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#!/usr/bin/perl

...
    $index += 3 while ( ($index + 3) < $positions{$key} );
    print "$key $positions{$key} " . substr($sequences{$key}, $index, 
+3) . "\n";
}

 
File 1:-
155369268 17 A 
...
>gi|269212605|ref|XM_401716884.1| some text 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCTATGAC
CTAATTGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT

155369268 17 CTA 
155369268 70 CGC
...
155369268 70 CGC
269212605 120 GGG