I have to count the number of overlapping dimers (AA, AG, AC, AT, GA, GG, GC, GT, CC, CG, CA, CT, TT, TA, TG, TC) in multiple sequences using PERL.

I wrote the following code but it only works for 1 sequence. How can I extend it to multiple sequences? 

#!/usr/bin/perl -w
open FH, "sample.txt";
$genome=<FH>;
%count=();
$count{substr($genome, $_, 2)}++ for 0..length($genome)-2;
print "AA: $count{AA}\n";
print "AG: $count{AG}\n";
print "AC: $count{AC}\n";
print "AT: $count{AT}\n";
print "TA: $count{TA}\n";
print "TG: $count{TG}\n";
print "TC: $count{TC}\n";
print "TT: $count{TT}\n";
print "GA: $count{GA}\n";
print "GG: $count{GG}\n";
print "GC: $count{GC}\n";
print "GT: $count{GT}\n";
print "CA: $count{CA}\n";
print "CG: $count{CG}\n";
print "CC: $count{CC}\n";
print "CT: $count{CT}\n";

[download]

I need 1. counts for each sequence and 2. the total counts

Input Example: Sample.txt 

ATGGGCTCCTCCGCCATCACCGTGAGCTTCCTCCTCTTTCTGGCATTTCAGCTCCCAGGGCAAACAGGAG
+CAAATCCCGTGTATGGCTCTGTGTCCAATGCAGACCTGATGGATTTCAAGTAAAAG ATGGTGAGAAAA
+TGGGCCCTGCTCCTGCCCATGCTGCTCTGCGGCCTGACTGGTCCCGCACACCTCTTCCAGCCAAGCCTG
+GTGCTGGAGATGGCCCAGGTCCTCTTGGATAACTACTGCTTCCCAGAGAACCTGATGGGGATGCAGGGA
+GCCATCGAGCAGGCCATCAAAAGTCAGGAGATTCTGTCTATCTCAGACCCTCAGACTCTGGCCCATGTG
+TTGACAGCTGGGGTGCAGAGCTCCTTGAATGACCCTCGCCTGGTCATCTCCTATGAGCCCAGCACCCTC
+GAGGCCCCTCCGCGAGCTCCAGCAGTCACGAACCTCACACTAGAGGAAATCATCGCAGGGCTGCAGGAT
+GGCCTTCGCCATGAGATTCTGGAAGGCAATGTGGGCTACCTGCGGGTGGACGACATCCCGGGCCAGGAG
+GTGATGAGCAAGCTGAGGAGCTTCCTGGTGGCCAACGTCTGGAGGAAGCTCGTGAACACGTCCGCCTTG
+GTGCTGGACCTCCGGCACTGCACTGGGGGACACGTGTCTGGCATCCCCTATGTCATCTCCTACCTGCAC
+CCAGGGAGCACAGTCTCGCACGTGGACACCGTCTACGACCGCCCCTCCAACACAACCACTGAGATCTGG
+ACCCTGCCTGAAGCCCTGGGAGAGAAGTACAGTGCAGACAAGGATGTGGTGGTCCTCACCAGCAGCCGC
+ACGGGGGGCGTGGCTGAGGACATCGCTTACATCCTCAAACAGATGCGCAGGGCCATCGTGGTGGGCGAG
+CGGACTGTTGGGGGGGCTCTGAACCTCCAGAAGCTGAGGGTAGGCCAGTCCGACTTCTTTCTCACTGTG
+CCTGTGTCCAGATCCCTGGGGCCCCTGGGTGAGGGCAGCCAGACGTGGGAGGGCAGTGGGGTGCTGCCC
+TGTGTGGGGACACCGGCCGAGCAGGCCCTGGAGAAAGCCCTGGCCGTTCTCATGCTGCGCAGGGCCCTG
+CCAGGAGTCATTCAGCGCCTTCAGGAGGCGCTGCGCGAGTACTACACGCTGGTGGACCGTGTGCCCGCC
+CTGCTGAGCCACCTGGCCGCCATGGACCTGTCCTCGGTGGTCTCCGAGGACGATCTGGTCACTAAGCTC
+AATGCTGGCCTGCAGGCTGTGTCTGAGGACCCCAGGCTCCAGGTGCAGGTGGTCAGACCCAAAGAAGCC
+TCTTCTGGGCCTGAGGAAGAAGCTGAAGAACCTCCAGAGGCGGTCCCGGAAGTGCCCGAGGACGAGGCT
+GTTCGGCGGGCTCTGGTGGACTCCGTGTTCCAGGTTTCTGTGCTGCCGGGCAACGTGGGCTACCTGCGC
+TTCGACAGTTTCGCTGATGCCTCTGTCCTGGAGGTGCTGGGCCCCTACATCCTGCACCAGGTGTGGGAG
+CCCCTGCAGGACACGGAGCACCTCATCATGGACCTGCGGCAGAACCCCGGGGGGCCGTCCTCCGCGGTG
+CCCCTGCTGCTCTCCTACTTCCAGAGCCCTGACGCCAGCCCCGTGCGCCTCTTCTCCACCTACGACCGG
+CGCACCAACATCACACGCGAGCACTTCAGCCAGACGGAGCTGCTGGGCCGGCCCTACGGCACCCAGCGT
+GGCGTGTACCTGCTCACTAGCCACCGCACCGCCACCGCGGCCGAGGAGCTGGCCTTCCTCATGCAGTCA
+CTGGGCTGGGCCACGCTGGTGGGCGAGATCACCGCGGGCAGCCTGCTGCACACACACACAGTATCCCTG
+CTGGAGACGCCCGAGGGCGGCCTGGCGCTCACGGTGCCTGTGCTCACCTTCATCGACAACCATGGCGAG
+TGCTGGCTGGGGGGCGGTGTGGTCCCCGATGCCATTGTGCTGGCCGAGGAAGCCCTAGACAGAGCCCAG
+GAGGTGCTGGAGTTCCACCGAAGCTTGGGGGAGTTGGTGGAAGGCACGGGGCGCCTGCTGGAGGCCCAC
+TACGCTCGGCCAGAGGTCGTGGGGCAGATGGGTGCCCTGCTGCGAGCCAAGCTGGCCCAGGGGGCCTAC
+CGCACCGCGGTGGACCTGGAGTCGCTGGCTTCCCAGCTTACGGCCGACCTGCAGGAGATGTCTGGGGAC
+CACCGTCTGCTGGTGTTCCACAGCCCCGGCGAAATGGTGGCTGAGGAGGCGCCCCCACCGCCTCCCGTC
+GTCCCCTCCCCGGAGGAGCTGTCCTATCTCATCGAGGCCCTGTTCAAGACTGAGGTGCTGCCCGGCCAG
+CTGGGCTACCTGCGTTTCGACGCCATGGCTGAGCTGGAGACGGTGAAGGCCGTCGGGCCACAGCTGGTG
+CAGCTGGTGTGGCAGAAGCTGGTGGACACGGCCGCGCTGGTGGTCGACCTGCGCTACAACCCCGGCAGC
+TACTCCACAGCCGTGCCTCTACTCTGCTCCTACTTCTTCGAGGCAGAGCCCCGCCGGCACCTCTACTCT
+GTCTTTGACAGGGCCACGTCAAGGGTCACAGAGGTATGGACCCTGCCCCACGTTACAGGCCAGCGCTAT
+GGCTCCCACAAGGACCTCTACGTTCTGGTGAGCCACACCAGCGGTTCAGCAGCTGAGGCTTTTGCTCAC
+ACCATGCAGGATCTGCAGCGAGCCACCATCATCGGGGAGCCCACGGCCGGAGGGGCACTCTCCGTGGGA
+ATCTACCAGGTGGGCAGCAGCGCCTTATACGCCTCCATGCCCACGCAGATGGCCATGAGTGCCAGCACC
+GGCGAGGCCTGGGATCTGGCTGGGGTGGAGCCGGACATCACTGTGCCCATGAGCGTGGCCCTCTCCACA
+GCCCGGGACATAGTGACCCTGCGTGCCAAGGTGCCCACTGTGCTGCAGACAGCTGGGAAGCTCGTAGCG
+GATAACTACGCCTCCCCTGAGCTGGGAGTCAAGATGGCAGCCGAACTGAGTGGTCTGCAGAGCCGCTAT
+GCCAGGGTGACCTCAGAAGCCGCCCTCGCCGAGCTGCTGCAAGCCGACCTGCAGGTGCTGTCCGGGGAC
+CCACACCTGAAGACAGCTCATATACCTGAGGATGCCAAAGACCGCATTCCTGGCATTGTACCCATGCAG
+TAACAG ATGGACATGATGGACGGCTGCCAGTTCTCGCCCTCTGAGTACTTCTACGACGGCTCCTGCAT
+CCCATCCCCCGACGGTGAGTTCGGGGACGAGTTTGAGCCGCGAGTGGCTGCTTTCGGGGCTCACAAGGC
+AGACCTGCAAGGCTCAGACGAGGACGAGCACGTGCGAGCACCCACGGGCCACCACCAGGCCGGCCACTG
+CCTCATGTGGGCCTGCAAAGCATGCAAAAGGAAGTCCACCACCATGGATCGGCGGAAGGCGGCCACCAT
+GCGCGAGCGGAGACGCCTGAAGAAGGTCAACCAGGCTTTCGACACGCTCAAGCGGTGCACCACGACCAA
+CCCTAACCAGAGGCTGCCCAAGGTGGAGATCCTCAGGAATGCCATCCGCTACATTGAGAGTCTGCAGGA
+GCTGCTTAGGGAACAGGTGGAAAACTACTATAGCCTGCCGGGGCAGAGCTGCTCTGAGCCCACCAGCCC
+CACCTCAAGTTGCTCTGATGGCATGTAAATG

[download]

Many thanks!

In reply to Counting overlapping dimers for multiple sequences by sally123

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