Main Window

overview

Krait2 graphical user interface is devided in five areas.

1.Toolbar

  • ssr search for perfect microsatellites.

  • cssr search for compound microsatellites.

  • gtr search for generic tandem repeats with any motif length.

  • issr search for imperfect microsatellites.

  • locating mapping microsatellites to gene features such as CDS, UTR, intron.

  • primer design primers for selected microsatellites.

  • statistics perform statistics analysis.

  • filter filter the rows in current table.

2.Input File List

The imported fasta/q file name will listed in this area.

_images/filelist.png

3.Main view

When clicking the file name in input file list, this view will display the corresponding file information, microsatellite tables, primer table and statistics information.

fileinfo

4.Annotation Tree

When there are microsatellites in the current table, click the annotated microsatellites, the annotation tree will display the gene feature information in where microsatellite located.

annotree

5.Sequence and Alignment Viewer

When clicking a microsatellite in current table, its sequence and flanking sequence will be displayed in sequence viewer.

seqview

If the clicked microsatellite is imperfect, the alignment between it and the perfect counterpart will be displayed in alignment viewer.

seqaln