If I've understood correctly I think one approach would break your sequences down into arrays of single letters and shift and compare a letter from each at a time.

use strict;
use warnings;

use 5.014;

open my $inFH, q{<}, \ <<EOD or die $!;
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctg
+aatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccgg
+c
atagctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctg
+aatcctgcggacgacccctctcgtggtcgtttggggctctgccgccctcttctccgcctgccgttcagg
+c
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctg
+aatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccgg
+c
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctg
+aatcctgcggacgacccctctcgtggtcgcttggggctctaccgccctcttctccgcctgccgttccgg
+c
EOD

chomp( my @sequences = <$inFH> );
close $inFH or die $!;

my @letters   = map { [ split m{} ] } @sequences;
my $consensus = q{};

while ( @{ $letters[ 0 ] } )
{
    my $seq0 = shift @{ $letters[ 0 ] };
    my $seq1 = shift @{ $letters[ 1 ] };
    my $seq2 = shift @{ $letters[ 2 ] };
    my $seq3 = shift @{ $letters[ 3 ] };
    if (
       $seq0 eq $seq1
       and
       $seq0 eq $seq2
       and
       $seq0 eq $seq3
       )
    {
        $consensus .= $seq0;
    }
    else
    {
        emitConsensus();
    }
}
emitConsensus();

sub emitConsensus
{
    say $consensus if length $consensus;
    $consensus = q{};
}

[download]

The output.

at
gctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaat
+cctgcggacgacccctctcgtggtcg
ttggggctct
ccgccctcttctccgcctgccgttc
ggc

[download]

I hope I have understood correctly and this is helpful.

Cheers,

JohnGG

In reply to Re: Comparing array of aligned sequences by johngg
in thread Comparing array of aligned sequences by newtoperlprog

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