in reply to find reverse complement of every 2nd line

For the pure ACGTacgt lines it is simple:

$in = 'GTAGGGGCTGCGCGAACGCAAACCCCCGCTGCCACAAATGATCGTCGGACTGTAGAACTCTGA
+ACGTGTAGATCTCGGTGGCCGCCGTATCATTAAAAAAA';;

( $out = reverse $in ) =~ tr[acgtACGT][tgcaTGCA];;

print $out;;
TTTTTTTAATGATACGGCGGCCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATCATTTGTGG
+CAGCGGGGGTTTGCGTTCGCGCAGCCCCTAC

[download]

Extending that to deal with the other letters and characters is just a case of knowing the complement rules -- which you presumably do -- and then extending the tr/// conversion strings appropriately.

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