in reply to values of hash table

Whether you use " " or \s+/ with the split, you don't need chomp.

On the other hand, if you want to use it, for clarity, the appropriate usage would be to chomp the lines as they are read in:

while ( $line = <$fh> ) { chomp $line; @r = split " ", $line; .....

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TTTATCGGTCGTTATATAGATGTTTGCA