This pseudocount value is added to each of the motif's letter counts in proportion to the background frequency before generating the postion specific scoring matrices.
This value sets the scale for calculating p-scores of motif hits. Hit p-values below this threshold get positive scores while hit p-values above this threshold get negative scores.
The p-score S for a hit with p-value p is:
S = -log2(p / hit p-value threshold)
This value specifies the longest distance allowed between two hits in a match. Hits separated by more than this value will be placed in different matches.
Large values for this field combined with large values for the hit p-value threshold may prevent MCAST from computing E-values.
This value sets the E-value threshold for displaying search results. If the E-value of a match is greater than this value, then the match will not be included in the output.
MCAST - Motif Cluster Alignment and Search Tool
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