AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0713780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0713780 MtrunA17_Chr5g0400901 93.631 157 10 0 1 157 1 157 3.07e-107 302
Msa0713780 MtrunA17_Chr4g0054291 55.172 174 61 6 1 157 1 174 3.28e-53 166
Msa0713780 MtrunA17_Chr3g0135061 41.085 129 60 3 11 136 16 131 1.17e-16 72.0
Msa0713780 MtrunA17_Chr1g0152241 53.086 81 38 0 60 140 59 139 2.60e-15 68.6
Msa0713780 MtrunA17_Chr7g0225661 40.625 96 50 1 58 153 81 169 1.16e-14 68.2
Msa0713780 MtrunA17_Chr4g0035414 43.210 81 46 0 58 138 27 107 3.91e-14 65.9
Msa0713780 MtrunA17_Chr8g0341311 39.583 96 51 1 58 153 71 159 1.14e-13 65.1
Msa0713780 MtrunA17_Chr3g0144941 37.500 96 52 1 58 145 27 122 3.64e-12 60.5
Msa0713780 MtrunA17_Chr1g0194681 36.667 90 42 2 36 125 8 82 6.97e-12 59.7
Msa0713780 MtrunA17_Chr1g0155551 36.792 106 63 1 36 137 1 106 1.13e-11 59.3
Msa0713780 MtrunA17_Chr8g0378901 42.683 82 39 3 59 136 33 110 1.16e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0713780 AT3G49760.1 38.129 139 85 1 5 142 15 153 2.03e-27 100
Msa0713780 AT4G37730.1 43.609 133 60 3 7 124 135 267 3.23e-19 82.4
Msa0713780 AT2G22850.1 47.059 85 45 0 59 143 127 211 3.13e-18 78.6
Msa0713780 AT2G22850.2 47.059 85 45 0 59 143 127 211 3.13e-18 78.6
Msa0713780 AT3G30530.1 40.000 120 67 2 27 146 49 163 4.82e-15 68.9
Msa0713780 AT1G75390.1 35.833 120 76 1 31 149 10 129 2.87e-13 64.3
Msa0713780 AT2G18160.1 50.820 61 23 1 52 105 15 75 9.12e-13 62.8
Msa0713780 AT1G75390.2 38.384 99 60 1 31 128 10 108 2.27e-12 60.8
Msa0713780 AT1G13600.1 45.679 81 37 1 58 138 83 156 4.56e-12 61.6
Msa0713780 AT4G34590.1 40.000 85 51 0 58 142 24 108 4.82e-12 60.8
Msa0713780 AT2G04038.1 38.835 103 51 2 36 138 54 144 1.79e-11 59.3
Msa0713780 AT4G36730.1 33.628 113 56 2 48 141 194 306 1.85e-11 61.2
Msa0713780 AT4G36730.2 33.628 113 56 2 48 141 192 304 2.05e-11 60.8
Msa0713780 AT5G15830.1 47.945 73 32 1 33 105 52 118 5.36e-11 58.5

Find 52 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGACATCTAGAGAATTTA+CGG 0.286559 5_1:-6221164 Msa0713780:CDS
GGATGGCTCGAACCGGAATA+TGG 0.309967 5_1:-6221253 Msa0713780:CDS
GGGCTGGTGGGTTGGAAGGG+TGG 0.313437 5_1:+6221327 None:intergenic
ATATCATTCTCCTCCGCTTT+CGG 0.329484 5_1:+6221226 None:intergenic
GCAACCCGTTGTTCAATTCC+CGG 0.358900 5_1:+6221112 None:intergenic
CAACCGGAGCCACTCACTTT+CGG 0.360505 5_1:+6221056 None:intergenic
GTGACCTCCGTGCCGATTCC+CGG 0.363167 5_1:+6221199 None:intergenic
TTCTTCTAACTCCGTGAAAT+CGG 0.384933 5_1:+6221383 None:intergenic
GCTTTCGGTCCTCCATATTC+CGG 0.399400 5_1:+6221241 None:intergenic
CTTAGGGCTGGTGGGTTGGA+AGG 0.408872 5_1:+6221323 None:intergenic
ACCGGTTTAGAGTTGAAAAC+CGG 0.409929 5_1:-6221131 Msa0713780:CDS
CCGGTTGGAACGAACCATGC+TGG 0.411515 5_1:-6221040 Msa0713780:CDS
TCTCTATGCCTCCGATTTCA+CGG 0.417032 5_1:-6221394 Msa0713780:CDS
CTCACTTCAAGCTCCGGTTC+AGG 0.426863 5_1:-6221300 Msa0713780:CDS
CCGGAGCTTGAAGTGAGCTT+AGG 0.429061 5_1:+6221306 None:intergenic
AAAACCGGGAATTGAACAAC+GGG 0.452979 5_1:-6221116 Msa0713780:CDS
ATTTACGGAACCAGGTGAAC+CGG 0.455271 5_1:-6221149 Msa0713780:CDS
CCAGCATGGTTCGTTCCAAC+CGG 0.461195 5_1:+6221040 None:intergenic
TGAAGTGAGCTTAGGGCTGG+TGG 0.471435 5_1:+6221314 None:intergenic
CAACTCTAAACCGGTTCACC+TGG 0.478647 5_1:+6221139 None:intergenic
CGGAGCTTGAAGTGAGCTTA+GGG 0.479442 5_1:+6221307 None:intergenic
TTAGGGCTGGTGGGTTGGAA+GGG 0.484445 5_1:+6221324 None:intergenic
CGGTCATGGATGGCTCGAAC+CGG 0.489104 5_1:-6221260 Msa0713780:CDS
CGGTTCGAGCCATCCATGAC+CGG 0.490515 5_1:+6221261 None:intergenic
TTCAACCTTTCTCATCTGCA+TGG 0.491200 5_1:-6220981 Msa0713780:CDS
GGAGGAGAATGATATCAAAC+CGG 0.491685 5_1:-6221218 Msa0713780:CDS
AATGATATCAAACCGGGAAT+CGG 0.493933 5_1:-6221211 Msa0713780:CDS
GAACCGAAAGTGAGTGGCTC+CGG 0.506432 5_1:-6221059 Msa0713780:CDS
TGAGCTTAGGGCTGGTGGGT+TGG 0.515513 5_1:+6221319 None:intergenic
CCTAAGCTCACTTCAAGCTC+CGG 0.518730 5_1:-6221306 Msa0713780:CDS
CGGTTGGAACGAACCATGCT+GGG 0.526524 5_1:-6221039 Msa0713780:CDS
GAAGTGAGCTTAGGGCTGGT+GGG 0.547493 5_1:+6221315 None:intergenic
GGCATAGAGAGAAGAGAGCA+TGG 0.571054 5_1:+6221407 None:intergenic
CATGGCCATGCAGATGAGAA+AGG 0.571565 5_1:+6220976 None:intergenic
GCTTGAAGTGAGCTTAGGGC+TGG 0.571567 5_1:+6221311 None:intergenic
AGAAGAAAGTTTAACGCCGT+GGG 0.579656 5_1:-6221367 Msa0713780:CDS
CCGGTTTAGAGTTGAAAACC+GGG 0.582456 5_1:-6221130 Msa0713780:CDS
TCTAGAGAATTTACGGAACC+AGG 0.588686 5_1:-6221157 Msa0713780:CDS
TAGAAGAAAGTTTAACGCCG+TGG 0.593173 5_1:-6221368 Msa0713780:CDS
CGAAAGTGAGTGGCTCCGGT+TGG 0.593366 5_1:-6221055 Msa0713780:CDS
TATCAAACCGGGAATCGGCA+CGG 0.599707 5_1:-6221206 Msa0713780:CDS
GTCTACGAACCGAAAGTGAG+TGG 0.602935 5_1:-6221065 Msa0713780:CDS
TTCTAACTCCGTGAAATCGG+AGG 0.604958 5_1:+6221386 None:intergenic
GGTCAAAAGTTGTCAAACAT+AGG 0.610074 5_1:-6221018 Msa0713780:CDS
GGAATATGGAGGACCGAAAG+CGG 0.611264 5_1:-6221239 Msa0713780:CDS
GAGGAGAATGATATCAAACC+GGG 0.616694 5_1:-6221217 Msa0713780:CDS
TCAGCTGTGACAATATTGCA+TGG 0.636378 5_1:+6220958 None:intergenic
GTCAAACATAGGTCAAAACA+TGG 0.654401 5_1:-6221007 Msa0713780:CDS
GAAAACCGGGAATTGAACAA+CGG 0.656607 5_1:-6221117 Msa0713780:CDS
ATATGGAGGACCGAAAGCGG+AGG 0.670255 5_1:-6221236 Msa0713780:CDS
TGGCTCGAACCGGAATATGG+AGG 0.676236 5_1:-6221250 Msa0713780:CDS
CAAACCGGGAATCGGCACGG+AGG 0.765542 5_1:-6221203 Msa0713780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGACATCTAGAGAATTTA+CGG - chr5_1:6221195-6221214 Msa0713780:CDS 25.0%
AGAATGTTAGAAAAATCCCA+CGG + chr5_1:6221011-6221030 None:intergenic 30.0%
TTCTTCTAACTCCGTGAAAT+CGG + chr5_1:6220979-6220998 None:intergenic 35.0%
AATGATATCAAACCGGGAAT+CGG - chr5_1:6221148-6221167 Msa0713780:CDS 35.0%
GGTCAAAAGTTGTCAAACAT+AGG - chr5_1:6221341-6221360 Msa0713780:CDS 35.0%
GTCAAACATAGGTCAAAACA+TGG - chr5_1:6221352-6221371 Msa0713780:CDS 35.0%
TAGAAGAAAGTTTAACGCCG+TGG - chr5_1:6220991-6221010 Msa0713780:CDS 40.0%
AGAAGAAAGTTTAACGCCGT+GGG - chr5_1:6220992-6221011 Msa0713780:CDS 40.0%
AGGCGAACCAAAAGAAAAAC+CGG - chr5_1:6221079-6221098 Msa0713780:CDS 40.0%
ACCAAAAGAAAAACCGGTCA+TGG - chr5_1:6221085-6221104 Msa0713780:CDS 40.0%
!! TCCATGACCGGTTTTTCTTT+TGG + chr5_1:6221089-6221108 None:intergenic 40.0%
AAAGAAAAACCGGTCATGGA+TGG - chr5_1:6221089-6221108 Msa0713780:CDS 40.0%
ATATCATTCTCCTCCGCTTT+CGG + chr5_1:6221136-6221155 None:intergenic 40.0%
GGAGGAGAATGATATCAAAC+CGG - chr5_1:6221141-6221160 Msa0713780:CDS 40.0%
GAGGAGAATGATATCAAACC+GGG - chr5_1:6221142-6221161 Msa0713780:CDS 40.0%
TCTAGAGAATTTACGGAACC+AGG - chr5_1:6221202-6221221 Msa0713780:CDS 40.0%
! ACCGGTTTAGAGTTGAAAAC+CGG - chr5_1:6221228-6221247 Msa0713780:CDS 40.0%
GAAAACCGGGAATTGAACAA+CGG - chr5_1:6221242-6221261 Msa0713780:CDS 40.0%
AAAACCGGGAATTGAACAAC+GGG - chr5_1:6221243-6221262 Msa0713780:CDS 40.0%
TTCAACCTTTCTCATCTGCA+TGG - chr5_1:6221378-6221397 Msa0713780:CDS 40.0%
TCAGCTGTGACAATATTGCA+TGG + chr5_1:6221404-6221423 None:intergenic 40.0%
TCTCTATGCCTCCGATTTCA+CGG - chr5_1:6220965-6220984 Msa0713780:CDS 45.0%
TTCTAACTCCGTGAAATCGG+AGG + chr5_1:6220976-6220995 None:intergenic 45.0%
!!! TTCTTTTGGTTCGCCTGAAC+CGG + chr5_1:6221075-6221094 None:intergenic 45.0%
ATTTACGGAACCAGGTGAAC+CGG - chr5_1:6221210-6221229 Msa0713780:CDS 45.0%
! CCCGGTTTTCAACTCTAAAC+CGG + chr5_1:6221232-6221251 None:intergenic 45.0%
! CCGGTTTAGAGTTGAAAACC+GGG - chr5_1:6221229-6221248 Msa0713780:CDS 45.0%
! TGACAACTTTTGACCCAGCA+TGG + chr5_1:6221336-6221355 None:intergenic 45.0%
CGGAGCTTGAAGTGAGCTTA+GGG + chr5_1:6221055-6221074 None:intergenic 50.0%
CCTAAGCTCACTTCAAGCTC+CGG - chr5_1:6221053-6221072 Msa0713780:CDS 50.0%
GCTTTCGGTCCTCCATATTC+CGG + chr5_1:6221121-6221140 None:intergenic 50.0%
GGAATATGGAGGACCGAAAG+CGG - chr5_1:6221120-6221139 Msa0713780:CDS 50.0%
TATCAAACCGGGAATCGGCA+CGG - chr5_1:6221153-6221172 Msa0713780:CDS 50.0%
! CAACTCTAAACCGGTTCACC+TGG + chr5_1:6221223-6221242 None:intergenic 50.0%
GCAACCCGTTGTTCAATTCC+CGG + chr5_1:6221250-6221269 None:intergenic 50.0%
GTCTACGAACCGAAAGTGAG+TGG - chr5_1:6221294-6221313 Msa0713780:CDS 50.0%
CATGGCCATGCAGATGAGAA+AGG + chr5_1:6221386-6221405 None:intergenic 50.0%
!! TTAGGGCTGGTGGGTTGGAA+GGG + chr5_1:6221038-6221057 None:intergenic 55.0%
! GAAGTGAGCTTAGGGCTGGT+GGG + chr5_1:6221047-6221066 None:intergenic 55.0%
TGAAGTGAGCTTAGGGCTGG+TGG + chr5_1:6221048-6221067 None:intergenic 55.0%
GCTTGAAGTGAGCTTAGGGC+TGG + chr5_1:6221051-6221070 None:intergenic 55.0%
CCGGAGCTTGAAGTGAGCTT+AGG + chr5_1:6221056-6221075 None:intergenic 55.0%
CTCACTTCAAGCTCCGGTTC+AGG - chr5_1:6221059-6221078 Msa0713780:CDS 55.0%
GGATGGCTCGAACCGGAATA+TGG - chr5_1:6221106-6221125 Msa0713780:CDS 55.0%
TGGCTCGAACCGGAATATGG+AGG - chr5_1:6221109-6221128 Msa0713780:CDS 55.0%
ATATGGAGGACCGAAAGCGG+AGG - chr5_1:6221123-6221142 Msa0713780:CDS 55.0%
GAACCGAAAGTGAGTGGCTC+CGG - chr5_1:6221300-6221319 Msa0713780:CDS 55.0%
CAACCGGAGCCACTCACTTT+CGG + chr5_1:6221306-6221325 None:intergenic 55.0%
CCAGCATGGTTCGTTCCAAC+CGG + chr5_1:6221322-6221341 None:intergenic 55.0%
CGGTTGGAACGAACCATGCT+GGG - chr5_1:6221320-6221339 Msa0713780:CDS 55.0%
!! CTTAGGGCTGGTGGGTTGGA+AGG + chr5_1:6221039-6221058 None:intergenic 60.0%
! TGAGCTTAGGGCTGGTGGGT+TGG + chr5_1:6221043-6221062 None:intergenic 60.0%
CGGTTCGAGCCATCCATGAC+CGG + chr5_1:6221101-6221120 None:intergenic 60.0%
CGGTCATGGATGGCTCGAAC+CGG - chr5_1:6221099-6221118 Msa0713780:CDS 60.0%
CGAAAGTGAGTGGCTCCGGT+TGG - chr5_1:6221304-6221323 Msa0713780:CDS 60.0%
CCGGTTGGAACGAACCATGC+TGG - chr5_1:6221319-6221338 Msa0713780:CDS 60.0%
CAAACCGGGAATCGGCACGG+AGG - chr5_1:6221156-6221175 Msa0713780:CDS 65.0%
!! GTGACCTCCGTGCCGATTCC+CGG + chr5_1:6221163-6221182 None:intergenic 65.0%
!! GGGCTGGTGGGTTGGAAGGG+TGG + chr5_1:6221035-6221054 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 6220954 6221427 6220954 ID=Msa0713780;Name=Msa0713780
chr5_1 mRNA 6220954 6221427 6220954 ID=Msa0713780-mRNA-1;Parent=Msa0713780;Name=Msa0713780-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|157
chr5_1 exon 6220954 6221427 6220954 ID=Msa0713780-mRNA-1:exon:2647;Parent=Msa0713780-mRNA-1
chr5_1 CDS 6220954 6221427 6220954 ID=Msa0713780-mRNA-1:cds;Parent=Msa0713780-mRNA-1
Gene Sequence

>Msa0713780

ATGCTCTCTTCTCTCTATGCCTCCGATTTCACGGAGTTAGAAGAAAGTTTAACGCCGTGGGATTTTTCTAACATTCTGCCACCCTTCCAACCCACCAGCCCTAAGCTCACTTCAAGCTCCGGTTCAGGCGAACCAAAAGAAAAACCGGTCATGGATGGCTCGAACCGGAATATGGAGGACCGAAAGCGGAGGAGAATGATATCAAACCGGGAATCGGCACGGAGGTCACGTATGAGAAAACAAAGACATCTAGAGAATTTACGGAACCAGGTGAACCGGTTTAGAGTTGAAAACCGGGAATTGAACAACGGGTTGCAGTTTTTGCTGTATCAATGCAATCGTCTACGAACCGAAAGTGAGTGGCTCCGGTTGGAACGAACCATGCTGGGTCAAAAGTTGTCAAACATAGGTCAAAACATGGTTTTTCAACCTTTCTCATCTGCATGGCCATGCAATATTGTCACAGCTGAATAA

Protein sequence

>Msa0713780

MLSSLYASDFTELEESLTPWDFSNILPPFQPTSPKLTSSSGSGEPKEKPVMDGSNRNMEDRKRRRMISNRESARRSRMRKQRHLENLRNQVNRFRVENRELNNGLQFLLYQCNRLRTESEWLRLERTMLGQKLSNIGQNMVFQPFSSAWPCNIVTAE*