parsing sequences from a file

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GENSCAN 1.0    Date run: 11-Mar-109    Time: 00:29:37

...
actctgaaagattcagcaactccagaagacaaggatcaagaagacaaacaagatgagaga
ggtgaagaaattcaagaacaacctcaagagatgtag

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#!/usr/bin/perl

...

    }
}

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seqfile1_uc.out
>scaffold_2|GENSCAN_predicted_CDS_1|144_bp
...
>scaffold_2|GENSCAN_predicted_peptide_2|51_aa
MRKNEGVDDADPLIEGMKEITLKDSATPEDKDQEDKQDERGEEIQEQPQEM
....... so on...from all the 40,000 files.

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