AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380015970.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015970.01.T01 MTR_3g080670 98.864 88 0 1 1 88 1 87 3.28e-57 171
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015970.01.T01 AT1G61570 59.302 86 33 2 1 85 1 85 1.04e-25 91.3

Find 36 sgRNAs with CRISPR-Local

Find 121 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGACATTATGTATTCTTT+TGG 0.251439 3:+77353702 MsG0380015970.01.T01:three_prime_UTR
CATGAAAGTAGCTCAAGTTT+TGG 0.292088 3:+77353662 MsG0380015970.01.T01:three_prime_UTR
TAAAATAACCGCAAATCTCT+TGG 0.345773 3:-77353753 None:intergenic
TGAGATCTTGTGGAGACAAT+TGG 0.346661 3:-77352097 None:intergenic
ATTAGCAAAGCATTATTTAG+TGG 0.385278 3:+77353606 MsG0380015970.01.T01:CDS
AGCATACTCCATAGCAAGTT+GGG 0.407741 3:-77352135 None:intergenic
AACTGGTCTTTGAGATCTTG+TGG 0.428429 3:-77352107 None:intergenic
GAGATCTTGTGGAGACAATT+GGG 0.444103 3:-77352096 None:intergenic
TAGCAAGTTGGGATTTCAAC+TGG 0.445555 3:-77352124 None:intergenic
TGCCCGTTGCCTCAATATAT+CGG 0.456646 3:-77353581 None:intergenic
AAAATAACCGCAAATCTCTT+GGG 0.462583 3:-77353752 None:intergenic
TTGTATGCCCAAGAGATTTG+CGG 0.473787 3:+77353745 MsG0380015970.01.T01:three_prime_UTR
GTGAAAGCAGTTGCATCTCT+AGG 0.509796 3:+77353550 MsG0380015970.01.T01:CDS
TGGGACGAAGGTCGACTTGG+TGG 0.513010 3:-77352077 None:intergenic
GACCGATATATTGAGGCAAC+GGG 0.513951 3:+77353579 MsG0380015970.01.T01:CDS
TTTATATATGCTCTGTTAAG+GGG 0.524665 3:+77353802 MsG0380015970.01.T01:three_prime_UTR
GTTGAAATCCCAACTTGCTA+TGG 0.532016 3:+77352127 MsG0380015970.01.T01:CDS
GAGCATACTCCATAGCAAGT+TGG 0.537182 3:-77352136 None:intergenic
GTTAAGGGGATATGCAAGAA+AGG 0.540861 3:+77353816 MsG0380015970.01.T01:three_prime_UTR
AATTGGGACGAAGGTCGACT+TGG 0.556046 3:-77352080 None:intergenic
TTTAGTGGTCAACAATGAAG+TGG 0.564069 3:+77353621 MsG0380015970.01.T01:exon
AAACCAAGTTCAAGCCTAAG+TGG 0.565557 3:+77353525 MsG0380015970.01.T01:CDS
AACCAAGTTCAAGCCTAAGT+GGG 0.569512 3:+77353526 MsG0380015970.01.T01:CDS
CACTTTCCTCTCACTGTCTG+CGG 0.572358 3:-77353483 None:intergenic
GGACCGATATATTGAGGCAA+CGG 0.576037 3:+77353578 MsG0380015970.01.T01:CDS
TGTATTCCGCAGACAGTGAG+AGG 0.592801 3:+77353477 MsG0380015970.01.T01:intron
GTGCGTGGACCGATATATTG+AGG 0.605495 3:+77353572 MsG0380015970.01.T01:CDS
ACCAAGTTCAAGCCTAAGTG+GGG 0.610079 3:+77353527 MsG0380015970.01.T01:CDS
GTATGCTCAACAATTTCTTG+AGG 0.618514 3:+77352151 MsG0380015970.01.T01:CDS
AATGAAGTGGATAACCTCCT+CGG 0.634098 3:+77353634 MsG0380015970.01.T01:exon
TGTGGAGACAATTGGGACGA+AGG 0.637876 3:-77352089 None:intergenic
CAGTTGCATCTCTAGGTGCG+TGG 0.638800 3:+77353557 MsG0380015970.01.T01:CDS
GCTACTTTCATGACTTGCCG+AGG 0.643716 3:-77353651 None:intergenic
ACTTTCATGACTTGCCGAGG+AGG 0.651534 3:-77353648 None:intergenic
AATTGATTAAATCTATAAGG+CGG 0.657771 3:-77353861 None:intergenic
CCAAGTTCAAGCCTAAGTGG+GGG 0.696199 3:+77353528 MsG0380015970.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTTATTAAATTGATTAGAAA+TGG + Chr3:77352220-77352239 MsG0380015970.01.T01:intron 15.0%
!!! CTTAATTTGTTAAAATTTCT+CGG + Chr3:77352363-77352382 MsG0380015970.01.T01:intron 15.0%
!! AAATAAGTTGTTTATCCAAA+TGG + Chr3:77352444-77352463 MsG0380015970.01.T01:intron 20.0%
!! AATTGATTAAATCTATAAGG+CGG - Chr3:77353864-77353883 None:intergenic 20.0%
!! ATGTTCAAAAAACAAATCAA+TGG - Chr3:77353197-77353216 None:intergenic 20.0%
!! ATTTGAAAGCAATAAATATC+AGG - Chr3:77353256-77353275 None:intergenic 20.0%
!! TAATATAAATAAGTGACTGT+GGG + Chr3:77352387-77352406 MsG0380015970.01.T01:intron 20.0%
!! TTAATATAAATAAGTGACTG+TGG + Chr3:77352386-77352405 MsG0380015970.01.T01:intron 20.0%
!!! AAAGAATTTAGAATTACAAG+TGG - Chr3:77353321-77353340 None:intergenic 20.0%
!!! ATTTCTGTTTTCTTAGTATT+GGG + Chr3:77352620-77352639 MsG0380015970.01.T01:intron 20.0%
!!! CTGTCTTTAAAAGATTAAAA+TGG - Chr3:77352742-77352761 None:intergenic 20.0%
!!! TATTTCTGTTTTCTTAGTAT+TGG + Chr3:77352619-77352638 MsG0380015970.01.T01:intron 20.0%
!!! TTTGACATTATGTATTCTTT+TGG + Chr3:77353702-77353721 MsG0380015970.01.T01:three_prime_UTR 20.0%
!!! TTTTATATATGCTCTGTTAA+GGG + Chr3:77353801-77353820 MsG0380015970.01.T01:three_prime_UTR 20.0%
! GATAGTGAAAATAGTGATTT+AGG + Chr3:77352244-77352263 MsG0380015970.01.T01:intron 25.0%
! GATTGAATACTGAATATGTT+TGG + Chr3:77353452-77353471 MsG0380015970.01.T01:intron 25.0%
! TTATTCTTACCCCATTAAAA+AGG + Chr3:77352991-77353010 MsG0380015970.01.T01:intron 25.0%
! TTTATATATGCTCTGTTAAG+GGG + Chr3:77353802-77353821 MsG0380015970.01.T01:three_prime_UTR 25.0%
!! AATTTAGAATTACAAGTGGA+TGG - Chr3:77353317-77353336 None:intergenic 25.0%
!! ATTAGCAAAGCATTATTTAG+TGG + Chr3:77353606-77353625 MsG0380015970.01.T01:CDS 25.0%
!! ATTTAGAATTACAAGTGGAT+GGG - Chr3:77353316-77353335 None:intergenic 25.0%
!! CTTTTATATATGCTCTGTTA+AGG + Chr3:77353800-77353819 MsG0380015970.01.T01:three_prime_UTR 25.0%
!! TTTCTGTTTTCTTAGTATTG+GGG + Chr3:77352621-77352640 MsG0380015970.01.T01:intron 25.0%
!!! ATTTTGATTTAGACACCATT+TGG - Chr3:77352462-77352481 None:intergenic 25.0%
!!! TGCAATATTTAAGGTTTTAG+AGG - Chr3:77352904-77352923 None:intergenic 25.0%
AAAATAACCGCAAATCTCTT+GGG - Chr3:77353755-77353774 None:intergenic 30.0%
AATTGTGGCTGCAATATTTA+AGG - Chr3:77352913-77352932 None:intergenic 30.0%
ACAAAATTGTCCTTCTATCA+AGG - Chr3:77352678-77352697 None:intergenic 30.0%
ATGTCAATTTAGACTGATGA+TGG + Chr3:77353130-77353149 MsG0380015970.01.T01:intron 30.0%
TAAAATAACCGCAAATCTCT+TGG - Chr3:77353756-77353775 None:intergenic 30.0%
TAACTACGTCTCTTTCTATA+TGG - Chr3:77353164-77353183 None:intergenic 30.0%
TCAAAGAACACTTCTGATTA+TGG - Chr3:77352539-77352558 None:intergenic 30.0%
TGGTGTCTAAATCAAAATCA+AGG + Chr3:77352464-77352483 MsG0380015970.01.T01:intron 30.0%
! AAAATGAAGCATCTTAGTCA+AGG + Chr3:77353352-77353371 MsG0380015970.01.T01:intron 30.0%
! AAATGAAGCATCTTAGTCAA+GGG + Chr3:77353353-77353372 MsG0380015970.01.T01:intron 30.0%
! AAGATCCTTTCATTCTTTTG+TGG + Chr3:77353393-77353412 MsG0380015970.01.T01:intron 30.0%
! ATGAAAGTAGCTCAAGTTTT+GGG + Chr3:77353663-77353682 MsG0380015970.01.T01:three_prime_UTR 30.0%
! GTATTTCTGTTTGTTGAGTT+AGG + Chr3:77352325-77352344 MsG0380015970.01.T01:intron 30.0%
! GTGATTTTCGATTTCAACAA+TGG + Chr3:77352040-77352059 MsG0380015970.01.T01:exon 30.0%
AGCTAATGAGAGATATTCCA+TGG + Chr3:77352705-77352724 MsG0380015970.01.T01:intron 35.0%
AGTGATTTAGGCAAATCAGT+TGG + Chr3:77352256-77352275 MsG0380015970.01.T01:intron 35.0%
AGTTTAGAAAGCAACGGAAT+CGG - Chr3:77352792-77352811 None:intergenic 35.0%
ATAAGTCCTAGGTAATGTCA+TGG + Chr3:77353429-77353448 MsG0380015970.01.T01:intron 35.0%
GCTAATGAGAGATATTCCAT+GGG + Chr3:77352706-77352725 MsG0380015970.01.T01:intron 35.0%
GTATGCTCAACAATTTCTTG+AGG + Chr3:77352151-77352170 MsG0380015970.01.T01:CDS 35.0%
GTCTAAATCAAAATCAAGGC+TGG + Chr3:77352468-77352487 MsG0380015970.01.T01:intron 35.0%
GTGATTTAGGCAAATCAGTT+GGG + Chr3:77352257-77352276 MsG0380015970.01.T01:intron 35.0%
TAAGTCCTAGGTAATGTCAT+GGG + Chr3:77353430-77353449 MsG0380015970.01.T01:intron 35.0%
TCACACCACAAAAGAATGAA+AGG - Chr3:77353401-77353420 None:intergenic 35.0%
TGATGAGACATTCTAATCTG+TGG + Chr3:77353032-77353051 MsG0380015970.01.T01:intron 35.0%
TGCTACTGTCAATGTAGATT+GGG + Chr3:77353094-77353113 MsG0380015970.01.T01:intron 35.0%
TTAATCCACAGCTACAATTG+TGG - Chr3:77352928-77352947 None:intergenic 35.0%
TTGCTACTGTCAATGTAGAT+TGG + Chr3:77353093-77353112 MsG0380015970.01.T01:intron 35.0%
TTTAGTGGTCAACAATGAAG+TGG + Chr3:77353621-77353640 MsG0380015970.01.T01:exon 35.0%
TTTGTTGAGTTAGGCTGTTT+GGG + Chr3:77352334-77352353 MsG0380015970.01.T01:intron 35.0%
! ACTACCATGCACCTTTTTAA+TGG - Chr3:77353005-77353024 None:intergenic 35.0%
! CATGAAAGTAGCTCAAGTTT+TGG + Chr3:77353662-77353681 MsG0380015970.01.T01:three_prime_UTR 35.0%
! CTACCATGCACCTTTTTAAT+GGG - Chr3:77353004-77353023 None:intergenic 35.0%
! GTGTTGTTAACCTTGATAGA+AGG + Chr3:77352665-77352684 MsG0380015970.01.T01:intron 35.0%
! TACCATGCACCTTTTTAATG+GGG - Chr3:77353003-77353022 None:intergenic 35.0%
! TGTGGTAGTTCTTTTCGTTT+TGG + Chr3:77353050-77353069 MsG0380015970.01.T01:intron 35.0%
!! TGTTTTCTTAGTATTGGGGT+TGG + Chr3:77352625-77352644 MsG0380015970.01.T01:intron 35.0%
!!! AAGTTTTGGGAATCACTTTG+TGG + Chr3:77353676-77353695 MsG0380015970.01.T01:three_prime_UTR 35.0%
AAACCAAGTTCAAGCCTAAG+TGG + Chr3:77353525-77353544 MsG0380015970.01.T01:CDS 40.0%
AAATGGATCCAATCTTCCCA+TGG - Chr3:77352725-77352744 None:intergenic 40.0%
AACCAAGTTCAAGCCTAAGT+GGG + Chr3:77353526-77353545 MsG0380015970.01.T01:CDS 40.0%
AATGAAGTGGATAACCTCCT+CGG + Chr3:77353634-77353653 MsG0380015970.01.T01:exon 40.0%
ACATTGACAGTAGCAACAAC+AGG - Chr3:77353089-77353108 None:intergenic 40.0%
AGCATACTCCATAGCAAGTT+GGG - Chr3:77352138-77352157 None:intergenic 40.0%
AGTCTCTGCAATTGCTTTAG+AGG + Chr3:77353285-77353304 MsG0380015970.01.T01:intron 40.0%
CACAATATTCCACAATCCCA+CGG - Chr3:77352832-77352851 None:intergenic 40.0%
CTGCAACTGTGTTTGCAATT+TGG + Chr3:77352869-77352888 MsG0380015970.01.T01:intron 40.0%
GAGATATTCCATGGGAAGAT+TGG + Chr3:77352714-77352733 MsG0380015970.01.T01:intron 40.0%
GAGATCTTGTGGAGACAATT+GGG - Chr3:77352099-77352118 None:intergenic 40.0%
GCCTAGAGTTTAGAAAGCAA+CGG - Chr3:77352798-77352817 None:intergenic 40.0%
GGCAATCACTTGCAAATACA+AGG - Chr3:77352770-77352789 None:intergenic 40.0%
GTTAAGGGGATATGCAAGAA+AGG + Chr3:77353816-77353835 MsG0380015970.01.T01:three_prime_UTR 40.0%
GTTTAGAAAGCAACGGAATC+GGG - Chr3:77352791-77352810 None:intergenic 40.0%
TCAATCCCATGACATTACCT+AGG - Chr3:77353438-77353457 None:intergenic 40.0%
TGAGATCTTGTGGAGACAAT+TGG - Chr3:77352100-77352119 None:intergenic 40.0%
TTGTATGCCCAAGAGATTTG+CGG + Chr3:77353745-77353764 MsG0380015970.01.T01:three_prime_UTR 40.0%
! ATTCTTTTGTGGTGTGACAC+TGG + Chr3:77353404-77353423 MsG0380015970.01.T01:intron 40.0%
! CAATTTTATCCGTGGGATTG+TGG + Chr3:77352820-77352839 MsG0380015970.01.T01:intron 40.0%
! GTCTCTGCAATTGCTTTAGA+GGG + Chr3:77353286-77353305 MsG0380015970.01.T01:intron 40.0%
! GTGACTGTGGGTTAAGTAAT+TGG + Chr3:77352399-77352418 MsG0380015970.01.T01:intron 40.0%
! GTTTGTTGAGTTAGGCTGTT+TGG + Chr3:77352333-77352352 MsG0380015970.01.T01:intron 40.0%
! TACCCCATTAAAAAGGTGCA+TGG + Chr3:77352998-77353017 MsG0380015970.01.T01:intron 40.0%
! TAGCAAGTTGGGATTTCAAC+TGG - Chr3:77352127-77352146 None:intergenic 40.0%
! TAGGCAGCAATTTTATCCGT+GGG + Chr3:77352813-77352832 MsG0380015970.01.T01:intron 40.0%
! TCCGTTGCTTTCTAAACTCT+AGG + Chr3:77352794-77352813 MsG0380015970.01.T01:intron 40.0%
! TGTGTGAAGGTTTTCTCTCA+AGG + Chr3:77352501-77352520 MsG0380015970.01.T01:intron 40.0%
! TTCTTTTGTGGTGTGACACT+GGG + Chr3:77353405-77353424 MsG0380015970.01.T01:intron 40.0%
! TTTCTTAGTATTGGGGTTGG+AGG + Chr3:77352628-77352647 MsG0380015970.01.T01:intron 40.0%
!! AACTGGTCTTTGAGATCTTG+TGG - Chr3:77352110-77352129 None:intergenic 40.0%
!! GTTGAAATCCCAACTTGCTA+TGG + Chr3:77352127-77352146 MsG0380015970.01.T01:CDS 40.0%
!!! TGGTTTTAGCTCATGTGTGA+AGG + Chr3:77352488-77352507 MsG0380015970.01.T01:intron 40.0%
ACCAAGTTCAAGCCTAAGTG+GGG + Chr3:77353527-77353546 MsG0380015970.01.T01:CDS 45.0%
GACCGATATATTGAGGCAAC+GGG + Chr3:77353579-77353598 MsG0380015970.01.T01:CDS 45.0%
GAGCATACTCCATAGCAAGT+TGG - Chr3:77352139-77352158 None:intergenic 45.0%
GGACCGATATATTGAGGCAA+CGG + Chr3:77353578-77353597 MsG0380015970.01.T01:CDS 45.0%
GTGAAAGCAGTTGCATCTCT+AGG + Chr3:77353550-77353569 MsG0380015970.01.T01:CDS 45.0%
TGCCCGTTGCCTCAATATAT+CGG - Chr3:77353584-77353603 None:intergenic 45.0%
TTGAGTTAGGCTGTTTGGGT+TGG + Chr3:77352338-77352357 MsG0380015970.01.T01:intron 45.0%
! AAAGGTGCATGGTAGTCTTG+AGG + Chr3:77353009-77353028 MsG0380015970.01.T01:intron 45.0%
! CTAGGCAGCAATTTTATCCG+TGG + Chr3:77352812-77352831 MsG0380015970.01.T01:intron 45.0%
! TCTTTTGTGGTGTGACACTG+GGG + Chr3:77353406-77353425 MsG0380015970.01.T01:intron 45.0%
AACTGCTTTCACCCCCACTT+AGG - Chr3:77353542-77353561 None:intergenic 50.0%
AATTGGGACGAAGGTCGACT+TGG - Chr3:77352083-77352102 None:intergenic 50.0%
CACTTTCCTCTCACTGTCTG+CGG - Chr3:77353486-77353505 None:intergenic 50.0%
CCAAGTTCAAGCCTAAGTGG+GGG + Chr3:77353528-77353547 MsG0380015970.01.T01:CDS 50.0%
GGGGTTGGAGGTTGTTACTA+TGG + Chr3:77352640-77352659 MsG0380015970.01.T01:intron 50.0%
GTGCGTGGACCGATATATTG+AGG + Chr3:77353572-77353591 MsG0380015970.01.T01:CDS 50.0%
TGACACTGGGGATAAGTCCT+AGG + Chr3:77353418-77353437 MsG0380015970.01.T01:intron 50.0%
TGCAGCCACAATTGTAGCTG+TGG + Chr3:77352920-77352939 MsG0380015970.01.T01:intron 50.0%
TGTATTCCGCAGACAGTGAG+AGG + Chr3:77353477-77353496 MsG0380015970.01.T01:intron 50.0%
TGTGGAGACAATTGGGACGA+AGG - Chr3:77352092-77352111 None:intergenic 50.0%
! ACTTTCATGACTTGCCGAGG+AGG - Chr3:77353651-77353670 None:intergenic 50.0%
! GCTACTTTCATGACTTGCCG+AGG - Chr3:77353654-77353673 None:intergenic 50.0%
CAGTTGCATCTCTAGGTGCG+TGG + Chr3:77353557-77353576 MsG0380015970.01.T01:CDS 55.0%
CCCCCACTTAGGCTTGAACT+TGG - Chr3:77353531-77353550 None:intergenic 55.0%
!! TGGGACGAAGGTCGACTTGG+TGG - Chr3:77352080-77352099 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 77352022 77353884 77352022 ID=MsG0380015970.01;Name=MsG0380015970.01
Chr3 mRNA 77352022 77353884 77352022 ID=MsG0380015970.01.T01;Parent=MsG0380015970.01;Name=MsG0380015970.01.T01;_AED=0.49;_eAED=0.49;_QI=37|0|0.5|1|0|0|2|246|88
Chr3 exon 77352022 77352172 77352022 ID=MsG0380015970.01.T01:exon:14586;Parent=MsG0380015970.01.T01
Chr3 exon 77353486 77353884 77353486 ID=MsG0380015970.01.T01:exon:14587;Parent=MsG0380015970.01.T01
Chr3 five_prime_UTR 77352022 77352058 77352022 ID=MsG0380015970.01.T01:five_prime_utr;Parent=MsG0380015970.01.T01
Chr3 CDS 77352059 77352172 77352059 ID=MsG0380015970.01.T01:cds;Parent=MsG0380015970.01.T01
Chr3 CDS 77353486 77353638 77353486 ID=MsG0380015970.01.T01:cds;Parent=MsG0380015970.01.T01
Chr3 three_prime_UTR 77353639 77353884 77353639 ID=MsG0380015970.01.T01:three_prime_utr;Parent=MsG0380015970.01.T01
Chr3 mRNA 77353635 77353637 77353635 ID=MsG0380015970.01.T02;Parent=MsG0380015970.01;Name=MsG0380015970.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|1
Chr3 exon 77353635 77353637 77353635 ID=MsG0380015970.01.T02:exon:14588;Parent=MsG0380015970.01.T02
Chr3 CDS 77353635 77353637 77353635 ID=MsG0380015970.01.T02:cds;Parent=MsG0380015970.01.T02
Gene Sequence

>MsG0380015970.01.T02

ATG

>MsG0380015970.01.T01

ATGGATTCATTCTCAGCTCCACCAAGTCGACCTTCGTCCCAATTGTCTCCACAAGATCTCAAAGACCAGTTGAAATCCCAACTTGCTATGGAGTATGCTCAACAATTTCTTGAGCAGACAGTGAGAGGAAAGTGTTTTGACAAGTGTATCACAAAACCAAGTTCAAGCCTAAGTGGGGGTGAAAGCAGTTGCATCTCTAGGTGCGTGGACCGATATATTGAGGCAACGGGCATAATTAGCAAAGCATTATTTAGTGGTCAACAATGA
Protein sequence

>MsG0380015970.01.T02

M

>MsG0380015970.01.T01

MDSFSAPPSRPSSQLSPQDLKDQLKSQLAMEYAQQFLEQTVRGKCFDKCITKPSSSLSGGESSCISRCVDRYIEATGIISKALFSGQQ*