AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380015900.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015900.01.T02 MTR_3g079520 97.674 43 1 0 9 51 93 135 3.14e-24 91.7
MsG0380015900.01.T02 MTR_3g479600 97.674 43 1 0 9 51 93 135 3.14e-24 91.7
MsG0380015900.01.T01 MTR_3g079520 93.088 217 15 0 1 217 1 217 1.00e-145 405
MsG0380015900.01.T01 MTR_3g479600 93.088 217 15 0 1 217 1 217 1.00e-145 405
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015900.01.T02 AT2G21530 59.615 52 19 1 9 58 92 143 2.85e-16 70.9
MsG0380015900.01.T01 AT2G21530 63.559 118 43 0 82 199 81 198 1.19e-50 164

Find 51 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATCTTCTTGTTATAGATT+TGG 0.263843 3:-76471840 MsG0380015900.01.T01:CDS
TCTGGGAGTTATATTACTTT+TGG 0.301923 3:-76471752 MsG0380015900.01.T01:intron
AGCATAGTACATTAAGATTA+AGG 0.304338 3:+76471957 None:intergenic
AATGCCAGGGGACACTAATT+TGG 0.313943 3:-76471525 MsG0380015900.01.T01:intron
CAATATGCTTTGTATCAAAA+TGG 0.318784 3:+76471329 None:intergenic
ACTTCTATACCTGTTGCAAC+TGG 0.344018 3:+76472057 None:intergenic
CAAATTATATTGTGATTCTC+TGG 0.352194 3:+76471923 None:intergenic
GCAGAACATGTTTGAGACTT+TGG 0.358567 3:+76472733 None:intergenic
GTAGTTACCACTGTATCTTC+TGG 0.366490 3:-76471770 MsG0380015900.01.T01:CDS
CCATCTCCTATCAAAATGAT+TGG 0.398371 3:+76472262 None:intergenic
CTTTGTGTAGCATTAGTTGT+TGG 0.401469 3:+76472535 None:intergenic
GCATTGGAGTGTAATAAAAT+TGG 0.429187 3:+76472694 None:intergenic
TAATACTCTAGCAACAATAA+TGG 0.429297 3:-76472791 MsG0380015900.01.T01:exon
GCTCATATGAGCTAGCTTTG+TGG 0.429557 3:+76472852 None:intergenic
TTGCTAGAGTATTATTAGCT+TGG 0.439298 3:+76472800 None:intergenic
ATCACTAAATCAGCTTTCTC+TGG 0.443107 3:+76472081 None:intergenic
ATGAATAATAAAGTTACTCT+TGG 0.447349 3:+76472892 None:intergenic
TTGATGCATGTATAGCTCCT+AGG 0.449624 3:+76472569 None:intergenic
ATGAGCTAGCTTTGTGGTGT+TGG 0.455619 3:+76472858 None:intergenic
TTAGTGATCCCAGTTGCAAC+AGG 0.462387 3:-76472066 MsG0380015900.01.T01:intron
TTCAAGGCATATAGGCTTCA+AGG 0.462486 3:-76472236 MsG0380015900.01.T01:CDS
GATGGTGATTCAAGGCATAT+AGG 0.467110 3:-76472244 MsG0380015900.01.T01:CDS
AGCACCAATGGAACATTCAT+TGG 0.469041 3:-76471815 MsG0380015900.01.T01:CDS
GAACATTCATTGGTGACAAA+AGG 0.471831 3:-76471805 MsG0380015900.01.T01:CDS
TAGTTACCACTGTATCTTCT+GGG 0.476442 3:-76471769 MsG0380015900.01.T01:CDS
GATTAAGGAGCTTATTTCAG+TGG 0.479303 3:+76471972 None:intergenic
CAACTAATGCTACACAAAGA+TGG 0.490326 3:-76472531 MsG0380015900.01.T01:CDS
TGATAGGAGATGGTGATTCA+AGG 0.491582 3:-76472252 MsG0380015900.01.T01:intron
ACTCTTGGTTGCGTAGGTCA+TGG 0.502974 3:+76472907 None:intergenic
GAAAGTTACTGAAGTGGCAT+TGG 0.511446 3:+76472678 None:intergenic
GTCACCAATGAATGTTCCAT+TGG 0.522297 3:+76471811 None:intergenic
GAGAAGGCTGCAGATACAGT+TGG 0.528528 3:-76471476 MsG0380015900.01.T01:CDS
AAAGTTACTCTTGGTTGCGT+AGG 0.529441 3:+76472901 None:intergenic
GGTGACAAAAGGCTGAAACC+TGG 0.545814 3:-76471794 MsG0380015900.01.T01:CDS
AGATGGATTCTTGAACCAGT+TGG 0.550406 3:-76472514 MsG0380015900.01.T01:intron
ATAGATTTGGATAGCACCAA+TGG 0.560750 3:-76471827 MsG0380015900.01.T01:CDS
GGCTTCAAGGTTGAGAGACC+AGG 0.565164 3:-76472223 MsG0380015900.01.T01:CDS
GATACAGTGGTAACTACTCC+AGG 0.567838 3:+76471776 None:intergenic
TGTTATACATCCCAAATCAC+AGG 0.568456 3:-76472602 MsG0380015900.01.T01:CDS
CTTCTATACCTGTTGCAACT+GGG 0.577256 3:+76472058 None:intergenic
CAGGTGTGCATGCACGCATT+CGG 0.581165 3:-76471874 MsG0380015900.01.T01:CDS
TGTGTCGAAAATAGAAGAGA+AGG 0.593642 3:-76471492 MsG0380015900.01.T01:CDS
TGTAGCATTAGTTGTTGGAG+TGG 0.594055 3:+76472540 None:intergenic
ACTCTAGCAACAATAATGGA+AGG 0.614859 3:-76472787 MsG0380015900.01.T01:exon
CCAGAAGGTAAAATAGACAA+TGG 0.633140 3:-76471449 MsG0380015900.01.T01:CDS
ATCTAGAATGAAGTCACTGT+AGG 0.636581 3:-76472111 MsG0380015900.01.T01:intron
TGAACTGAAAGTTACTGAAG+TGG 0.650521 3:+76472672 None:intergenic
GATACAGTTGGAGAACCAGA+AGG 0.673218 3:-76471464 MsG0380015900.01.T01:CDS
GAAGTAATTTCATAAGCACC+TGG 0.674584 3:+76472205 None:intergenic
TTGGGATGTATAACACGACC+TGG 0.687791 3:+76472610 None:intergenic
ATAACTCCCAGAAGATACAG+TGG 0.690459 3:+76471763 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAAGTATTTGTTTCAATA+TGG - Chr3:76471870-76471889 MsG0380015900.01.T01:CDS 15.0%
!!! GATTTTAACAATTTTTCAAT+TGG + Chr3:76471741-76471760 None:intergenic 15.0%
!! ACATAATTATTCAACAGAAA+AGG + Chr3:76472505-76472524 None:intergenic 20.0%
!! ATGAATAATAAAGTTACTCT+TGG + Chr3:76471305-76471324 None:intergenic 20.0%
!! TATTTGTAGTAATATCATGA+AGG + Chr3:76471828-76471847 None:intergenic 20.0%
!! TGAAACAAATACTTAAAAAG+TGG + Chr3:76471867-76471886 None:intergenic 20.0%
!! TTCATGATATTACTACAAAT+AGG - Chr3:76471827-76471846 MsG0380015900.01.T01:CDS 20.0%
!! TTTGTAACTGTAAGAAAAAT+AGG + Chr3:76472194-76472213 None:intergenic 20.0%
!!! TATCATTTTGAAATTCTCTT+AGG + Chr3:76472597-76472616 None:intergenic 20.0%
! ACTTAAAAAGTGGTTAATTG+AGG + Chr3:76471857-76471876 None:intergenic 25.0%
! AGCATAGTACATTAAGATTA+AGG + Chr3:76472240-76472259 None:intergenic 25.0%
! ATAATAGCAGAGGTTAAATA+TGG + Chr3:76472648-76472667 None:intergenic 25.0%
! CAAATTATATTGTGATTCTC+TGG + Chr3:76472274-76472293 None:intergenic 25.0%
! CAATATGCTTTGTATCAAAA+TGG + Chr3:76472868-76472887 None:intergenic 25.0%
! CAATATGGTCAATATTAACA+AGG - Chr3:76471885-76471904 MsG0380015900.01.T01:intron 25.0%
! CTCAATCAAGATAAGAAAAA+TGG + Chr3:76471787-76471806 None:intergenic 25.0%
! CTTAAAAAGTGGTTAATTGA+GGG + Chr3:76471856-76471875 None:intergenic 25.0%
! TAATACTCTAGCAACAATAA+TGG - Chr3:76471403-76471422 MsG0380015900.01.T01:exon 25.0%
! TTGAAATTCTCTTAGGAATA+TGG + Chr3:76472590-76472609 None:intergenic 25.0%
!! CAATCTTCTTGTTATAGATT+TGG - Chr3:76472354-76472373 MsG0380015900.01.T01:intron 25.0%
!!! ACAAAACCAATCATTTTGAT+AGG - Chr3:76471926-76471945 MsG0380015900.01.T01:intron 25.0%
CAGAGGTTAAATATGGAATA+GGG + Chr3:76472641-76472660 None:intergenic 30.0%
GCATTGGAGTGTAATAAAAT+TGG + Chr3:76471503-76471522 None:intergenic 30.0%
TATATAACCCTGTTTGTAGA+AGG - Chr3:76472551-76472570 MsG0380015900.01.T01:CDS 30.0%
TTAAGATCCTTCTACAAACA+GGG + Chr3:76472561-76472580 None:intergenic 30.0%
! ATCAGAATCAATGATTTGTG+TGG - Chr3:76472022-76472041 MsG0380015900.01.T01:intron 30.0%
! TCTGGGAGTTATATTACTTT+TGG - Chr3:76472442-76472461 MsG0380015900.01.T01:intron 30.0%
! TGTTTTGTATTTACAGTGTC+AGG - Chr3:76472301-76472320 MsG0380015900.01.T01:intron 30.0%
! TTGCTAGAGTATTATTAGCT+TGG + Chr3:76471397-76471416 None:intergenic 30.0%
! TTTAAGATCCTTCTACAAAC+AGG + Chr3:76472562-76472581 None:intergenic 30.0%
!! AACAAGGTGTTTTATCACTT+TGG - Chr3:76471901-76471920 MsG0380015900.01.T01:intron 30.0%
!!! GAGACTTTGGAATTTTTGTT+AGG + Chr3:76471451-76471470 None:intergenic 30.0%
!!! TTCACTTTTTCCTGTGATTT+GGG + Chr3:76471605-76471624 None:intergenic 30.0%
ATAGATTTGGATAGCACCAA+TGG - Chr3:76472367-76472386 MsG0380015900.01.T01:intron 35.0%
ATCACTAAATCAGCTTTCTC+TGG + Chr3:76472116-76472135 None:intergenic 35.0%
CAACTAATGCTACACAAAGA+TGG - Chr3:76471663-76471682 MsG0380015900.01.T01:intron 35.0%
CCAGAAGGTAAAATAGACAA+TGG - Chr3:76472745-76472764 MsG0380015900.01.T01:CDS 35.0%
CCATCTCCTATCAAAATGAT+TGG + Chr3:76471935-76471954 None:intergenic 35.0%
CTTTGTGTAGCATTAGTTGT+TGG + Chr3:76471662-76471681 None:intergenic 35.0%
GAAGTAATTTCATAAGCACC+TGG + Chr3:76471992-76472011 None:intergenic 35.0%
GATTAAGGAGCTTATTTCAG+TGG + Chr3:76472225-76472244 None:intergenic 35.0%
GCAGAGGTTAAATATGGAAT+AGG + Chr3:76472642-76472661 None:intergenic 35.0%
TAGTTACCACTGTATCTTCT+GGG - Chr3:76472425-76472444 MsG0380015900.01.T01:intron 35.0%
TGAACTGAAAGTTACTGAAG+TGG + Chr3:76471525-76471544 None:intergenic 35.0%
TGTGTCGAAAATAGAAGAGA+AGG - Chr3:76472702-76472721 MsG0380015900.01.T01:CDS 35.0%
TGTTATACATCCCAAATCAC+AGG - Chr3:76471592-76471611 MsG0380015900.01.T01:intron 35.0%
! ACTCTAGCAACAATAATGGA+AGG - Chr3:76471407-76471426 MsG0380015900.01.T01:CDS 35.0%
! AGAAAGTGTAACTAACCAAC+TGG + Chr3:76471698-76471717 None:intergenic 35.0%
! ATCTAGAATGAAGTCACTGT+AGG - Chr3:76472083-76472102 MsG0380015900.01.T01:CDS 35.0%
! CCATTGTCTATTTTACCTTC+TGG + Chr3:76472748-76472767 None:intergenic 35.0%
! GAACATTCATTGGTGACAAA+AGG - Chr3:76472389-76472408 MsG0380015900.01.T01:intron 35.0%
! TCTCTTCTATTTTCGACACA+CGG + Chr3:76472702-76472721 None:intergenic 35.0%
!! CCAATCATTTTGATAGGAGA+TGG - Chr3:76471932-76471951 MsG0380015900.01.T01:intron 35.0%
!!! GTTCACTTTTTCCTGTGATT+TGG + Chr3:76471606-76471625 None:intergenic 35.0%
AAAGTTACTCTTGGTTGCGT+AGG + Chr3:76471296-76471315 None:intergenic 40.0%
ACTTCTATACCTGTTGCAAC+TGG + Chr3:76472140-76472159 None:intergenic 40.0%
AGCACCAATGGAACATTCAT+TGG - Chr3:76472379-76472398 MsG0380015900.01.T01:intron 40.0%
ATAACTCCCAGAAGATACAG+TGG + Chr3:76472434-76472453 None:intergenic 40.0%
CTCTGCTATTATGAATGCCA+GGG - Chr3:76472656-76472675 MsG0380015900.01.T01:CDS 40.0%
CTTCTATACCTGTTGCAACT+GGG + Chr3:76472139-76472158 None:intergenic 40.0%
GAAAGTTACTGAAGTGGCAT+TGG + Chr3:76471519-76471538 None:intergenic 40.0%
GATGGTGATTCAAGGCATAT+AGG - Chr3:76471950-76471969 MsG0380015900.01.T01:intron 40.0%
GTAGTTACCACTGTATCTTC+TGG - Chr3:76472424-76472443 MsG0380015900.01.T01:intron 40.0%
GTCACCAATGAATGTTCCAT+TGG + Chr3:76472386-76472405 None:intergenic 40.0%
TCACAGGAAAAAGTGAACCT+AGG - Chr3:76471608-76471627 MsG0380015900.01.T01:intron 40.0%
TCTGCTATTATGAATGCCAG+GGG - Chr3:76472657-76472676 MsG0380015900.01.T01:CDS 40.0%
TGATAGGAGATGGTGATTCA+AGG - Chr3:76471942-76471961 MsG0380015900.01.T01:intron 40.0%
TGTAGCATTAGTTGTTGGAG+TGG + Chr3:76471657-76471676 None:intergenic 40.0%
TTCAAGGCATATAGGCTTCA+AGG - Chr3:76471958-76471977 MsG0380015900.01.T01:intron 40.0%
TTGATGCATGTATAGCTCCT+AGG + Chr3:76471628-76471647 None:intergenic 40.0%
! AGATGGATTCTTGAACCAGT+TGG - Chr3:76471680-76471699 MsG0380015900.01.T01:intron 40.0%
! GCAGAACATGTTTGAGACTT+TGG + Chr3:76471464-76471483 None:intergenic 40.0%
!!! TGCTTTCTTTTTCAGCAACC+AGG - Chr3:76471566-76471585 MsG0380015900.01.T01:intron 40.0%
AATGCCAGGGGACACTAATT+TGG - Chr3:76472669-76472688 MsG0380015900.01.T01:CDS 45.0%
ATAGCCAAATTAGTGTCCCC+TGG + Chr3:76472676-76472695 None:intergenic 45.0%
CCTCTGCTATTATGAATGCC+AGG - Chr3:76472655-76472674 MsG0380015900.01.T01:CDS 45.0%
CCTGGCATTCATAATAGCAG+AGG + Chr3:76472658-76472677 None:intergenic 45.0%
GATACAGTGGTAACTACTCC+AGG + Chr3:76472421-76472440 None:intergenic 45.0%
GATACAGTTGGAGAACCAGA+AGG - Chr3:76472730-76472749 MsG0380015900.01.T01:CDS 45.0%
TTAGTGATCCCAGTTGCAAC+AGG - Chr3:76472128-76472147 MsG0380015900.01.T01:intron 45.0%
TTGGGATGTATAACACGACC+TGG + Chr3:76471587-76471606 None:intergenic 45.0%
!! ATGAGCTAGCTTTGTGGTGT+TGG + Chr3:76471339-76471358 None:intergenic 45.0%
!! GCTCATATGAGCTAGCTTTG+TGG + Chr3:76471345-76471364 None:intergenic 45.0%
ACTCTTGGTTGCGTAGGTCA+TGG + Chr3:76471290-76471309 None:intergenic 50.0%
GAGAAGGCTGCAGATACAGT+TGG - Chr3:76472718-76472737 MsG0380015900.01.T01:CDS 50.0%
GGTGACAAAAGGCTGAAACC+TGG - Chr3:76472400-76472419 MsG0380015900.01.T01:intron 50.0%
CAGGTGTGCATGCACGCATT+CGG - Chr3:76472320-76472339 MsG0380015900.01.T01:intron 55.0%
GGCTTCAAGGTTGAGAGACC+AGG - Chr3:76471971-76471990 MsG0380015900.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
Chr3 gene 76471280 76472936 76471280 ID=MsG0380015900.01;Name=MsG0380015900.01
Chr3 mRNA 76471280 76472936 76471280 ID=MsG0380015900.01.T01;Parent=MsG0380015900.01;Name=MsG0380015900.01.T01;_AED=0.43;_eAED=0.43;_QI=142|1|1|1|0.5|0.6|5|126|228
Chr3 exon 76471280 76471539 76471280 ID=MsG0380015900.01.T01:exon:32039;Parent=MsG0380015900.01.T01
Chr3 exon 76471753 76471899 76471753 ID=MsG0380015900.01.T01:exon:32038;Parent=MsG0380015900.01.T01
Chr3 exon 76472067 76472127 76472067 ID=MsG0380015900.01.T01:exon:32037;Parent=MsG0380015900.01.T01
Chr3 exon 76472204 76472268 76472204 ID=MsG0380015900.01.T01:exon:32036;Parent=MsG0380015900.01.T01
Chr3 exon 76472515 76472936 76472515 ID=MsG0380015900.01.T01:exon:32035;Parent=MsG0380015900.01.T01
Chr3 five_prime_UTR 76472795 76472936 76472795 ID=MsG0380015900.01.T01:five_prime_utr;Parent=MsG0380015900.01.T01
Chr3 CDS 76472515 76472794 76472515 ID=MsG0380015900.01.T01:cds;Parent=MsG0380015900.01.T01
Chr3 CDS 76472204 76472268 76472204 ID=MsG0380015900.01.T01:cds;Parent=MsG0380015900.01.T01
Chr3 CDS 76472067 76472127 76472067 ID=MsG0380015900.01.T01:cds;Parent=MsG0380015900.01.T01
Chr3 CDS 76471753 76471899 76471753 ID=MsG0380015900.01.T01:cds;Parent=MsG0380015900.01.T01
Chr3 CDS 76471406 76471539 76471406 ID=MsG0380015900.01.T01:cds;Parent=MsG0380015900.01.T01
Chr3 three_prime_UTR 76471280 76471405 76471280 ID=MsG0380015900.01.T01:three_prime_utr;Parent=MsG0380015900.01.T01
Chr3 mRNA 76471927 76472296 76471927 ID=MsG0380015900.01.T02;Parent=MsG0380015900.01;Name=MsG0380015900.01.T02;_AED=0.48;_eAED=0.70;_QI=0|1|0|1|1|1|2|0|97
Chr3 exon 76472204 76472296 76472204 ID=MsG0380015900.01.T02:exon:32041;Parent=MsG0380015900.01.T02
Chr3 exon 76471927 76472127 76471927 ID=MsG0380015900.01.T02:exon:32040;Parent=MsG0380015900.01.T02
Chr3 CDS 76472204 76472296 76472204 ID=MsG0380015900.01.T02:cds;Parent=MsG0380015900.01.T02
Chr3 CDS 76471927 76472127 76471927 ID=MsG0380015900.01.T02:cds;Parent=MsG0380015900.01.T02
Gene Sequence

>MsG0380015900.01.T02

TTGGAAACAAAACCAATCATTTTGATAGGAGATGGTGATTCAAGGCATATAGGCTTCAAGGTTGAGAGACCAGGTGCTTATGAAATTACTTCTAATGAAGTCACTGTAGGACGTGTTCCAGAGAAAGCTGATTTAGTGATCCCAGTTGCAACAGGTATAGAAGTTCAAGTTAATAAACTGTTGTGTATTTCGATTCCTATTTTTCTTACAGTTACAAACATTTTTTCCACTGAAATAAGCTCCTTAATCTTAATGTACTATGCTTTGTTTATGTTCCAGAGAATCACAATATAA

>MsG0380015900.01.T01

ATGGAAGGCATTGTAAAATCTCTCTACCTAACAAAAATTCCAAAGTCTCAAACATGTTCTGCTTCTCTGTTGAACTCACCAATTTTATTACACTCCAATGCCACTTCAGTAACTTTCAGTTCAGCAACAAATCATCTGCACAAGTGCTTTCTTTTTCAGCAACCAGGTCGTGTTATACATCCCAAATCACAGGAAAAAGTGAACCTAGGAGCTATACATGCATCAAAAGCTACCACTCCAACAACTAATGCTACACAAAGATGGATTCTTGAACCAGTTGGAGATGGTGATTCAAGGCATATAGGCTTCAAGGTTGAGAGACCAGGTGCTTATGAAATTACTTCTAATGAAGTCACTGTAGGACGTGTTCCAGAGAAAGCTGATTTAGTGATCCCAGTTGCAACAGTGTCAGGTGTGCATGCACGCATTCGGATGAAACAAGACAATCTTCTTGTTATAGATTTGGATAGCACCAATGGAACATTCATTGGTGACAAAAGGCTGAAACCTGGAGTAGTTACCACTGTATCTTCTGGGAGTTATATTACTTTTGGGGACACTAATTTGGCTATGTTCCGTGTGTCGAAAATAGAAGAGAAGGCTGCAGATACAGTTGGAGAACCAGAAGGTAAAATAGACAATGGTGACAAATCTGATAGTACTGAAACAAGTTCAACTTCTAGTTGA

Protein sequence

>MsG0380015900.01.T02

LETKPIILIGDGDSRHIGFKVERPGAYEITSNEVTVGRVPEKADLVIPVATGIEVQVNKLLCISIPIFLTVTNIFSTEISSLILMYYALFMFQRITI*

>MsG0380015900.01.T01

MEGIVKSLYLTKIPKSQTCSASLLNSPILLHSNATSVTFSSATNHLHKCFLFQQPGRVIHPKSQEKVNLGAIHASKATTPTTNATQRWILEPVGDGDSRHIGFKVERPGAYEITSNEVTVGRVPEKADLVIPVATVSGVHARIRMKQDNLLVIDLDSTNGTFIGDKRLKPGVVTTVSSGSYITFGDTNLAMFRVSKIEEKAADTVGEPEGKIDNGDKSDSTETSSTSS*