Target 4 Track Settings
 
Target 4   (All Custom Tracks)

Display mode:          

Color track by bases: Help on base coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion


Display data as a density graph:

Display data as a rearrangement graph:
Data schema/format description and download
Data last updated at UCSC: 2024-02-07 17:30:00

Description

This track shows the BLAT alignments of your sequence(s) to the genome assembly. The data display can also be toggled to a density graph, or rearrangement display. In the Genome Browser, alignments of nucleotides use color to highlight differences as follows:

  • red: Genome and query sequence have different bases at this position.
  • orange: The query sequence has an insertion (or genome has a deletion / alignment gap) at this point.
  • purple: The query sequence extends beyond the end of the alignment.
  • green: The query sequence appears to have a polyA tail that is not aligned to the genome.

Also, when the alignment has gaps in both the genome and query sequence, double horizontal lines are drawn.

Credits

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