From: PILER-CR: Fast and accurate identification of CRISPR repeats
Parameter | Description | Default |
---|---|---|
minrepeat | Minimum length of a repeat. Smaller values might increase sensitivity, though repeats < 16 bases are not currently known. | 16 |
maxrepeat | Maximum length of a repeat. Larger values might increase sensitivity, though repeats > 64 bases are not currently known. Larger values may also tend to give more false positives, such as RNAs. | 64 |
minspacer | Minimum spacer length. | 8 |
minarray | Minimum number of repeats in an array. A value < 3 will give large numbers of false positives. A value > 3 might increase specificity at the expense of missing shorter arrays. | 3 |
maxspacer | Maximum spacer length. | 64 |
minrepeatratio | Repeat length ratio (see caption for definition of ratio). | 0.9 |
minspacerratio | Spacer length ratio (see caption for definition of ratio). | 0.75 |
mincons | A run of minarray repeats with at least mincons similarity is required for an array to be reported. The value is specified as fractional identity 0.0 .. 1.0, with 1.0 meaning identical sequences. Increasing this value will tend to increase specificity by reducing the number of degraded or mutated repeats reported. | 0.90 |