AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66352


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66352.t1 MTR_6g091630 99.174 121 1 0 1 121 1 121 1.12e-84 243
MS.gene66352.t1 MTR_8g101980 96.694 121 4 0 1 121 1 121 1.18e-82 237
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66352.t1 AT5G56710 83.333 114 19 0 8 121 6 119 5.97e-67 197
MS.gene66352.t1 AT4G26230 84.211 114 18 0 8 121 6 119 7.43e-67 197
MS.gene66352.t1 AT2G19740 80.833 120 22 1 2 121 1 119 7.12e-66 195
MS.gene66352.t1 AT5G56710 57.895 114 14 1 8 121 6 85 1.15e-37 122

Find 38 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGATCTCCTTGATAGCTTT+TGG 0.199036 6.4:+63068072 None:intergenic
ATTCCTAAAGAAGAGTTAAA+AGG 0.277484 6.4:-63067868 MS.gene66352:CDS
TAAAGAAGAGTTAAAAGGTT+TGG 0.305277 6.4:-63067863 MS.gene66352:CDS
TCAAGCTGAACAAGGCTATC+TGG 0.323250 6.4:-63068002 MS.gene66352:CDS
AAAGAAGAGTTAAAAGGTTT+GGG 0.335880 6.4:-63067862 MS.gene66352:CDS
GATCAGAAAATTTGCTCAAA+AGG 0.384063 6.4:-63068055 MS.gene66352:CDS
TTGGGACACTTCTGATTCCC+TGG 0.397200 6.4:+63067977 None:intergenic
GAAGTGTCCCAAGGAGGATC+AGG 0.403517 6.4:-63067966 MS.gene66352:CDS
GTCTTCATCATCGATGATCT+TGG 0.459511 6.4:+63067837 None:intergenic
ATGCGTACCCTGATCCTCCT+TGG 0.463330 6.4:+63067958 None:intergenic
AAGATTGAAATTACCATCCA+TGG 0.468912 6.4:+63070053 None:intergenic
GAAGGCACCAAAAGCTATCA+AGG 0.472855 6.4:-63068079 MS.gene66352:CDS
TGCGTACCCTGATCCTCCTT+GGG 0.477887 6.4:+63067959 None:intergenic
GAACAAGGCTATCTGGAGCC+AGG 0.480113 6.4:-63067995 MS.gene66352:CDS
ATGGTGGAGAAGGGTGCAGC+AGG 0.507040 6.4:-63070130 MS.gene66352:CDS
GAGACGCTTGTGGAGATTGA+TGG 0.526766 6.4:+63070075 None:intergenic
GAAGCTGAAAATGGTGGAGA+AGG 0.536786 6.4:-63070140 None:intergenic
AAACAGCACCTTCAAGAAGA+AGG 0.555549 6.4:-63068097 MS.gene66352:intron
AATCTCCACAAGCGTCTCCA+TGG 0.563199 6.4:-63070070 MS.gene66352:CDS
TCCACAAGCGTCTCCATGGA+TGG 0.567901 6.4:-63070066 MS.gene66352:intron
TGCAGCAGGTAGAAAAGAAG+AGG 0.581022 6.4:-63070116 MS.gene66352:CDS
TCTAACATCGTTAGTACCCA+TGG 0.582220 6.4:+63068032 None:intergenic
AAAATTTGCTCAAAAGGCCA+TGG 0.583183 6.4:-63068049 MS.gene66352:CDS
AAAAGAAGAGGTGGTTACAC+GGG 0.584738 6.4:-63070104 MS.gene66352:CDS
GAAAAGAAGAGGTGGTTACA+CGG 0.586191 6.4:-63070105 MS.gene66352:CDS
ACCATCCATGGAGACGCTTG+TGG 0.589153 6.4:+63070065 None:intergenic
GAATTTCAACGACAGTGACA+AGG 0.604839 6.4:+63067887 None:intergenic
AAGCTGAAAATGGTGGAGAA+GGG 0.607163 6.4:-63070139 None:intergenic
AACAAGGCTATCTGGAGCCA+GGG 0.614836 6.4:-63067994 MS.gene66352:CDS
GAATGACGACGAAGATGCAA+AGG 0.619084 6.4:-63067923 MS.gene66352:CDS
AAGTGTCCCAAGGAGGATCA+GGG 0.621071 6.4:-63067965 MS.gene66352:CDS
AAATTTGCTCAAAAGGCCAT+GGG 0.623564 6.4:-63068048 MS.gene66352:CDS
AGTTGATGTCAAGCTGAACA+AGG 0.626602 6.4:-63068010 MS.gene66352:CDS
AGCAGGTAGAAAAGAAGAGG+TGG 0.632837 6.4:-63070113 MS.gene66352:CDS
AGGGAATCAGAAGTGTCCCA+AGG 0.639457 6.4:-63067975 MS.gene66352:CDS
AATTTCAACGACAGTGACAA+GGG 0.644182 6.4:+63067888 None:intergenic
GGGTACGCATTGCTCGCAAG+AGG 0.652748 6.4:-63067945 MS.gene66352:CDS
GAATCAGAAGTGTCCCAAGG+AGG 0.720888 6.4:-63067972 MS.gene66352:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTATAAGTGTTAATTAA+CGG - chr6.4:63068256-63068275 MS.gene66352:intron 10.0%
!!! ATAATCTTTTAAAGAATTAT+GGG + chr6.4:63068338-63068357 None:intergenic 10.0%
!!! TATAATCTTTTAAAGAATTA+TGG + chr6.4:63068339-63068358 None:intergenic 10.0%
!! TTATGTAACACAATAATTAT+GGG + chr6.4:63068563-63068582 None:intergenic 15.0%
!!! TGTTTTAAAAAAAAACATCA+TGG + chr6.4:63068936-63068955 None:intergenic 15.0%
!! AAATGAACAGCATATATTTA+GGG + chr6.4:63069530-63069549 None:intergenic 20.0%
!! ATTAAACTGTTAATCAAAAC+AGG + chr6.4:63069052-63069071 None:intergenic 20.0%
!! CTATTCATGATTTGAAAAAT+CGG - chr6.4:63069659-63069678 MS.gene66352:intron 20.0%
!! CTTATGTAACACAATAATTA+TGG + chr6.4:63068564-63068583 None:intergenic 20.0%
!! TACTAATTTCTGTTTATGTT+TGG - chr6.4:63069825-63069844 MS.gene66352:intron 20.0%
!! TATGTAACACAATAATTATG+GGG + chr6.4:63068562-63068581 None:intergenic 20.0%
!! TTAAACTGTTAATCAAAACA+GGG + chr6.4:63069051-63069070 None:intergenic 20.0%
!! TTGATATTCATATTGTGAAT+TGG + chr6.4:63069689-63069708 None:intergenic 20.0%
!!! TAAGCTATTTCTATTTCAAA+AGG - chr6.4:63068402-63068421 MS.gene66352:intron 20.0%
! AAAGAAGAGTTAAAAGGTTT+GGG - chr6.4:63070102-63070121 MS.gene66352:CDS 25.0%
! ACTAAGTTATTTATCCATAC+AGG + chr6.4:63068096-63068115 None:intergenic 25.0%
! ATGAATTCAAAAACAGCTTA+TGG + chr6.4:63069421-63069440 None:intergenic 25.0%
! ATGTAACACAATAATTATGG+GGG + chr6.4:63068561-63068580 None:intergenic 25.0%
! ATTCCTAAAGAAGAGTTAAA+AGG - chr6.4:63070096-63070115 MS.gene66352:CDS 25.0%
! CAAATGAACAGCATATATTT+AGG + chr6.4:63069531-63069550 None:intergenic 25.0%
! CTAAATATATGCTGTTCATT+TGG - chr6.4:63069529-63069548 MS.gene66352:intron 25.0%
! CTAAGTTATTTATCCATACA+GGG + chr6.4:63068095-63068114 None:intergenic 25.0%
! GTGAGTAAATTAATAGTTTG+TGG - chr6.4:63069551-63069570 MS.gene66352:intron 25.0%
! TAAAATAAGCCAATCTAAAC+AGG + chr6.4:63068232-63068251 None:intergenic 25.0%
! TAAAGAAGAGTTAAAAGGTT+TGG - chr6.4:63070101-63070120 MS.gene66352:CDS 25.0%
! TATGAAAATAAGCTGAATAC+AGG + chr6.4:63068907-63068926 None:intergenic 25.0%
! TTATTTGCATCTAATCCAAA+TGG - chr6.4:63068312-63068331 MS.gene66352:intron 25.0%
! TTTCATGATCTAACTACATT+AGG - chr6.4:63069025-63069044 MS.gene66352:intron 25.0%
!! AGTGATGAAATTGATGATTA+TGG + chr6.4:63068994-63069013 None:intergenic 25.0%
!! CTCAAATAAGCTATTTCAAA+AGG - chr6.4:63069263-63069282 MS.gene66352:intron 25.0%
!! TACACTGTGTTAGATAATTT+TGG - chr6.4:63068455-63068474 MS.gene66352:intron 25.0%
!! TCAATTTTGTAGATCTACTA+GGG - chr6.4:63068776-63068795 MS.gene66352:intron 25.0%
!! TGGATTAGATGCAAATAAAT+AGG + chr6.4:63068310-63068329 None:intergenic 25.0%
!! TTCAATTTTGTAGATCTACT+AGG - chr6.4:63068775-63068794 MS.gene66352:intron 25.0%
!!! AAACCTTTTAACTCTTCTTT+AGG + chr6.4:63070102-63070121 None:intergenic 25.0%
!!! TCCTGTAATATTGTTTTAGT+TGG - chr6.4:63068749-63068768 MS.gene66352:intron 25.0%
!!! TGAGATCAAGTTATTTTTTG+TGG - chr6.4:63069731-63069750 MS.gene66352:intron 25.0%
!!! TGTGGTTTTAATATGAATTG+AGG - chr6.4:63069569-63069588 MS.gene66352:intron 25.0%
AAGATTGAAATTACCATCCA+TGG + chr6.4:63067914-63067933 None:intergenic 30.0%
ATTCTCTAATGGCATAACAT+TGG + chr6.4:63069243-63069262 None:intergenic 30.0%
GAAATAAGCTGAAACAACTT+AGG - chr6.4:63069176-63069195 MS.gene66352:intron 30.0%
GCCAACTAAAACAATATTAC+AGG + chr6.4:63068753-63068772 None:intergenic 30.0%
GCTATGTGTAATTGCATAAT+TGG - chr6.4:63069763-63069782 MS.gene66352:intron 30.0%
TGTCATCAACTGTTTCAATA+AGG + chr6.4:63068875-63068894 None:intergenic 30.0%
TTAAAGAATTATGGGCCATT+TGG + chr6.4:63068330-63068349 None:intergenic 30.0%
! GATCAGAAAATTTGCTCAAA+AGG - chr6.4:63069909-63069928 MS.gene66352:intron 30.0%
! GCATATATTTAGGGTTTGTT+TGG + chr6.4:63069521-63069540 None:intergenic 30.0%
! GCTTATTTGAGATTCTCTAA+TGG + chr6.4:63069254-63069273 None:intergenic 30.0%
! TATTTAGGGTTTGTTTGGAT+AGG + chr6.4:63069516-63069535 None:intergenic 30.0%
! TCAGTTTTCTGTGTTTACAT+TGG - chr6.4:63068695-63068714 MS.gene66352:intron 30.0%
!! CGTTTCAAATTTGTTGATCT+AGG - chr6.4:63068584-63068603 MS.gene66352:intron 30.0%
!! TAATATGAATTGAGGTGTTG+TGG - chr6.4:63069577-63069596 MS.gene66352:intron 30.0%
!!! TGTTTTTTATAAGCGACTCT+TGG - chr6.4:63069143-63069162 MS.gene66352:intron 30.0%
AACACAATAATTATGGGGGA+AGG + chr6.4:63068557-63068576 None:intergenic 35.0%
AATTTCAACGACAGTGACAA+GGG + chr6.4:63070079-63070098 None:intergenic 35.0%
TGTCATTGTTCATAAGTTGC+TGG + chr6.4:63069462-63069481 None:intergenic 35.0%
! AAAATTTGCTCAAAAGGCCA+TGG - chr6.4:63069915-63069934 MS.gene66352:intron 35.0%
! AAATTTGCTCAAAAGGCCAT+GGG - chr6.4:63069916-63069935 MS.gene66352:intron 35.0%
AAAAGAAGAGGTGGTTACAC+GGG - chr6.4:63067860-63067879 MS.gene66352:CDS 40.0%
AAACAGCACCTTCAAGAAGA+AGG - chr6.4:63069867-63069886 MS.gene66352:intron 40.0%
AGCTAAGTGCCTGTTTAGAT+TGG - chr6.4:63068220-63068239 MS.gene66352:intron 40.0%
CTATAGATCTAGACCCTGTA+TGG - chr6.4:63068079-63068098 MS.gene66352:CDS 40.0%
CTATTTGCATAAGCTCCTGT+TGG - chr6.4:63068836-63068855 MS.gene66352:intron 40.0%
GAAAAGAAGAGGTGGTTACA+CGG - chr6.4:63067859-63067878 MS.gene66352:CDS 40.0%
GAATTTCAACGACAGTGACA+AGG + chr6.4:63070080-63070099 None:intergenic 40.0%
GTCTTCATCATCGATGATCT+TGG + chr6.4:63070130-63070149 None:intergenic 40.0%
TCTAACATCGTTAGTACCCA+TGG + chr6.4:63069935-63069954 None:intergenic 40.0%
! AGTTGATGTCAAGCTGAACA+AGG - chr6.4:63069954-63069973 MS.gene66352:intron 40.0%
! ATCTACTAGGGTGTTAGGAT+CGG - chr6.4:63068788-63068807 MS.gene66352:intron 40.0%
! TGTAGATCTACTAGGGTGTT+AGG - chr6.4:63068783-63068802 MS.gene66352:intron 40.0%
! TTCATAAGTTGCTGGCTGTT+TGG + chr6.4:63069454-63069473 None:intergenic 40.0%
!! CTGATCTCCTTGATAGCTTT+TGG + chr6.4:63069895-63069914 None:intergenic 40.0%
!!! TTTTGGTGCCTTCTTCTTGA+AGG + chr6.4:63069878-63069897 None:intergenic 40.0%
AAGCTCCTGTTGGACTGTTT+GGG - chr6.4:63068846-63068865 MS.gene66352:intron 45.0%
AGCAGGTAGAAAAGAAGAGG+TGG - chr6.4:63067851-63067870 MS.gene66352:CDS 45.0%
GAATGACGACGAAGATGCAA+AGG - chr6.4:63070041-63070060 MS.gene66352:intron 45.0%
TAAGCTCCTGTTGGACTGTT+TGG - chr6.4:63068845-63068864 MS.gene66352:intron 45.0%
TCAAGCTGAACAAGGCTATC+TGG - chr6.4:63069962-63069981 MS.gene66352:intron 45.0%
TGCAGCAGGTAGAAAAGAAG+AGG - chr6.4:63067848-63067867 MS.gene66352:CDS 45.0%
!! GAAGGCACCAAAAGCTATCA+AGG - chr6.4:63069885-63069904 MS.gene66352:intron 45.0%
!! TTAATTAAAATTAAAATCAT+GGG + chr6.4:63068049-63068068 None:intergenic 5.0%
!! TTTAATTAAAATTAAAATCA+TGG + chr6.4:63068050-63068069 None:intergenic 5.0%
AAGTGTCCCAAGGAGGATCA+GGG - chr6.4:63069999-63070018 MS.gene66352:intron 50.0%
AATCTCCACAAGCGTCTCCA+TGG - chr6.4:63067894-63067913 MS.gene66352:CDS 50.0%
AGCGACTCTTGGAGAGCTTA+TGG - chr6.4:63069154-63069173 MS.gene66352:intron 50.0%
GAGACGCTTGTGGAGATTGA+TGG + chr6.4:63067892-63067911 None:intergenic 50.0%
TTGGGACACTTCTGATTCCC+TGG + chr6.4:63069990-63070009 None:intergenic 50.0%
! AACAAGGCTATCTGGAGCCA+GGG - chr6.4:63069970-63069989 MS.gene66352:intron 50.0%
! CTAGGGTGTTAGGATCGGTT+TGG - chr6.4:63068793-63068812 MS.gene66352:intron 50.0%
!! AGGGAATCAGAAGTGTCCCA+AGG - chr6.4:63069989-63070008 MS.gene66352:intron 50.0%
!! GAATCAGAAGTGTCCCAAGG+AGG - chr6.4:63069992-63070011 MS.gene66352:intron 50.0%
ACCATCCATGGAGACGCTTG+TGG + chr6.4:63067902-63067921 None:intergenic 55.0%
ATGCGTACCCTGATCCTCCT+TGG + chr6.4:63070009-63070028 None:intergenic 55.0%
GGTCTCCCAAACAGTCCAAC+AGG + chr6.4:63068854-63068873 None:intergenic 55.0%
TCCACAAGCGTCTCCATGGA+TGG - chr6.4:63067898-63067917 MS.gene66352:CDS 55.0%
TGCGTACCCTGATCCTCCTT+GGG + chr6.4:63070008-63070027 None:intergenic 55.0%
! GAACAAGGCTATCTGGAGCC+AGG - chr6.4:63069969-63069988 MS.gene66352:intron 55.0%
! GAAGTGTCCCAAGGAGGATC+AGG - chr6.4:63069998-63070017 MS.gene66352:intron 55.0%
GGGTACGCATTGCTCGCAAG+AGG - chr6.4:63070019-63070038 MS.gene66352:intron 60.0%
! ATGGTGGAGAAGGGTGCAGC+AGG - chr6.4:63067834-63067853 MS.gene66352:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 63067834 63070152 63067834 ID=MS.gene66352
chr6.4 mRNA 63067834 63070152 63067834 ID=MS.gene66352.t1;Parent=MS.gene66352
chr6.4 exon 63070067 63070152 63070067 ID=MS.gene66352.t1.exon1;Parent=MS.gene66352.t1
chr6.4 CDS 63070067 63070152 63070067 ID=cds.MS.gene66352.t1;Parent=MS.gene66352.t1
chr6.4 exon 63067834 63068113 63067834 ID=MS.gene66352.t1.exon2;Parent=MS.gene66352.t1
chr6.4 CDS 63067834 63068113 63067834 ID=cds.MS.gene66352.t1;Parent=MS.gene66352.t1
Gene Sequence

>MS.gene66352

ATGGTGGAGAAGGGTGCAGCAGGTAGAAAAGAAGAGGTGGTTACACGGGAGTATACCATCAATCTCCACAAGCGTCTCCATGGATGGTAATTTCAATCTTTCGATTATTTGCTTCTCATGATTCAACTCTCTGTGTTTCATAGCAAGTCTTGATTCATCATTTTTGTTGTTAATTTCATGATTTAACTGCTAATCAGTAATTTTCTCACTTGCCCATGATTTTAATTTTAATTAAAGTTCAATTTCTATAGATCTAGACCCTGTATGGATAAATAACTTAGTTTGCAGCTTATATTGTAAAGTTAAATTGTTCTTATAAGCGCTTAGTTATAAGCTACTTTTATGACGAGAGAAAAATTAAGTTTAATTGTTTTTTGTAAGTTATAAGCTAAGTGCCTGTTTAGATTGGCTTATTTTATGTTAATTTATAAGTGTTAATTAACGGAAATTATGTTTTGAAAAATACATAAAAGCCTATTTATTTGCATCTAATCCAAATGGCCCATAATTCTTTAAAAGATTATATAAATTATTTTTTACAAGCGTTGTCATGATAAGCGCTTCTATATAAGCTATTTCTATTTCAAAAGGTAATCAAAATTATTGTTTTTTAATAAGCTATACACTGTGTTAGATAATTTTGGAGAGTTTATGAAAAATAGTTGAAAACAACTTGTGCAATAGATGCTCAAATAAGCTTGTTATTCAGTAATTTTCTCACCTTCCCCCATAATTATTGTGTTACATAAGCGTTTCAAATTTGTTGATCTAGGATCTGTTTGTTAAACTATGTTAGATAACATATGAAAAGAAGCTGATAACACGTAATAACATGTAACAAGTAATTTTGACTTTTGTGATTCAGTTTTCTGTGTTTACATTGGAAATTACAACTTATCAGTAATTTTCTCACTTTCCTGTAATATTGTTTTAGTTGGCATTTCAATTTTGTAGATCTACTAGGGTGTTAGGATCGGTTTGGATCGACTTATTTATGCTTATCTATTTGCATAAGCTCCTGTTGGACTGTTTGGGAGACCTTATTGAAACAGTTGATGACATTTTCATAACCTGTATTCAGCTTATTTTCATAATCTCTCCATGATGTTTTTTTTTAAAACAGCTTATAACTACTAATCAGTAATTTTCTCACTTTTCCATAATCATCAATTTCATCACTTTAATTGTTAATTTCATGATCTAACTACATTAGGCCCTGTTTTGATTAACAGTTTAATTTGCAGCTTATAGTATTATAAGTGCTTAGTTATAAGCTATTTTTATAACAAAAGATAAAATAAATTTAAATTGTTTTTTATAAGCGACTCTTGGAGAGCTTATGGAAATAAGCTGAAACAACTTAGGCACAAAGTCATTAGCTGTTTTAATAAGCTCTTACAGTCATTCCAATGTTATGCCATTAGAGAATCTCAAATAAGCTATTTCAAAAGGCTCTAAGTATTTATGCTGTTCATTTGATGTTAATGAGTAAATTATTATAGTTTGTGAACAATGTCATTAGCTGTTTGTGTATGTTATCTGCGAGAACTTATAAAATATGCTGAAAGCAGCTTATGAACAATGCCATAAGCTGTTTTTGAATTCATATATGTTTTTCCAAACAGCCAGCAACTTATGAACAATGACAAAATTTATGTGAGTAAATAAGCTCAAATAAGCCTATCCAAACAAACCCTAAATATATGCTGTTCATTTGGTGAGTAAATTAATAGTTTGTGGTTTTAATATGAATTGAGGTGTTGTGGACTCACAGTTTTTTAGTCATATTGATTTTTGACTTGTTTCTTTTTTACTGTGTATCTTACTATTCATGATTTGAAAAATCGGTATGCCAATTCACAATATGAATATCAATATAAGCTCTGTTTCGTTGCTTTGAGATCAAGTTATTTTTTGTGGATGATTCATGCTATGTGTAATTGCATAATTGGATCTGTTTATAGTTTCTGTAATTGTATAACTAGATCTCTTACTAATTTCTGTTTATGTTTGGTATTTTTTTGTATGTAAAAAAACAGCACCTTCAAGAAGAAGGCACCAAAAGCTATCAAGGAGATCAGAAAATTTGCTCAAAAGGCCATGGGTACTAACGATGTTAGAGTTGATGTCAAGCTGAACAAGGCTATCTGGAGCCAGGGAATCAGAAGTGTCCCAAGGAGGATCAGGGTACGCATTGCTCGCAAGAGGAATGACGACGAAGATGCAAAGGAAGAGTTATACTCCCTTGTCACTGTCGTTGAAATTCCTAAAGAAGAGTTAAAAGGTTTGGGCACCAAGATCATCGATGATGAAGACTGA

Protein sequence

>MS.gene66352.t1

MVEKGAAGRKEEVVTREYTINLHKRLHGCTFKKKAPKAIKEIRKFAQKAMGTNDVRVDVKLNKAIWSQGIRSVPRRIRVRIARKRNDDEDAKEELYSLVTVVEIPKEELKGLGTKIIDDED