Dear members,
I have a problem with a perl script pasted below. Since it is not a
short script I was reluctant to paste all of it but then I thought it
may be easier to understand if I pasted all of it. I greatly welcome any
recommendations to refine the script (I predict many of you will have
something to say about it), but my main concern is where it is going
wrong? Below is part of the output, A and B. Snip A is ok but lines in
snip B starting with "B: nomatch>" are wrong, which is why half of these
lines are empty. Lines with "nomatch>" are expected but on manual
inspection some are incorrectly labelled as such, including some of the
B: lines I have here. I have included some parts of the input files
after the script. Since it is a lot to take in I thank you all in
advance for giving it a shot of any sort. I have tried but I cannot get
my head round where I have made the mistake(s).
Cheers. Aim.
__OUTPUT START__
A: CLUSTALFILE> CDSs_Contig_File_2
A: ismatch> M63553.1 1 1.000 0.957 55 70 FPrintScan
3.9e-04 frame f1 <=> frame f3 335565.2 5 66 81 FPrintScan
5.3e-04 --
A: ismatch> M63553.1 2 1.000 0.946 84 96 FPrintScan
4.7e-04 frame f1 <=> frame f3 335565.2 6 95 107 FPrintScan
6.3e-04 --
A: framehits> 0 0 7 0.000 0.000 1.000 1.000 7
B: CLUSTALFILE> CDSs_Contig_File_1
B: nomatch> X64146.1 1 1.000 0.000 16 40 FPrintScan
8.0e-12
B: nomatch> X64146.1 2 1.000 0.000 41 70 FPrintScan
8.0e-12
B: nomatch> X64146.1 3 1.000 0.000 71 100 FPrintScan
8.0e-12
B: nomatch> X64146.1 4 1.000 0.000 101 130 FPrintScan
8.0e-12
B: nomatch> X64146.1 5 1.000 0.000 146 165 FPrintScan
5.6e-08
B: ismatch> X64146.1 6 1.000 0.998 11 170 HMMPfam
8.6e-107 frame f1 <=> frame f2 335884.1 1 59 218 HMMPfam
8.6e-107
B: ismatch> X64146.1 7 1.000 0.997 11 118 HMMSmart
7.0e-77 frame f1 <=> frame f2 335884.1 2 59 166 HMMSmart
7.0e-77
__OUTPUT END__
__SCRIPT START__
!/usr/bin/perl -w
use strict;
( @ARGV > 0 ) or die "usage: ????? {in-file}\n";
my @clust_file = @ARGV;
my ($cds,$nc,$contig,$is_matched,$nhits,$coverage);
my %cdscount = ();
my %cds_frame = ();
my %cds_db = ();
my %cds_start = ();
my %cds_end = ();
my %cds_score = ();
my %contigcount = ();
my %contig_frame = ();
my %contig_db = ();
my %contig_start = ();
my %contig_end = ();
my %contig_score = ();
my %apos1 = ();
my %apos2 = ();
#
# read in cds data first
#
my $CDS_file = "File_A.data";
open(CDS, $CDS_file) or die "DEBUG2: unable to open file $CDS_file: $!
\n";
while ( <CDS> ) {
if (
/(^\S+\.\d+)\.(f\d)\s+\S+\s+\S+\s+(\S+)\s+\S+\s+\S+\s+(\S+)\s+(\S+)\s+(\S+)\s/
) {
$cds = $1;
$cdscount{$cds}++;
$nc=$cdscount{$cds};
$cds_frame{$cds}[$nc] = $2;
$cds_db{$cds}[$nc] = $3;
$cds_start{$cds}[$nc] = 3*$4; # convert amino acid to nucleotide
positions
$cds_end{$cds}[$nc] = 3*$5; # convert amino acid to nucleotide
positions
$cds_score{$cds}[$nc] = ScoreFix($6);
}
}
close(CDS);
# read in contig data
my $CONTIG_file = "File_B.data";
open(CONTIG, $CONTIG_file) or die "DEBUG2: unable to open file
$CONTIG_file: $! \n";
while ( <CONTIG> ) {
if (
/(^\S+\.\d+)\.(f\d)\s+\S+\s+\S+\s+(\S+)\s+\S+\s+\S+\s+(\S+)\s+(\S+)\s+(\S+)\s/
) {
$contig = $1;
$contigcount{$contig}++;
$nc=$contigcount{$contig};
$contig_frame{$contig}[$nc] = $2;
$contig_db{$contig}[$nc] = $3;
$contig_start{$contig}[$nc] = 3*$4; # convert amino acid to
nucleotide positions
$contig_end{$contig}[$nc] = 3*$5; # convert amino acid to
nucleotide positions
$contig_score{$contig}[$nc] = ScoreFix($6);
}
}
close(CONTIG);
# read clustalw data one file at a time
my ($key,$seq,$contigname,$cdsname);
foreach my $file ( @clust_file ) {
open(CLUSTAL, $file) or die "DEBUG1: unable to open file $file: $! \n";
print "CLUSTALFILE> $file\n";
$contig = "";
$cds = "";
while ( <CLUSTAL> ) {
next if ( /^\s*$/ || /\*/ || /^CLUST/);
chomp;
if (/^(\S+)\s+(\S+)/) { #seq1#
$key = $1;
$seq = $2;
if ( $key =~ /^\d/ ) {
$contig .= $seq;
$contigname = $key;
} else {
$cds .= $seq;
$cdsname = $key;
}
}
}
close(CLUSTAL);
# create indexing arrays
my $rpos1 = 0; my $rpos2 = 0;
my ($a,$b);
foreach my $pos (1..length $contig) {
$a = substr($cds,$pos-1,1);
$b = substr($contig,$pos-1,1);
$rpos1++ if ( $a ne '-' );
$rpos2++ if ( $b ne '-' );
$apos1{$rpos1}=$pos;
$apos2{$rpos2}=$pos;
}
my %fh = (); my $th = 0;
$fh{'f1'} = 0; $fh{'f2'} = 0; $fh{'f3'} = 0;
# CDS point of view
my ($s1,$e1,$s2,$e2,$overlap,$mh);
if ( defined $cdscount{$cdsname} ) {
foreach $nhits ( 1..$cdscount{$cdsname} ) {
if ( $cds_frame{$cdsname}[$nhits] eq "f1" ) {
$is_matched = 0;
$s1 = $cds_start{$cdsname}[$nhits];
$e1 = $cds_end{$cdsname}[$nhits];
if ( ! defined $contigcount{$contigname} ) { #value if contig not
in have IPR hit#
if ( $cds_db{$cdsname}[$nhits] ne "Coil" ) {
$coverage = GetCoverage($s1,$e1,$contig);
printf "nomatch> %-10.10s %3d %5.3f %5.3f %4d %4d %-12.12s %8.1e
contig %s has no hits\n",
$cdsname,$nhits,$coverage,0.0,$s1/3,$e1/3,$cds_db{$cdsname}[$nhits],
$cds_score{$cdsname}[$nhits],$contigname;
}
next;
}
foreach my $mhits ( 1..$contigcount{$contigname} ) {
if ( $cds_db{$cdsname}[$nhits] eq $contig_db{$contigname}[$mhits] )
{
$s2 = $contig_start{$contigname}[$mhits];
$e2 = $contig_end{$contigname}[$mhits];
$overlap = GetOverlap($s1,$e1,$s2,$e2);
$coverage = GetCoverage($s1,$e1,$contig);
if ( $overlap > 0.7 ) {
$is_matched = 1;
printf "ismatch> %-10.10s %3d %5.3f %5.3f %4d %4d %-12.12s
%8.1e ",
$cdsname,$nhits,$coverage,$overlap,$s1/3,$e1/3,
$cds_db{$cdsname}[$nhits],$cds_score{$cdsname}[$nhits];
printf " frame f1 <=> frame %2s %-10.10s %3d %4d %4d %-12.12s
%8.1e ",
$contig_frame{$contigname}[$mhits],$contigname,$mhits,$s2/3,$e2/3,
$contig_db{$contigname}[$mhits],$contig_score{$contigname}[$mhits];
if ( $contig_score{$contigname}[$mhits] >
$cds_score{$cdsname}[$nhits] ) {
print " -- \n";
} elsif ($contig_score{$contigname}[$mhits] <
$cds_score{$cdsname}[$nhits] ) {
print " ++ \n";
} else {
print "\n";
}
$fh{$contig_frame{$contigname}[$mhits]}++;
$th++;
$mhits = $contigcount{$contigname};
}
}
}
if ( ! $is_matched && $cds_db{$cdsname}[$nhits] ne "Coil" ) {
printf "nomatch> %-10.10s %3d %5.3f %5.3f %4d %4d %-12.12s %8.1e
%-10.10s\n",
$cdsname,$nhits,$coverage,0.0,$s1/3,$e1/3,
$cds_db{$cdsname}[$nhits],$cds_score{$cdsname}[$nhits],$contigname;
}
}
}
} else {
print "nothit> $cdsname has no hits \n";
}
$mh = ( $fh{'f1'} > $fh{'f2'} ) ? $fh{'f1'} : $fh{'f2'};
$mh = ( $mh > $fh{"f3"} ) ? $mh : $fh{"f3"};
if ( $th > 0 ) {
printf "framehits> %3d %3d %3d %5.3f %5.3f %5.3f %5.3f %4d \n",
$fh{"f1"},$fh{"f2"},$fh{"f3"},$fh{"f1"}/$th,$fh{"f2"}/$th,$fh{"f3"}/$th,$mh/$th,$th;
}
}
exit;
sub GetCoverage {
my ($s, $e, $contig) = @_;
my ($n, $m);
$n = $m = 0;
for ( my $i=$s; $i<=$e; $i++) {
$n++;
$m++ if ( substr($contig,$i,1) ne '-' );
}
return $m/$n;
}
sub GetOverlap {
my ($s1,$e1,$s2,$e2) = @_;
my ($ns1, $ns2, $ne1, $ne2);
$ns1 = $apos1{$s1};
$ne1 = $apos1{$e1};
$ns2 = $apos2{$s2};
$ne2 = $apos2{$e2};
my $smax = ($ns1 > $ns2) ? $ns1 : $ns2;
my $emin = ($ne1 > $ne2) ? $ne2 : $ne1;
my $overlap = ($emin - $smax + 1)/($e1 - $s1 + 1);
return $overlap;
}
sub ScoreFix {
my $s = shift;
$s =~ s/^e/1e/;
return $s;
}
__SCRIPT END___
__File_A.data START __
M63553.1.f1 0169C0C2E528E25B 208 FPrintScan
PR00153 CSAPPISMRASE 55 70 0.000392 T
11-Dec-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
M63553.1.f1 0169C0C2E528E25B 208 FPrintScan
PR00153 CSAPPISMRASE 84 96 0.0004696 T
11-Dec-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
M63553.1.f1 0169C0C2E528E25B 208 FPrintScan
PR00153 CSAPPISMRASE 127 142 2.184e-05 T
11-Dec-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
M63553.1.f1 0169C0C2E528E25B 208 FPrintScan
PR00153 CSAPPISMRASE 142 154 0.00264 T
11-Dec-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
M63553.1.f1 0169C0C2E528E25B 208 FPrintScan
PR00153 CSAPPISMRASE 155 170 2.464e-06 T
11-Dec-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
M63553.1.f1 0169C0C2E528E25B 208 HMMPfam PF00160
pro_isomerase 36 197 1.7e-114 T
11-Dec-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
M63553.1.f1 0169C0C2E528E25B 208 ProfileScan PS50072
CSA_PPIASE_2 38 195 47.499 T 11-Dec-2002
IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase
Molecular Function: peptidylprolyl isomerase (GO:0003755), Cellular
Component: cytoplasm (GO:0005737), Biological Process: protein folding
(GO:0006457)
M63553.1.f2 D4C09FEDAE405814 207 ProfileScan PS50323
ARG_RICH 2 65 9.497 T 11-Dec-2002
NULL NULL
M63553.1.f3 23501CA3B611B62A 207 ProfileScan PS50323
ARG_RICH 19 139 10.014 T 11-Dec-2002
NULL NULL
M63553.1.f3 23501CA3B611B62A 207 ProfileScan PS50315
GLY_RICH 2 173 10.279 T 11-Dec-2002
NULL NULL
X64146.1.f1 89FA4BA1BFCBCEA2 171 FPrintScan
PR00310 ANTIPRLFBTG1 16 40 8e-12 T
12-Dec-2002 IPR002087 Anti-proliferative protein
X64146.1.f1 89FA4BA1BFCBCEA2 171 FPrintScan
PR00310 ANTIPRLFBTG1 41 70 8e-12 T
12-Dec-2002 IPR002087 Anti-proliferative protein
X64146.1.f1 89FA4BA1BFCBCEA2 171 FPrintScan
PR00310 ANTIPRLFBTG1 71 100 8e-12 T
12-Dec-2002 IPR002087 Anti-proliferative protein
X64146.1.f1 89FA4BA1BFCBCEA2 171 FPrintScan
PR00310 ANTIPRLFBTG1 101 130 8e-12 T
12-Dec-2002 IPR002087 Anti-proliferative protein
X64146.1.f1 89FA4BA1BFCBCEA2 171 FPrintScan
PR00310 ANTIPRLFBTG1 146 165 5.584e-08 T
12-Dec-2002 IPR002087 Anti-proliferative protein
X64146.1.f1 89FA4BA1BFCBCEA2 171 HMMPfam PF01211
Anti_proliferat 11 170 8.6e-107 T
12-Dec-2002 IPR002087 Anti-proliferative protein
X64146.1.f1 89FA4BA1BFCBCEA2 171 HMMSmart SM00099
btg1 11 118 7e-77 T 12-Dec-2002
IPR002087 Anti-proliferative protein
__File_A.data END__
__File_B.data START__
335565.2.f3 B0DC0087DC4FBE8B 304 HMMPfam PF00160
pro_isomerase 47 208 4.2e-115 T 25-Jul-2002
IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase
Molecular Function: peptidylprolyl isomerase (GO:0003755), Cellular
Component: cytoplasm (GO:0005737), Biological Process: protein folding
(GO:0006457)
335565.2.f3 B0DC0087DC4FBE8B 304 FPrintScan
PR00153 CSAPPISMRASE 138 153 2.944e-05 T
25-Jul-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
335565.2.f3 B0DC0087DC4FBE8B 304 FPrintScan
PR00153 CSAPPISMRASE 153 165 0.001728 T
25-Jul-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
335565.2.f3 B0DC0087DC4FBE8B 304 FPrintScan
PR00153 CSAPPISMRASE 166 181 3.32e-06 T
25-Jul-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
335565.2.f3 B0DC0087DC4FBE8B 304 FPrintScan
PR00153 CSAPPISMRASE 66 81 0.0005272 T
25-Jul-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
335565.2.f3 B0DC0087DC4FBE8B 304 FPrintScan
PR00153 CSAPPISMRASE 95 107 0.000632 T
25-Jul-2002 IPR002130 Cyclophilin-type peptidyl-prolyl
cis-trans isomerase Molecular Function: peptidylprolyl isomerase
(GO:0003755), Cellular Component: cytoplasm (GO:0005737), Biological
Process: protein folding (GO:0006457)
335565.2.f1 A58984EC37123726 304 ProfileScan PS50323
ARG_RICH 3 77 9.670 T 25-Jul-2002 NULL
NULL
335565.2.f2 22ED3D4C8B838162 304 ProfileScan PS50323
ARG_RICH 31 151 10.014 T 25-Jul-2002 NULL
NULL
335565.2.f3 B0DC0087DC4FBE8B 304 ProfileScan PS50072
CSA_PPIASE_2 49 206 47.731 T 25-Jul-2002
IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase
Molecular Function: peptidylprolyl isomerase (GO:0003755), Cellular
Component: cytoplasm (GO:0005737), Biological Process: protein folding
(GO:0006457)
335565.2.f2 22ED3D4C8B838162 304 ProfileScan PS50315
GLY_RICH 14 113 9.456 T 25-Jul-2002 NULL
NULL
335884.1.f2 269B66FBEF17C478 527 HMMPfam PF01211
Anti_proliferat 59 218 8.6e-107 T 20-Jul-2002
IPR002087 Anti-proliferative protein
335884.1.f2 AEC0A2BB26E70AC1 526 HMMSmart SM00099
btg1 59 166 7e-77 T 20-Jul-2002 IPR002087
Anti-proliferative protein
335884.1.f3 9D1D86D4577130FA 526 ProfileScan PS50099
PRO_RICH 27 76 13.052 T 20-Jul-2002
IPR000694 Proline-rich region
__File_B.data END__
__ CDSs_Contig_File_1 START (entered on command line)__
X64146.1
-------------------------ATGCATCCCGCCCTGTACACCCGGGCCAGCATGAT
335884.1
CTGGCTGCCGGCCGCCGCCGCCTCCATGCATCCCGCCCTGTACACCCGGGCCAGCATGAT
***********************************
X64146.1
ACGCGAGATCGCCGCGGCCGTGGCCTTCATCTCCAAGTTCCTGCGCACCAAGGGGCTGAT
335884.1
ACGCGAGATCGCCGCGGCCGTGGCCTTCATCTCCAAGTTCCTGCGCACCAAGGGGCTGAT
************************************************************
X64146.1
GAACGAACGGCAGTTACAGACCTTCAGCCAGAGCCTGCAGGAGCTGCTGGCAGAACATTA
335884.1
GAACGAACGGCAGTTACAGACCTTCAGCCAGAGCCTGCAGGAGCTGCTGGCAGAACATTA
************************************************************
X64146.1
TAAACACCACTGGTTCCCAGAAAAGCCATGCAAGGGATCAGGTTACCGATGTATCCGGAT
335884.1
TAAACACCACTGGTTCCCAGAAAAGCCATGCAAGGGATCAGGTTACCGATGTATCCGGAT
************************************************************
X64146.1
CAACCATAAAATGGATCCTCTCATTGGACAGGCAGCACAGCGGATTGGATTGAGCAGTCA
335884.1
CAACCATAAAATGGATCCTCTCATTGGACAGGCAGCACAGCGGATTGGATTGAGCAGTCA
************************************************************
X64146.1
GGAACTGTTCCAGCTTCTTCCGAGCGAACTCACTCTATGGGTTGACCCGTATGAAGTGTC
335884.1
GGAACTGTTCCAGCTTCTTCCGAGCGAACTCACTCTATGGGTTGACCCGTATGAAGTGTC
************************************************************
X64146.1
CTATCGTATTGGAGAGGATGGCTCAATCTGTGTGCTGTATGAAGCTGCACCAGCAGGAGG
335884.1
CTATCGTATTGGAGAGGATGGCTCAATCTGTGTGCTGTATGAAGCTGCACCAGCAGGAGG
************************************************************
X64146.1
TAGCCAAAATAACACCAACATGCAAATGGTAGACAGCAGAATAAGCTGTAAGGAGGAACT
335884.1
TAGCCAAAATAACACCAACATGCAAATGGTAGACAGCAGAATAAGCTGTAAGGAGGAACT
************************************************************
X64146.1
TCTCTTGGGCAGAACTAGCCCTTCCAAAAGCTACAATATGATGACTGTATCGGGTTAA--
335884.1
TCTCTTGGGCAGAACTAGCCCTTCCAAAAGCTACAATATGATGACTGTATCGGGTTAAGA
**********************************************************
X64146.1
------------------------------------------------------------
335884.1
TATAGTCAGTGGATGGATCACCTTAAAATGGATGGATAAGTTTGGTTTTTACTTTGGGTG
__ CDSs_Contig_File_1 END__
__ CDSs_Contig_File_2 START (entered on command line)__
M63553.1
-----------------------------------ATGAAGGCTTTGGTGGCGGCGACGG
335565.2
GGCGGGCGCTGCGGCCGGGCTGCGATCGGCGGAGGATGAAGGCTTTGGTGGCGGCGACGG
*************************
M63553.1
CGCTGGGGCCGGCGCTCCTACTGCTGCTGCCCGCCGCCTCGAGGGCCGACGAGCGCAAGA
335565.2
CGCTGGGCGCGGCGCTCCTACTGCTGCTGCCCGCCGCCTCGAGGGCCGACGAGCGCAAGA
*******
***************************************************
M63553.1
AGGGCCCCAAGGTCACGGCCAAGGTGTTCTTCGACCTCCGCGTGGGCGAGGAGGATGCGG
335565.2
AGGGCCCCAAGGTCACGGCCAAGGTGTTCTTCGACCTCCGCGTGGGCGAGGAGGATGCGG
************************************************************
M63553.1
GCCGCGTCGTCATCGGGCTCTTCGGCAAAACGGTGCCCAAAACGGTGGAGAACTTCGTGG
335565.2
GCCGCGTCGTCATCGGGCTCTTCGGCAAAACGGTGCCCAAAACGGTGGAGAACTTCGTGG
************************************************************
M63553.1
CTTTGGCCACCGGGGAGAAAGGGTTCGGCTTCAAGGGCAGCAAGTTCCACCGCGTCATCA
335565.2
CTTTGGCCACCGGGGAGAAAGGGTTCGGCTTCAAGGGCAGCAAGTTCCACCGCGTCATCA
************************************************************
M63553.1
AGGACTTCATGATCCAGGGAGGGGACTTCACCCGCGGGGACGGCACCGGAGGGAAGAGCA
335565.2
AGGACTTCATGATCCAGGGAGGGGACTTCACCCGCGGGGACGGCACCGGAGGGAAGAGCA
************************************************************
M63553.1
TCTACGGAGACCGCTTCCCTGACGAGAACTTCAAGCTGAAGCACTACGGCCCCGGCTGGG
335565.2
TCTACGGAGACCGCTTCCCTGACGAGAACTTCAAGCTGAAGCACTACGGCCCCGGCTGGG
************************************************************
M63553.1
TGAGCATGGCCAACGCCGGCAAGGACACCAACGGCTCCCAGTTCTTCATCACCACGGTGA
335565.2
TGAGCATGGCCAACGCCGGCAAGGACACCAACGGCTCCCAGTTCTTCATCACCACGGTGA
************************************************************
M63553.1
AGACGGCGTGGCTGGATGGCAAGCACGTGGTGTTCGGCAAAGTGCTGGAGGGCATGGACG
335565.2
AGACGCCGTGGCTGGATGGCAAGCACGTGGTGTTCGGCAAAGTGCTGGAGGGCATGGACG
*****
******************************************************
M63553.1
TGGTGAGGAAGGTGGAGAACACCAAGACAGACAGCCGGGACAAACCCCTGAAGGACGTCA
335565.2
TGGTGAGGAAGGTGGAGAACACCAAGACAGACAGCCGGGACAAACCCCTGAAGGACGTCA
************************************************************
M63553.1
CCATTGCTGACTGCGGCACCATCGAGGTGGAGAAGCCCTTCG-CCATCGCCAAGGAGTGA
335565.2
CCATTGCTGACTGCGGCACCATCGAGGTGGAGAAGCCCTTCGGCCATCGCCAAGGAGTGA
******************************************
*****************
__ CDSs_Contig_File_2 END__
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