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Russel88 / CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
https://typer.crispr.dk
MIT License
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About spacer sequences #18

Closed wfgui closed 2 years ago

wfgui commented 2 years ago

I use the the software to construct the CRISPRCas database from the bacterial genome in the Refseq database. But I found that some spacer sequences are not in the genome，for example（spacers/NC_015711.1_1.fa）：>NC_015711.1_1:1

>NC_015711.1_1:1
TCAACCAGCATTAGCACCGTCCGCGTGGCGCCCGTGT
>NC_015711.1_1:2
CTGGAGTTGTCCCCCGAGGCTGAGCCGGTGTCCCGCGT
>NC_015711.1_1:3
TCTTCCATCTGCGTCTGCGTCTGACCCTTGAACTTCG
>NC_015711.1_1:4
ATGCAGAACAGCGGCAAGGAGGCGATTATCGACCT
>NC_015711.1_1:5
GGGCAGTGAAACCCTTGGGTGGGGAAGGAGTTCTGGGGGC
>NC_015711.1_1:6
AGGAGCGCCCGCCGGCCAGACGCATAGACGACGCA

Am i missing something？

Thanks！

GCF_000219105.zip

Russel88 commented 2 years ago

Dear wfgui,

Not sure what the problem is here. When I blast these 6 spacer sequences against NC_015711.1 I find perfect matches for all, as expected.

See attached BLASTn table: BLASTn-Alignment.txt

Cheers, Jakob