Thanks Limbic~Region and BrowserUk for your good advice. I have had a quick go with BrowserUk's script and it seems to work OK. However, the merge is not so clean and results after the merge seem not to be in equal chunks (I have posted this on to my scratchpad). I am speculating that this will continue as > continue to add more block (i.e thousands). I have adapted your script as follows: 

#! perl -slw
use strict;



if (scalar(@ARGV) != 1) {
    print "\n";
    print "Usage: script.pl <alignment file>";
    print "\n";
    exit();
  }

my ($FILENAME) = @ARGV; #read in file
open(DATA, $FILENAME);

my( $id, %accu, @order );

## remove existing files    
my $remove = "new_alignment_".$FILENAME;  #remove any existing results
+ file
    if (unlink($remove) == 1) {
                        print "Existing \"$remove\" file was removed\n
+";
                          }



## generate a temporary storage file    
my $outputfile = "new_alignment_".$FILENAME; #make a big file in which
+ the final results will be printed
    unless ( open(POS, ">>$outputfile") ) {
    print "Cannot open file \"$outputfile\" to write to!!\n\n";
        exit;
        }

while( <DATA> ) {
    chomp;
    if( m[^(\S+_\S+_\S+)\s+(.+)\s*$] ) {
        $id = $1;
        unless( exists $accu{ $id } ) {
            push @order, $id;
            $accu{ $id } = $2;
        }
        else {
            $accu{ $id } .= ' ' . $2;
        }
    }
    else {
        $accu{ $id } .= ' ' . $_;
    }
}

for my $key ( @order ) {
    printf POS "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' );
    print POS substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $
+key };
    print POS '';
}

[download]
I must also confess I do not understand the last bit of code: 
for my $key ( @order ) {
    printf POS "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' );
    print POS substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $
+key };
    print POS '';
}

[download]
Could you kindly please explain it to me.

PS: Still thinking of how to implement what Limbic~Region has pointed out.

$new_guy

In reply to Re^2: concatenating identical sequences by $new_guy
in thread concatenating identical sequences by $new_guy

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