STREME motif significance

[Ariana Treat]

From the STREME paper,

1. Motif significance computation. STREME computes the statistical significance of the motif by using the motif and the optimal discriminative score threshold (based on the primary and control sequences) to classify the hold-out set sequences, and then applying the statistical test to the classification. Classification is based on the best match to the motif in each sequence (on either strand when the alphabet is complementable).

This is unclear to me; how should we interpret the ordering of motifs in significance? Some motifs that are considered more significant by STREME show up much less frequently in my list of sequences than less significant motifs (I determined this by searching the sequences with STREME motifs using FIMO and tallying motif occurrences). Are more significant motifs also more significant biologically?

Thank you,

Ariana Treat