Define input parameters:
Define ouput parameters:
Genome file in multifasta format.
To print accepted clusters, select one of the following options:
First contig selected (0 means all).
0: not print anything
Last contig selected (if the first is nonzero)
1: print the list of accepted clusters.
Minimum number of repeats of the pattern into a cluster.
2: print the list of accepted clusters with a representative repeat in fasta format.
Minimum length of the cluster
3: print the list of accepted clusters with all repeats.
Length of the pattern.
4: print the list of accepted clusters with only the selected repeats.
With these parameters the program searches for the clusters. After that, each pattern determines a repeat that starts with the pattern and ends before the next pattern (The patterns into the cluster can be find with
errors). These repeats are grouped according to its length, and consecutive lengths are grouped into intervals of width ...
To print rejected clusters select one of the following options:
Width of the interval.
0: not print anything.
Now we check if there is an interval with enough number of repeats according to this parameters:
1: print the list of rejected clusters.
Minimum percentage (1..100) of repeats.
2: print the list of rejected clusters with all repeats.
Minimum number of repeats.
The repeats can be aligned and the concensus sequence can be printed:
Now we have for each cluster a selected set of repeats. We can select those clusters according to the length of the repeats:
To print aligned repeats of a cluster select one of the following options:
Minimum length of the repeats (0 no matter).
0: Do not align the repeats.
Maximum length of the repeats. (0 no matter)
1: Print the concesus of all repeats.
The repeats can be aligned with the following parameters:
2: Print the concesus of selected repeats.
3: Print the alignment of all repeats.
4: Print the alignment of selected repeats.
Gap openning penalty.
Gap extension penalty.
Gap extrem penalty.