AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0726770

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCCATGAGTTTCATTAATA+TGG 0.183207 5_1:-28156469 Msa0726770:CDS
AAGAGAATATGGTTGGAGTT+TGG 0.225607 5_1:-28156503 Msa0726770:CDS
GGGCAACTTTGAAGAGAATA+TGG 0.298068 5_1:-28156514 Msa0726770:CDS
AGAGAATATGGTTGGAGTTT+GGG 0.298441 5_1:-28156502 Msa0726770:CDS
CAAGTATATGTATCTATTTA+TGG 0.308121 5_1:-28156433 Msa0726770:CDS
TCTTCAAAGTTGCCCCAAAA+AGG 0.390045 5_1:+28156522 None:intergenic
TCTGAAAACAAGCATGGAAA+TGG 0.391099 5_1:-28156546 Msa0726770:CDS
TAAATGTCAAATGGATTCAT+TGG 0.413489 5_1:-28156409 None:intergenic
ATTTATGGCTAAATGTCAAA+TGG 0.431655 5_1:-28156418 Msa0726770:CDS
TATGGTTGGAGTTTGGGGTC+AGG 0.432917 5_1:-28156496 Msa0726770:CDS
AGATACATATACTTGTCCTT+TGG 0.454505 5_1:+28156441 None:intergenic
TACATATACTTGTCCTTTGG+TGG 0.475426 5_1:+28156444 None:intergenic
GAGAATATGGTTGGAGTTTG+GGG 0.481399 5_1:-28156501 Msa0726770:CDS
TCCATATTAATGAAACTCAT+GGG 0.503316 5_1:+28156468 None:intergenic
GTCCATATTAATGAAACTCA+TGG 0.514913 5_1:+28156467 None:intergenic
AACTTTGAAGAGAATATGGT+TGG 0.531598 5_1:-28156510 Msa0726770:CDS
GGTTGGAGTTTGGGGTCAGG+AGG 0.545206 5_1:-28156493 Msa0726770:CDS
ACATATACTTGTCCTTTGGT+GGG 0.584233 5_1:+28156445 None:intergenic
GCTGAATCTGAAAACAAGCA+TGG 0.598695 5_1:-28156552 Msa0726770:CDS
CATTAATATGGACCCACCAA+AGG 0.600842 5_1:-28156457 Msa0726770:CDS
CCATATTAATGAAACTCATG+GGG 0.681211 5_1:+28156469 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATTTCCTTTTAGTTTTA+AGG - chr5_1:28156537-28156556 Msa0726770:CDS 15.0%
!!! TATCTAATGATTTTAAATCG+CGG + chr5_1:28156448-28156467 None:intergenic 20.0%
!! AGTATTACAGTATACAAATT+TGG + chr5_1:28156500-28156519 None:intergenic 20.0%
!! CAAGTATATGTATCTATTTA+TGG - chr5_1:28156794-28156813 Msa0726770:intron 20.0%
! CAACAAACCTTAAAACTAAA+AGG + chr5_1:28156547-28156566 None:intergenic 25.0%
! TCCATATTAATGAAACTCAT+GGG + chr5_1:28156762-28156781 None:intergenic 25.0%
! ATTTATGGCTAAATGTCAAA+TGG - chr5_1:28156809-28156828 Msa0726770:intron 25.0%
AGAAAAACCAAAAACAAGCA+TGG + chr5_1:28156590-28156609 None:intergenic 30.0%
! GGTTTTTCTGTCTTGTAATT+AGG - chr5_1:28156601-28156620 Msa0726770:intron 30.0%
AAGGTAGAGAATGTTGTAAA+AGG - chr5_1:28156647-28156666 Msa0726770:intron 30.0%
AGGTAGAGAATGTTGTAAAA+GGG - chr5_1:28156648-28156667 Msa0726770:intron 30.0%
! AACTTTGAAGAGAATATGGT+TGG - chr5_1:28156717-28156736 Msa0726770:intron 30.0%
CCATATTAATGAAACTCATG+GGG + chr5_1:28156761-28156780 None:intergenic 30.0%
GTCCATATTAATGAAACTCA+TGG + chr5_1:28156763-28156782 None:intergenic 30.0%
AGATACATATACTTGTCCTT+TGG + chr5_1:28156789-28156808 None:intergenic 30.0%
CCAAAAACAAGCATGGAAAT+GGG + chr5_1:28156583-28156602 None:intergenic 35.0%
ACCAAAAACAAGCATGGAAA+TGG + chr5_1:28156584-28156603 None:intergenic 35.0%
GGTAGAGAATGTTGTAAAAG+GGG - chr5_1:28156649-28156668 Msa0726770:intron 35.0%
TCTGAAAACAAGCATGGAAA+TGG - chr5_1:28156681-28156700 Msa0726770:intron 35.0%
AAGAGAATATGGTTGGAGTT+TGG - chr5_1:28156724-28156743 Msa0726770:intron 35.0%
AGAGAATATGGTTGGAGTTT+GGG - chr5_1:28156725-28156744 Msa0726770:intron 35.0%
CCCCATGAGTTTCATTAATA+TGG - chr5_1:28156758-28156777 Msa0726770:intron 35.0%
ACATATACTTGTCCTTTGGT+GGG + chr5_1:28156785-28156804 None:intergenic 35.0%
TACATATACTTGTCCTTTGG+TGG + chr5_1:28156786-28156805 None:intergenic 35.0%
TTTAAATCGCGGTTGCAGTT+AGG + chr5_1:28156437-28156456 None:intergenic 40.0%
!! CCCATTTCCATGCTTGTTTT+TGG - chr5_1:28156580-28156599 Msa0726770:intron 40.0%
TCTCACACAACACAACTCTA+TGG + chr5_1:28156628-28156647 None:intergenic 40.0%
TAGAGTTGTGTTGTGTGAGA+AGG - chr5_1:28156628-28156647 Msa0726770:intron 40.0%
GCTGAATCTGAAAACAAGCA+TGG - chr5_1:28156675-28156694 Msa0726770:intron 40.0%
! AGCATGGAAATGGACCTTTT+TGG - chr5_1:28156691-28156710 Msa0726770:intron 40.0%
! GCATGGAAATGGACCTTTTT+GGG - chr5_1:28156692-28156711 Msa0726770:intron 40.0%
! CATGGAAATGGACCTTTTTG+GGG - chr5_1:28156693-28156712 Msa0726770:intron 40.0%
TCTTCAAAGTTGCCCCAAAA+AGG + chr5_1:28156708-28156727 None:intergenic 40.0%
! GGGCAACTTTGAAGAGAATA+TGG - chr5_1:28156713-28156732 Msa0726770:intron 40.0%
GAGAATATGGTTGGAGTTTG+GGG - chr5_1:28156726-28156745 Msa0726770:intron 40.0%
CATTAATATGGACCCACCAA+AGG - chr5_1:28156770-28156789 Msa0726770:intron 40.0%
! TATGGTTGGAGTTTGGGGTC+AGG - chr5_1:28156731-28156750 Msa0726770:intron 50.0%
! GGTTGGAGTTTGGGGTCAGG+AGG - chr5_1:28156734-28156753 Msa0726770:intron 60.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 28156410 28156839 28156410 ID=Msa0726770;Name=Msa0726770
chr5_1 mRNA 28156410 28156839 28156410 ID=Msa0726770-mRNA-1;Parent=Msa0726770;Name=Msa0726770-mRNA-1;_AED=0.36;_eAED=0.36;_QI=0|0|0|0.33|0|0|3|0|61
chr5_1 exon 28156835 28156839 28156835 ID=Msa0726770-mRNA-1:exon:9833;Parent=Msa0726770-mRNA-1
chr5_1 exon 28156691 28156697 28156691 ID=Msa0726770-mRNA-1:exon:9832;Parent=Msa0726770-mRNA-1
chr5_1 exon 28156410 28156580 28156410 ID=Msa0726770-mRNA-1:exon:9831;Parent=Msa0726770-mRNA-1
chr5_1 CDS 28156835 28156839 28156835 ID=Msa0726770-mRNA-1:cds;Parent=Msa0726770-mRNA-1
chr5_1 CDS 28156691 28156697 28156691 ID=Msa0726770-mRNA-1:cds;Parent=Msa0726770-mRNA-1
chr5_1 CDS 28156410 28156580 28156410 ID=Msa0726770-mRNA-1:cds;Parent=Msa0726770-mRNA-1
Gene Sequence

>Msa0726770

ATGTTTTTTAAGGGGAGAGCTGAATCTGAAAACAAGCATGGAAATGGACCTTTTTGGGGCAACTTTGAAGAGAATATGGTTGGAGTTTGGGGTCAGGAGGACCCCATGAGTTTCATTAATATGGACCCACCAAAGGACAAGTATATGTATCTATTTATGGCTAAATGTCAAATGGATTCATTG
Protein sequence

>Msa0726770

MFFKGRAESENKHGNGPFWGNFEENMVGVWGQEDPMSFINMDPPKDKYMYLFMAKCQMDSL