Off hand I'd say that you aren't accounting for the newlines in the data. You're trying to match across all six lines explicitly, but aren't matching the newlines. Try changing where you set content to look like this: 

chomp(my @content = <FILE>);

[download]
And then there shouldn't be any newlines in $allseq

Oh, and if you're trying to match the same pattern several times, you can do something like this: /pattern{6}/ Though in your case that'll throw a kink into how you get the values out with $1 and friends.

duff

In reply to Re^5: Regex /g and interpolated lengths by duff
in thread Regex /g and interpolated lengths by Anonymous Monk

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