Select Code to Download

My File 1 looks like this:- 
155369268 300
...
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
TGTGGCCTAACCATGGTCGTGTTGTGCTGGACGTCACAGCAGAGGAGGAGGCGCAGAACAAAGGCTGC

I am getting this error /warning:-
Substr outside of the string at line 42. <$fh> line 2.
Use of Uninitialized value in concatenation or string at line 42. <$fh
+> line 4.
Use of uninitialized value in hash element at line 34. <$fh> line 4. 
...................................

#!/usr/bin/perl

...

   }
}