AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54889

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54889.t1 MTR_4g039340 80.916 131 17 2 1 123 1 131 1.05e-60 182
MS.gene54889.t1 MTR_4g039380 80.645 124 16 2 1 123 1 117 1.84e-60 181
MS.gene54889.t1 MTR_4g039640 68.702 131 19 3 1 123 1 117 3.19e-44 140
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGGTTATT+TGG 0.175696 4.4:+65703449 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4.4:+65703227 None:intergenic
CTTGATTCTAATATATAATC+TGG 0.305373 4.4:+65703488 None:intergenic
TGTTTAATTTCTCATTCATC+TGG 0.344042 4.4:+65703218 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4.4:+65703228 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.452210 4.4:+65703455 None:intergenic
TTGAGGTCGAAAGCTTGAAC+AGG 0.493044 4.4:+65703254 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 4.4:+65703275 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.509510 4.4:+65703452 None:intergenic
CGAAAGCTTGAACAGGAGGC+TGG 0.520977 4.4:+65703261 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.4:+65703287 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.4:+65703293 None:intergenic
ACTGTTAAAGCTTCTCGAGA+TGG 0.587984 4.4:+65703533 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.4:+65703237 None:intergenic
AGGTCGAAAGCTTGAACAGG+AGG 0.614849 4.4:+65703257 None:intergenic
ATATTAGAATCAAGTAAACA+AGG 0.665430 4.4:-65703479 MS.gene54889:CDS
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.4:+65703290 None:intergenic
TCAAAGCTAGAATTCTTATG+CGG 0.715209 4.4:-65703575 MS.gene54889:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTAGAATCAAGTAAACA+AGG - chr4.4:65703328-65703347 MS.gene54889:CDS 20.0%
!! CTTGATTCTAATATATAATC+TGG + chr4.4:65703322-65703341 None:intergenic 20.0%
TCAAAGCTAGAATTCTTATG+CGG - chr4.4:65703232-65703251 MS.gene54889:CDS 30.0%
! TGATGTTCAACATTTTGTGG+TGG + chr4.4:65703397-65703416 None:intergenic 35.0%
! TGTTCAACATTTTGTGGTTG+AGG + chr4.4:65703394-65703413 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr4.4:65703400-65703419 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG + chr4.4:65703523-65703542 None:intergenic 40.0%
ACTGTTAAAGCTTCTCGAGA+TGG + chr4.4:65703277-65703296 None:intergenic 40.0%
CTGGTGTATAAGGGAGATTG+AGG + chr4.4:65703573-65703592 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr4.4:65703520-65703539 None:intergenic 45.0%
TTGAGGTCGAAAGCTTGAAC+AGG + chr4.4:65703556-65703575 None:intergenic 45.0%
! GGTTGAGGTTGAGCATTTTC+TGG + chr4.4:65703379-65703398 None:intergenic 45.0%
! TCTGGTTCAGGCTGGTTATT+TGG + chr4.4:65703361-65703380 None:intergenic 45.0%
!!! GGTTGAGCATTTTCTGGTTC+AGG + chr4.4:65703373-65703392 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG + chr4.4:65703517-65703536 None:intergenic 50.0%
AGGTCGAAAGCTTGAACAGG+AGG + chr4.4:65703553-65703572 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG + chr4.4:65703535-65703554 None:intergenic 50.0%
! GGTGGAGCTAGTGCATTTTG+TGG + chr4.4:65703421-65703440 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG + chr4.4:65703358-65703377 None:intergenic 50.0%
! TCAGGCTGGTTATTTGGTGG+TGG + chr4.4:65703355-65703374 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr4.4:65703505-65703524 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG + chr4.4:65703369-65703388 None:intergenic 50.0%
CGAAAGCTTGAACAGGAGGC+TGG + chr4.4:65703549-65703568 None:intergenic 55.0%
! GGAGCTGGTGCATTTTGTGG+TGG + chr4.4:65703460-65703479 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG + chr4.4:65703502-65703521 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr4.4:65703463-65703482 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG + chr4.4:65703475-65703494 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 65703229 65703600 65703229 ID=MS.gene54889
chr4.4 mRNA 65703229 65703600 65703229 ID=MS.gene54889.t1;Parent=MS.gene54889
chr4.4 exon 65703229 65703600 65703229 ID=MS.gene54889.t1.exon1;Parent=MS.gene54889.t1
chr4.4 CDS 65703229 65703600 65703229 ID=cds.MS.gene54889.t1;Parent=MS.gene54889.t1
Gene Sequence

>MS.gene54889

ATGTCAAAGCTAGAATTCTTATGCGGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAACAGTGCATGTTATCGAAGAACATCATCCAGATTATATATTAGAATCAAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCAGAAAATGCTCAACCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACTAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCAAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene54889.t1

MSKLEFLCGECDTMFPSREALTVHVIEEHHPDYILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNALAPPQNVEHQPQNAPAPPQNAPAPPQNAPPPHVQPFDLNQPPVQAFDLNLPYTPDE