1. Input sequence and parameters
Type a species name in the text box:
Paste a (Multi)FASTA sequence :
[ or use a sample :
E.coli K-12 substr.
Cronobacter sakazakii ES15
Pectobacterium sp. SCC3193
Upload a sequence file in (Multi)FASTA/GBK format:
Left flank length:
Right flank length:
2. Search putative CRISPRs using the following options
Minimum word repetition >=
Maximum distance between words:
3. Filter out poor CRISPRs using one or more of the following parameters
Min. repeat length >=
Min. number of repeats >=
CRISPR likelihood score >=
[can be modified once the output is generated]
A. Correct common insertion(s) in all repeats of an array.
B. Correct gap(s) at repeat ends
C. Attempt to extend arrays both side with matching repeat identity >=
%, use dynamic search
(it reveals degenerated missing repeats at the end)
D. Search for unidentified mutated repeat(s) in spacer sequences with >=
% identity, use dynamic search
E. Trim repeat end(s) with >=
% mismatch in region.
force trimming LEFT
F. Extend repeats (length) on either side with >=
% identity in region.
force extend on LEFT by
and/or RIGHT by
G. Remove degenerated repeats from both ends with matching repeat identity <=
force removing from TOP
H. Attempt to verify the orientation of the array and adjust repeats length based on an experimentally determined repeat library.
You can add comma separated repeat(s) for this analysis:
I. Reverse selected array(s).
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