AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG030560

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG030560 MtrunA17_Chr6g0460691 84.333 300 6 3 1 259 1 300 1.30e-180 498
MsaG030560 MtrunA17_Chr7g0254251 51.071 280 108 7 1 259 1 272 5.19e-76 231
MsaG030560 MtrunA17_Chr7g0223471 62.857 70 26 0 24 93 39 108 7.61e-28 110
MsaG030560 MtrunA17_Chr2g0283141 62.500 72 27 0 24 95 47 118 1.59e-27 110
MsaG030560 MtrunA17_Chr8g0392991 43.333 90 50 1 11 99 75 164 2.45e-17 80.5
MsaG030560 MtrunA17_Chr4g0043891 40.909 66 39 0 31 96 7 72 7.98e-15 72.0
MsaG030560 MtrunA17_Chr1g0212511 46.875 64 34 0 28 91 81 144 3.90e-14 70.5
MsaG030560 MtrunA17_Chr3g0144021 45.070 71 39 0 28 98 78 148 1.41e-13 67.8
MsaG030560 MtrunA17_Chr5g0436661 34.524 84 55 0 12 95 13 96 1.62e-12 64.3
MsaG030560 MtrunA17_Chr4g0031341 40.299 67 40 0 32 98 25 91 2.61e-12 65.1
MsaG030560 MtrunA17_Chr5g0405351 40.625 64 37 1 31 93 29 92 3.84e-12 65.1
MsaG030560 MtrunA17_Chr7g0238431 40.625 64 38 0 31 94 7 70 5.10e-12 63.5
MsaG030560 MtrunA17_Chr7g0222981 41.538 65 38 0 29 93 65 129 3.74e-11 60.5
MsaG030560 MtrunA17_Chr1g0153171 42.188 64 37 0 31 94 89 152 7.91e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG030560 AT5G17810.3 50.362 276 93 7 13 256 3 266 1.39e-73 226
MsaG030560 AT5G17810.1 50.362 276 94 7 13 256 3 267 2.40e-73 225
MsaG030560 AT5G17810.2 50.362 276 94 7 13 256 3 267 2.40e-73 225
MsaG030560 AT3G03660.1 54.710 276 93 6 3 256 2 267 3.11e-73 225
MsaG030560 AT3G03660.4 54.945 273 91 6 3 253 2 264 2.09e-71 221
MsaG030560 AT3G03660.2 49.508 305 93 8 3 256 2 296 1.09e-67 211
MsaG030560 AT3G03660.3 49.669 302 91 8 3 253 2 293 1.01e-65 207
MsaG030560 AT2G33880.1 62.162 74 28 0 23 96 46 119 1.27e-27 109
MsaG030560 AT2G33880.2 62.162 74 28 0 23 96 46 119 1.46e-27 109
MsaG030560 AT5G45980.1 57.534 73 31 0 30 102 53 125 8.85e-26 103
MsaG030560 AT4G35550.1 47.692 65 34 0 28 92 95 159 2.17e-14 71.6
MsaG030560 AT3G18010.1 40.000 80 47 1 29 107 73 152 4.69e-14 71.2
MsaG030560 AT5G59340.1 39.706 68 41 0 31 98 13 80 5.27e-13 67.4
MsaG030560 AT1G20700.2 42.254 71 41 0 28 98 29 99 1.26e-12 64.3
MsaG030560 AT2G28610.1 38.889 72 44 0 26 97 2 73 2.89e-12 65.1
MsaG030560 AT1G20700.1 42.254 71 41 0 28 98 91 161 2.90e-12 64.7
MsaG030560 AT1G20700.3 42.254 71 41 0 28 98 91 161 3.00e-12 64.3
MsaG030560 AT2G17950.1 42.188 64 36 1 31 93 37 100 4.28e-12 65.1
MsaG030560 AT3G11260.1 39.062 64 39 0 32 95 24 87 6.60e-12 63.2
MsaG030560 AT1G46480.2 42.188 64 37 0 31 94 89 152 9.97e-12 62.8
MsaG030560 AT1G46480.1 42.188 64 37 0 31 94 89 152 4.60e-11 62.0
MsaG030560 AT5G05770.1 37.500 64 40 0 32 95 29 92 5.01e-11 59.3

Find 49 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAAACTTCTTGAGAAATT+TGG 0.100600 6:+10049091 MsaT030560.1:CDS
ATTCTCACGGTTTCATCTTT+TGG 0.207436 6:-10049067 None:intergenic
GACCATTCCACTATTGAAAA+TGG 0.216187 6:-10049038 None:intergenic
ATAAGGATTTGTTCAGGTTT+TGG 0.291953 6:-10049007 None:intergenic
TGAAAATGGATTCAAGTATA+AGG 0.302638 6:-10049024 None:intergenic
CTTGGTGCTGCACTTGGTCT+TGG 0.327659 6:+10049274 MsaT030560.1:CDS
CTGCACTGGTATTGGTGATA+TGG 0.337777 6:-10049229 None:intergenic
CTGTCTCTTGGTGCTGCACT+TGG 0.345570 6:+10049268 MsaT030560.1:CDS
GTAATATTGGTTCATTCCTC+TGG 0.359362 6:+10051165 MsaT030560.1:CDS
TCAGTTCCAACCAATGAGTT+TGG 0.369989 6:+10051192 MsaT030560.1:CDS
GTTTGGTGAAGATGTAATAT+TGG 0.373946 6:+10051152 MsaT030560.1:CDS
TCAAATCAATTTGCCTCAAA+TGG 0.378394 6:+10049483 MsaT030560.1:CDS
TGTTGGTGCTGCACTGGTAT+TGG 0.396373 6:-10049237 None:intergenic
TCAAGTATAAGGATTTGTTC+AGG 0.405750 6:-10049013 None:intergenic
CAGTACTGCCACCGCTTAGT+TGG 0.406811 6:-10049201 None:intergenic
GTACCTCTTGGCATTTCTGT+TGG 0.409908 6:-10051108 None:intergenic
AGTACTGCCACCGCTTAGTT+GGG 0.417375 6:-10049200 None:intergenic
GCATGGTGAAAGCTACTATC+TGG 0.420994 6:+10051236 MsaT030560.1:CDS
CTTGAGAAATTTGGAGCTGT+TGG 0.435040 6:+10049100 MsaT030560.1:CDS
GGTGCTGCACTTGGTCTTGG+TGG 0.436302 6:+10049277 MsaT030560.1:CDS
ATTGACATGAAAACAATGTT+TGG 0.438397 6:+10051135 MsaT030560.1:CDS
GTTGTTTGGATTATTAGTAT+TGG 0.439777 6:-10048948 None:intergenic
CATCTGCCTCTGACGGCGTC+GGG 0.463584 6:-10049167 None:intergenic
GCATCTGCCTCTGACGGCGT+CGG 0.466933 6:-10049168 None:intergenic
GCTGAAGTATTGTCCATTTG+AGG 0.472860 6:-10049496 None:intergenic
TCAAATTTCAACTATTACCC+AGG 0.481334 6:+10049553 MsaT030560.1:CDS
AACAGTACCTCTCTGTCTCT+TGG 0.490108 6:+10049256 MsaT030560.1:CDS
CATCAAGAAACCAAACTCAT+TGG 0.493495 6:-10051202 None:intergenic
AAGAAACCAAACTCATTGGT+TGG 0.499044 6:-10051198 None:intergenic
GTGATCACAGTGTTTATCAA+TGG 0.505244 6:+10051081 MsaT030560.1:CDS
ATGTCAATTGCAGTACCTCT+TGG 0.508431 6:-10051120 None:intergenic
AGGTACTGTTGGTGCTGCAC+TGG 0.511056 6:-10049243 None:intergenic
CTCGCTCCCGACGCCGTCAG+AGG 0.513233 6:+10049161 MsaT030560.1:CDS
CGGCCTGCATCTGCCTCTGA+CGG 0.528621 6:-10049174 None:intergenic
ACGCCGTCAGAGGCAGATGC+AGG 0.537355 6:+10049171 MsaT030560.1:CDS
GACGGCGTCGGGAGCGAGAG+CGG 0.542417 6:-10049156 None:intergenic
AAATTTGAAGCATTATCAGA+AGG 0.574791 6:-10049538 None:intergenic
GCCGCCGCCCAACTAAGCGG+TGG 0.588442 6:+10049193 MsaT030560.1:CDS
GTGAAACTGTGAGATCAAGA+TGG 0.590101 6:+10048981 MsaT030560.1:CDS
ACTGCCACCGCTTAGTTGGG+CGG 0.608647 6:-10049197 None:intergenic
AGAATTCATAGTGAAAGTTG+AGG 0.624134 6:-10049302 None:intergenic
GCCACCGCTTAGTTGGGCGG+CGG 0.641411 6:-10049194 None:intergenic
CAGGCCGCCGCCCAACTAAG+CGG 0.643678 6:+10049190 MsaT030560.1:CDS
TGCAGCACCAAGAGACAGAG+AGG 0.645908 6:-10049263 None:intergenic
AACTTTGAGACTGAACATGT+TGG 0.650519 6:-10048925 None:intergenic
AAGAGACAGAGAGGTACTGT+TGG 0.665242 6:-10049254 None:intergenic
TTGATGCAGAACTTGCAGCA+TGG 0.678300 6:+10051219 MsaT030560.1:CDS
GGTTGGAACTGAGACTCCAG+AGG 0.711041 6:-10051181 None:intergenic
GTTCCAACAGAAATGCCAAG+AGG 0.748646 6:+10051105 MsaT030560.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 10048905 10051563 10048905 ID=MsaG030560
Chr6 mRNA 10048905 10051563 10048905 ID=MsaT030560.1;Parent=MsaG030560
Chr6 exon 10048905 10049358 10048905 ID=MsaT030560.1.exon1;Parent=MsaT030560.1
Chr6 CDS 10048905 10049358 10048905 ID=cds.MsaT030560.1;Parent=MsaT030560.1
Chr6 exon 10049476 10049574 10049476 ID=MsaT030560.1.exon2;Parent=MsaT030560.1
Chr6 CDS 10049476 10049574 10049476 ID=cds.MsaT030560.1;Parent=MsaT030560.1
Chr6 exon 10051055 10051257 10051055 ID=MsaT030560.1.exon3;Parent=MsaT030560.1
Chr6 CDS 10051055 10051257 10051055 ID=cds.MsaT030560.1;Parent=MsaT030560.1
Chr6 exon 10051540 10051563 10051540 ID=MsaT030560.1.exon4;Parent=MsaT030560.1
Chr6 CDS 10051540 10051563 10051540 ID=cds.MsaT030560.1;Parent=MsaT030560.1
Gene Sequence

>MsaT030560.1

ATGGAAGATCAACAACAAAACCAACATGTTCAGTCTCAAAGTTCCAATACTAATAATCCAAACAACACTGAAAAGAGTGAAACTGTGAGATCAAGATGGACACCAAAACCTGAACAAATCCTTATACTTGAATCCATTTTCAATAGTGGAATGGTCAATCCACCAAAAGATGAAACCGTGAGAATAAGAAAACTTCTTGAGAAATTTGGAGCTGTTGGTGATGCTAATGTTTTTTATTGGTTTCAGAATCGCCGCTCTCGCTCCCGACGCCGTCAGAGGCAGATGCAGGCCGCCGCCCAACTAAGCGGTGGCAGTACTGCAAATCCATATCACCAATACCAGTGCAGCACCAACAGTACCTCTCTGTCTCTTGGTGCTGCACTTGGTCTTGGTGGTTCCTCAACTTTCACTATGAATTCTTCTTCTTGTTCTACTTATAATAATAACTTTTCGGGCTCTACTCAAATCAATTTGCCTCAAATGGACAATACTTCAGCTGCTTCATCAATTTTGCAGCCTTCTGATAATGCTTCAAATTTCAACTATTACCCAGGATATGGGGGGAGTAATGTTTCAGGTGTGATCACAGTGTTTATCAATGGAGTTCCAACAGAAATGCCAAGAGGTACTGCAATTGACATGAAAACAATGTTTGGTGAAGATGTAATATTGGTTCATTCCTCTGGAGTCTCAGTTCCAACCAATGAGTTTGGTTTCTTGATGCAGAACTTGCAGCATGGTGAAAGCTACTATCTGGTGTCAAAGCAAGCACAAGCTTGA
Protein sequence

>MsaT030560.1

MEDQQQNQHVQSQSSNTNNPNNTEKSETVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGAVGDANVFYWFQNRRSRSRRRQRQMQAAAQLSGGSTANPYHQYQCSTNSTSLSLGAALGLGGSSTFTMNSSSCSTYNNNFSGSTQINLPQMDNTSAASSILQPSDNASNFNYYPGYGGSNVSGVITVFINGVPTEMPRGTAIDMKTMFGEDVILVHSSGVSVPTNEFGFLMQNLQHGESYYLVSKQAQA*