canFam2.chr30 3361632 3361632 382 - +9 canFam2.chr30_insert 1 hg18.chr1 55378 55379 367 + panTro2.chrUn 9721572 9721573 402 + canFam2.chr30 3361651 3361651 382 - +9 canFam2.chr30_insert 1 hg18.chr1 55396 55397 367 + panTro2.chrUn 9721625 9721626 402 + canFam2.chr30 3361703 3361703 382 - +9 canFam2.chr30_insert 2 hg18.chr1 55444 55445 367 + panTro2.chrUn 9721673 9721674 402 + canFam2.chr30 3361752 3361753 382 - +10 canFam2.chr30_insert 1 hg18.chr1 55776 55777 272 + panTro2.chrUn 9721772 9721773 307 + canFam2.chr30 3360902 3360902 265 - +10 canFam2.chr30_insert 5 hg18.chr1 55864 55865 272 + panTro2.chrUn 9721860 9721861 307 + canFam2.chr30 3360991 3360995 265 - +10 canFam2.chr30_insert 2 hg18.chr1 55969 55970 272 + panTro2.chrUn 9721965 9721966 307 + canFam2.chr30 3361087 3361088 265 - +10 canFam2.chr30_insert 2 hg18.chr1 55980 55981 272 + panTro2.chrUn 9721976 9721977 307 + canFam2.chr30 3361100 3361101 265 - +12 canFam2.chr30_insert 33 hg18.chr1 56722 56723 802 + panTro2.chrUn 9723901 9723902 801 + canFam2.chr30 3360035 3360067 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56746 56747 802 + panTro2.chrUn 9723925 9723926 801 + canFam2.chr30 3360092 3360092 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56836 56837 802 + panTro2.chrUn 9724015 9724016 801 + canFam2.chr30 3360183 3360183 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56864 56865 802 + panTro2.chrUn 9724043 9724044 801 + canFam2.chr30 3360212 3360212 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56894 56895 802 + panTro2.chrUn 9724073 9724074 801 + canFam2.chr30 3360243 3360243 805 - +12 canFam2.chr30_insert 2 hg18.chr1 57161 57162 802 + panTro2.chrUn 9724340 9724341 801 + canFam2.chr30 3360496 3360497 805 - +12 canFam2.chr30_insert 1 hg18.chr1 57352 57353 802 + panTro2.chrUn 9724530 9724531 801 + canFam2.chr30 3360680 3360680 805 - +13 canFam2.chr30_insert 2 hg18.chr1 58529 58530 176 + panTro2.chrUn 9725707 9725708 176 + canFam2.chr30 3359565 3359566 148 - +14 canFam2.chr30_insert 1 hg18.chr1 58700 58701 1628 + panTro2.chrUn 9725878 9725879 1631 + canFam2.chr30 3356984 3356984 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 58709 58710 1628 + panTro2.chrUn 9725887 9725888 1631 + canFam2.chr30 3356994 3356994 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 58770 58771 1628 + panTro2.chrUn 9725949 9725950 1631 + canFam2.chr30 3357057 3357057 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 58772 58773 1628 + panTro2.chrUn 9725955 9725956 1631 + canFam2.chr30 3357064 3357064 1623 - +14 canFam2.chr30_insert 15 hg18.chr1 58800 58801 1628 + panTro2.chrUn 9725983 9725984 1631 + canFam2.chr30 3357093 3357107 1623 - +14 canFam2.chr30_insert 9 hg18.chr1 58808 58809 1628 + panTro2.chrUn 9725991 9725992 1631 + canFam2.chr30 3357116 3357124 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 60032 60033 1628 + panTro2.chrUn 9727214 9727215 1631 + canFam2.chr30 3358319 3358319 1623 - +14 canFam2.chr30_insert 4 hg18.chr1 60148 60149 1628 + panTro2.chrUn 9727330 9727331 1631 + canFam2.chr30 3358426 3358429 1623 - +15 canFam2.chr30_insert 1 hg18.chr1 60326 60327 230 + panTro2.chrUn 9727507 9727508 230 + canFam2.chr30 3356643 3356643 218 - +15 canFam2.chr30_insert 2 hg18.chr1 60353 60354 230 + panTro2.chrUn 9727534 9727535 230 + canFam2.chr30 3356671 3356672 218 - +15 canFam2.chr30_insert 1 hg18.chr1 60391 60392 230 + panTro2.chrUn 9727572 9727573 230 + canFam2.chr30 3356711 3356711 218 - +15 canFam2.chr30_insert 1 hg18.chr1 60466 60467 230 + panTro2.chrUn 9727647 9727648 230 + canFam2.chr30 3356783 3356783 218 - +15 canFam2.chr30_insert 5 hg18.chr1 60476 60477 230 + panTro2.chrUn 9727657 9727658 230 + canFam2.chr30 3356794 3356798 218 - +1 canFam2.chr30_delete 1 hg18.chr1 46857 46857 143 + panTro2.chrUn 9712464 9712464 145 + canFam2.chr30 3368190 3368191 145 - +1 canFam2.chr30_delete 1 hg18.chr1 46900 46900 143 + panTro2.chrUn 9712509 9712509 145 + canFam2.chr30 3368232 3368233 145 - +2 canFam2.chr30_delete 7 hg18.chr1 47080 47086 1380 + panTro2.chrUn 9712689 9712695 1384 + canFam2.chr30 3366677 3366678 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 47168 47168 1380 + panTro2.chrUn 9712777 9712777 1384 + canFam2.chr30 3366766 3366767 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 47482 47482 1380 + panTro2.chrUn 9713091 9713091 1384 + canFam2.chr30 3367091 3367092 1415 - +2 canFam2.chr30_delete 2 hg18.chr1 47703 47704 1380 + panTro2.chrUn 9713312 9713313 1384 + canFam2.chr30 3367330 3367331 1415 - +2 canFam2.chr30_delete 15 hg18.chr1 48139 48153 1380 + panTro2.chrUn 9713752 9713766 1384 + canFam2.chr30 3367793 3367794 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 48160 48160 1380 + panTro2.chrUn 9713773 9713773 1384 + canFam2.chr30 3367799 3367800 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 48174 48174 1380 + panTro2.chrUn 9713787 9713787 1384 + canFam2.chr30 3367812 3367813 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 48197 48197 1380 + panTro2.chrUn 9713810 9713810 1384 + canFam2.chr30 3367834 3367835 1415 - +2 canFam2.chr30_delete 5 hg18.chr1 48280 48284 1380 + panTro2.chrUn 9713893 9713897 1384 + canFam2.chr30 3367917 3367918 1415 - +3 canFam2.chr30_delete 4 hg18.chr1 48344 48347 455 + panTro2.chrUn 9714254 9714257 455 + canFam2.chr30 3366005 3366006 483 - +3 canFam2.chr30_delete 4 hg18.chr1 48410 48413 455 + panTro2.chrUn 9714320 9714323 455 + canFam2.chr30 3366082 3366083 483 - +3 canFam2.chr30_delete 1 hg18.chr1 48470 48470 455 + panTro2.chrUn 9714380 9714380 455 + canFam2.chr30 3366159 3366160 483 - +4 canFam2.chr30_delete 4 hg18.chr1 52639 52642 183 + panTro2.chrUn 9718542 9718545 183 + canFam2.chr30 3364767 3364768 193 - +5 canFam2.chr30_delete 3 hg18.chr1 52707 52709 115 + panTro2.chrUn 9718610 9718612 115 + canFam2.chr30 3364524 3364525 118 - +5 canFam2.chr30_delete 2 hg18.chr1 52743 52744 115 + panTro2.chrUn 9718646 9718647 115 + canFam2.chr30 3364560 3364561 118 - +7 canFam2.chr30_delete 2 hg18.chr1 53879 53880 335 + panTro2.chrUn 9719782 9719783 335 + canFam2.chr30 3363148 3363149 356 - +7 canFam2.chr30_delete 4 hg18.chr1 54052 54055 335 + panTro2.chrUn 9719955 9719958 335 + canFam2.chr30 3363336 3363337 356 - +8 canFam2.chr30_delete 1 hg18.chr1 54634 54634 582 + panTro2.chrUn 9720825 9720825 585 + canFam2.chr30 3362526 3362527 600 - +8 canFam2.chr30_delete 3 hg18.chr1 54710 54712 582 + panTro2.chrUn 9720901 9720903 585 + canFam2.chr30 3362603 3362604 600 - +8 canFam2.chr30_delete 4 hg18.chr1 54876 54879 582 + panTro2.chrUn 9721071 9721074 585 + canFam2.chr30 3362785 3362786 600 - +8 canFam2.chr30_delete 1 hg18.chr1 54984 54984 582 + panTro2.chrUn 9721178 9721178 585 + canFam2.chr30 3362894 3362895 600 - +9 canFam2.chr30_delete 1 hg18.chr1 55131 55131 367 + panTro2.chrUn 9721325 9721325 402 + canFam2.chr30 3361420 3361421 382 - +9 canFam2.chr30_delete 6 hg18.chr1 55213 55218 367 + panTro2.chrUn 9721407 9721412 402 + canFam2.chr30 3361501 3361502 382 - +9 canFam2.chr30_delete 1 hg18.chr1 55308 55308 367 + panTro2.chrUn 9721502 9721502 402 + canFam2.chr30 3361590 3361591 382 - +9 canFam2.chr30_delete 4 hg18.chr1 55324 55327 367 + panTro2.chrUn 9721518 9721521 402 + canFam2.chr30 3361605 3361606 382 - +9 canFam2.chr30_delete 7 hg18.chr1 55340 55346 367 + panTro2.chrUn 9721534 9721540 402 + canFam2.chr30 3361617 3361618 382 - +9 canFam2.chr30_delete 2 hg18.chr1 55386 55387 367 + panTro2.chrUn 9721580 9721581 402 + canFam2.chr30 3361658 3361659 382 - +9 canFam2.chr30_delete 4 hg18.chr1 55457 55460 367 + panTro2.chrUn 9721686 9721689 402 + canFam2.chr30 3361765 3361766 382 - +10 canFam2.chr30_delete 11 hg18.chr1 55893 55903 272 + panTro2.chrUn 9721889 9721899 307 + canFam2.chr30 3361023 3361024 265 - +10 canFam2.chr30_delete 1 hg18.chr1 55924 55924 272 + panTro2.chrUn 9721920 9721920 307 + canFam2.chr30 3361043 3361044 265 - +10 canFam2.chr30_delete 1 hg18.chr1 55939 55939 272 + panTro2.chrUn 9721935 9721935 307 + canFam2.chr30 3361057 3361058 265 - +10 canFam2.chr30_delete 1 hg18.chr1 55959 55959 272 + panTro2.chrUn 9721955 9721955 307 + canFam2.chr30 3361076 3361077 265 - +10 canFam2.chr30_delete 3 hg18.chr1 56001 56003 272 + panTro2.chrUn 9722032 9722034 307 + canFam2.chr30 3361121 3361122 265 - +12 canFam2.chr30_delete 6 hg18.chr1 56611 56616 802 + panTro2.chrUn 9723790 9723795 801 + canFam2.chr30 3359929 3359930 805 - +12 canFam2.chr30_delete 1 hg18.chr1 56696 56696 802 + panTro2.chrUn 9723875 9723875 801 + canFam2.chr30 3360008 3360009 805 - +12 canFam2.chr30_delete 7 hg18.chr1 56911 56917 802 + panTro2.chrUn 9724090 9724096 801 + canFam2.chr30 3360259 3360260 805 - +12 canFam2.chr30_delete 3 hg18.chr1 56991 56993 802 + panTro2.chrUn 9724170 9724172 801 + canFam2.chr30 3360332 3360333 805 - +12 canFam2.chr30_delete 5 hg18.chr1 57110 57114 802 + panTro2.chrUn 9724289 9724293 801 + canFam2.chr30 3360448 3360449 805 - +12 canFam2.chr30_delete 1 hg18.chr1 57217 57217 802 + panTro2.chrUn 9724395 9724395 801 + canFam2.chr30 3360551 3360552 805 - +12 canFam2.chr30_delete 5 hg18.chr1 57247 57251 802 + panTro2.chrUn 9724425 9724429 801 + canFam2.chr30 3360580 3360581 805 - +12 canFam2.chr30_delete 2 hg18.chr1 57310 57311 802 + panTro2.chrUn 9724488 9724489 801 + canFam2.chr30 3360638 3360639 805 - +12 canFam2.chr30_delete 2 hg18.chr1 57379 57380 802 + panTro2.chrUn 9724557 9724558 801 + canFam2.chr30 3360706 3360707 805 - +12 canFam2.chr30_delete 4 hg18.chr1 57387 57390 802 + panTro2.chrUn 9724565 9724568 801 + canFam2.chr30 3360712 3360713 805 - +13 canFam2.chr30_delete 3 hg18.chr1 58409 58411 176 + panTro2.chrUn 9725587 9725589 176 + canFam2.chr30 3359468 3359469 148 - +13 canFam2.chr30_delete 1 hg18.chr1 58434 58434 176 + panTro2.chrUn 9725612 9725612 176 + canFam2.chr30 3359490 3359491 148 - +13 canFam2.chr30_delete 2 hg18.chr1 58446 58447 176 + panTro2.chrUn 9725624 9725625 176 + canFam2.chr30 3359501 3359502 148 - +13 canFam2.chr30_delete 8 hg18.chr1 58470 58477 176 + panTro2.chrUn 9725648 9725655 176 + canFam2.chr30 3359523 3359524 148 - +13 canFam2.chr30_delete 5 hg18.chr1 58488 58492 176 + panTro2.chrUn 9725666 9725670 176 + canFam2.chr30 3359533 3359534 148 - +13 canFam2.chr30_delete 6 hg18.chr1 58510 58515 176 + panTro2.chrUn 9725688 9725693 176 + canFam2.chr30 3359550 3359551 148 - +13 canFam2.chr30_delete 5 hg18.chr1 58565 58569 176 + panTro2.chrUn 9725743 9725747 176 + canFam2.chr30 3359601 3359602 148 - +14 canFam2.chr30_delete 1 hg18.chr1 58669 58669 1628 + panTro2.chrUn 9725847 9725847 1631 + canFam2.chr30 3356952 3356953 1623 - +14 canFam2.chr30_delete 3 hg18.chr1 58849 58851 1628 + panTro2.chrUn 9726032 9726034 1631 + canFam2.chr30 3357164 3357165 1623 - +14 canFam2.chr30_delete 10 hg18.chr1 59342 59351 1628 + panTro2.chrUn 9726524 9726533 1631 + canFam2.chr30 3357654 3357655 1623 - +14 canFam2.chr30_delete 1 hg18.chr1 59561 59561 1628 + panTro2.chrUn 9726743 9726743 1631 + canFam2.chr30 3357863 3357864 1623 - +14 canFam2.chr30_delete 11 hg18.chr1 59887 59897 1628 + panTro2.chrUn 9727069 9727079 1631 + canFam2.chr30 3358188 3358189 1623 - +14 canFam2.chr30_delete 5 hg18.chr1 59908 59912 1628 + panTro2.chrUn 9727090 9727094 1631 + canFam2.chr30 3358198 3358199 1623 - +14 canFam2.chr30_delete 6 hg18.chr1 60052 60057 1628 + panTro2.chrUn 9727234 9727239 1631 + canFam2.chr30 3358338 3358339 1623 - +14 canFam2.chr30_delete 4 hg18.chr1 60111 60114 1628 + panTro2.chrUn 9727293 9727296 1631 + canFam2.chr30 3358391 3358392 1623 - +14 canFam2.chr30_delete 2 hg18.chr1 60183 60184 1628 + panTro2.chrUn 9727365 9727366 1631 + canFam2.chr30 3358463 3358464 1623 - +15 canFam2.chr30_delete 4 hg18.chr1 60400 60403 230 + panTro2.chrUn 9727581 9727584 230 + canFam2.chr30 3356719 3356720 218 - +15 canFam2.chr30_delete 8 hg18.chr1 60506 60513 230 + panTro2.chrUn 9727687 9727694 230 + canFam2.chr30 3356827 3356828 218 - +15 canFam2.chr30_delete 10 hg18.chr1 60520 60529 230 + panTro2.chrUn 9727701 9727710 230 + canFam2.chr30 3356833 3356834 218 -