There is a very high volume of traffic coming from your site (IP address 3.229.142.91) as of Thu Oct 28 02:38:17 2021 (California time). So that other users get a fair share of our bandwidth, we are putting in a delay of 13.4 seconds before we service your request. This delay will slowly decrease over a half hour as activity returns to normal. This high volume of traffic is likely due to program-driven rather than interactive access, or the submission of queries on a large number of sequences. If you are making large batch queries, please write to our genome@soe.ucsc.edu public mailing list and inquire about more efficient ways to access our data. If you are sharing an IP address with someone who is submitting large batch queries, we apologize for the inconvenience. To use the genome browser functionality from a Unix command line, please read <a href='http://genome.ucsc.edu/FAQ/FAQdownloads.html#download36'>our FAQ</a> on this topic. For further help on[...] Short Match Track Settings
Short Match Track Settings
 
Perfect Match to Short Sequence   (All Mapping and Sequencing tracks)

Display mode:   

Short (2-30 base) sequence:
Examples: TATAWAAR, AAAAA


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.