AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0925210

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0925210 MtrunA17_Chr4g0019921 82.456 171 20 1 1 161 1 171 1.41e-100 300
Msa0925210 MtrunA17_Chr8g0355501 81.287 171 22 1 1 161 77 247 4.26e-99 297
Msa0925210 MtrunA17_Chr8g0355431 80.000 165 23 1 1 155 77 241 1.97e-95 277
Msa0925210 MtrunA17_Chr2g0332321 82.456 171 20 1 1 161 170 340 2.18e-95 296
Msa0925210 MtrunA17_Chr3g0087111 69.412 170 39 2 1 160 160 326 3.12e-82 245
Msa0925210 MtrunA17_Chr6g0471851 67.836 171 42 2 1 161 25 192 6.20e-82 241
Msa0925210 MtrunA17_Chr3g0087121 67.836 171 42 2 1 161 25 192 1.43e-80 239
Msa0925210 MtrunA17_Chr6g0467971 64.912 171 47 2 1 161 69 236 2.11e-78 233
Msa0925210 MtrunA17_Chr4g0074241 76.724 116 17 1 1 106 128 243 2.76e-60 187
Msa0925210 MtrunA17_Chr6g0469401 75.893 112 17 1 27 128 1 112 5.74e-56 172
Msa0925210 MtrunA17_Chr8g0358571 76.667 90 11 1 1 80 109 198 1.04e-44 145
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACACTTTCTTTGTGGATT+GGG 0.290896 6_2:+68006385 Msa0925210:CDS
GCACCCTTCACCCACGCTTT+TGG 0.299769 6_2:-68006649 None:intergenic
AACTGGTGCTCACATGTTCT+TGG 0.308087 6_2:+68006775 Msa0925210:CDS
TTGCAACTTTCGAAGTTTGC+AGG 0.338886 6_2:-68006813 None:intergenic
CTTCTAATATGTGCGCATAT+TGG 0.390895 6_2:-68006729 None:intergenic
AGCGGACTTCCACTTCCTAA+TGG 0.393907 6_2:+68006843 Msa0925210:CDS
CTGGGGTATCATCTTATAAC+TGG 0.409514 6_2:+68006758 Msa0925210:CDS
AAAAGTCCACACTTTCTTTG+TGG 0.413967 6_2:+68006379 Msa0925210:CDS
ACTTTGACAAAGAGAACATA+TGG 0.418859 6_2:+68006417 Msa0925210:CDS
TCCACACTTTCTTTGTGGAT+TGG 0.419046 6_2:+68006384 Msa0925210:CDS
CTCTTTCAATGGAAGTACCT+TGG 0.423989 6_2:-68006456 None:intergenic
TGTACATCTTCCTCTTTCAA+TGG 0.427894 6_2:-68006467 None:intergenic
GAATGTTGCATATATGCAAC+TGG 0.434180 6_2:+68006354 None:intergenic
AATATATATTGATCACCATT+AGG 0.440739 6_2:-68006858 None:intergenic
TTAATCTGCTTCCCCGCCAT+TGG 0.441073 6_2:-68006506 None:intergenic
AGGAAGTGGAAGTCCGCTAA+TGG 0.450533 6_2:-68006838 None:intergenic
GTGTATGAGCTTCCAATGGC+GGG 0.469992 6_2:+68006494 Msa0925210:CDS
ACTGGTGCTCACATGTTCTT+GGG 0.481155 6_2:+68006776 Msa0925210:CDS
GAAAGAGGAAGATGTACATA+TGG 0.483357 6_2:+68006472 Msa0925210:CDS
AGATACAAAGCTACTATTAG+TGG 0.497139 6_2:-68006704 None:intergenic
GATACAAAGCTACTATTAGT+GGG 0.506158 6_2:-68006703 None:intergenic
TTATAAGATGATACCCCAGC+TGG 0.526208 6_2:-68006754 None:intergenic
GAAAGTTGCAAATCCATTAG+CGG 0.538378 6_2:+68006825 Msa0925210:CDS
GTTCTTGGGTATATGAAAGA+AGG 0.541111 6_2:+68006790 Msa0925210:CDS
CACATATTAGAAGATCCAGC+TGG 0.543608 6_2:+68006739 Msa0925210:CDS
GAAACCAAAAGCGTGGGTGA+AGG 0.554072 6_2:+68006645 Msa0925210:CDS
TATTGATCACCATTAGGAAG+TGG 0.555102 6_2:-68006852 None:intergenic
CAAGGTACTTCCATTGAAAG+AGG 0.558826 6_2:+68006457 Msa0925210:CDS
AAACCAAAAGCGTGGGTGAA+GGG 0.563573 6_2:+68006646 Msa0925210:CDS
CCCAATCCACAAAGAAAGTG+TGG 0.589593 6_2:-68006385 None:intergenic
ACATATTAGAAGATCCAGCT+GGG 0.592494 6_2:+68006740 Msa0925210:CDS
CACTAGAGAAACCAAAAGCG+TGG 0.593065 6_2:+68006638 Msa0925210:CDS
GGTGTATGAGCTTCCAATGG+CGG 0.622320 6_2:+68006493 Msa0925210:CDS
TATGGTGTATGAGCTTCCAA+TGG 0.654344 6_2:+68006490 Msa0925210:CDS
ACTAGAGAAACCAAAAGCGT+GGG 0.657073 6_2:+68006639 Msa0925210:CDS
TGTATGAGCTTCCAATGGCG+GGG 0.670381 6_2:+68006495 Msa0925210:CDS
GATTGTATTAAGCAAGACCA+AGG 0.690147 6_2:+68006439 Msa0925210:CDS
ATACAAAGCTACTATTAGTG+GGG 0.694074 6_2:-68006702 None:intergenic
CATATTAGAAGATCCAGCTG+GGG 0.720326 6_2:+68006741 Msa0925210:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATATTGATCACCATT+AGG - chr6_2:68006861-68006880 None:intergenic 20.0%
! AAGAGATTGAGGAAAAAATT+AGG + chr6_2:68006556-68006575 Msa0925210:intron 25.0%
!!! TAATTATTCTGCTTTTGTGA+GGG + chr6_2:68006588-68006607 Msa0925210:CDS 25.0%
ACTTTGACAAAGAGAACATA+TGG + chr6_2:68006417-68006436 Msa0925210:CDS 30.0%
AGGAAAAAATTAGGACTGAA+TGG + chr6_2:68006565-68006584 Msa0925210:CDS 30.0%
!! GTAATTATTCTGCTTTTGTG+AGG + chr6_2:68006587-68006606 Msa0925210:CDS 30.0%
ATACAAAGCTACTATTAGTG+GGG - chr6_2:68006705-68006724 None:intergenic 30.0%
GATACAAAGCTACTATTAGT+GGG - chr6_2:68006706-68006725 None:intergenic 30.0%
AGATACAAAGCTACTATTAG+TGG - chr6_2:68006707-68006726 None:intergenic 30.0%
AAAAGTCCACACTTTCTTTG+TGG + chr6_2:68006379-68006398 Msa0925210:CDS 35.0%
GATTGTATTAAGCAAGACCA+AGG + chr6_2:68006439-68006458 Msa0925210:CDS 35.0%
TGTACATCTTCCTCTTTCAA+TGG - chr6_2:68006470-68006489 None:intergenic 35.0%
GAAAGAGGAAGATGTACATA+TGG + chr6_2:68006472-68006491 Msa0925210:CDS 35.0%
CTTCTAATATGTGCGCATAT+TGG - chr6_2:68006732-68006751 None:intergenic 35.0%
ACATATTAGAAGATCCAGCT+GGG + chr6_2:68006740-68006759 Msa0925210:CDS 35.0%
GTTCTTGGGTATATGAAAGA+AGG + chr6_2:68006790-68006809 Msa0925210:CDS 35.0%
GAAAGTTGCAAATCCATTAG+CGG + chr6_2:68006825-68006844 Msa0925210:CDS 35.0%
TATTGATCACCATTAGGAAG+TGG - chr6_2:68006855-68006874 None:intergenic 35.0%
TCCACACTTTCTTTGTGGAT+TGG + chr6_2:68006384-68006403 Msa0925210:CDS 40.0%
CCACACTTTCTTTGTGGATT+GGG + chr6_2:68006385-68006404 Msa0925210:CDS 40.0%
!! CTCTTTCAATGGAAGTACCT+TGG - chr6_2:68006459-68006478 None:intergenic 40.0%
! CAAGGTACTTCCATTGAAAG+AGG + chr6_2:68006457-68006476 Msa0925210:CDS 40.0%
TATGGTGTATGAGCTTCCAA+TGG + chr6_2:68006490-68006509 Msa0925210:CDS 40.0%
GCGGCAAAAAAAAGAGATTG+AGG + chr6_2:68006545-68006564 Msa0925210:intron 40.0%
! TTTTGTGAGGGTGACAGATT+TGG + chr6_2:68006600-68006619 Msa0925210:CDS 40.0%
! ACTAGAGAAACCAAAAGCGT+GGG + chr6_2:68006639-68006658 Msa0925210:CDS 40.0%
CACATATTAGAAGATCCAGC+TGG + chr6_2:68006739-68006758 Msa0925210:CDS 40.0%
CATATTAGAAGATCCAGCTG+GGG + chr6_2:68006741-68006760 Msa0925210:CDS 40.0%
TTATAAGATGATACCCCAGC+TGG - chr6_2:68006757-68006776 None:intergenic 40.0%
! CTGGGGTATCATCTTATAAC+TGG + chr6_2:68006758-68006777 Msa0925210:CDS 40.0%
TTGCAACTTTCGAAGTTTGC+AGG - chr6_2:68006816-68006835 None:intergenic 40.0%
CCCAATCCACAAAGAAAGTG+TGG - chr6_2:68006388-68006407 None:intergenic 45.0%
TAATGTCGATCTCTGCTCTG+CGG + chr6_2:68006526-68006545 Msa0925210:intron 45.0%
CACTAGAGAAACCAAAAGCG+TGG + chr6_2:68006638-68006657 Msa0925210:CDS 45.0%
! AAACCAAAAGCGTGGGTGAA+GGG + chr6_2:68006646-68006665 Msa0925210:CDS 45.0%
AACTGGTGCTCACATGTTCT+TGG + chr6_2:68006775-68006794 Msa0925210:CDS 45.0%
ACTGGTGCTCACATGTTCTT+GGG + chr6_2:68006776-68006795 Msa0925210:CDS 45.0%
GGTGTATGAGCTTCCAATGG+CGG + chr6_2:68006493-68006512 Msa0925210:CDS 50.0%
GTGTATGAGCTTCCAATGGC+GGG + chr6_2:68006494-68006513 Msa0925210:CDS 50.0%
TGTATGAGCTTCCAATGGCG+GGG + chr6_2:68006495-68006514 Msa0925210:CDS 50.0%
TTAATCTGCTTCCCCGCCAT+TGG - chr6_2:68006509-68006528 None:intergenic 50.0%
! GAAACCAAAAGCGTGGGTGA+AGG + chr6_2:68006645-68006664 Msa0925210:CDS 50.0%
AGGAAGTGGAAGTCCGCTAA+TGG - chr6_2:68006841-68006860 None:intergenic 50.0%
! AGCGGACTTCCACTTCCTAA+TGG + chr6_2:68006843-68006862 Msa0925210:CDS 50.0%
! GCACCCTTCACCCACGCTTT+TGG - chr6_2:68006652-68006671 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 68006356 68006891 68006356 ID=Msa0925210;Name=Msa0925210
chr6_2 mRNA 68006356 68006891 68006356 ID=Msa0925210-mRNA-1;Parent=Msa0925210;Name=Msa0925210-mRNA-1;_AED=0.38;_eAED=0.43;_QI=0|0|0|1|0|0.5|2|0|168
chr6_2 exon 68006356 68006529 68006356 ID=Msa0925210-mRNA-1:exon:10782;Parent=Msa0925210-mRNA-1
chr6_2 exon 68006559 68006891 68006559 ID=Msa0925210-mRNA-1:exon:10783;Parent=Msa0925210-mRNA-1
chr6_2 CDS 68006356 68006529 68006356 ID=Msa0925210-mRNA-1:cds;Parent=Msa0925210-mRNA-1
chr6_2 CDS 68006559 68006891 68006559 ID=Msa0925210-mRNA-1:cds;Parent=Msa0925210-mRNA-1
Gene Sequence

>Msa0925210

ATGTTGCATATATGCAACTGGAAAAAAGTCCACACTTTCTTTGTGGATTGGGTTGTTAGAAACTTTGACAAAGAGAACATATGGATTGTATTAAGCAAGACCAAGGTACTTCCATTGAAAGAGGAAGATGTACATATGGTGTATGAGCTTCCAATGGCGGGGAAGCAGATTAATAGATTGAGGAAAAAATTAGGACTGAATGGTAATTATTCTGCTTTTGTGAGGGTGACAGATTTGGAGAGAATATTGAAGACACTAGAGAAACCAAAAGCGTGGGTGAAGGGTGCAATCTGTTTTATCATTCACAAAATTTTGTGCCCCACTAATAGTAGCTTTGTATCTCTCCAATATGCGCACATATTAGAAGATCCAGCTGGGGTATCATCTTATAACTGGTGCTCACATGTTCTTGGGTATATGAAAGAAGGCCTGCAAACTTCGAAAGTTGCAAATCCATTAGCGGACTTCCACTTCCTAATGGTGATCAATATATATTTGTATTTTTAA
Protein sequence

>Msa0925210

MLHICNWKKVHTFFVDWVVRNFDKENIWIVLSKTKVLPLKEEDVHMVYELPMAGKQINRLRKKLGLNGNYSAFVRVTDLERILKTLEKPKAWVKGAICFIIHKILCPTNSSFVSLQYAHILEDPAGVSSYNWCSHVLGYMKEGLQTSKVANPLADFHFLMVINIYLYF*