AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071847

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071847.t1 MTR_2g035320 96.815 157 5 0 1 157 1 157 9.74e-108 304
MS.gene071847.t1 MTR_2g035190 94.268 157 9 0 1 157 1 157 8.40e-105 296
MS.gene071847.t1 MTR_2g035210 89.809 157 16 0 1 157 1 157 1.27e-100 286
MS.gene071847.t1 MTR_2g035220 86.624 157 21 0 1 157 1 157 1.93e-96 275
MS.gene071847.t1 MTR_6g033450 64.968 157 55 0 1 157 1 157 4.02e-70 209
MS.gene071847.t1 MTR_4g120970 64.968 157 55 0 1 157 1 157 4.02e-70 209
MS.gene071847.t1 MTR_2g035100 63.694 157 57 0 1 157 1 157 8.32e-68 203
MS.gene071847.t1 MTR_2g035105 63.057 157 58 0 1 157 1 157 8.48e-67 200
MS.gene071847.t1 MTR_2g035130 61.783 157 60 0 1 157 1 157 7.74e-66 198
MS.gene071847.t1 MTR_2g035150 61.783 157 60 0 1 157 1 157 2.67e-65 196
MS.gene071847.t1 MTR_2g035320 93.000 100 7 0 58 157 23 122 1.29e-62 188
MS.gene071847.t1 MTR_2g035120 56.051 157 69 0 1 157 1 157 1.60e-59 182
MS.gene071847.t1 MTR_2g035170 45.860 157 85 0 1 157 1 157 6.98e-47 150
MS.gene071847.t1 MTR_4g120950 42.236 161 86 5 1 157 1 158 5.51e-32 112
MS.gene071847.t1 MTR_2g435310 32.051 156 105 1 1 155 1 156 6.73e-30 107
MS.gene071847.t1 MTR_4g120760 33.121 157 104 1 1 156 1 157 5.21e-29 104
MS.gene071847.t1 MTR_4g120760 33.121 157 104 1 1 156 1 157 5.21e-29 104
MS.gene071847.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:+53668687 None:intergenic
CTTCAACAATTTCAACAGTT+TGG 0.243960 2.2:+53668728 None:intergenic
GGATAACTTCTTAATGGTTC+CGG 0.295277 2.2:+53668693 None:intergenic
TTCAACAATTTCAACAGTTT+GGG 0.345097 2.2:+53668729 None:intergenic
TACAGCTTAGTAGGAGGAAC+AGG 0.356588 2.2:-53668138 MS.gene071847:CDS
GTTGAAATTGTTGAAGGAAA+TGG 0.360922 2.2:-53668721 MS.gene071847:CDS
GAAACTAAGGCCAGAGGAAC+TGG 0.366866 2.2:-53667982 MS.gene071847:CDS
TGGGCAGCAGAAATCACCTT+TGG 0.390043 2.2:+53668748 None:intergenic
GATAACTTCTTAATGGTTCC+GGG 0.390267 2.2:+53668694 None:intergenic
AGAGCTTTGTAGAGTTTAGC+TGG 0.394931 2.2:+53668796 None:intergenic
TGCAGTAGATGAGGCAAACT+TGG 0.396721 2.2:-53668169 MS.gene071847:CDS
CTTGATAAGTCCAGTTCCTC+TGG 0.419380 2.2:+53667972 None:intergenic
GGATACAACTACAGCTTAGT+AGG 0.431725 2.2:-53668147 MS.gene071847:CDS
AGATAGAGCTGCATCACCTT+TGG 0.442558 2.2:+53668020 None:intergenic
CTCTTAATTACCTTCAACAA+TGG 0.448029 2.2:+53668672 None:intergenic
GGGCAGCAGAAATCACCTTT+GGG 0.452332 2.2:+53668749 None:intergenic
AAGAAGTTATCCATTGTTGA+AGG 0.479062 2.2:-53668682 MS.gene071847:intron
AAAATTGTGGCTGGCTCTGA+TGG 0.498760 2.2:-53668078 MS.gene071847:CDS
CAAACTGTTGAAATTGTTGA+AGG 0.498891 2.2:-53668727 MS.gene071847:CDS
TAATTTGTGTAGCACAAAGT+TGG 0.501990 2.2:+53668194 None:intergenic
CAGAGGAACTGGACTTATCA+AGG 0.507213 2.2:-53667971 MS.gene071847:CDS
GGACTTATCAAGGCCATTGA+GGG 0.514208 2.2:-53667961 MS.gene071847:CDS
TTTCACTGTAATCTTAGCAA+TGG 0.523574 2.2:+53668050 None:intergenic
CTCTGGCCTTAGTTTCATCA+CGG 0.532674 2.2:+53667989 None:intergenic
TGCAGTCCGTGATGAAACTA+AGG 0.533307 2.2:-53667995 MS.gene071847:CDS
TGCCACGACGTAGCCCTCAA+TGG 0.549026 2.2:+53667948 None:intergenic
TGGACTTATCAAGGCCATTG+AGG 0.572485 2.2:-53667962 MS.gene071847:CDS
CAAATTAGATGCAGTAGATG+AGG 0.587202 2.2:-53668178 MS.gene071847:CDS
ATTGTGGCTGGCTCTGATGG+TGG 0.588345 2.2:-53668075 MS.gene071847:CDS
GCAGTAGATGAGGCAAACTT+GGG 0.598362 2.2:-53668168 MS.gene071847:CDS
GTTGAAGGAAATGGAGGACC+CGG 0.599694 2.2:-53668712 MS.gene071847:CDS
GTAGAGTTTAGCTGGAGCCA+CGG 0.602676 2.2:+53668804 None:intergenic
TGCTGATGAAATCGTCCCAA+AGG 0.606260 2.2:-53668764 MS.gene071847:CDS
CTTAGTAGGAGGAACAGGGT+TGG 0.609437 2.2:-53668133 MS.gene071847:CDS
GAAATTGTTGAAGGAAATGG+AGG 0.626795 2.2:-53668718 MS.gene071847:CDS
TACAACTACAGCTTAGTAGG+AGG 0.637578 2.2:-53668144 MS.gene071847:CDS
GGCCATTGAGGGCTACGTCG+TGG 0.646344 2.2:-53667950 MS.gene071847:CDS
GAGCTGCATCACCTTTGGTG+TGG 0.654393 2.2:+53668025 None:intergenic
ACAGTGAAATACCACACCAA+AGG 0.661287 2.2:-53668036 MS.gene071847:CDS
CGTGATGAAACTAAGGCCAG+AGG 0.688505 2.2:-53667988 MS.gene071847:CDS
TGATGAACATGTCTCAACCG+TGG 0.717160 2.2:-53668821 MS.gene071847:CDS
ACAGCTTAGTAGGAGGAACA+GGG 0.723853 2.2:-53668137 MS.gene071847:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTATATAAATAATTATAA+TGG - chr2.2:53668537-53668556 MS.gene071847:intron 0.0%
!! AAATAAGTTAAATTCATTAT+GGG - chr2.2:53668330-53668349 MS.gene071847:intron 10.0%
!!! TTTGTCAATTTTTAAATAAA+AGG + chr2.2:53668251-53668270 None:intergenic 10.0%
!! AATAAGTTAAATTCATTATG+GGG - chr2.2:53668331-53668350 MS.gene071847:intron 15.0%
!! CAAATAAGTTAAATTCATTA+TGG - chr2.2:53668329-53668348 MS.gene071847:intron 15.0%
!!! GACTTTAAAAAAAATGATTC+AGG - chr2.2:53668433-53668452 MS.gene071847:intron 20.0%
! AACAATGGATAACTTCTTAA+TGG + chr2.2:53668090-53668109 None:intergenic 25.0%
! ATTACATCATTCATTTCTCA+TGG + chr2.2:53668376-53668395 None:intergenic 25.0%
! TGAATTCGAAACAAAAATTG+TGG - chr2.2:53668683-53668702 MS.gene071847:CDS 25.0%
! TTCAACAATTTCAACAGTTT+GGG + chr2.2:53668048-53668067 None:intergenic 25.0%
AAGAAGTTATCCATTGTTGA+AGG - chr2.2:53668092-53668111 MS.gene071847:CDS 30.0%
ATAATTATTAGACATACCCC+TGG + chr2.2:53668350-53668369 None:intergenic 30.0%
CAAACTGTTGAAATTGTTGA+AGG - chr2.2:53668047-53668066 MS.gene071847:CDS 30.0%
CTCTTAATTACCTTCAACAA+TGG + chr2.2:53668105-53668124 None:intergenic 30.0%
CTTCAACAATTTCAACAGTT+TGG + chr2.2:53668049-53668068 None:intergenic 30.0%
GTTGAAATTGTTGAAGGAAA+TGG - chr2.2:53668053-53668072 MS.gene071847:CDS 30.0%
TATAATGGTTGTATTGCAGA+TGG - chr2.2:53668552-53668571 MS.gene071847:intron 30.0%
TGGGGTATGTCTAATAATTA+TGG - chr2.2:53668349-53668368 MS.gene071847:intron 30.0%
TTCAGGTGATTAATGATACT+CGG - chr2.2:53668450-53668469 MS.gene071847:intron 30.0%
TTTCACTGTAATCTTAGCAA+TGG + chr2.2:53668727-53668746 None:intergenic 30.0%
! AGGGGTATGTCTAATAATTA+TGG - chr2.2:53668411-53668430 MS.gene071847:intron 30.0%
! TAATTTGTGTAGCACAAAGT+TGG + chr2.2:53668583-53668602 None:intergenic 30.0%
CAAATTAGATGCAGTAGATG+AGG - chr2.2:53668596-53668615 MS.gene071847:intron 35.0%
GAAATTGTTGAAGGAAATGG+AGG - chr2.2:53668056-53668075 MS.gene071847:CDS 35.0%
GATAACTTCTTAATGGTTCC+GGG + chr2.2:53668083-53668102 None:intergenic 35.0%
GGATAACTTCTTAATGGTTC+CGG + chr2.2:53668084-53668103 None:intergenic 35.0%
TAATACATAAGCTCGTTCCA+GGG - chr2.2:53668392-53668411 MS.gene071847:intron 35.0%
TTCGAAACAAAAATTGTGGC+TGG - chr2.2:53668687-53668706 MS.gene071847:CDS 35.0%
! TACACAATTCTTTGTTGTGC+TGG + chr2.2:53668224-53668243 None:intergenic 35.0%
AATACATAAGCTCGTTCCAG+GGG - chr2.2:53668393-53668412 MS.gene071847:intron 40.0%
ACAGTGAAATACCACACCAA+AGG - chr2.2:53668738-53668757 MS.gene071847:CDS 40.0%
GGATACAACTACAGCTTAGT+AGG - chr2.2:53668627-53668646 MS.gene071847:intron 40.0%
GTAATACATAAGCTCGTTCC+AGG - chr2.2:53668391-53668410 MS.gene071847:intron 40.0%
TACAACTACAGCTTAGTAGG+AGG - chr2.2:53668630-53668649 MS.gene071847:intron 40.0%
! AGAGCTTTGTAGAGTTTAGC+TGG + chr2.2:53667981-53668000 None:intergenic 40.0%
ACAGCTTAGTAGGAGGAACA+GGG - chr2.2:53668637-53668656 MS.gene071847:intron 45.0%
AGATAGAGCTGCATCACCTT+TGG + chr2.2:53668757-53668776 None:intergenic 45.0%
CAGAGGAACTGGACTTATCA+AGG - chr2.2:53668803-53668822 MS.gene071847:CDS 45.0%
CTTGATAAGTCCAGTTCCTC+TGG + chr2.2:53668805-53668824 None:intergenic 45.0%
GCAGTAGATGAGGCAAACTT+GGG - chr2.2:53668606-53668625 MS.gene071847:intron 45.0%
GGACTTATCAAGGCCATTGA+GGG - chr2.2:53668813-53668832 MS.gene071847:CDS 45.0%
GGCGAACTTTGATCAGTTGT+CGG + chr2.2:53668203-53668222 None:intergenic 45.0%
TACAGCTTAGTAGGAGGAAC+AGG - chr2.2:53668636-53668655 MS.gene071847:intron 45.0%
TGATGAACATGTCTCAACCG+TGG - chr2.2:53667953-53667972 MS.gene071847:CDS 45.0%
TGCAGTAGATGAGGCAAACT+TGG - chr2.2:53668605-53668624 MS.gene071847:intron 45.0%
TGCAGTCCGTGATGAAACTA+AGG - chr2.2:53668779-53668798 MS.gene071847:CDS 45.0%
TGCTGATGAAATCGTCCCAA+AGG - chr2.2:53668010-53668029 MS.gene071847:CDS 45.0%
TGGACTTATCAAGGCCATTG+AGG - chr2.2:53668812-53668831 MS.gene071847:CDS 45.0%
!! AAAATTGTGGCTGGCTCTGA+TGG - chr2.2:53668696-53668715 MS.gene071847:CDS 45.0%
!! CTCTGGCCTTAGTTTCATCA+CGG + chr2.2:53668788-53668807 None:intergenic 45.0%
CGTGATGAAACTAAGGCCAG+AGG - chr2.2:53668786-53668805 MS.gene071847:CDS 50.0%
CTTAGTAGGAGGAACAGGGT+TGG - chr2.2:53668641-53668660 MS.gene071847:intron 50.0%
GAAACTAAGGCCAGAGGAAC+TGG - chr2.2:53668792-53668811 MS.gene071847:CDS 50.0%
GGGCAGCAGAAATCACCTTT+GGG + chr2.2:53668028-53668047 None:intergenic 50.0%
GTAGAGTTTAGCTGGAGCCA+CGG + chr2.2:53667973-53667992 None:intergenic 50.0%
GTTGAAGGAAATGGAGGACC+CGG - chr2.2:53668062-53668081 MS.gene071847:CDS 50.0%
TGGGCAGCAGAAATCACCTT+TGG + chr2.2:53668029-53668048 None:intergenic 50.0%
GAGCTGCATCACCTTTGGTG+TGG + chr2.2:53668752-53668771 None:intergenic 55.0%
!! ATTGTGGCTGGCTCTGATGG+TGG - chr2.2:53668699-53668718 MS.gene071847:CDS 55.0%
TGCCACGACGTAGCCCTCAA+TGG + chr2.2:53668829-53668848 None:intergenic 60.0%
GGCCATTGAGGGCTACGTCG+TGG - chr2.2:53668824-53668843 MS.gene071847:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53667933 53668863 53667933 ID=MS.gene071847
chr2.2 mRNA 53667933 53668863 53667933 ID=MS.gene071847.t1;Parent=MS.gene071847
chr2.2 exon 53668683 53668863 53668683 ID=MS.gene071847.t1.exon1;Parent=MS.gene071847.t1
chr2.2 CDS 53668683 53668863 53668683 ID=cds.MS.gene071847.t1;Parent=MS.gene071847.t1
chr2.2 exon 53667933 53668225 53667933 ID=MS.gene071847.t1.exon2;Parent=MS.gene071847.t1
chr2.2 CDS 53667933 53668225 53667933 ID=cds.MS.gene071847.t1;Parent=MS.gene071847.t1
Gene Sequence

>MS.gene071847

ATGGGTGTTTTTACTTTCAATGATGAACATGTCTCAACCGTGGCTCCAGCTAAACTCTACAAAGCTCTTGCAAAAGATGCTGATGAAATCGTCCCAAAGGTGATTTCTGCTGCCCAAACTGTTGAAATTGTTGAAGGAAATGGAGGACCCGGAACCATTAAGAAGTTATCCATTGTTGAAGGTAATTAAGAGCATATACTATGTACAAATATATAATACTTGAGATCAAATGATACATATATAGTGTTCGTGTAAAATTGTTTTACACCGACAACTGATCAAAGTTCGCCAGCACAACAAAGAATTGTGTAACTACCTTTTATTTAAAAATTGACAAACATGATGTGACAAATTAAAGAGTTGTGATTGATTAAATAATTTTGATTAAATGATTCACAAATAAGTTAAATTCATTATGGGGTATGTCTAATAATTATGGACCATGAGAAATGAATGATGTAATACATAAGCTCGTTCCAGGGGTATGTCTAATAATTATGGACTTTAAAAAAAATGATTCAGGTGATTAATGATACTCGGTAAAGTTCAAATCGATCTTTAAACGAAAGAGTTTTTAGTCAAACTTTACTCATATTGAAAAAATAATTATATAAATAATTATAATGGTTGTATTGCAGATGGCAAAACCAACTTTGTGCTACACAAATTAGATGCAGTAGATGAGGCAAACTTGGGATACAACTACAGCTTAGTAGGAGGAACAGGGTTGGATGAAAGTTTAGAGAAAGTTGAATTCGAAACAAAAATTGTGGCTGGCTCTGATGGTGGATCCATTGCTAAGATTACAGTGAAATACCACACCAAAGGTGATGCAGCTCTATCTGATGCAGTCCGTGATGAAACTAAGGCCAGAGGAACTGGACTTATCAAGGCCATTGAGGGCTACGTCGTGGCAAACCCTAATTACTAA
Protein sequence

>MS.gene071847.t1

MGVFTFNDEHVSTVAPAKLYKALAKDADEIVPKVISAAQTVEIVEGNGGPGTIKKLSIVEDGKTNFVLHKLDAVDEANLGYNYSLVGGTGLDESLEKVEFETKIVAGSDGGSIAKITVKYHTKGDAALSDAVRDETKARGTGLIKAIEGYVVANPNY