Matrix Alignment and COparison
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INPUT Position Frequency Matrix (PFM):
Choose format: Choose to input raw PFM or in Fasta format

Paste Matrix(s) here


Paste PFM here row by row, in A C G T order

PARAMETERS:
General Parameters
Scoring method: Choose scoring method. Must be above 3.0
Dataset Specify the dataset.
Cutoff: Choose Cutoff value. PFM that scores lower than cutoff is discarded. Must be above 3
Min. Core Length: The minimum length of core overlap.
Min. Subcore Length: The minimum length of overlaps flanking the core overlap. Must be above 2
Spacer Limit: The maxium shift of sub overlaps. Must be above 0.
Reverse Complement? If checked, perform reverse complement comparison.
Loose Tolerance? If checked, loose letter tolerance in alignment.
Truncate Input? If checked, truncate input PFM into fragments and compare independently.

Interface and CGI developed by G.Su. Email!