Actually, my first thought on reading this was to make sure that you read in the whole document, or at least all the relevant section. If you're reading line-by-line, you can match on a regional basis:
if ( m|QBlastInfoEnd|...0 ) { # continue till end of file if ( m|-->|...m|</form>| ) { print; } }
--
TTTATCGGTCGTTATATAGATGTTTGCA
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