FindM is a tool that finds the occurrences of predefined motifs in a set of DNA sequences aligned with respect to a functional site (e.g. a transcription start site). For example it can extract all promoters that contain a TATA-box.
Inputs can be one of the available data sets, a user provided FASTA file or a users' FPS file.
A motif can be selected from the available libraries, a user provided Position Weight Matrix or a consensus sequence.
Sequence range: is the range around the functional site that FindM scans for the motif
Sequence Selection: output can be restricted to sequences with or without a match, all matches, best matches, etc...
FindM output: in this example all the sequences with a TATA-box (in the region -99 to 100)