Pattern


Input
Sequence   Input file - nucleotide sequences in FASTA-format
Output
Result  Name of the output file
Print N best patterns pairs  Print N best patterns pairs
Options
Search in both chain  Search for pattern in both chain
Threshold for include fragment   Threshold for include fragment to pattern.
Minimal distance for patterns in pair  Minimal distance for patterns in pair
Maximal distance for patterns in pair  Maximal distance for patterns in pair
Number of stored best patterns  Number of stored best patterns
Initial length  Initial length. Minimal value is 3, maximal value is 12.
Try to expand  Try to expand to xx position left and right. If this option is switched off, the pattern will not extend in the parties. Default value is 2, minimal value is 1, maximal value is 10.
Pair selection methodsPair selection methods:
Both pattern must present
One of pattern must present