AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0934540

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0934540 MtrunA17_Chr6g0449651 93.571 140 9 0 1 140 59 198 3.13e-97 278
Msa0934540 MtrunA17_Chr6g0449641 87.234 141 18 0 1 141 1 141 5.78e-90 257
Msa0934540 MtrunA17_Chr7g0227511 84.821 112 17 0 2 113 4 115 9.48e-69 205
Msa0934540 MtrunA17_Chr3g0117121 79.130 115 23 1 1 114 1 115 3.57e-64 194
Msa0934540 MtrunA17_Chr4g0058651 78.505 107 23 0 7 113 9 115 2.61e-62 189
Msa0934540 MtrunA17_Chr3g0115431 64.602 113 40 0 1 113 1 113 9.25e-48 153
Msa0934540 MtrunA17_Chr2g0311601 61.607 112 42 1 8 118 12 123 9.45e-48 151
Msa0934540 MtrunA17_Chr4g0043421 62.857 105 39 0 8 112 14 118 1.65e-47 151
Msa0934540 MtrunA17_Chr5g0437571 50.000 146 62 1 7 141 4 149 2.99e-47 150
Msa0934540 MtrunA17_Chr8g0353981 66.964 112 35 1 1 112 1 110 3.74e-46 149
Msa0934540 MtrunA17_Chr5g0402611 63.636 110 40 0 3 112 2 111 3.83e-46 152
Msa0934540 MtrunA17_Chr3g0114061 52.857 140 57 3 6 136 5 144 1.50e-45 145
Msa0934540 MtrunA17_Chr3g0097221 62.727 110 41 0 4 113 2 111 6.31e-44 145
Msa0934540 MtrunA17_Chr3g0106101 52.000 125 58 1 7 129 5 129 1.07e-43 141
Msa0934540 MtrunA17_Chr5g0437401 62.264 106 40 0 6 111 8 113 9.75e-42 136
Msa0934540 MtrunA17_Chr3g0129071 57.143 105 45 0 8 112 46 150 2.52e-40 135
Msa0934540 MtrunA17_Chr5g0438091 56.075 107 47 0 6 112 36 142 3.03e-40 133
Msa0934540 MtrunA17_Chr3g0113891 64.948 97 34 0 6 102 11 107 3.08e-40 133
Msa0934540 MtrunA17_Chr4g0030001 44.366 142 66 2 8 136 23 164 3.59e-40 133
Msa0934540 MtrunA17_Chr1g0200201 51.327 113 55 0 10 122 73 185 4.71e-38 129
Msa0934540 MtrunA17_Chr1g0184281 50.000 142 63 4 6 139 12 153 4.08e-37 125
Msa0934540 MtrunA17_Chr7g0260971 57.407 108 45 1 3 109 8 115 5.58e-37 125
Msa0934540 MtrunA17_Chr5g0432451 54.867 113 51 0 8 120 42 154 3.57e-36 124
Msa0934540 MtrunA17_Chr8g0351701 54.286 105 47 1 9 112 23 127 9.81e-34 117
Msa0934540 MtrunA17_Chr8g0351721 55.769 104 45 1 7 109 16 119 2.65e-33 116
Msa0934540 MtrunA17_Chr6g0460951 48.276 116 57 2 8 120 39 154 5.19e-33 115
Msa0934540 MtrunA17_Chr7g0245871 57.895 95 39 1 9 102 27 121 1.01e-32 115
Msa0934540 MtrunA17_Chr5g0435641 54.639 97 43 1 8 103 6 102 2.48e-32 113
Msa0934540 MtrunA17_Chr8g0374601 45.217 115 63 0 9 123 26 140 1.92e-31 113
Msa0934540 MtrunA17_Chr7g0261031 54.082 98 44 1 6 102 5 102 1.13e-30 109
Msa0934540 MtrunA17_Chr5g0444351 48.000 100 52 0 10 109 6 105 1.79e-30 107
Msa0934540 MtrunA17_Chr1g0184271 53.684 95 43 1 9 102 12 106 3.21e-30 108
Msa0934540 MtrunA17_Chr7g0225111 45.098 102 56 0 8 109 4 105 5.76e-30 104
Msa0934540 MtrunA17_Chr8g0374591 44.231 104 58 0 9 112 8 111 9.19e-30 104
Msa0934540 MtrunA17_Chr6g0452661 45.918 98 52 1 7 103 7 104 2.53e-28 104
Msa0934540 MtrunA17_Chr4g0059901 47.000 100 53 0 10 109 11 110 9.73e-28 103
Msa0934540 MtrunA17_Chr7g0245861 53.763 93 40 2 6 95 9 101 1.65e-27 99.4
Msa0934540 MtrunA17_Chr6g0452691 42.593 108 61 1 1 107 1 108 1.13e-25 95.9
Msa0934540 MtrunA17_Chr6g0452671 42.000 100 58 0 6 105 8 107 1.54e-25 95.9
Msa0934540 MtrunA17_Chr6g0460941 48.864 88 44 1 9 95 7 94 5.84e-25 91.7
Msa0934540 MtrunA17_Chr8g0374581 46.667 105 55 1 9 112 8 112 7.93e-25 94.7
Msa0934540 MtrunA17_Chr8g0342351 40.777 103 61 0 10 112 13 115 1.01e-24 95.5
Msa0934540 MtrunA17_Chr2g0330201 43.750 96 54 0 10 105 20 115 2.08e-24 95.1
Msa0934540 MtrunA17_Chr5g0439111 43.878 98 54 1 7 103 7 104 6.91e-22 87.4
Msa0934540 MtrunA17_Chr4g0055441 40.000 95 56 1 10 103 3 97 1.84e-21 84.3
Msa0934540 MtrunA17_Chr4g0040831 43.011 93 53 0 10 102 16 108 5.07e-21 84.3
Msa0934540 MtrunA17_Chr2g0326041 60.345 58 23 0 1 58 25 82 7.13e-21 80.9
Msa0934540 MtrunA17_Chr4g0046201 32.955 88 59 0 10 97 7 94 3.61e-16 72.8
Msa0934540 MtrunA17_Chr2g0326051 49.275 69 35 0 54 122 5 73 1.61e-15 68.2
Msa0934540 MtrunA17_Chr1g0207471 29.655 145 88 2 10 140 3 147 4.87e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0934540 AT3G27650.1 79.091 110 23 0 3 112 33 142 3.33e-64 193
Msa0934540 AT5G63090.4 72.441 127 33 1 1 125 1 127 5.94e-63 191
Msa0934540 AT5G63090.3 72.441 127 33 1 1 125 1 127 5.94e-63 191
Msa0934540 AT5G63090.2 72.441 127 33 1 1 125 1 127 5.94e-63 191
Msa0934540 AT5G63090.1 72.441 127 33 1 1 125 1 127 5.94e-63 191
Msa0934540 AT2G30130.1 57.627 118 50 0 7 124 6 123 6.91e-47 150
Msa0934540 AT1G65620.1 64.655 116 41 0 1 116 1 116 8.07e-47 150
Msa0934540 AT1G65620.4 64.655 116 41 0 1 116 1 116 8.07e-47 150
Msa0934540 AT1G65620.3 64.655 116 41 0 1 116 1 116 8.07e-47 150
Msa0934540 AT1G65620.5 64.655 116 41 0 1 116 1 116 8.07e-47 150
Msa0934540 AT1G65620.2 64.655 116 41 0 1 116 1 116 8.07e-47 150
Msa0934540 AT2G23660.2 60.748 107 42 0 6 112 2 108 1.93e-45 150
Msa0934540 AT2G23660.3 60.748 107 42 0 6 112 2 108 1.93e-45 150
Msa0934540 AT2G23660.1 60.748 107 42 0 6 112 2 108 1.93e-45 150
Msa0934540 AT5G66870.1 61.062 113 42 1 1 113 1 111 1.62e-44 148
Msa0934540 AT1G31320.1 68.182 88 28 0 8 95 12 99 7.79e-43 139
Msa0934540 AT1G16530.1 60.577 104 40 1 8 110 13 116 4.30e-41 135
Msa0934540 AT2G30340.1 53.982 113 52 0 8 120 51 163 5.39e-41 137
Msa0934540 AT2G30340.2 53.982 113 52 0 8 120 52 164 5.52e-41 137
Msa0934540 AT1G07900.1 52.174 115 55 0 8 122 32 146 2.91e-40 133
Msa0934540 AT2G28500.1 53.043 115 54 0 8 122 54 168 1.43e-39 133
Msa0934540 AT3G11090.1 55.856 111 47 1 6 116 8 116 8.77e-39 129
Msa0934540 AT2G40470.2 58.333 108 45 0 8 115 19 126 6.94e-38 127
Msa0934540 AT2G40470.1 58.879 107 44 0 8 114 44 150 1.23e-37 128
Msa0934540 AT3G26620.1 45.082 122 61 1 10 131 6 121 3.66e-37 123
Msa0934540 AT3G26660.1 44.262 122 62 1 10 131 6 121 1.23e-36 122
Msa0934540 AT3G03760.1 55.769 104 45 1 8 110 50 153 3.80e-36 125
Msa0934540 AT2G42430.1 52.500 120 54 2 6 124 12 129 5.85e-35 121
Msa0934540 AT4G00210.1 56.863 102 43 1 9 109 11 112 9.84e-34 117
Msa0934540 AT4G00220.1 56.566 99 42 1 12 109 20 118 6.05e-33 116
Msa0934540 AT2G45420.1 56.566 99 42 1 12 109 40 138 3.67e-32 115
Msa0934540 AT5G06080.1 45.378 119 64 1 8 125 6 124 1.84e-31 110
Msa0934540 AT2G45410.1 45.185 135 67 3 12 139 19 153 8.56e-31 109
Msa0934540 AT2G31310.1 51.042 96 46 1 8 102 6 101 4.28e-30 107
Msa0934540 AT2G42440.1 48.485 99 50 1 6 103 4 102 8.89e-30 108
Msa0934540 AT3G58190.1 52.083 96 45 1 9 103 11 106 9.30e-30 107
Msa0934540 AT3G50510.1 45.714 105 57 0 8 112 11 115 7.27e-29 104
Msa0934540 AT3G50510.2 45.714 105 57 0 8 112 11 115 7.27e-29 104
Msa0934540 AT3G13850.1 40.777 103 61 0 10 112 37 139 9.22e-26 98.6
Msa0934540 AT3G47870.1 39.423 104 63 0 6 109 33 136 2.96e-25 98.2
Msa0934540 AT5G35900.1 36.719 128 74 1 10 137 6 126 1.62e-24 94.0
Msa0934540 AT1G72980.1 40.187 107 64 0 3 109 7 113 2.67e-22 88.2
Msa0934540 AT1G06280.1 46.753 77 41 0 10 86 25 101 1.06e-18 79.0
Msa0934540 AT4G22700.1 34.127 126 81 2 10 134 6 130 3.70e-17 74.3
Msa0934540 AT2G19820.1 37.363 91 56 1 6 95 9 99 3.47e-16 70.1
Msa0934540 AT5G15060.1 38.356 73 43 1 10 80 18 90 5.66e-13 62.4
Msa0934540 AT3G27940.3 35.616 73 47 0 8 80 4 76 6.54e-12 59.7
Msa0934540 AT3G27940.1 35.616 73 47 0 8 80 4 76 6.54e-12 59.7
Msa0934540 AT3G27940.2 35.616 73 47 0 8 80 4 76 6.54e-12 59.7

Find 24 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCAATGTTCACAAAGTATT+TGG 0.182732 6_3:+4382309 Msa0934540:CDS
ACAAATTTATGAGGCTCTTC+TGG 0.285297 6_3:-4382288 None:intergenic
AATCCTTGCTTCAGCTTCAT+AGG 0.299183 6_3:-4382403 None:intergenic
GGCTCTTCTGGTGGGAAATA+AGG 0.304156 6_3:-4382276 None:intergenic
GGTTCTTCTTCTCTTGGTCT+TGG 0.305065 6_3:+4382540 Msa0934540:CDS
CATGAAGGTTCTTCTTCTCT+TGG 0.312102 6_3:+4382534 Msa0934540:CDS
TTGTAGCATCAAGTTCCTTT+TGG 0.323860 6_3:-4382488 None:intergenic
TGAACATTGACAAATTTATG+AGG 0.442843 6_3:-4382297 None:intergenic
GGAGCTATTTCAGCGCTTCA+AGG 0.465943 6_3:+4382450 Msa0934540:CDS
GTGTCATTGCTAAAATTTGA+AGG 0.469256 6_3:-4382594 None:intergenic
ATGAAGTCTTACCTCATCAA+AGG 0.530030 6_3:+4382358 Msa0934540:CDS
ACAACTCTGTAGGCTCCAAA+AGG 0.532237 6_3:+4382473 Msa0934540:CDS
TGAAGTCTTACCTCATCAAA+GGG 0.542775 6_3:+4382359 Msa0934540:CDS
AATTTATGAGGCTCTTCTGG+TGG 0.551183 6_3:-4382285 None:intergenic
AATCCAGTGTATGGTTGTGT+TGG 0.555823 6_3:+4382429 Msa0934540:CDS
TGTCATTGCTAAAATTTGAA+GGG 0.561675 6_3:-4382593 None:intergenic
ATTTATGAGGCTCTTCTGGT+GGG 0.585354 6_3:-4382284 None:intergenic
AGGAACTTGCAAGCAGCACA+TGG 0.591215 6_3:-4382219 None:intergenic
CGCTTCAAGGACAACTCTGT+AGG 0.607990 6_3:+4382463 Msa0934540:CDS
GCTCCAACACAACCATACAC+TGG 0.615806 6_3:-4382432 None:intergenic
TTGCCTATGAAGCTGAAGCA+AGG 0.624248 6_3:+4382400 Msa0934540:CDS
TGGAGAATTTGAGTAGCTTG+AGG 0.626001 6_3:-4382199 None:intergenic
ACTGTATCCTCCCTTTGATG+AGG 0.648075 6_3:-4382369 None:intergenic
AGTCTTACCTCATCAAAGGG+AGG 0.699522 6_3:+4382362 Msa0934540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAACATTGACAAATTTATG+AGG - chr6_3:4382300-4382319 None:intergenic 25.0%
! TGTCATTGCTAAAATTTGAA+GGG - chr6_3:4382596-4382615 None:intergenic 25.0%
! CTGATATGCATTTTCTTCTT+AGG - chr6_3:4382242-4382261 None:intergenic 30.0%
! GTCAATGTTCACAAAGTATT+TGG + chr6_3:4382309-4382328 Msa0934540:CDS 30.0%
AGGATTAAAAATCCAGTGTA+TGG + chr6_3:4382420-4382439 Msa0934540:CDS 30.0%
!! TTGATTCGTTTTACTCATGA+AGG + chr6_3:4382519-4382538 Msa0934540:CDS 30.0%
! GTGTCATTGCTAAAATTTGA+AGG - chr6_3:4382597-4382616 None:intergenic 30.0%
ACAAATTTATGAGGCTCTTC+TGG - chr6_3:4382291-4382310 None:intergenic 35.0%
ATGAAGTCTTACCTCATCAA+AGG + chr6_3:4382358-4382377 Msa0934540:CDS 35.0%
TGAAGTCTTACCTCATCAAA+GGG + chr6_3:4382359-4382378 Msa0934540:CDS 35.0%
! TTGTAGCATCAAGTTCCTTT+TGG - chr6_3:4382491-4382510 None:intergenic 35.0%
TGGAGAATTTGAGTAGCTTG+AGG - chr6_3:4382202-4382221 None:intergenic 40.0%
ATTTATGAGGCTCTTCTGGT+GGG - chr6_3:4382287-4382306 None:intergenic 40.0%
AATTTATGAGGCTCTTCTGG+TGG - chr6_3:4382288-4382307 None:intergenic 40.0%
AATCCTTGCTTCAGCTTCAT+AGG - chr6_3:4382406-4382425 None:intergenic 40.0%
AATCCAGTGTATGGTTGTGT+TGG + chr6_3:4382429-4382448 Msa0934540:CDS 40.0%
CATGAAGGTTCTTCTTCTCT+TGG + chr6_3:4382534-4382553 Msa0934540:CDS 40.0%
AGTCTTACCTCATCAAAGGG+AGG + chr6_3:4382362-4382381 Msa0934540:CDS 45.0%
ACTGTATCCTCCCTTTGATG+AGG - chr6_3:4382372-4382391 None:intergenic 45.0%
TTGCCTATGAAGCTGAAGCA+AGG + chr6_3:4382400-4382419 Msa0934540:CDS 45.0%
ACAACTCTGTAGGCTCCAAA+AGG + chr6_3:4382473-4382492 Msa0934540:CDS 45.0%
GGTTCTTCTTCTCTTGGTCT+TGG + chr6_3:4382540-4382559 Msa0934540:CDS 45.0%
AGGAACTTGCAAGCAGCACA+TGG - chr6_3:4382222-4382241 None:intergenic 50.0%
GGCTCTTCTGGTGGGAAATA+AGG - chr6_3:4382279-4382298 None:intergenic 50.0%
GCTCCAACACAACCATACAC+TGG - chr6_3:4382435-4382454 None:intergenic 50.0%
! GGAGCTATTTCAGCGCTTCA+AGG + chr6_3:4382450-4382469 Msa0934540:CDS 50.0%
CGCTTCAAGGACAACTCTGT+AGG + chr6_3:4382463-4382482 Msa0934540:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 4382195 4382620 4382195 ID=Msa0934540;Name=Msa0934540
chr6_3 mRNA 4382195 4382620 4382195 ID=Msa0934540-mRNA-1;Parent=Msa0934540;Name=Msa0934540-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|141
chr6_3 exon 4382195 4382620 4382195 ID=Msa0934540-mRNA-1:exon:1323;Parent=Msa0934540-mRNA-1
chr6_3 CDS 4382195 4382620 4382195 ID=Msa0934540-mRNA-1:cds;Parent=Msa0934540-mRNA-1
Gene Sequence

>Msa0934540

ATGGCCTCAAGCTACTCAAATTCTCCATGTGCTGCTTGCAAGTTCCTAAGAAGAAAATGCATATCAGATTGCATTTTTGCACCTTATTTCCCACCAGAAGAGCCTCATAAATTTGTCAATGTTCACAAAGTATTTGGTGCAAGCAATGTTAGCAAAATTCTTAATGAAGTCTTACCTCATCAAAGGGAGGATACAGTGAGTTCTCTTGCCTATGAAGCTGAAGCAAGGATTAAAAATCCAGTGTATGGTTGTGTTGGAGCTATTTCAGCGCTTCAAGGACAACTCTGTAGGCTCCAAAAGGAACTTGATGCTACAAATGCTGATTTGATTCGTTTTACTCATGAAGGTTCTTCTTCTCTTGGTCTTGGACATGTTCACTCTGATGACTTTTTAAATTACCCTTCAAATTTTAGCAATGACACGTGA
Protein sequence

>Msa0934540

MASSYSNSPCAACKFLRRKCISDCIFAPYFPPEEPHKFVNVHKVFGASNVSKILNEVLPHQREDTVSSLAYEAEARIKNPVYGCVGAISALQGQLCRLQKELDATNADLIRFTHEGSSSLGLGHVHSDDFLNYPSNFSNDT*