AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071849

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071849.t1 MTR_2g035320 96.815 157 5 0 1 157 1 157 9.74e-108 304
MS.gene071849.t1 MTR_2g035190 94.268 157 9 0 1 157 1 157 8.40e-105 296
MS.gene071849.t1 MTR_2g035210 89.809 157 16 0 1 157 1 157 1.27e-100 286
MS.gene071849.t1 MTR_2g035220 86.624 157 21 0 1 157 1 157 1.93e-96 275
MS.gene071849.t1 MTR_6g033450 64.968 157 55 0 1 157 1 157 4.02e-70 209
MS.gene071849.t1 MTR_4g120970 64.968 157 55 0 1 157 1 157 4.02e-70 209
MS.gene071849.t1 MTR_2g035100 63.694 157 57 0 1 157 1 157 8.32e-68 203
MS.gene071849.t1 MTR_2g035105 63.057 157 58 0 1 157 1 157 8.48e-67 200
MS.gene071849.t1 MTR_2g035130 61.783 157 60 0 1 157 1 157 7.74e-66 198
MS.gene071849.t1 MTR_2g035150 61.783 157 60 0 1 157 1 157 2.67e-65 196
MS.gene071849.t1 MTR_2g035320 93.000 100 7 0 58 157 23 122 1.29e-62 188
MS.gene071849.t1 MTR_2g035120 56.051 157 69 0 1 157 1 157 1.60e-59 182
MS.gene071849.t1 MTR_2g035170 45.860 157 85 0 1 157 1 157 6.98e-47 150
MS.gene071849.t1 MTR_4g120950 42.236 161 86 5 1 157 1 158 5.51e-32 112
MS.gene071849.t1 MTR_2g435310 32.051 156 105 1 1 155 1 156 6.73e-30 107
MS.gene071849.t1 MTR_4g120760 33.121 157 104 1 1 156 1 157 5.21e-29 104
MS.gene071849.t1 MTR_4g120760 33.121 157 104 1 1 156 1 157 5.21e-29 104
MS.gene071849.t1 MTR_4g120940 61.644 73 28 0 85 157 47 119 5.62e-24 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 42 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAATGGATAACTTCTTAA+TGG 0.186795 2.2:+53636418 None:intergenic
CTTCAACAATTTCAACAGTT+TGG 0.243960 2.2:+53636459 None:intergenic
GGATAACTTCTTAATGGTTC+CGG 0.295277 2.2:+53636424 None:intergenic
TTCAACAATTTCAACAGTTT+GGG 0.345097 2.2:+53636460 None:intergenic
TACAGCTTAGTAGGAGGAAC+AGG 0.356588 2.2:-53635869 MS.gene071849:CDS
GTTGAAATTGTTGAAGGAAA+TGG 0.360922 2.2:-53636452 MS.gene071849:CDS
GAAACTAAGGCCAGAGGAAC+TGG 0.366866 2.2:-53635713 MS.gene071849:CDS
TGGGCAGCAGAAATCACCTT+TGG 0.390043 2.2:+53636479 None:intergenic
GATAACTTCTTAATGGTTCC+GGG 0.390267 2.2:+53636425 None:intergenic
AGAGCTTTGTAGAGTTTAGC+TGG 0.394931 2.2:+53636527 None:intergenic
TGCAGTAGATGAGGCAAACT+TGG 0.396721 2.2:-53635900 MS.gene071849:CDS
CTTGATAAGTCCAGTTCCTC+TGG 0.419380 2.2:+53635703 None:intergenic
GGATACAACTACAGCTTAGT+AGG 0.431725 2.2:-53635878 MS.gene071849:CDS
AGATAGAGCTGCATCACCTT+TGG 0.442558 2.2:+53635751 None:intergenic
CTCTTAATTACCTTCAACAA+TGG 0.448029 2.2:+53636403 None:intergenic
GGGCAGCAGAAATCACCTTT+GGG 0.452332 2.2:+53636480 None:intergenic
AAGAAGTTATCCATTGTTGA+AGG 0.479062 2.2:-53636413 MS.gene071849:intron
AAAATTGTGGCTGGCTCTGA+TGG 0.498760 2.2:-53635809 MS.gene071849:CDS
CAAACTGTTGAAATTGTTGA+AGG 0.498891 2.2:-53636458 MS.gene071849:CDS
TAATTTGTGTAGCACAAAGT+TGG 0.501990 2.2:+53635925 None:intergenic
CAGAGGAACTGGACTTATCA+AGG 0.507213 2.2:-53635702 MS.gene071849:CDS
GGACTTATCAAGGCCATTGA+GGG 0.514208 2.2:-53635692 MS.gene071849:CDS
TTTCACTGTAATCTTAGCAA+TGG 0.523574 2.2:+53635781 None:intergenic
CTCTGGCCTTAGTTTCATCA+CGG 0.532674 2.2:+53635720 None:intergenic
TGCAGTCCGTGATGAAACTA+AGG 0.533307 2.2:-53635726 MS.gene071849:CDS
TGCCACGACGTAGCCCTCAA+TGG 0.549026 2.2:+53635679 None:intergenic
TGGACTTATCAAGGCCATTG+AGG 0.572485 2.2:-53635693 MS.gene071849:CDS
CAAATTAGATGCAGTAGATG+AGG 0.587202 2.2:-53635909 MS.gene071849:CDS
ATTGTGGCTGGCTCTGATGG+TGG 0.588345 2.2:-53635806 MS.gene071849:CDS
GCAGTAGATGAGGCAAACTT+GGG 0.598362 2.2:-53635899 MS.gene071849:CDS
GTTGAAGGAAATGGAGGACC+CGG 0.599694 2.2:-53636443 MS.gene071849:CDS
GTAGAGTTTAGCTGGAGCCA+CGG 0.602676 2.2:+53636535 None:intergenic
TGCTGATGAAATCGTCCCAA+AGG 0.606260 2.2:-53636495 MS.gene071849:CDS
CTTAGTAGGAGGAACAGGGT+TGG 0.609437 2.2:-53635864 MS.gene071849:CDS
GAAATTGTTGAAGGAAATGG+AGG 0.626795 2.2:-53636449 MS.gene071849:CDS
TACAACTACAGCTTAGTAGG+AGG 0.637578 2.2:-53635875 MS.gene071849:CDS
GGCCATTGAGGGCTACGTCG+TGG 0.646344 2.2:-53635681 MS.gene071849:CDS
GAGCTGCATCACCTTTGGTG+TGG 0.654393 2.2:+53635756 None:intergenic
ACAGTGAAATACCACACCAA+AGG 0.661287 2.2:-53635767 MS.gene071849:CDS
CGTGATGAAACTAAGGCCAG+AGG 0.688505 2.2:-53635719 MS.gene071849:CDS
TGATGAACATGTCTCAACCG+TGG 0.717160 2.2:-53636552 MS.gene071849:CDS
ACAGCTTAGTAGGAGGAACA+GGG 0.723853 2.2:-53635868 MS.gene071849:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTATATAAATAATTATAA+TGG - chr2.2:53636268-53636287 MS.gene071849:intron 0.0%
!! AAATAAGTTAAATTCATTAT+GGG - chr2.2:53636061-53636080 MS.gene071849:intron 10.0%
!!! TTTGTCAATTTTTAAATAAA+AGG + chr2.2:53635982-53636001 None:intergenic 10.0%
!! AATAAGTTAAATTCATTATG+GGG - chr2.2:53636062-53636081 MS.gene071849:intron 15.0%
!! CAAATAAGTTAAATTCATTA+TGG - chr2.2:53636060-53636079 MS.gene071849:intron 15.0%
!!! GACTTTAAAAAAAATGATTC+AGG - chr2.2:53636164-53636183 MS.gene071849:intron 20.0%
! AACAATGGATAACTTCTTAA+TGG + chr2.2:53635821-53635840 None:intergenic 25.0%
! ATTACATCATTCATTTCTCA+TGG + chr2.2:53636107-53636126 None:intergenic 25.0%
! TGAATTCGAAACAAAAATTG+TGG - chr2.2:53636414-53636433 MS.gene071849:CDS 25.0%
! TTCAACAATTTCAACAGTTT+GGG + chr2.2:53635779-53635798 None:intergenic 25.0%
AAGAAGTTATCCATTGTTGA+AGG - chr2.2:53635823-53635842 MS.gene071849:CDS 30.0%
ATAATTATTAGACATACCCC+TGG + chr2.2:53636081-53636100 None:intergenic 30.0%
CAAACTGTTGAAATTGTTGA+AGG - chr2.2:53635778-53635797 MS.gene071849:CDS 30.0%
CTCTTAATTACCTTCAACAA+TGG + chr2.2:53635836-53635855 None:intergenic 30.0%
CTTCAACAATTTCAACAGTT+TGG + chr2.2:53635780-53635799 None:intergenic 30.0%
GTTGAAATTGTTGAAGGAAA+TGG - chr2.2:53635784-53635803 MS.gene071849:CDS 30.0%
TATAATGGTTGTATTGCAGA+TGG - chr2.2:53636283-53636302 MS.gene071849:intron 30.0%
TGGGGTATGTCTAATAATTA+TGG - chr2.2:53636080-53636099 MS.gene071849:intron 30.0%
TTCAGGTGATTAATGATACT+CGG - chr2.2:53636181-53636200 MS.gene071849:intron 30.0%
TTTCACTGTAATCTTAGCAA+TGG + chr2.2:53636458-53636477 None:intergenic 30.0%
! AGGGGTATGTCTAATAATTA+TGG - chr2.2:53636142-53636161 MS.gene071849:intron 30.0%
! TAATTTGTGTAGCACAAAGT+TGG + chr2.2:53636314-53636333 None:intergenic 30.0%
CAAATTAGATGCAGTAGATG+AGG - chr2.2:53636327-53636346 MS.gene071849:intron 35.0%
GAAATTGTTGAAGGAAATGG+AGG - chr2.2:53635787-53635806 MS.gene071849:CDS 35.0%
GATAACTTCTTAATGGTTCC+GGG + chr2.2:53635814-53635833 None:intergenic 35.0%
GGATAACTTCTTAATGGTTC+CGG + chr2.2:53635815-53635834 None:intergenic 35.0%
TAATACATAAGCTCGTTCCA+GGG - chr2.2:53636123-53636142 MS.gene071849:intron 35.0%
TTCGAAACAAAAATTGTGGC+TGG - chr2.2:53636418-53636437 MS.gene071849:CDS 35.0%
! TACACAATTCTTTGTTGTGC+TGG + chr2.2:53635955-53635974 None:intergenic 35.0%
AATACATAAGCTCGTTCCAG+GGG - chr2.2:53636124-53636143 MS.gene071849:intron 40.0%
ACAGTGAAATACCACACCAA+AGG - chr2.2:53636469-53636488 MS.gene071849:CDS 40.0%
GGATACAACTACAGCTTAGT+AGG - chr2.2:53636358-53636377 MS.gene071849:intron 40.0%
GTAATACATAAGCTCGTTCC+AGG - chr2.2:53636122-53636141 MS.gene071849:intron 40.0%
TACAACTACAGCTTAGTAGG+AGG - chr2.2:53636361-53636380 MS.gene071849:intron 40.0%
! AGAGCTTTGTAGAGTTTAGC+TGG + chr2.2:53635712-53635731 None:intergenic 40.0%
ACAGCTTAGTAGGAGGAACA+GGG - chr2.2:53636368-53636387 MS.gene071849:intron 45.0%
AGATAGAGCTGCATCACCTT+TGG + chr2.2:53636488-53636507 None:intergenic 45.0%
CAGAGGAACTGGACTTATCA+AGG - chr2.2:53636534-53636553 MS.gene071849:CDS 45.0%
CTTGATAAGTCCAGTTCCTC+TGG + chr2.2:53636536-53636555 None:intergenic 45.0%
GCAGTAGATGAGGCAAACTT+GGG - chr2.2:53636337-53636356 MS.gene071849:intron 45.0%
GGACTTATCAAGGCCATTGA+GGG - chr2.2:53636544-53636563 MS.gene071849:CDS 45.0%
GGCGAACTTTGATCAGTTGT+CGG + chr2.2:53635934-53635953 None:intergenic 45.0%
TACAGCTTAGTAGGAGGAAC+AGG - chr2.2:53636367-53636386 MS.gene071849:intron 45.0%
TGATGAACATGTCTCAACCG+TGG - chr2.2:53635684-53635703 MS.gene071849:CDS 45.0%
TGCAGTAGATGAGGCAAACT+TGG - chr2.2:53636336-53636355 MS.gene071849:intron 45.0%
TGCAGTCCGTGATGAAACTA+AGG - chr2.2:53636510-53636529 MS.gene071849:CDS 45.0%
TGCTGATGAAATCGTCCCAA+AGG - chr2.2:53635741-53635760 MS.gene071849:CDS 45.0%
TGGACTTATCAAGGCCATTG+AGG - chr2.2:53636543-53636562 MS.gene071849:CDS 45.0%
!! AAAATTGTGGCTGGCTCTGA+TGG - chr2.2:53636427-53636446 MS.gene071849:CDS 45.0%
!! CTCTGGCCTTAGTTTCATCA+CGG + chr2.2:53636519-53636538 None:intergenic 45.0%
CGTGATGAAACTAAGGCCAG+AGG - chr2.2:53636517-53636536 MS.gene071849:CDS 50.0%
CTTAGTAGGAGGAACAGGGT+TGG - chr2.2:53636372-53636391 MS.gene071849:intron 50.0%
GAAACTAAGGCCAGAGGAAC+TGG - chr2.2:53636523-53636542 MS.gene071849:CDS 50.0%
GGGCAGCAGAAATCACCTTT+GGG + chr2.2:53635759-53635778 None:intergenic 50.0%
GTAGAGTTTAGCTGGAGCCA+CGG + chr2.2:53635704-53635723 None:intergenic 50.0%
GTTGAAGGAAATGGAGGACC+CGG - chr2.2:53635793-53635812 MS.gene071849:CDS 50.0%
TGGGCAGCAGAAATCACCTT+TGG + chr2.2:53635760-53635779 None:intergenic 50.0%
GAGCTGCATCACCTTTGGTG+TGG + chr2.2:53636483-53636502 None:intergenic 55.0%
!! ATTGTGGCTGGCTCTGATGG+TGG - chr2.2:53636430-53636449 MS.gene071849:CDS 55.0%
TGCCACGACGTAGCCCTCAA+TGG + chr2.2:53636560-53636579 None:intergenic 60.0%
GGCCATTGAGGGCTACGTCG+TGG - chr2.2:53636555-53636574 MS.gene071849:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53635664 53636594 53635664 ID=MS.gene071849
chr2.2 mRNA 53635664 53636594 53635664 ID=MS.gene071849.t1;Parent=MS.gene071849
chr2.2 exon 53636414 53636594 53636414 ID=MS.gene071849.t1.exon1;Parent=MS.gene071849.t1
chr2.2 CDS 53636414 53636594 53636414 ID=cds.MS.gene071849.t1;Parent=MS.gene071849.t1
chr2.2 exon 53635664 53635956 53635664 ID=MS.gene071849.t1.exon2;Parent=MS.gene071849.t1
chr2.2 CDS 53635664 53635956 53635664 ID=cds.MS.gene071849.t1;Parent=MS.gene071849.t1
Gene Sequence

>MS.gene071849

ATGGGTGTTTTTACTTTCAATGATGAACATGTCTCAACCGTGGCTCCAGCTAAACTCTACAAAGCTCTTGCAAAAGATGCTGATGAAATCGTCCCAAAGGTGATTTCTGCTGCCCAAACTGTTGAAATTGTTGAAGGAAATGGAGGACCCGGAACCATTAAGAAGTTATCCATTGTTGAAGGTAATTAAGAGCATATACTATGTACAAATATATAATACTTGAGATCAAATGATACATATATAGTGTTCGTGTAAAATTGTTTTACACCGACAACTGATCAAAGTTCGCCAGCACAACAAAGAATTGTGTAACTACCTTTTATTTAAAAATTGACAAACATGATGTGACAAATTAAAGAGTTGTGATTGATTAAATAATTTTGATTAAATGATTCACAAATAAGTTAAATTCATTATGGGGTATGTCTAATAATTATGGACCATGAGAAATGAATGATGTAATACATAAGCTCGTTCCAGGGGTATGTCTAATAATTATGGACTTTAAAAAAAATGATTCAGGTGATTAATGATACTCGGTAAAGTTCAAATCGATCTTTAAACGAAAGAGTTTTTAGTCAAACTTTACTCATATTGAAAAAATAATTATATAAATAATTATAATGGTTGTATTGCAGATGGCAAAACCAACTTTGTGCTACACAAATTAGATGCAGTAGATGAGGCAAACTTGGGATACAACTACAGCTTAGTAGGAGGAACAGGGTTGGATGAAAGTTTAGAGAAAGTTGAATTCGAAACAAAAATTGTGGCTGGCTCTGATGGTGGATCCATTGCTAAGATTACAGTGAAATACCACACCAAAGGTGATGCAGCTCTATCTGATGCAGTCCGTGATGAAACTAAGGCCAGAGGAACTGGACTTATCAAGGCCATTGAGGGCTACGTCGTGGCAAACCCTAATTACTAA
Protein sequence

>MS.gene071849.t1

MGVFTFNDEHVSTVAPAKLYKALAKDADEIVPKVISAAQTVEIVEGNGGPGTIKKLSIVEDGKTNFVLHKLDAVDEANLGYNYSLVGGTGLDESLEKVEFETKIVAGSDGGSIAKITVKYHTKGDAALSDAVRDETKARGTGLIKAIEGYVVANPNY