Traces Window

The Traces window contains a complex series of columns. From left to right these are;

Scale and Consensus sequence

indicates position within the sequence in base pairs

Base Calls

Dots in the column indicate agreement with the consensus sequece. The number of dots indicates the number of overlaping reads in the portion of the sequence being displayed. Blue bars located in the "dot" columns indicate vector sequence.

Locator bar

The length of the green locator bar indicates the proportion of the sequence which is displayed in the trace columns. Clicking on the green bar brings the contig display window to the front

Scale 2

Base pair position and consensus sequence relative to the trace display

Traces

Intensity traces from the sequencer are displayed with a color code; A in green, T in red, G in black and C in blue. The number of traces which are displayed depends on selections under Show button. The numbers at the top of trace columns indicate the position within the individual read. A blue background indicates that the read has be designated as high quality (generally a reflection of the sequencing protocol). Triangles at the top indicate the direction of the read. Clicking on a triangle removes the trace from the display window. A second character (a t g c) with a highlighted background in the base call column is a suggestion for an edit to the sequence calls, and occurs at positions where the ACEDB base calling procedure conflicts with the sequence of the SCF file. Machine edited positions are shown with a green background, while manually edited positions are shown with a yellow background. Regions which have been removed from base calling (clipped sequences) are shown as yellow bars over the sequence read.

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