AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0539080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0539080 MtrunA17_Chr4g0014131 84.422 199 30 1 4 201 3 201 1.18e-111 318
Msa0539080 MtrunA17_Chr4g0014031 88.202 178 20 1 4 180 3 180 5.40e-107 306
Msa0539080 MtrunA17_Chr8g0351751 64.319 213 65 5 4 211 3 209 1.70e-85 253
Msa0539080 MtrunA17_Chr4g0014321 58.962 212 72 5 1 211 1 198 2.07e-79 237
Msa0539080 MtrunA17_Chr4g0014121 79.870 154 30 1 4 156 31 184 8.11e-78 231
Msa0539080 MtrunA17_Chr4g0013041 56.522 207 59 4 6 211 5 181 1.92e-74 223
Msa0539080 MtrunA17_Chr3g0110131 61.146 157 61 0 4 160 3 159 3.82e-58 183
Msa0539080 MtrunA17_Chr3g0107381 53.289 152 71 0 4 155 3 154 4.29e-57 180
Msa0539080 MtrunA17_Chr2g0296831 71.667 120 34 0 4 123 3 122 6.99e-49 155
Msa0539080 MtrunA17_Chr3g0107331 43.750 160 90 0 4 163 2 161 2.84e-44 145
Msa0539080 MtrunA17_Chr3g0107351 43.312 157 89 0 4 160 2 158 2.15e-41 138
Msa0539080 MtrunA17_Chr5g0432691 42.953 149 85 0 6 154 5 153 1.30e-40 135
Msa0539080 MtrunA17_Chr3g0107361 41.401 157 92 0 4 160 2 158 4.50e-39 132
Msa0539080 MtrunA17_Chr5g0420351 43.137 153 86 1 4 156 3 154 8.86e-39 131
Msa0539080 MtrunA17_Chr3g0107341 42.038 157 91 0 4 160 2 158 9.61e-39 131
Msa0539080 MtrunA17_Chr3g0107461 39.873 158 86 2 4 156 3 156 2.85e-37 127
Msa0539080 MtrunA17_Chr2g0283941 40.132 152 90 1 6 156 5 156 8.78e-36 126
Msa0539080 MtrunA17_Chr1g0188681 39.869 153 91 1 4 156 3 154 2.56e-34 119
Msa0539080 MtrunA17_Chr1g0197461 38.562 153 93 1 4 156 2 153 3.44e-34 119
Msa0539080 MtrunA17_Chr1g0197261 38.065 155 95 1 4 158 3 156 3.50e-33 117
Msa0539080 MtrunA17_Chr1g0193311 42.484 153 87 1 4 156 3 154 7.25e-32 113
Msa0539080 MtrunA17_Chr1g0188661 41.830 153 88 1 4 156 3 154 7.71e-32 113
Msa0539080 MtrunA17_Chr1g0197321 39.375 160 92 4 1 158 1 157 3.71e-31 111
Msa0539080 MtrunA17_Chr7g0218151 41.176 153 89 1 4 156 3 154 3.96e-31 111
Msa0539080 MtrunA17_Chr4g0012761 41.176 153 89 1 4 156 3 154 6.65e-31 111
Msa0539080 MtrunA17_Chr3g0105791 41.270 126 73 1 30 154 1 126 1.60e-29 107
Msa0539080 MtrunA17_Chr4g0031421 38.686 137 83 1 30 165 1 137 2.83e-28 103
Msa0539080 MtrunA17_Chr1g0188651 41.176 153 87 2 4 156 3 152 1.19e-27 102
Msa0539080 MtrunA17_Chr3g0106421 37.681 138 85 1 30 166 1 138 2.98e-26 100
Msa0539080 MtrunA17_Chr2g0296851 59.794 97 37 2 75 169 1 97 1.44e-24 92.8
Msa0539080 MtrunA17_Chr7g0267601 37.179 156 81 3 3 157 5 144 6.11e-23 95.9
Msa0539080 MtrunA17_Chr4g0008701 37.821 156 80 3 3 157 5 144 7.34e-23 95.5
Msa0539080 MtrunA17_Chr3g0128721 28.497 193 126 3 3 194 5 186 2.57e-22 94.4
Msa0539080 MtrunA17_Chr2g0296861 33.333 150 100 0 7 156 6 155 4.52e-22 88.2
Msa0539080 MtrunA17_Chr3g0106501 31.343 134 91 1 30 162 1 134 3.57e-17 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0539080 AT5G48670.1 46.734 199 99 2 4 199 3 197 2.22e-46 155
Msa0539080 AT1G65300.1 39.344 183 98 1 4 186 2 171 1.84e-41 142
Msa0539080 AT1G65330.1 40.217 184 97 1 4 187 2 172 1.45e-40 139
Msa0539080 AT5G26630.1 49.342 152 77 0 4 155 3 154 5.06e-40 136
Msa0539080 AT5G26650.1 39.264 163 99 0 6 168 3 165 4.98e-36 130
Msa0539080 AT5G27960.1 38.650 163 100 0 6 168 3 165 2.95e-35 127
Msa0539080 AT1G31630.1 34.254 181 105 2 4 184 2 168 3.29e-34 124
Msa0539080 AT1G31640.1 31.579 209 134 3 4 204 2 209 7.53e-32 120
Msa0539080 AT3G05860.2 38.095 147 91 0 4 150 3 149 8.81e-30 110
Msa0539080 AT5G27810.1 52.632 95 45 0 30 124 1 95 2.54e-29 106
Msa0539080 AT3G05860.3 38.095 147 91 0 4 150 3 149 3.70e-29 109
Msa0539080 AT3G05860.1 38.095 147 91 0 4 150 3 149 4.55e-29 109
Msa0539080 AT2G28700.1 35.802 162 104 0 4 165 3 164 6.63e-27 105
Msa0539080 AT5G26580.1 35.484 155 85 2 1 155 1 140 3.05e-25 101
Msa0539080 AT1G22590.2 31.056 161 107 2 1 161 1 157 8.46e-24 93.2
Msa0539080 AT5G06500.1 35.099 151 97 1 4 154 3 152 4.51e-21 88.2
Msa0539080 AT2G40210.1 38.636 132 80 1 4 134 3 134 1.80e-18 82.8
Msa0539080 AT5G58890.1 37.903 124 66 5 7 121 6 127 3.46e-14 70.1

Find 52 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCATGAGTCAATGTCTTAA+TGG 0.213476 4_1:+19432578 Msa0539080:CDS
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4_1:+19432537 Msa0539080:CDS
GAGTGAAGAAATGGCAATTA+TGG 0.233693 4_1:+19432796 Msa0539080:CDS
TCAATTTCTCTTCAGCCTTC+AGG 0.259829 4_1:-19432514 None:intergenic
AACGAAGGGTCTATTGAAAA+AGG 0.335070 4_1:+19432304 Msa0539080:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4_1:+19432384 Msa0539080:CDS
CCGCCATTTCGAGTTGGACT+TGG 0.347668 4_1:-19432739 None:intergenic
ATAATGTCATCATCATTAAT+AGG 0.359787 4_1:-19432839 None:intergenic
GAAGCCTTTGCCATAGTGTA+TGG 0.388094 4_1:+19432356 Msa0539080:CDS
ATCTCAGGTTGAGGCTCATA+AGG 0.418788 4_1:-19432380 None:intergenic
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4_1:+19432538 Msa0539080:CDS
AGTGAAGAAATGGCAATTAT+GGG 0.424565 4_1:+19432797 Msa0539080:CDS
GAAGGACGTTAGTAGACGTT+TGG 0.432671 4_1:+19432670 Msa0539080:CDS
GTTGATTGACCACAATTTGA+AGG 0.436294 4_1:+19432652 Msa0539080:CDS
AAACCAAGTCCAACTCGAAA+TGG 0.452175 4_1:+19432736 Msa0539080:CDS
AGCATCTAGGAGTGAAGAAA+TGG 0.457574 4_1:+19432787 Msa0539080:CDS
CTCATAAGGTCCATACACTA+TGG 0.467279 4_1:-19432366 None:intergenic
AGCATAGATTGGACACCCTC+TGG 0.468177 4_1:-19432413 None:intergenic
TTATGGGTCATGGCCATCTT+GGG 0.468268 4_1:+19432813 Msa0539080:CDS
ATTATGGGTCATGGCCATCT+TGG 0.475028 4_1:+19432812 Msa0539080:CDS
AACTATGGGTAGAAGAAGTA+AGG 0.492866 4_1:+19432226 None:intergenic
TCTGGTAGAGGCCAAATCTC+AGG 0.493519 4_1:-19432395 None:intergenic
TGGATATGAGTTATCTTGCT+TGG 0.509186 4_1:+19432630 Msa0539080:CDS
TTAGTAGACGTTTGGAAGCA+TGG 0.511917 4_1:+19432678 Msa0539080:CDS
TGCAACATCATTGACAATGA+AGG 0.517037 4_1:-19432258 None:intergenic
TTTGCGTCAAGAAAGTCTCT+TGG 0.520457 4_1:-19432487 None:intergenic
AGAGACTTTCTTGACGCAAA+GGG 0.522386 4_1:+19432490 Msa0539080:CDS
CAATGCTCAAAATCAAATCA+TGG 0.522605 4_1:+19432706 Msa0539080:CDS
CACCACTTCTAGCAGCATCT+AGG 0.525777 4_1:+19432774 Msa0539080:CDS
GATTGGACACCCTCTGGTAG+AGG 0.527894 4_1:-19432407 None:intergenic
GAAATGGCAATTATGGGTCA+TGG 0.549964 4_1:+19432803 Msa0539080:CDS
TAGTAGACGTTTGGAAGCAT+GGG 0.557707 4_1:+19432679 Msa0539080:CDS
CTCCTAGATGCTGCTAGAAG+TGG 0.571630 4_1:-19432776 None:intergenic
TACTAACGTCCTTCAAATTG+TGG 0.573371 4_1:-19432661 None:intergenic
CATTAATAGGTATCCCAAGA+TGG 0.574332 4_1:-19432826 None:intergenic
CTTGACGCAAAGGGTCCTGA+AGG 0.584070 4_1:+19432499 Msa0539080:CDS
TTGTTGCCGCCATTTCGAGT+TGG 0.584691 4_1:-19432745 None:intergenic
AAGAGACTTTCTTGACGCAA+AGG 0.588013 4_1:+19432489 Msa0539080:CDS
TCATTGTCAATGATGTTGCA+AGG 0.595963 4_1:+19432261 Msa0539080:CDS
CTAGATGCTGCTAGAAGTGG+TGG 0.605478 4_1:-19432773 None:intergenic
AAAGGCTTCAATGCCACAGA+GGG 0.618725 4_1:-19432342 None:intergenic
ATCATACAAGAAAAGAACGA+AGG 0.618898 4_1:+19432289 Msa0539080:CDS
TCATACAAGAAAAGAACGAA+GGG 0.620354 4_1:+19432290 Msa0539080:CDS
AGAGGCCAAATCTCAGGTTG+AGG 0.620704 4_1:-19432389 None:intergenic
CCAAGTCCAACTCGAAATGG+CGG 0.631061 4_1:+19432739 Msa0539080:CDS
GATGCTGCTAGAAGTGGTGG+TGG 0.633563 4_1:-19432770 None:intergenic
GAGATTTGGCCTCTACCAGA+GGG 0.634065 4_1:+19432398 Msa0539080:CDS
TGAGATTTGGCCTCTACCAG+AGG 0.636282 4_1:+19432397 Msa0539080:CDS
AGGTCCATACACTATGGCAA+AGG 0.638234 4_1:-19432360 None:intergenic
GCATGACAATATGTCAACAA+TGG 0.671130 4_1:+19432610 Msa0539080:CDS
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4_1:+19432329 Msa0539080:CDS
CAAAGGCTTCAATGCCACAG+AGG 0.706392 4_1:-19432343 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAACAAAGAAAAGAAAAT+AGG + chr4_1:19432537-19432556 Msa0539080:CDS 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG + chr4_1:19432538-19432557 Msa0539080:CDS 20.0%
!! ATAATGTCATCATCATTAAT+AGG - chr4_1:19432842-19432861 None:intergenic 20.0%
ATCATACAAGAAAAGAACGA+AGG + chr4_1:19432289-19432308 Msa0539080:CDS 30.0%
TCATACAAGAAAAGAACGAA+GGG + chr4_1:19432290-19432309 Msa0539080:CDS 30.0%
!! TGAATTTTGAGAGCATAGAT+TGG - chr4_1:19432427-19432446 None:intergenic 30.0%
CAATGCTCAAAATCAAATCA+TGG + chr4_1:19432706-19432725 Msa0539080:CDS 30.0%
AGTGAAGAAATGGCAATTAT+GGG + chr4_1:19432797-19432816 Msa0539080:CDS 30.0%
TGCAACATCATTGACAATGA+AGG - chr4_1:19432261-19432280 None:intergenic 35.0%
TCATTGTCAATGATGTTGCA+AGG + chr4_1:19432261-19432280 Msa0539080:CDS 35.0%
AACGAAGGGTCTATTGAAAA+AGG + chr4_1:19432304-19432323 Msa0539080:CDS 35.0%
CTCATGAGTCAATGTCTTAA+TGG + chr4_1:19432578-19432597 Msa0539080:CDS 35.0%
GCATGACAATATGTCAACAA+TGG + chr4_1:19432610-19432629 Msa0539080:CDS 35.0%
TGGATATGAGTTATCTTGCT+TGG + chr4_1:19432630-19432649 Msa0539080:CDS 35.0%
GTTGATTGACCACAATTTGA+AGG + chr4_1:19432652-19432671 Msa0539080:CDS 35.0%
TACTAACGTCCTTCAAATTG+TGG - chr4_1:19432664-19432683 None:intergenic 35.0%
GAGTGAAGAAATGGCAATTA+TGG + chr4_1:19432796-19432815 Msa0539080:CDS 35.0%
CATTAATAGGTATCCCAAGA+TGG - chr4_1:19432829-19432848 None:intergenic 35.0%
CTCATAAGGTCCATACACTA+TGG - chr4_1:19432369-19432388 None:intergenic 40.0%
TTTGCGTCAAGAAAGTCTCT+TGG - chr4_1:19432490-19432509 None:intergenic 40.0%
AAGAGACTTTCTTGACGCAA+AGG + chr4_1:19432489-19432508 Msa0539080:CDS 40.0%
AGAGACTTTCTTGACGCAAA+GGG + chr4_1:19432490-19432509 Msa0539080:CDS 40.0%
TCAATTTCTCTTCAGCCTTC+AGG - chr4_1:19432517-19432536 None:intergenic 40.0%
TTAGTAGACGTTTGGAAGCA+TGG + chr4_1:19432678-19432697 Msa0539080:CDS 40.0%
! TAGTAGACGTTTGGAAGCAT+GGG + chr4_1:19432679-19432698 Msa0539080:CDS 40.0%
AAACCAAGTCCAACTCGAAA+TGG + chr4_1:19432736-19432755 Msa0539080:CDS 40.0%
AGCATCTAGGAGTGAAGAAA+TGG + chr4_1:19432787-19432806 Msa0539080:CDS 40.0%
GAAATGGCAATTATGGGTCA+TGG + chr4_1:19432803-19432822 Msa0539080:CDS 40.0%
AAAGGCTTCAATGCCACAGA+GGG - chr4_1:19432345-19432364 None:intergenic 45.0%
GAAGCCTTTGCCATAGTGTA+TGG + chr4_1:19432356-19432375 Msa0539080:CDS 45.0%
AGGTCCATACACTATGGCAA+AGG - chr4_1:19432363-19432382 None:intergenic 45.0%
!! ATCTCAGGTTGAGGCTCATA+AGG - chr4_1:19432383-19432402 None:intergenic 45.0%
ATGAGCCTCAACCTGAGATT+TGG + chr4_1:19432384-19432403 Msa0539080:CDS 45.0%
GAAGGACGTTAGTAGACGTT+TGG + chr4_1:19432670-19432689 Msa0539080:CDS 45.0%
ATTATGGGTCATGGCCATCT+TGG + chr4_1:19432812-19432831 Msa0539080:CDS 45.0%
TTATGGGTCATGGCCATCTT+GGG + chr4_1:19432813-19432832 Msa0539080:CDS 45.0%
CAAAGGCTTCAATGCCACAG+AGG - chr4_1:19432346-19432365 None:intergenic 50.0%
! AGAGGCCAAATCTCAGGTTG+AGG - chr4_1:19432392-19432411 None:intergenic 50.0%
TCTGGTAGAGGCCAAATCTC+AGG - chr4_1:19432398-19432417 None:intergenic 50.0%
TGAGATTTGGCCTCTACCAG+AGG + chr4_1:19432397-19432416 Msa0539080:CDS 50.0%
GAGATTTGGCCTCTACCAGA+GGG + chr4_1:19432398-19432417 Msa0539080:CDS 50.0%
AGCATAGATTGGACACCCTC+TGG - chr4_1:19432416-19432435 None:intergenic 50.0%
CCAAGTCCAACTCGAAATGG+CGG + chr4_1:19432739-19432758 Msa0539080:CDS 50.0%
! TTGTTGCCGCCATTTCGAGT+TGG - chr4_1:19432748-19432767 None:intergenic 50.0%
CTAGATGCTGCTAGAAGTGG+TGG - chr4_1:19432776-19432795 None:intergenic 50.0%
CACCACTTCTAGCAGCATCT+AGG + chr4_1:19432774-19432793 Msa0539080:CDS 50.0%
CTCCTAGATGCTGCTAGAAG+TGG - chr4_1:19432779-19432798 None:intergenic 50.0%
GCTGAACTTAGCACCCTCTG+TGG + chr4_1:19432329-19432348 Msa0539080:CDS 55.0%
GATTGGACACCCTCTGGTAG+AGG - chr4_1:19432410-19432429 None:intergenic 55.0%
CTTGACGCAAAGGGTCCTGA+AGG + chr4_1:19432499-19432518 Msa0539080:CDS 55.0%
!! CCGCCATTTCGAGTTGGACT+TGG - chr4_1:19432742-19432761 None:intergenic 55.0%
GATGCTGCTAGAAGTGGTGG+TGG - chr4_1:19432773-19432792 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 19432230 19432865 19432230 ID=Msa0539080;Name=Msa0539080
chr4_1 mRNA 19432230 19432865 19432230 ID=Msa0539080-mRNA-1;Parent=Msa0539080;Name=Msa0539080-mRNA-1;_AED=0.19;_eAED=0.19;_QI=0|-1|0|1|-1|1|1|0|211
chr4_1 exon 19432230 19432865 19432230 ID=Msa0539080-mRNA-1:exon:5656;Parent=Msa0539080-mRNA-1
chr4_1 CDS 19432230 19432865 19432230 ID=Msa0539080-mRNA-1:cds;Parent=Msa0539080-mRNA-1
Gene Sequence

>Msa0539080

ATGGGTAGAAGAAGTAAGGTTAAACTTGCCTTCATTGTCAATGATGTTGCAAGGAAAGCATCATACAAGAAAAGAACGAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTTTGCCATAGTGTATGGACCTTATGAGCCTCAACCTGAGATTTGGCCTCTACCAGAGGGTGTCCAATCTATGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACGCAAAGGGTCCTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGACAATACTCATGAGTCAATGTCTTAATGGTAAAGTTGTGCATGACAATATGTCAACAATGGATATGAGTTATCTTGCTTGGTTGATTGACCACAATTTGAAGGACGTTAGTAGACGTTTGGAAGCATGGGATAACAATGCTCAAAATCAAATCATGGCTATTCAAAACCAAGTCCAACTCGAAATGGCGGCAACAATACCACCACCACTTCTAGCAGCATCTAGGAGTGAAGAAATGGCAATTATGGGTCATGGCCATCTTGGGATACCTATTAATGATGATGACATTATATAA
Protein sequence

>Msa0539080

MGRRSKVKLAFIVNDVARKASYKKRTKGLLKKVAELSTLCGIEAFAIVYGPYEPQPEIWPLPEGVQSMLSKFMTMHEFQKCKKMMNQETFLTQRVLKAEEKLKKQRKENREQEMTILMSQCLNGKVVHDNMSTMDMSYLAWLIDHNLKDVSRRLEAWDNNAQNQIMAIQNQVQLEMAATIPPPLLAASRSEEMAIMGHGHLGIPINDDDII*