AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0933690

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0933690 MtrunA17_Chr6g0449651 92.958 142 10 0 1 142 58 199 2.43e-98 281
Msa0933690 MtrunA17_Chr6g0449641 87.857 140 17 0 2 141 1 140 8.84e-90 257
Msa0933690 MtrunA17_Chr7g0227511 68.387 155 32 4 3 141 4 157 4.73e-69 206
Msa0933690 MtrunA17_Chr3g0117121 78.261 115 25 0 1 115 1 115 8.72e-64 193
Msa0933690 MtrunA17_Chr4g0058651 79.439 107 22 0 8 114 9 115 5.71e-62 188
Msa0933690 MtrunA17_Chr5g0437571 52.055 146 59 1 8 142 4 149 8.00e-49 154
Msa0933690 MtrunA17_Chr4g0043421 54.074 135 61 1 9 142 14 148 1.07e-48 154
Msa0933690 MtrunA17_Chr2g0311601 60.714 112 43 1 9 119 12 123 3.12e-48 152
Msa0933690 MtrunA17_Chr3g0115431 63.717 113 41 0 2 114 1 113 9.33e-47 150
Msa0933690 MtrunA17_Chr8g0353981 67.857 112 34 1 2 113 1 110 2.18e-46 150
Msa0933690 MtrunA17_Chr5g0402611 64.545 110 39 0 4 113 2 111 2.23e-46 152
Msa0933690 MtrunA17_Chr3g0106101 53.600 125 56 1 8 130 5 129 2.27e-45 145
Msa0933690 MtrunA17_Chr3g0114061 62.857 105 39 0 7 111 5 109 6.37e-45 144
Msa0933690 MtrunA17_Chr3g0097221 64.220 109 39 0 5 113 2 110 5.01e-44 145
Msa0933690 MtrunA17_Chr3g0113891 67.010 97 32 0 7 103 11 107 1.74e-42 139
Msa0933690 MtrunA17_Chr5g0437401 63.208 106 39 0 7 112 8 113 2.02e-42 138
Msa0933690 MtrunA17_Chr5g0438091 57.944 107 45 0 7 113 36 142 2.19e-41 136
Msa0933690 MtrunA17_Chr3g0129071 59.048 105 43 0 9 113 46 150 2.90e-41 137
Msa0933690 MtrunA17_Chr4g0030001 44.366 142 66 2 9 137 23 164 2.34e-38 128
Msa0933690 MtrunA17_Chr7g0260971 58.333 108 44 1 4 110 8 115 1.74e-37 127
Msa0933690 MtrunA17_Chr5g0432451 56.250 112 49 0 9 120 42 153 7.73e-37 125
Msa0933690 MtrunA17_Chr1g0184281 58.491 106 43 1 7 111 12 117 5.75e-36 122
Msa0933690 MtrunA17_Chr1g0200201 54.455 101 46 0 11 111 73 173 1.05e-35 122
Msa0933690 MtrunA17_Chr7g0245871 60.000 95 37 1 10 103 27 121 6.53e-34 118
Msa0933690 MtrunA17_Chr8g0351721 52.941 119 52 2 7 121 15 133 6.82e-34 117
Msa0933690 MtrunA17_Chr8g0351701 55.046 109 46 2 10 117 23 129 8.20e-34 118
Msa0933690 MtrunA17_Chr6g0460951 48.276 116 57 2 9 121 39 154 2.07e-32 114
Msa0933690 MtrunA17_Chr5g0435641 53.608 97 44 1 9 104 6 102 6.04e-32 112
Msa0933690 MtrunA17_Chr5g0444351 49.000 100 51 0 11 110 6 105 1.21e-31 110
Msa0933690 MtrunA17_Chr7g0261031 55.102 98 43 1 7 103 5 102 4.81e-31 110
Msa0933690 MtrunA17_Chr8g0374591 44.231 104 58 0 10 113 8 111 2.24e-30 106
Msa0933690 MtrunA17_Chr7g0225111 45.098 102 56 0 9 110 4 105 4.26e-30 105
Msa0933690 MtrunA17_Chr1g0184271 52.632 95 44 1 10 103 12 106 7.27e-30 108
Msa0933690 MtrunA17_Chr8g0374601 46.154 104 56 0 10 113 26 129 1.68e-29 108
Msa0933690 MtrunA17_Chr6g0452661 45.918 98 52 1 8 104 7 104 6.53e-29 105
Msa0933690 MtrunA17_Chr4g0059901 47.000 100 53 0 11 110 11 110 1.65e-28 105
Msa0933690 MtrunA17_Chr7g0245861 56.383 94 36 3 7 96 9 101 4.02e-28 100
Msa0933690 MtrunA17_Chr6g0452671 42.000 100 58 0 7 106 8 107 1.06e-26 99.0
Msa0933690 MtrunA17_Chr6g0452691 43.689 103 57 1 7 108 6 108 1.30e-26 98.2
Msa0933690 MtrunA17_Chr6g0460941 50.000 88 43 1 10 96 7 94 3.73e-26 94.7
Msa0933690 MtrunA17_Chr8g0374581 46.667 105 55 1 10 113 8 112 4.13e-26 98.2
Msa0933690 MtrunA17_Chr8g0342351 40.777 103 61 0 11 113 13 115 2.35e-24 94.4
Msa0933690 MtrunA17_Chr2g0330201 42.708 96 55 0 11 106 20 115 8.54e-24 93.6
Msa0933690 MtrunA17_Chr5g0439111 42.857 98 55 1 8 104 7 104 3.19e-22 88.2
Msa0933690 MtrunA17_Chr4g0040831 43.011 93 53 0 11 103 16 108 6.21e-22 86.7
Msa0933690 MtrunA17_Chr4g0055441 40.000 95 56 1 11 104 3 97 8.21e-22 85.1
Msa0933690 MtrunA17_Chr2g0326041 58.621 58 24 0 2 59 25 82 2.59e-20 79.3
Msa0933690 MtrunA17_Chr4g0046201 32.955 88 59 0 11 98 7 94 2.15e-15 70.9
Msa0933690 MtrunA17_Chr2g0326051 47.826 69 36 0 55 123 5 73 9.50e-15 66.2
Msa0933690 MtrunA17_Chr1g0207471 34.021 97 59 1 11 102 3 99 2.68e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0933690 AT3G27650.1 73.171 123 29 1 4 122 33 155 1.70e-64 194
Msa0933690 AT5G63090.4 73.600 125 31 1 2 124 1 125 9.57e-63 190
Msa0933690 AT5G63090.3 73.600 125 31 1 2 124 1 125 9.57e-63 190
Msa0933690 AT5G63090.2 73.600 125 31 1 2 124 1 125 9.57e-63 190
Msa0933690 AT5G63090.1 73.600 125 31 1 2 124 1 125 9.57e-63 190
Msa0933690 AT1G65620.1 63.934 122 39 1 2 123 1 117 2.40e-47 152
Msa0933690 AT1G65620.4 63.934 122 39 1 2 123 1 117 2.40e-47 152
Msa0933690 AT1G65620.3 63.934 122 39 1 2 123 1 117 2.40e-47 152
Msa0933690 AT1G65620.5 63.934 122 39 1 2 123 1 117 2.40e-47 152
Msa0933690 AT1G65620.2 63.934 122 39 1 2 123 1 117 2.40e-47 152
Msa0933690 AT2G30130.1 64.423 104 37 0 8 111 6 109 7.26e-47 150
Msa0933690 AT5G66870.1 62.832 113 40 1 2 114 1 111 2.27e-45 150
Msa0933690 AT2G23660.2 61.682 107 41 0 7 113 2 108 4.13e-45 149
Msa0933690 AT2G23660.3 61.682 107 41 0 7 113 2 108 4.13e-45 149
Msa0933690 AT2G23660.1 61.682 107 41 0 7 113 2 108 4.13e-45 149
Msa0933690 AT1G31320.1 69.318 88 27 0 9 96 12 99 9.34e-44 142
Msa0933690 AT1G16530.1 57.895 114 45 2 9 119 13 126 1.04e-41 136
Msa0933690 AT2G30340.1 54.867 113 51 0 9 121 51 163 1.48e-41 139
Msa0933690 AT2G30340.2 54.867 113 51 0 9 121 52 164 1.57e-41 139
Msa0933690 AT3G11090.1 59.048 105 43 0 7 111 8 112 4.77e-41 135
Msa0933690 AT1G07900.1 47.407 135 65 1 9 137 32 166 1.47e-39 132
Msa0933690 AT2G28500.1 45.223 157 63 3 9 142 54 210 2.27e-39 132
Msa0933690 AT2G40470.2 61.905 105 40 0 9 113 19 123 2.54e-39 131
Msa0933690 AT2G40470.1 61.905 105 40 0 9 113 44 148 4.86e-39 131
Msa0933690 AT3G26620.1 45.902 122 60 1 11 132 6 121 2.32e-37 124
Msa0933690 AT3G26660.1 45.082 122 61 1 11 132 6 121 1.18e-36 122
Msa0933690 AT3G03760.1 55.769 104 45 1 9 111 50 153 3.71e-35 123
Msa0933690 AT2G42430.1 47.287 129 67 1 7 134 12 140 2.62e-34 120
Msa0933690 AT5G06080.1 50.926 108 52 1 9 115 6 113 2.97e-33 115
Msa0933690 AT4G00210.1 58.763 97 39 1 8 103 9 105 4.72e-33 116
Msa0933690 AT4G00220.1 57.576 99 41 1 13 110 20 118 7.78e-33 115
Msa0933690 AT2G45420.1 57.576 99 41 1 13 110 40 138 4.37e-32 114
Msa0933690 AT3G58190.1 53.125 96 44 1 10 104 11 106 6.68e-31 110
Msa0933690 AT2G45410.1 46.667 135 65 3 13 140 19 153 7.07e-31 109
Msa0933690 AT2G31310.1 51.546 97 46 1 8 103 5 101 1.04e-30 109
Msa0933690 AT3G50510.1 45.283 106 58 0 8 113 10 115 5.02e-30 107
Msa0933690 AT3G50510.2 45.283 106 58 0 8 113 10 115 5.02e-30 107
Msa0933690 AT2G42440.1 49.495 99 49 1 7 104 4 102 8.36e-30 108
Msa0933690 AT3G13850.1 40.777 103 61 0 11 113 37 139 7.09e-26 99.0
Msa0933690 AT3G47870.1 38.182 110 68 0 1 110 27 136 1.74e-25 99.0
Msa0933690 AT5G35900.1 36.719 128 74 1 11 138 6 126 5.26e-25 95.1
Msa0933690 AT1G72980.1 41.121 107 63 0 4 110 7 113 1.49e-23 91.7
Msa0933690 AT1G06280.1 48.052 77 40 0 11 87 25 101 5.26e-20 82.0
Msa0933690 AT4G22700.1 34.586 133 71 4 11 135 6 130 4.30e-18 77.0
Msa0933690 AT2G19820.1 36.264 91 57 1 7 96 9 99 4.16e-16 70.1
Msa0933690 AT5G15060.1 36.986 73 44 1 11 81 18 90 2.21e-12 60.8
Msa0933690 AT3G27940.3 29.245 106 75 0 10 115 5 110 5.22e-12 60.1
Msa0933690 AT3G27940.1 29.245 106 75 0 10 115 5 110 5.22e-12 60.1
Msa0933690 AT3G27940.2 29.245 106 75 0 10 115 5 110 5.22e-12 60.1

Find 23 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAATGTTCACAAAGTATT+TGG 0.212072 6_3:-2297442 Msa0933690:CDS
GTTTCTTCTTCTCTTGGTCT+TGG 0.291584 6_3:-2297211 Msa0933690:CDS
AATCCTTGCTTCAGCTTCAT+AGG 0.299183 6_3:+2297348 None:intergenic
CATGAAGTTTCTTCTTCTCT+TGG 0.303347 6_3:-2297217 Msa0933690:CDS
GGCTCTTCTTGTGGGAAATA+AGG 0.309872 6_3:+2297475 None:intergenic
TTGTAGCATCAAGTTCCTTT+TGG 0.323860 6_3:+2297263 None:intergenic
CGCTTCAAGGACAACTCTTT+AGG 0.341714 6_3:-2297288 Msa0933690:CDS
TGAACATTTGCAAACTTATG+AGG 0.383834 6_3:+2297454 None:intergenic
ACTTATGAGGCTCTTCTTGT+GGG 0.457572 6_3:+2297467 None:intergenic
ATGTCATTGCTGAAATTTGA+AGG 0.464467 6_3:+2297157 None:intergenic
GGAGCTATTTCAGCGCTTCA+AGG 0.465943 6_3:-2297301 Msa0933690:CDS
AACTTATGAGGCTCTTCTTG+TGG 0.480033 6_3:+2297466 None:intergenic
ATGAAGTCTTACCTCATCAA+AGG 0.530030 6_3:-2297393 Msa0933690:CDS
ACAACTCTTTAGGCTCCAAA+AGG 0.536437 6_3:-2297278 Msa0933690:CDS
TGAAGTCTTACCTCATCAAA+GGG 0.542775 6_3:-2297392 Msa0933690:CDS
AATCCAGTGTATGGTTGTGT+TGG 0.555823 6_3:-2297322 Msa0933690:CDS
TGTCATTGCTGAAATTTGAA+GGG 0.589927 6_3:+2297158 None:intergenic
AGAAACTTGCAAGCAGCACA+TGG 0.591215 6_3:+2297532 None:intergenic
ACTGTATCCTCCCTTTGATG+AGG 0.610482 6_3:+2297382 None:intergenic
GCTCCAACACAACCATACAC+TGG 0.615806 6_3:+2297319 None:intergenic
TTGCCTATGAAGCTGAAGCA+AGG 0.624248 6_3:-2297351 Msa0933690:CDS
TGGAGAATTTGAGTAGCTTG+AGG 0.626001 6_3:+2297552 None:intergenic
AGTCTTACCTCATCAAAGGG+AGG 0.699522 6_3:-2297389 Msa0933690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGAACATTTGCAAACTTATG+AGG + chr6_3:2297261-2297280 None:intergenic 30.0%
! GCAAATGTTCACAAAGTATT+TGG - chr6_3:2297270-2297289 Msa0933690:CDS 30.0%
AGGATTAAAAATCCAGTGTA+TGG - chr6_3:2297381-2297400 Msa0933690:CDS 30.0%
TGTCATTGCTGAAATTTGAA+GGG + chr6_3:2297557-2297576 None:intergenic 30.0%
ATGTCATTGCTGAAATTTGA+AGG + chr6_3:2297558-2297577 None:intergenic 30.0%
AAGGTGCAAAAATGCAATCT+TGG + chr6_3:2297221-2297240 None:intergenic 35.0%
ATGAAGTCTTACCTCATCAA+AGG - chr6_3:2297319-2297338 Msa0933690:CDS 35.0%
TGAAGTCTTACCTCATCAAA+GGG - chr6_3:2297320-2297339 Msa0933690:CDS 35.0%
! TTGTAGCATCAAGTTCCTTT+TGG + chr6_3:2297452-2297471 None:intergenic 35.0%
CATGAAGTTTCTTCTTCTCT+TGG - chr6_3:2297495-2297514 Msa0933690:CDS 35.0%
TGGAGAATTTGAGTAGCTTG+AGG + chr6_3:2297163-2297182 None:intergenic 40.0%
ACTTATGAGGCTCTTCTTGT+GGG + chr6_3:2297248-2297267 None:intergenic 40.0%
AACTTATGAGGCTCTTCTTG+TGG + chr6_3:2297249-2297268 None:intergenic 40.0%
AATCCTTGCTTCAGCTTCAT+AGG + chr6_3:2297367-2297386 None:intergenic 40.0%
AATCCAGTGTATGGTTGTGT+TGG - chr6_3:2297390-2297409 Msa0933690:CDS 40.0%
ACAACTCTTTAGGCTCCAAA+AGG - chr6_3:2297434-2297453 Msa0933690:CDS 40.0%
GTTTCTTCTTCTCTTGGTCT+TGG - chr6_3:2297501-2297520 Msa0933690:CDS 40.0%
AGAAACTTGCAAGCAGCACA+TGG + chr6_3:2297183-2297202 None:intergenic 45.0%
GGCTCTTCTTGTGGGAAATA+AGG + chr6_3:2297240-2297259 None:intergenic 45.0%
AGTCTTACCTCATCAAAGGG+AGG - chr6_3:2297323-2297342 Msa0933690:CDS 45.0%
ACTGTATCCTCCCTTTGATG+AGG + chr6_3:2297333-2297352 None:intergenic 45.0%
TTGCCTATGAAGCTGAAGCA+AGG - chr6_3:2297361-2297380 Msa0933690:CDS 45.0%
CGCTTCAAGGACAACTCTTT+AGG - chr6_3:2297424-2297443 Msa0933690:CDS 45.0%
GCTCCAACACAACCATACAC+TGG + chr6_3:2297396-2297415 None:intergenic 50.0%
! GGAGCTATTTCAGCGCTTCA+AGG - chr6_3:2297411-2297430 Msa0933690:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 2297153 2297581 2297153 ID=Msa0933690;Name=Msa0933690
chr6_3 mRNA 2297153 2297581 2297153 ID=Msa0933690-mRNA-1;Parent=Msa0933690;Name=Msa0933690-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|142
chr6_3 exon 2297153 2297581 2297153 ID=Msa0933690-mRNA-1:exon:911;Parent=Msa0933690-mRNA-1
chr6_3 CDS 2297153 2297581 2297153 ID=Msa0933690-mRNA-1:cds;Parent=Msa0933690-mRNA-1
Gene Sequence

>Msa0933690

ATGATGGCCTCAAGCTACTCAAATTCTCCATGTGCTGCTTGCAAGTTTCTAAGAAGAAAATGCAACCAAGATTGCATTTTTGCACCTTATTTCCCACAAGAAGAGCCTCATAAGTTTGCAAATGTTCACAAAGTATTTGGTGCAAGCAATGTTAGCAAAATTCTTAATGAAGTCTTACCTCATCAAAGGGAGGATACAGTGAATTCTCTTGCCTATGAAGCTGAAGCAAGGATTAAAAATCCAGTGTATGGTTGTGTTGGAGCTATTTCAGCGCTTCAAGGACAACTCTTTAGGCTCCAAAAGGAACTTGATGCTACAAATGCTGATTTGATTCGTTTTACTCATGAAGTTTCTTCTTCTCTTGGTCTTGGACAATTTCACTCTGATGACTTTTTAAATTACCCTTCAAATTTCAGCAATGACATGTGA
Protein sequence

>Msa0933690

MMASSYSNSPCAACKFLRRKCNQDCIFAPYFPQEEPHKFANVHKVFGASNVSKILNEVLPHQREDTVNSLAYEAEARIKNPVYGCVGAISALQGQLFRLQKELDATNADLIRFTHEVSSSLGLGQFHSDDFLNYPSNFSNDM*