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#!/usr/bin/perl

...
      my  $Location = $position + 1;
        print "$sequences{$key}";
 }

File 1:-
155369268 5 C 
...
>gi|169212695|ref|XM_001716884.1| Its the code 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT

 
>gi|155369268|ref|NM_001100917.1| After all
AAACCATGTCGATTCTATGATGCGAACGCAGCATTTCAGGGACTGGATGAGGAGCTTACGGTTTTTTACT
...
>gi|169212695|ref|XM_001716884.1| Its the code 
AGACAATCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT