Traces
Color of traces:
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A trace color Color of A nucleotide in alignment. Click on arrow on the right to change the color.
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C trace color Color of C nucleotide in alignment. Click on arrow on the right to change the color.
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G trace color Color of G nucleotide in alignment. Click on arrow on the right to change the color.
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T trace color Color of T nucleotide in alignment. Click on arrow on the right to change the color.
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N trace color Color of N nucleotide in alignment. Click on arrow on the right to change the color.
DNA:
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Show letter in color True or false.
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Show ambiguity letter True or false.
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Show confidence levels True or false.
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Show confidence methods Numbers correspond to the methods in the following paper:"Assignment of position-specific error probability to primary DNA sequence data." by C. B. Lawrence and V. V. SolovyevDepartment of Cell Biology, Baylor College of Medicine, Houston, TX 77030. In Nucleic Acid Research, 1994, Vol 22, No7, Page 12741 = Average (algorithm/characteristic 1)2 = AverageDiff (algorithm/characteristic 2)3 = AverageAndAverageDiff (algorithm/characteristic 2)4 = DiffWithOtherMax (algorithm/characteristic 6)8 = Peakwidth (algorithm/characteristic 16)16 = MaxDiffBetween (algorithm/characteristic 23)
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Use confidence levels True or false.
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Minimum level of confidence All nucleotides with confidence below the minimum level of confidence are displayed in gray, if the Disable low confidence nucleotides option is selected.
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Base caller level This value is used to calculate the threshold level, depending on the selected algorithm.
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Base caller method Two algorithms are currently available, the Average method and the Max value method. For more details on the algorithms click here.
Genbank:
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Genbank timeout Seconds before timeout. E.g. 60 means that in the sequence alignment (BLAST) the software will try for max 60 seconds to get an answer from Genbank.When no answer is returned within the 60 seconds then the BLAST will be stopped.
Click Save to save the changes made and to close the Options dialog.
