AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0274260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0274260 MtrunA17_Chr2g0284621 95.620 137 6 0 1 137 1 137 1.08e-98 279
Msa0274260 MtrunA17_Chr4g0020691 87.591 137 17 0 1 137 1 137 1.51e-89 256
Msa0274260 MtrunA17_Chr8g0371681 54.464 112 48 2 10 119 13 123 2.82e-38 126
Msa0274260 MtrunA17_Chr5g0405631 55.556 108 45 2 10 115 30 136 4.88e-35 118
Msa0274260 MtrunA17_Chr5g0406281 40.179 112 66 1 12 123 75 185 6.14e-27 99.0
Msa0274260 MtrunA17_Chr7g0258361 28.448 116 60 2 18 110 55 170 8.28e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0274260 AT2G21045.1 64.748 139 45 3 1 137 30 166 7.57e-64 192
Msa0274260 AT5G66170.3 44.628 121 64 2 1 119 5 124 1.89e-33 114
Msa0274260 AT2G17850.1 50.000 112 53 2 10 119 32 142 5.40e-33 114
Msa0274260 AT5G66170.2 44.715 123 63 3 1 119 5 126 6.12e-32 110
Msa0274260 AT5G66040.1 46.296 108 57 1 12 119 10 116 4.61e-28 100
Msa0274260 AT4G35770.1 38.983 118 66 2 11 128 71 182 2.78e-26 97.8
Msa0274260 AT2G17850.3 38.889 144 53 3 10 119 32 174 4.45e-26 97.4
Msa0274260 AT2G17850.2 50.588 85 39 2 10 92 32 115 1.18e-23 89.4
Msa0274260 AT5G66170.1 43.878 98 52 2 1 96 5 101 1.36e-23 89.4
Msa0274260 AT4G35770.3 39.785 93 55 1 11 103 71 162 8.93e-19 78.2
Msa0274260 AT4G35770.2 42.353 85 48 1 12 96 72 155 1.74e-18 77.0
Msa0274260 AT4G35770.5 40.541 74 43 1 12 85 72 144 1.73e-14 66.6
Msa0274260 AT5G66040.2 45.763 59 32 0 61 119 3 61 3.86e-13 60.5

Find 30 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTGTTTGGAACATATA+GGG 0.248410 2_3:+6047480 None:intergenic
GCAACTTGGTTAACAAAATC+AGG 0.314294 2_3:+6047306 None:intergenic
AGATATTACCTTCTTCTGTT+TGG 0.320745 2_3:+6047469 None:intergenic
TTTGAACACTTACTCCTTTG+TGG 0.354183 2_3:+6047820 None:intergenic
TGGGTGGACGCTGGATTTGC+AGG 0.388509 2_3:-6046919 Msa0274260:CDS
TTCTTCTGTTTGGAACATAT+AGG 0.391220 2_3:+6047479 None:intergenic
TTAATTCAGGCTTGCAATAG+TGG 0.393156 2_3:-6047165 Msa0274260:intron
AGATGAATGTAATAGATCTT+TGG 0.398666 2_3:+6047683 None:intergenic
AAAGATCTATTACATTCATC+TGG 0.432420 2_3:-6047681 Msa0274260:CDS
TTTGGCAGCATGGACATCTA+AGG 0.433360 2_3:+6047701 None:intergenic
GGGAGGCTATTCTGCGTGGG+TGG 0.453900 2_3:-6046935 Msa0274260:CDS
GTCATAGACTTACTGAATCA+TGG 0.464191 2_3:+6047112 None:intergenic
TATATGTTCCAAACAGAAGA+AGG 0.504174 2_3:-6047477 Msa0274260:intron
CTTCTGTTTGGAACATATAG+GGG 0.513278 2_3:+6047481 None:intergenic
TCTTACATATTGCTGCAACT+TGG 0.515579 2_3:+6047292 None:intergenic
CATTAATAGCATTCTCAACA+TGG 0.531780 2_3:+6047505 None:intergenic
ATTTCAACATATTGTGAACA+TGG 0.543412 2_3:-6046959 Msa0274260:CDS
TATTCTGCGTGGGTGGACGC+TGG 0.551007 2_3:-6046928 Msa0274260:CDS
GTAATAGATCTTTGGCAGCA+TGG 0.556298 2_3:+6047691 None:intergenic
TTTCAACATATTGTGAACAT+GGG 0.587874 2_3:-6046958 Msa0274260:CDS
CATATATATAACATTATGGA+CGG 0.597708 2_3:+6046854 None:intergenic
GTTACAATTATCTTGATGTG+AGG 0.616591 2_3:-6047659 Msa0274260:intron
GAAAATAATGGACTCCACAA+AGG 0.616932 2_3:-6047834 None:intergenic
GAGTGAGGATCACTTAGTTG+TGG 0.619130 2_3:-6047271 Msa0274260:intron
ATTCAGGCTTGCAATAGTGG+AGG 0.624070 2_3:-6047162 Msa0274260:intron
CAACATATTGTGAACATGGG+GGG 0.627212 2_3:-6046955 Msa0274260:CDS
TGAATCATGGAGATCAACGC+AGG 0.638826 2_3:+6047125 None:intergenic
TGCAGCAATATGTAAGAGTG+AGG 0.640119 2_3:-6047286 Msa0274260:CDS
TTCAACATATTGTGAACATG+GGG 0.642487 2_3:-6046957 Msa0274260:CDS
TCAACATATTGTGAACATGG+GGG 0.699731 2_3:-6046956 Msa0274260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATGTAACATAATATTGAA+AGG + chr2_3:6046907-6046926 None:intergenic 15.0%
!! TTTCAATATTATGTTACATA+TGG - chr2_3:6046906-6046925 Msa0274260:CDS 15.0%
!!! TTATGTTCTAGAAAATTAAA+AGG + chr2_3:6047455-6047474 None:intergenic 15.0%
!! ATATGTAACATAATATTGAA+AGG + chr2_3:6046907-6046926 None:intergenic 15.0%
!! TTTCAATATTATGTTACATA+TGG - chr2_3:6046906-6046925 Msa0274260:CDS 15.0%
!!! TTATGTTCTAGAAAATTAAA+AGG + chr2_3:6047455-6047474 None:intergenic 15.0%
!!! CCTAATTCTTTTAAAATTTG+AGG + chr2_3:6047617-6047636 None:intergenic 20.0%
!!! CCTCAAATTTTAAAAGAATT+AGG - chr2_3:6047614-6047633 Msa0274260:intron 20.0%
!!! CCTAATTCTTTTAAAATTTG+AGG + chr2_3:6047617-6047636 None:intergenic 20.0%
!!! CCTCAAATTTTAAAAGAATT+AGG - chr2_3:6047614-6047633 Msa0274260:intron 20.0%
! AGATGAATGTAATAGATCTT+TGG + chr2_3:6047014-6047033 None:intergenic 25.0%
! AAAGATCTATTACATTCATC+TGG - chr2_3:6047013-6047032 Msa0274260:intron 25.0%
! AAATTACAAATGATCGAAGA+AGG + chr2_3:6047092-6047111 None:intergenic 25.0%
!! CGATCATTTGTAATTTTCAA+AGG - chr2_3:6047096-6047115 Msa0274260:intron 25.0%
! ATATGCAAGCATCATAAAAT+AGG - chr2_3:6047479-6047498 Msa0274260:CDS 25.0%
! TAATGGAGTACAATTAATTC+AGG - chr2_3:6047516-6047535 Msa0274260:CDS 25.0%
!! AAAGCATTTGTAATATGATG+TGG - chr2_3:6047701-6047720 Msa0274260:CDS 25.0%
! ATTTCAACATATTGTGAACA+TGG - chr2_3:6047735-6047754 Msa0274260:intron 25.0%
! TTTCAACATATTGTGAACAT+GGG - chr2_3:6047736-6047755 Msa0274260:intron 25.0%
! AGATGAATGTAATAGATCTT+TGG + chr2_3:6047014-6047033 None:intergenic 25.0%
! AAAGATCTATTACATTCATC+TGG - chr2_3:6047013-6047032 Msa0274260:intron 25.0%
! AAATTACAAATGATCGAAGA+AGG + chr2_3:6047092-6047111 None:intergenic 25.0%
!! CGATCATTTGTAATTTTCAA+AGG - chr2_3:6047096-6047115 Msa0274260:intron 25.0%
! ATATGCAAGCATCATAAAAT+AGG - chr2_3:6047479-6047498 Msa0274260:CDS 25.0%
! TAATGGAGTACAATTAATTC+AGG - chr2_3:6047516-6047535 Msa0274260:CDS 25.0%
!! AAAGCATTTGTAATATGATG+TGG - chr2_3:6047701-6047720 Msa0274260:CDS 25.0%
! ATTTCAACATATTGTGAACA+TGG - chr2_3:6047735-6047754 Msa0274260:intron 25.0%
! TTTCAACATATTGTGAACAT+GGG - chr2_3:6047736-6047755 Msa0274260:intron 25.0%
GTTACAATTATCTTGATGTG+AGG - chr2_3:6047035-6047054 Msa0274260:intron 30.0%
TGATGTGAGGTAATTAACAA+AGG - chr2_3:6047048-6047067 Msa0274260:intron 30.0%
AAATGATCGAAGAAGGAAAT+TGG + chr2_3:6047085-6047104 None:intergenic 30.0%
GAAAGAAAATGACTTCAGTT+AGG + chr2_3:6047126-6047145 None:intergenic 30.0%
CATTAATAGCATTCTCAACA+TGG + chr2_3:6047192-6047211 None:intergenic 30.0%
! TCTTCTGTTTGGAACATATA+GGG + chr2_3:6047217-6047236 None:intergenic 30.0%
! TTCTTCTGTTTGGAACATAT+AGG + chr2_3:6047218-6047237 None:intergenic 30.0%
TATATGTTCCAAACAGAAGA+AGG - chr2_3:6047217-6047236 Msa0274260:intron 30.0%
AGATATTACCTTCTTCTGTT+TGG + chr2_3:6047228-6047247 None:intergenic 30.0%
ATGTATTCCAAATGATCAAC+AGG - chr2_3:6047352-6047371 Msa0274260:intron 30.0%
TTCAACATATTGTGAACATG+GGG - chr2_3:6047737-6047756 Msa0274260:intron 30.0%
GTTACAATTATCTTGATGTG+AGG - chr2_3:6047035-6047054 Msa0274260:intron 30.0%
TGATGTGAGGTAATTAACAA+AGG - chr2_3:6047048-6047067 Msa0274260:intron 30.0%
AAATGATCGAAGAAGGAAAT+TGG + chr2_3:6047085-6047104 None:intergenic 30.0%
GAAAGAAAATGACTTCAGTT+AGG + chr2_3:6047126-6047145 None:intergenic 30.0%
CATTAATAGCATTCTCAACA+TGG + chr2_3:6047192-6047211 None:intergenic 30.0%
! TCTTCTGTTTGGAACATATA+GGG + chr2_3:6047217-6047236 None:intergenic 30.0%
! TTCTTCTGTTTGGAACATAT+AGG + chr2_3:6047218-6047237 None:intergenic 30.0%
TATATGTTCCAAACAGAAGA+AGG - chr2_3:6047217-6047236 Msa0274260:intron 30.0%
AGATATTACCTTCTTCTGTT+TGG + chr2_3:6047228-6047247 None:intergenic 30.0%
ATGTATTCCAAATGATCAAC+AGG - chr2_3:6047352-6047371 Msa0274260:intron 30.0%
TTCAACATATTGTGAACATG+GGG - chr2_3:6047737-6047756 Msa0274260:intron 30.0%
TTTGAACACTTACTCCTTTG+TGG + chr2_3:6046877-6046896 None:intergenic 35.0%
!! TTCTTTTGCCCCTTTTGTTT+AGG - chr2_3:6047143-6047162 Msa0274260:CDS 35.0%
TCAACTGACCTAAACAAAAG+GGG + chr2_3:6047154-6047173 None:intergenic 35.0%
CTCAACTGACCTAAACAAAA+GGG + chr2_3:6047155-6047174 None:intergenic 35.0%
! CTTCTGTTTGGAACATATAG+GGG + chr2_3:6047216-6047235 None:intergenic 35.0%
ATTCCAAATGATCAACAGGA+AGG - chr2_3:6047356-6047375 Msa0274260:intron 35.0%
TTCCAAATGATCAACAGGAA+GGG - chr2_3:6047357-6047376 Msa0274260:intron 35.0%
GCAACTTGGTTAACAAAATC+AGG + chr2_3:6047391-6047410 None:intergenic 35.0%
TCTTACATATTGCTGCAACT+TGG + chr2_3:6047405-6047424 None:intergenic 35.0%
!! AGGTTGATGTGTGACTATAA+TGG - chr2_3:6047499-6047518 Msa0274260:CDS 35.0%
TTAATTCAGGCTTGCAATAG+TGG - chr2_3:6047529-6047548 Msa0274260:CDS 35.0%
GTCATAGACTTACTGAATCA+TGG + chr2_3:6047585-6047604 None:intergenic 35.0%
TAATATGATGTGGTAAACGC+AGG - chr2_3:6047711-6047730 Msa0274260:CDS 35.0%
AATATGATGTGGTAAACGCA+GGG - chr2_3:6047712-6047731 Msa0274260:CDS 35.0%
TCAACATATTGTGAACATGG+GGG - chr2_3:6047738-6047757 Msa0274260:intron 35.0%
TTTGAACACTTACTCCTTTG+TGG + chr2_3:6046877-6046896 None:intergenic 35.0%
!! TTCTTTTGCCCCTTTTGTTT+AGG - chr2_3:6047143-6047162 Msa0274260:CDS 35.0%
TCAACTGACCTAAACAAAAG+GGG + chr2_3:6047154-6047173 None:intergenic 35.0%
CTCAACTGACCTAAACAAAA+GGG + chr2_3:6047155-6047174 None:intergenic 35.0%
! CTTCTGTTTGGAACATATAG+GGG + chr2_3:6047216-6047235 None:intergenic 35.0%
ATTCCAAATGATCAACAGGA+AGG - chr2_3:6047356-6047375 Msa0274260:intron 35.0%
TTCCAAATGATCAACAGGAA+GGG - chr2_3:6047357-6047376 Msa0274260:intron 35.0%
GCAACTTGGTTAACAAAATC+AGG + chr2_3:6047391-6047410 None:intergenic 35.0%
TCTTACATATTGCTGCAACT+TGG + chr2_3:6047405-6047424 None:intergenic 35.0%
!! AGGTTGATGTGTGACTATAA+TGG - chr2_3:6047499-6047518 Msa0274260:CDS 35.0%
TTAATTCAGGCTTGCAATAG+TGG - chr2_3:6047529-6047548 Msa0274260:CDS 35.0%
GTCATAGACTTACTGAATCA+TGG + chr2_3:6047585-6047604 None:intergenic 35.0%
TAATATGATGTGGTAAACGC+AGG - chr2_3:6047711-6047730 Msa0274260:CDS 35.0%
AATATGATGTGGTAAACGCA+GGG - chr2_3:6047712-6047731 Msa0274260:CDS 35.0%
TCAACATATTGTGAACATGG+GGG - chr2_3:6047738-6047757 Msa0274260:intron 35.0%
GTAATAGATCTTTGGCAGCA+TGG + chr2_3:6047006-6047025 None:intergenic 40.0%
CCTCAACTGACCTAAACAAA+AGG + chr2_3:6047156-6047175 None:intergenic 40.0%
!! CCTTTTGTTTAGGTCAGTTG+AGG - chr2_3:6047153-6047172 Msa0274260:CDS 40.0%
TGCAGCAATATGTAAGAGTG+AGG - chr2_3:6047408-6047427 Msa0274260:intron 40.0%
CAACATATTGTGAACATGGG+GGG - chr2_3:6047739-6047758 Msa0274260:intron 40.0%
GTAATAGATCTTTGGCAGCA+TGG + chr2_3:6047006-6047025 None:intergenic 40.0%
CCTCAACTGACCTAAACAAA+AGG + chr2_3:6047156-6047175 None:intergenic 40.0%
!! CCTTTTGTTTAGGTCAGTTG+AGG - chr2_3:6047153-6047172 Msa0274260:CDS 40.0%
TGCAGCAATATGTAAGAGTG+AGG - chr2_3:6047408-6047427 Msa0274260:intron 40.0%
CAACATATTGTGAACATGGG+GGG - chr2_3:6047739-6047758 Msa0274260:intron 40.0%
TTTGGCAGCATGGACATCTA+AGG + chr2_3:6046996-6047015 None:intergenic 45.0%
CACCCTTCCTGTTGATCATT+TGG + chr2_3:6047362-6047381 None:intergenic 45.0%
GAGTGAGGATCACTTAGTTG+TGG - chr2_3:6047423-6047442 Msa0274260:intron 45.0%
ATTCAGGCTTGCAATAGTGG+AGG - chr2_3:6047532-6047551 Msa0274260:CDS 45.0%
TGAATCATGGAGATCAACGC+AGG + chr2_3:6047572-6047591 None:intergenic 45.0%
TTTGGCAGCATGGACATCTA+AGG + chr2_3:6046996-6047015 None:intergenic 45.0%
CACCCTTCCTGTTGATCATT+TGG + chr2_3:6047362-6047381 None:intergenic 45.0%
GAGTGAGGATCACTTAGTTG+TGG - chr2_3:6047423-6047442 Msa0274260:intron 45.0%
ATTCAGGCTTGCAATAGTGG+AGG - chr2_3:6047532-6047551 Msa0274260:CDS 45.0%
TGAATCATGGAGATCAACGC+AGG + chr2_3:6047572-6047591 None:intergenic 45.0%
CATATTGTGAACATGGGGGG+AGG - chr2_3:6047742-6047761 Msa0274260:intron 50.0%
CATATTGTGAACATGGGGGG+AGG - chr2_3:6047742-6047761 Msa0274260:intron 50.0%
!! GCTGTTTTGAGCTCGTCTGC+AGG + chr2_3:6047811-6047830 None:intergenic 55.0%
!! GCTGTTTTGAGCTCGTCTGC+AGG + chr2_3:6047811-6047830 None:intergenic 55.0%
TATTCTGCGTGGGTGGACGC+TGG - chr2_3:6047766-6047785 Msa0274260:intron 60.0%
TGGGTGGACGCTGGATTTGC+AGG - chr2_3:6047775-6047794 Msa0274260:intron 60.0%
TATTCTGCGTGGGTGGACGC+TGG - chr2_3:6047766-6047785 Msa0274260:intron 60.0%
TGGGTGGACGCTGGATTTGC+AGG - chr2_3:6047775-6047794 Msa0274260:intron 60.0%
TGGGGGGAGGCTATTCTGCG+TGG - chr2_3:6047755-6047774 Msa0274260:intron 65.0%
GGGGGGAGGCTATTCTGCGT+GGG - chr2_3:6047756-6047775 Msa0274260:intron 65.0%
GGGAGGCTATTCTGCGTGGG+TGG - chr2_3:6047759-6047778 Msa0274260:intron 65.0%
TGGGGGGAGGCTATTCTGCG+TGG - chr2_3:6047755-6047774 Msa0274260:intron 65.0%
GGGGGGAGGCTATTCTGCGT+GGG - chr2_3:6047756-6047775 Msa0274260:intron 65.0%
GGGAGGCTATTCTGCGTGGG+TGG - chr2_3:6047759-6047778 Msa0274260:intron 65.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 6046867 6047849 6046867 ID=Msa0274260;Name=Msa0274260
chr2_3 mRNA 6046867 6047849 6046867 ID=Msa0274260-mRNA-1;Parent=Msa0274260;Name=Msa0274260-mRNA-1;_AED=0.30;_eAED=0.31;_QI=0|0|0|0.83|1|1|6|0|137
chr2_3 exon 6047833 6047849 6047833 ID=Msa0274260-mRNA-1:exon:2801;Parent=Msa0274260-mRNA-1
chr2_3 exon 6047660 6047740 6047660 ID=Msa0274260-mRNA-1:exon:2800;Parent=Msa0274260-mRNA-1
chr2_3 exon 6047478 6047551 6047478 ID=Msa0274260-mRNA-1:exon:2799;Parent=Msa0274260-mRNA-1
chr2_3 exon 6047272 6047342 6047272 ID=Msa0274260-mRNA-1:exon:2798;Parent=Msa0274260-mRNA-1
chr2_3 exon 6047125 6047178 6047125 ID=Msa0274260-mRNA-1:exon:2797;Parent=Msa0274260-mRNA-1
chr2_3 exon 6046867 6046983 6046867 ID=Msa0274260-mRNA-1:exon:2796;Parent=Msa0274260-mRNA-1
chr2_3 CDS 6047833 6047849 6047833 ID=Msa0274260-mRNA-1:cds;Parent=Msa0274260-mRNA-1
chr2_3 CDS 6047660 6047740 6047660 ID=Msa0274260-mRNA-1:cds;Parent=Msa0274260-mRNA-1
chr2_3 CDS 6047478 6047551 6047478 ID=Msa0274260-mRNA-1:cds;Parent=Msa0274260-mRNA-1
chr2_3 CDS 6047272 6047342 6047272 ID=Msa0274260-mRNA-1:cds;Parent=Msa0274260-mRNA-1
chr2_3 CDS 6047125 6047178 6047125 ID=Msa0274260-mRNA-1:cds;Parent=Msa0274260-mRNA-1
chr2_3 CDS 6046867 6046983 6046867 ID=Msa0274260-mRNA-1:cds;Parent=Msa0274260-mRNA-1
Gene Sequence

>Msa0274260

ATGGACTCCACAAAGGATCATCAAAATGTTGTTACCTTAGATGTCCATGCTGCCAAAGATCTATTACATTCATCTGGTTACAATTATCTTGATGTGAGGTCAGTTGAGGAATTCAATAAAAGCCATGTTGAGAATGCTATTAATGTCCCCTATATGTTCCAAACAGAAGAAGGAAGGGTGAAAAATCCTGATTTTGTTAACCAAGTTGCAGCAATATGTAAGAGTGAGGATCACTTAGTTGTGGCTTGCAATAGTGGAGGAAGATCAAGTCGAGCCTGCGTTGATCTCCATGATTCAGGATTTCAACATATTGTGAACATGGGGGGAGGCTATTCTGCGTGGGTGGACGCTGGATTTGCAGGTGATGACAAGCCTGCAGACGAGCTCAAAACAGCTTGCAAGTTCCGTCCATAA

Protein sequence

>Msa0274260

MDSTKDHQNVVTLDVHAAKDLLHSSGYNYLDVRSVEEFNKSHVENAINVPYMFQTEEGRVKNPDFVNQVAAICKSEDHLVVACNSGGRSSRACVDLHDSGFQHIVNMGGGYSAWVDAGFAGDDKPADELKTACKFRP*