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#!/usr/bin/perl

use warnings;
...
TCAGCTAGCNA
ACTGSCGACAAAA
GTCTGAGTTATTT

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ACTGCTAGGGGGGG -> 5 -> ACTGCTAGG
TCAGCTAGCNA -> 
ACTGSCGACAAAA -> 2 -> ACTGSCGACAA
GTCTGAGTTATTT -> 1 -> GTCTGAGTTATT