Description

This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the "+" strand is shown.

The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the track's description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.

To see how to create a bed file of the short match data see this mailing list question here.

Credits

This track was generated by Jim Kent of the UCSC Genome Bioinformatics Group.