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Working with Hit Results

Hit results are shown in a clickable image. The query sequence is shown in black, and the hits are shown below it. If the alignment was generated using a BLAST program, the hits will be color-coded by BLAST score and the BLAST scoring color key is provided above the hit image alignment score. Hits generated from all other tools will be displayed in black, regardless of score.

For each hit, a scaffold number is shown to the left and an alignment score is shown to the right. The graphical alignment summary page offers several controls for customizing the image.

• Xsize The width of the result image in pixels. The scale adjusts to fit the full query sequence into the image.
• Ysize The height of the result image in pixels. Setting this number too low may cut off some of the hits. (In this case, a warning appears above the image.) If set to zero, Ysize will adapt to show all the hits.
• minScore The minimum alignment score a hit must have to be shown. (A higher number gives you fewer hits.)
• min%id the minimum percentage identity a hit must have to be shown.
• min%pos The minimum percentage of positives (identical or similar matches) a hit must have to be shown.
• minLength The minimum alignment length in base pairs a hit must have to be shown.
• Start The start of the shown portion of the query sequence. If this number is higher than the actual start of the query sequence, you can use the navigation buttons to jump toward the start or end.
• End The end of the shown portion of the query sequence. If this number is less than the actual end of the query sequence, you can use the navigation buttons to jump toward the start or end.