Please format your code (and your question) better, next time.

Running your code with just the one line in the input file gives on stdout:

ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagttccaggg
+ctgatgaggg
The first occurance of little a is: 48
The first occurance of little c is: 47
The first occurance of little g is: 46
The first occurance of little t is: 55
[download]

and in out.index.7.19.04:

ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagttccaggg
+ctgatgaggg
Mon Jul 19 20:20:27 2004
The first occurance of little a is: 48
The first occurance of little c is: 47
The first occurance of little g is: 46
The first occurance of little t is: 55


ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagttccaggg
+ctgatgaggg
Mon Jul 19 20:20:27 2004
The first occurance of little a is: 48
The first occurance of little c is: 47
The first occurance of little g is: 46
The first occurance of little t is: 55
[download]

So it works correctly for me, using perl 5.8.5 RC2 and 5.8.4 on debian linux. Your particular perl binary might be broken; you seem to have an "unoffical" release - what does perl -V give after the "Locally applied patches:" line?