AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0506180

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0506180 MtrunA17_Chr3g0107461 89.441 161 17 0 1 161 1 161 1.75e-105 298
Msa0506180 MtrunA17_Chr4g0031421 78.195 133 29 0 29 161 1 133 8.49e-73 215
Msa0506180 MtrunA17_Chr3g0105791 77.444 133 30 0 29 161 1 133 1.71e-71 211
Msa0506180 MtrunA17_Chr3g0107381 55.195 154 68 1 1 154 1 153 1.76e-56 176
Msa0506180 MtrunA17_Chr3g0110131 50.323 155 76 1 1 155 1 154 1.93e-42 141
Msa0506180 MtrunA17_Chr2g0283941 43.590 156 88 0 5 160 5 160 2.07e-41 138
Msa0506180 MtrunA17_Chr2g0296861 48.387 155 79 1 1 155 1 154 1.37e-40 134
Msa0506180 MtrunA17_Chr5g0432691 39.610 154 92 1 1 154 1 153 3.88e-37 125
Msa0506180 MtrunA17_Chr8g0351751 41.509 159 91 1 1 157 1 159 1.57e-36 126
Msa0506180 MtrunA17_Chr4g0014321 38.312 154 95 0 1 154 1 154 3.15e-36 125
Msa0506180 MtrunA17_Chr4g0014131 43.478 161 91 0 1 161 1 161 6.05e-34 119
Msa0506180 MtrunA17_Chr4g0014031 43.590 156 88 0 1 156 1 156 6.14e-34 119
Msa0506180 MtrunA17_Chr2g0296831 51.282 117 57 0 1 117 1 117 1.31e-33 115
Msa0506180 MtrunA17_Chr3g0107331 40.397 151 89 1 3 153 2 151 1.68e-33 115
Msa0506180 MtrunA17_Chr3g0106421 44.697 132 73 0 29 160 1 132 1.70e-33 117
Msa0506180 MtrunA17_Chr3g0106501 44.961 129 71 0 29 157 1 129 4.13e-31 109
Msa0506180 MtrunA17_Chr4g0014121 39.744 156 94 0 1 156 29 184 4.76e-31 110
Msa0506180 MtrunA17_Chr4g0013041 37.791 172 86 4 1 157 1 166 5.25e-31 110
Msa0506180 MtrunA17_Chr5g0420351 38.854 157 94 2 1 157 1 155 7.97e-31 108
Msa0506180 MtrunA17_Chr3g0107351 36.774 155 97 1 3 157 2 155 3.90e-30 107
Msa0506180 MtrunA17_Chr1g0188681 38.854 157 94 2 1 157 1 155 8.89e-29 103
Msa0506180 MtrunA17_Chr1g0197461 34.839 155 99 2 3 157 2 154 2.03e-27 100
Msa0506180 MtrunA17_Chr3g0107341 36.129 155 98 1 3 157 2 155 2.08e-27 100
Msa0506180 MtrunA17_Chr3g0107361 36.129 155 98 1 3 157 2 155 2.58e-27 100
Msa0506180 MtrunA17_Chr1g0188661 38.608 158 93 3 1 157 1 155 1.99e-26 97.8
Msa0506180 MtrunA17_Chr4g0012761 38.854 157 94 2 1 157 1 155 2.84e-26 97.4
Msa0506180 MtrunA17_Chr7g0218151 36.943 157 97 2 1 157 1 155 1.03e-24 93.6
Msa0506180 MtrunA17_Chr1g0188651 37.267 161 97 2 1 161 1 157 1.49e-24 93.2
Msa0506180 MtrunA17_Chr1g0197261 32.911 158 102 3 1 157 1 155 5.16e-24 91.7
Msa0506180 MtrunA17_Chr1g0197321 33.333 159 101 3 1 157 1 156 1.27e-23 90.5
Msa0506180 MtrunA17_Chr1g0193311 36.709 158 96 3 1 157 1 155 1.55e-23 90.5
Msa0506180 MtrunA17_Chr4g0008701 27.703 148 103 1 3 150 6 149 6.30e-15 71.2
Msa0506180 MtrunA17_Chr7g0267601 28.947 114 81 0 5 118 8 121 1.52e-13 67.0
Msa0506180 MtrunA17_Chr6g0457851 29.204 113 73 3 1 107 11 122 5.40e-12 62.4
Msa0506180 MtrunA17_Chr3g0128721 26.271 118 87 0 5 122 8 125 8.95e-12 62.0
Msa0506180 MtrunA17_Chr1g0212151 28.448 116 76 3 1 110 1 115 9.74e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0506180 AT5G48670.1 50.000 156 75 2 1 155 1 154 1.82e-38 133
Msa0506180 AT3G05860.2 53.535 99 46 0 1 99 1 99 7.99e-31 110
Msa0506180 AT3G05860.3 53.535 99 46 0 1 99 1 99 1.57e-30 111
Msa0506180 AT3G05860.1 53.535 99 46 0 1 99 1 99 2.20e-30 111
Msa0506180 AT1G65330.1 41.892 148 85 1 3 150 2 148 2.41e-30 111
Msa0506180 AT1G65300.1 40.127 157 92 2 5 161 4 158 6.97e-30 110
Msa0506180 AT5G27810.1 53.933 89 41 0 29 117 1 89 4.04e-29 103
Msa0506180 AT5G26650.1 36.601 153 96 1 5 157 3 154 7.40e-26 101
Msa0506180 AT5G27960.1 35.294 153 98 1 5 157 3 154 1.47e-24 97.1
Msa0506180 AT1G31630.1 38.776 147 76 4 3 143 2 140 7.97e-24 95.5
Msa0506180 AT1G22590.2 33.750 160 89 2 1 157 1 146 2.54e-23 90.5
Msa0506180 AT1G31640.1 39.623 159 82 4 3 155 2 152 3.16e-23 95.1
Msa0506180 AT2G28700.1 32.667 150 100 1 1 150 1 149 1.34e-21 89.4
Msa0506180 AT5G26630.1 33.548 155 102 1 1 155 1 154 9.34e-21 85.1
Msa0506180 AT5G06500.1 33.333 147 88 3 1 147 1 137 5.69e-19 80.9
Msa0506180 AT2G40210.1 34.653 101 66 0 1 101 1 101 2.34e-14 69.7
Msa0506180 AT5G26580.1 37.624 101 49 1 1 101 1 87 8.47e-14 67.8
Msa0506180 AT3G57230.1 29.012 162 100 4 1 161 1 148 3.96e-12 62.4
Msa0506180 AT3G57230.4 29.012 162 100 4 1 161 1 148 3.96e-12 62.4

Find 34 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAGTCATTTCCTGCTTTC+TGG 0.078990 3_4:-52395580 None:intergenic
ATTCATACCACAGAATTTAA+TGG 0.196701 3_4:+52395618 Msa0506180:CDS
CAGGTTTGGCCATCAGATTC+AGG 0.224706 3_4:+52395423 Msa0506180:CDS
CCTGGGCTTGAGGATTGTTT+TGG 0.292217 3_4:-52395404 None:intergenic
GATGAAATTAGCACTCTTTG+TGG 0.382102 3_4:+52395354 Msa0506180:CDS
GTTCAGGAGTTTGCCTGGAC+TGG 0.382826 3_4:+52395467 Msa0506180:CDS
CTGAATCTGATGGCCAAACC+TGG 0.394792 3_4:-52395422 None:intergenic
GAAGTGTGATATCCAGGTTC+AGG 0.406864 3_4:+52395451 Msa0506180:CDS
AGGTTTGGCCATCAGATTCA+GGG 0.444978 3_4:+52395424 Msa0506180:CDS
TCCAGGTTCAGGAGTTTGCC+TGG 0.447666 3_4:+52395462 Msa0506180:CDS
ACAATCCTCAAGCCCAGGTT+TGG 0.451431 3_4:+52395409 Msa0506180:CDS
TATTCTTGAGGCAAAGCATT+GGG 0.452810 3_4:+52395520 Msa0506180:CDS
GGGTTAGAAGTGTGATATCC+AGG 0.506627 3_4:+52395445 Msa0506180:CDS
CACTATCATGGCTAGAGGTA+AGG 0.508320 3_4:+52395057 None:intergenic
TCCAGGCAAACTCCTGAACC+TGG 0.517673 3_4:-52395463 None:intergenic
AAGGAAGGAAACCAGAAAGC+AGG 0.520416 3_4:+52395569 Msa0506180:CDS
GGAGGATGACATTCAGAAAG+AGG 0.520726 3_4:+52395113 Msa0506180:CDS
CAAATTCCCAGCAATAAAAG+AGG 0.540558 3_4:-52395676 None:intergenic
ACTCTTTGTGGAATAGAAGC+TGG 0.543874 3_4:+52395366 Msa0506180:CDS
TAAATATCCATTAAATTCTG+TGG 0.554522 3_4:-52395625 None:intergenic
GTATTCTTGAGGCAAAGCAT+TGG 0.555152 3_4:+52395519 Msa0506180:CDS
GATGGCCAAACCTGGGCTTG+AGG 0.558655 3_4:-52395414 None:intergenic
CCAAAACAATCCTCAAGCCC+AGG 0.591446 3_4:+52395404 Msa0506180:CDS
TGAATCTGATGGCCAAACCT+GGG 0.592740 3_4:-52395421 None:intergenic
GAGGTCGATCAAAAGATGAA+AGG 0.605953 3_4:+52395702 Msa0506180:CDS
CTTCTAACCCCTGAATCTGA+TGG 0.608216 3_4:-52395432 None:intergenic
ATGAGCAGTTGATGAAACAA+AGG 0.608842 3_4:+52395550 Msa0506180:CDS
ACATAACATGTGACTCGAAG+AGG 0.616371 3_4:+52395092 Msa0506180:CDS
GGTTTGGCCATCAGATTCAG+GGG 0.621539 3_4:+52395425 Msa0506180:CDS
GCAGTTGATGAAACAAAGGA+AGG 0.627441 3_4:+52395554 Msa0506180:CDS
TATTGCTGGGAATTTGAGGG+AGG 0.633594 3_4:+52395683 Msa0506180:CDS
TAACATGTGACTCGAAGAGG+AGG 0.651743 3_4:+52395095 Msa0506180:CDS
ATCCTCACTATCATGGCTAG+AGG 0.659018 3_4:+52395052 None:intergenic
TGGATCAAGAGGTATTCTTG+AGG 0.709854 3_4:+52395508 Msa0506180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATTTAGAATTTTACTAT+AGG + chr3_4:52395279-52395298 Msa0506180:intron 10.0%
!!! ATGGATATATTTTTTTTAAT+AGG + chr3_4:52395315-52395334 Msa0506180:intron 10.0%
!! TATAGGTTATATATTGTTTA+TGG + chr3_4:52395296-52395315 Msa0506180:intron 15.0%
!! TAAATATCCATTAAATTCTG+TGG - chr3_4:52395628-52395647 None:intergenic 20.0%
! ATTCATACCACAGAATTTAA+TGG + chr3_4:52395618-52395637 Msa0506180:CDS 25.0%
ACATTCAGAAAGAGGAAAAA+TGG + chr3_4:52395121-52395140 Msa0506180:CDS 30.0%
TATGTATGATATGCAAAGAG+AGG - chr3_4:52395157-52395176 None:intergenic 30.0%
ACTGGAACAAAGTAAAAAGA+TGG + chr3_4:52395485-52395504 Msa0506180:CDS 30.0%
! ATTTGTCCTCTTTTATTGCT+GGG + chr3_4:52395670-52395689 Msa0506180:CDS 30.0%
! TTTTATTGCTGGGAATTTGA+GGG + chr3_4:52395680-52395699 Msa0506180:CDS 30.0%
GATGAAATTAGCACTCTTTG+TGG + chr3_4:52395354-52395373 Msa0506180:CDS 35.0%
! TTTTTACTTTGTTCCAGTCC+AGG - chr3_4:52395483-52395502 None:intergenic 35.0%
GGAACAAAGTAAAAAGATGG+TGG + chr3_4:52395488-52395507 Msa0506180:CDS 35.0%
!! TAAAAAGATGGTGGATCAAG+AGG + chr3_4:52395497-52395516 Msa0506180:CDS 35.0%
! TATTCTTGAGGCAAAGCATT+GGG + chr3_4:52395520-52395539 Msa0506180:CDS 35.0%
!! ATGAGCAGTTGATGAAACAA+AGG + chr3_4:52395550-52395569 Msa0506180:CDS 35.0%
ATTAGTCATTTCCTGCTTTC+TGG - chr3_4:52395583-52395602 None:intergenic 35.0%
! GATTTGTCCTCTTTTATTGC+TGG + chr3_4:52395669-52395688 Msa0506180:CDS 35.0%
CAAATTCCCAGCAATAAAAG+AGG - chr3_4:52395679-52395698 None:intergenic 35.0%
! CTTTTATTGCTGGGAATTTG+AGG + chr3_4:52395679-52395698 Msa0506180:CDS 35.0%
ACATAACATGTGACTCGAAG+AGG + chr3_4:52395092-52395111 Msa0506180:CDS 40.0%
ACTCTTTGTGGAATAGAAGC+TGG + chr3_4:52395366-52395385 Msa0506180:CDS 40.0%
!! TGGATCAAGAGGTATTCTTG+AGG + chr3_4:52395508-52395527 Msa0506180:CDS 40.0%
GTATTCTTGAGGCAAAGCAT+TGG + chr3_4:52395519-52395538 Msa0506180:CDS 40.0%
!! GCAGTTGATGAAACAAAGGA+AGG + chr3_4:52395554-52395573 Msa0506180:CDS 40.0%
GAGGTCGATCAAAAGATGAA+AGG + chr3_4:52395702-52395721 Msa0506180:CDS 40.0%
TAACATGTGACTCGAAGAGG+AGG + chr3_4:52395095-52395114 Msa0506180:CDS 45.0%
GGAGGATGACATTCAGAAAG+AGG + chr3_4:52395113-52395132 Msa0506180:CDS 45.0%
TGAATCTGATGGCCAAACCT+GGG - chr3_4:52395424-52395443 None:intergenic 45.0%
AGGTTTGGCCATCAGATTCA+GGG + chr3_4:52395424-52395443 Msa0506180:CDS 45.0%
CTTCTAACCCCTGAATCTGA+TGG - chr3_4:52395435-52395454 None:intergenic 45.0%
! GGGTTAGAAGTGTGATATCC+AGG + chr3_4:52395445-52395464 Msa0506180:CDS 45.0%
GAAGTGTGATATCCAGGTTC+AGG + chr3_4:52395451-52395470 Msa0506180:CDS 45.0%
AAGGAAGGAAACCAGAAAGC+AGG + chr3_4:52395569-52395588 Msa0506180:CDS 45.0%
TATTGCTGGGAATTTGAGGG+AGG + chr3_4:52395683-52395702 Msa0506180:CDS 45.0%
! CCTGGGCTTGAGGATTGTTT+TGG - chr3_4:52395407-52395426 None:intergenic 50.0%
CCAAAACAATCCTCAAGCCC+AGG + chr3_4:52395404-52395423 Msa0506180:CDS 50.0%
ACAATCCTCAAGCCCAGGTT+TGG + chr3_4:52395409-52395428 Msa0506180:CDS 50.0%
CTGAATCTGATGGCCAAACC+TGG - chr3_4:52395425-52395444 None:intergenic 50.0%
CAGGTTTGGCCATCAGATTC+AGG + chr3_4:52395423-52395442 Msa0506180:CDS 50.0%
GGTTTGGCCATCAGATTCAG+GGG + chr3_4:52395425-52395444 Msa0506180:CDS 50.0%
TCCAGGTTCAGGAGTTTGCC+TGG + chr3_4:52395462-52395481 Msa0506180:CDS 55.0%
TCCAGGCAAACTCCTGAACC+TGG - chr3_4:52395466-52395485 None:intergenic 55.0%
GTTCAGGAGTTTGCCTGGAC+TGG + chr3_4:52395467-52395486 Msa0506180:CDS 55.0%
GATGGCCAAACCTGGGCTTG+AGG - chr3_4:52395417-52395436 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 52395064 52395743 52395064 ID=Msa0506180;Name=Msa0506180
chr3_4 mRNA 52395064 52395743 52395064 ID=Msa0506180-mRNA-1;Parent=Msa0506180;Name=Msa0506180-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|0|0|1|1|1|2|0|161
chr3_4 exon 52395064 52395142 52395064 ID=Msa0506180-mRNA-1:exon:11417;Parent=Msa0506180-mRNA-1
chr3_4 exon 52395337 52395743 52395337 ID=Msa0506180-mRNA-1:exon:11418;Parent=Msa0506180-mRNA-1
chr3_4 CDS 52395064 52395142 52395064 ID=Msa0506180-mRNA-1:cds;Parent=Msa0506180-mRNA-1
chr3_4 CDS 52395337 52395743 52395337 ID=Msa0506180-mRNA-1:cds;Parent=Msa0506180-mRNA-1
Gene Sequence

>Msa0506180

ATGGCTAGAGGTAAGGTGAAACTAGCATACATAACATGTGACTCGAAGAGGAGGATGACATTCAGAAAGAGGAAAAATGGAATTATGAAGAAGATTGATGAAATTAGCACTCTTTGTGGAATAGAAGCTGGTGCAATAATTTACGACCAAAACAATCCTCAAGCCCAGGTTTGGCCATCAGATTCAGGGGTTAGAAGTGTGATATCCAGGTTCAGGAGTTTGCCTGGACTGGAACAAAGTAAAAAGATGGTGGATCAAGAGGTATTCTTGAGGCAAAGCATTGGGAAAGTCTATGAGCAGTTGATGAAACAAAGGAAGGAAACCAGAAAGCAGGAAATGACTAATATCATTCATCATTTCATTCATACCACAGAATTTAATGGATATTTAATGAGCAAACATGATCTTAATGATTTGTCCTCTTTTATTGCTGGGAATTTGAGGGAGGTCGATCAAAAGATGAAAGGAATGCTAATCGAAGATTGA
Protein sequence

>Msa0506180

MARGKVKLAYITCDSKRRMTFRKRKNGIMKKIDEISTLCGIEAGAIIYDQNNPQAQVWPSDSGVRSVISRFRSLPGLEQSKKMVDQEVFLRQSIGKVYEQLMKQRKETRKQEMTNIIHHFIHTTEFNGYLMSKHDLNDLSSFIAGNLREVDQKMKGMLIED*