The data I am working with are DNA sequences. (I know of the Bioperl project but have found nothing there that could help.) I have distilled the data to the DNA sequences alone. I have a second file with the sequence IDs, which is why I also print out the indicies from the matching strings. The data look like this.

ATGGAGAACATCACATCAGGACTCCTAGGACCCCTTCTCGTGTTACAGGC
ATGGAGAACATCACATCACGACTCCTAGGACCCCTTCACGTGAAACAGGC
ATGCTCAACGTCACATCAGGACTCCTAGGACCACGTCTCGTGTTACAGGG
ATGGTGTACATCACGACAGGATTCCTCGGAATCGCGCTGGTGACACAGGC

With the sequence IDs the data would look like this.

>seq1
ATGGAGAACATCACATCAGGACTCCTAGGACCCCTTCTCGTGTTACAGGC
>seq2
ATGGAGAACATCACATCACGACTCCTAGGACCCCTTCACGTGAAACAGGC
>seq3
ATGCTCAACGTCACATCAGGACTCCTAGGACCACGTCTCGTGTTACAGGG
>seq4
ATGGTGTACATCACGACAGGATTCCTCGGAATCGCGCTGGTGACACAGGC

### update ###

I have placed real data in my public scratchpad.

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