In addition to the other numerous things that have been pointed out, I can't help but notice that of the two same lines of input you provide, 1 of those don't acctually start with an 'R'...

Results:1582 1640 6 9.8 6 90 0 69 55 16 13 13 1.68 GACAAT GACAATGACAAT
+GACAATGACAATGACAGAGACAGTAACAATAACAATAACAATAACAA
"Results:5184 5214 6 5.2 6 96 0 55 16 0 45 38 1.47 TGGTGA TGGTGATGGTGA
+TGGTGATGGTGATGTTGAT";
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That second line starts with the '"' character, which means this regexp...

      if ($line =~/^R.*/) {
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...will ignore that line, because the '^' says the line must start with the 'R'.

Maybe this was jsut a typo in your post ... or maybe a bunch of lines of your data accutally look like that, and are causing problems.