Just few changes: 
--- 1.pl        2015-03-30 22:58:28.434954333 +0200
+++ 2.pl        2015-03-30 22:58:11.261833250 +0200
@@ -3,16 +3,18 @@
 use warnings;
 use Syntax::Construct qw{ // };
 
-my ($startpos, $endpos, $count);
+my $endpos = 0;
+my ($startpos, $count);
 my %occurrences;
 while (<DATA>) {
-    if (/^\s+ ([0-9]+) \s+ ([0-9]+) \s*$/x) {
-        ($startpos, $endpos) = ($1, $2);
+    if (/^ +$/) {
+        $startpos = $endpos + 1;
         $count = 0;
 
     } elsif (/\s+ ([-actg]+) \s*$/x) {
         ++$count;
         my @nucleotides = split //, $1;
+        $endpos = $endpos + length $1 if $startpos == $endpos + 1;
         for my $pos (0 .. $#nucleotides) {
             ++$occurrences{ $nucleotides[$pos] }[$startpos + $pos]
                 unless '-' eq $nucleotides[$pos];

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In reply to Re^3: Alignment and matrix generation by choroba
in thread Alignment and matrix generation by newtoperlprog

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