AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0973120

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0973120 MtrunA17_Chr6g0449651 93.662 142 9 0 1 142 58 199 1.67e-99 283
Msa0973120 MtrunA17_Chr6g0449641 88.571 140 16 0 2 141 1 140 7.41e-91 259
Msa0973120 MtrunA17_Chr7g0227511 69.032 155 31 4 3 141 4 157 8.12e-70 207
Msa0973120 MtrunA17_Chr3g0117121 79.130 115 24 0 1 115 1 115 5.54e-65 196
Msa0973120 MtrunA17_Chr4g0058651 80.374 107 21 0 8 114 9 115 5.68e-63 191
Msa0973120 MtrunA17_Chr5g0437571 52.055 146 59 1 8 142 4 149 1.04e-48 154
Msa0973120 MtrunA17_Chr4g0043421 58.678 121 49 1 9 128 14 134 1.22e-48 154
Msa0973120 MtrunA17_Chr2g0311601 60.714 112 43 1 9 119 12 123 2.59e-48 152
Msa0973120 MtrunA17_Chr3g0115431 64.602 113 40 0 2 114 1 113 5.70e-48 154
Msa0973120 MtrunA17_Chr5g0402611 65.455 110 38 0 4 113 2 111 1.05e-47 156
Msa0973120 MtrunA17_Chr8g0353981 68.750 112 33 1 2 113 1 110 1.16e-47 153
Msa0973120 MtrunA17_Chr3g0097221 65.138 109 38 0 5 113 2 110 1.93e-45 149
Msa0973120 MtrunA17_Chr3g0106101 53.600 125 56 1 8 130 5 129 3.47e-45 145
Msa0973120 MtrunA17_Chr3g0114061 62.857 105 39 0 7 111 5 109 9.85e-45 144
Msa0973120 MtrunA17_Chr5g0438091 58.879 107 44 0 7 113 36 142 1.27e-42 139
Msa0973120 MtrunA17_Chr3g0129071 60.000 105 42 0 9 113 46 150 1.44e-42 140
Msa0973120 MtrunA17_Chr3g0113891 67.010 97 32 0 7 103 11 107 2.81e-42 138
Msa0973120 MtrunA17_Chr5g0437401 63.208 106 39 0 7 112 8 113 2.92e-42 138
Msa0973120 MtrunA17_Chr4g0030001 45.070 142 65 2 9 137 23 164 1.00e-39 132
Msa0973120 MtrunA17_Chr5g0432451 57.143 112 48 0 9 120 42 153 5.13e-38 129
Msa0973120 MtrunA17_Chr7g0260971 58.333 108 44 1 4 110 8 115 2.14e-37 127
Msa0973120 MtrunA17_Chr1g0200201 55.446 101 45 0 11 111 73 173 6.91e-37 125
Msa0973120 MtrunA17_Chr1g0184281 58.491 106 43 1 7 111 12 117 4.95e-36 123
Msa0973120 MtrunA17_Chr7g0245871 60.000 95 37 1 10 103 27 121 7.36e-34 118
Msa0973120 MtrunA17_Chr8g0351701 55.046 109 46 2 10 117 23 129 1.08e-33 117
Msa0973120 MtrunA17_Chr8g0351721 52.941 119 52 2 7 121 15 133 1.10e-33 117
Msa0973120 MtrunA17_Chr6g0460951 48.276 116 57 2 9 121 39 154 2.51e-32 114
Msa0973120 MtrunA17_Chr5g0435641 53.608 97 44 1 9 104 6 102 1.02e-31 111
Msa0973120 MtrunA17_Chr5g0444351 49.000 100 51 0 11 110 6 105 1.27e-31 110
Msa0973120 MtrunA17_Chr7g0225111 46.078 102 55 0 9 110 4 105 1.83e-31 108
Msa0973120 MtrunA17_Chr8g0374601 47.115 104 55 0 10 113 26 129 1.02e-30 111
Msa0973120 MtrunA17_Chr7g0261031 55.102 98 43 1 7 103 5 102 1.09e-30 110
Msa0973120 MtrunA17_Chr8g0374591 44.231 104 58 0 10 113 8 111 6.16e-30 105
Msa0973120 MtrunA17_Chr1g0184271 52.632 95 44 1 10 103 12 106 1.31e-29 107
Msa0973120 MtrunA17_Chr6g0452661 45.918 98 52 1 8 104 7 104 5.62e-29 106
Msa0973120 MtrunA17_Chr4g0059901 47.000 100 53 0 11 110 11 110 1.57e-28 105
Msa0973120 MtrunA17_Chr7g0245861 54.839 93 39 2 7 96 9 101 7.97e-28 100
Msa0973120 MtrunA17_Chr6g0452671 42.000 100 58 0 7 106 8 107 9.76e-27 99.4
Msa0973120 MtrunA17_Chr6g0452691 43.689 103 57 1 7 108 6 108 1.72e-26 98.2
Msa0973120 MtrunA17_Chr8g0374581 46.667 105 55 1 10 113 8 112 4.90e-26 98.2
Msa0973120 MtrunA17_Chr6g0460941 50.000 88 43 1 10 96 7 94 9.30e-26 93.6
Msa0973120 MtrunA17_Chr8g0342351 40.777 103 61 0 11 113 13 115 5.90e-24 93.2
Msa0973120 MtrunA17_Chr2g0330201 41.000 100 59 0 7 106 16 115 1.79e-23 92.8
Msa0973120 MtrunA17_Chr5g0439111 42.857 98 55 1 8 104 7 104 3.74e-22 88.2
Msa0973120 MtrunA17_Chr4g0040831 43.011 93 53 0 11 103 16 108 5.77e-22 87.0
Msa0973120 MtrunA17_Chr4g0055441 40.000 95 56 1 11 104 3 97 1.09e-21 85.1
Msa0973120 MtrunA17_Chr2g0326041 60.345 58 23 0 2 59 25 82 2.35e-21 82.0
Msa0973120 MtrunA17_Chr4g0046201 32.222 90 61 0 9 98 5 94 2.33e-15 70.5
Msa0973120 MtrunA17_Chr2g0326051 47.826 69 36 0 55 123 5 73 8.91e-15 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0973120 AT3G27650.1 73.984 123 28 1 4 122 33 155 1.04e-65 197
Msa0973120 AT5G63090.4 74.400 125 30 1 2 124 1 125 1.22e-63 192
Msa0973120 AT5G63090.3 74.400 125 30 1 2 124 1 125 1.22e-63 192
Msa0973120 AT5G63090.2 74.400 125 30 1 2 124 1 125 1.22e-63 192
Msa0973120 AT5G63090.1 74.400 125 30 1 2 124 1 125 1.22e-63 192
Msa0973120 AT1G65620.1 64.754 122 38 1 2 123 1 117 1.70e-48 155
Msa0973120 AT1G65620.4 64.754 122 38 1 2 123 1 117 1.70e-48 155
Msa0973120 AT1G65620.3 64.754 122 38 1 2 123 1 117 1.70e-48 155
Msa0973120 AT1G65620.5 64.754 122 38 1 2 123 1 117 1.70e-48 155
Msa0973120 AT1G65620.2 64.754 122 38 1 2 123 1 117 1.70e-48 155
Msa0973120 AT2G30130.1 65.385 104 36 0 8 111 6 109 4.32e-48 154
Msa0973120 AT5G66870.1 63.717 113 39 1 2 114 1 111 1.43e-46 153
Msa0973120 AT2G23660.2 62.617 107 40 0 7 113 2 108 2.38e-46 152
Msa0973120 AT2G23660.3 62.617 107 40 0 7 113 2 108 2.38e-46 152
Msa0973120 AT2G23660.1 62.617 107 40 0 7 113 2 108 2.38e-46 152
Msa0973120 AT1G31320.1 69.318 88 27 0 9 96 12 99 9.98e-44 142
Msa0973120 AT2G30340.1 55.752 113 50 0 9 121 51 163 8.40e-43 142
Msa0973120 AT2G30340.2 55.752 113 50 0 9 121 52 164 9.29e-43 142
Msa0973120 AT1G16530.1 57.895 114 45 2 9 119 13 126 1.09e-41 136
Msa0973120 AT1G07900.1 48.148 135 64 1 9 137 32 166 4.21e-41 135
Msa0973120 AT3G11090.1 59.048 105 43 0 7 111 8 112 6.98e-41 134
Msa0973120 AT2G28500.1 45.860 157 62 3 9 142 54 210 1.02e-40 136
Msa0973120 AT2G40470.2 62.857 105 39 0 9 113 19 123 2.02e-40 134
Msa0973120 AT2G40470.1 62.857 105 39 0 9 113 44 148 4.11e-40 134
Msa0973120 AT3G26620.1 46.721 122 59 1 11 132 6 121 1.22e-38 127
Msa0973120 AT3G26660.1 45.902 122 60 1 11 132 6 121 5.61e-38 125
Msa0973120 AT3G03760.1 55.769 104 45 1 9 111 50 153 4.08e-35 122
Msa0973120 AT2G42430.1 47.287 129 67 1 7 134 12 140 2.43e-34 120
Msa0973120 AT5G06080.1 50.926 108 52 1 9 115 6 113 3.10e-33 115
Msa0973120 AT4G00210.1 58.763 97 39 1 8 103 9 105 9.11e-33 115
Msa0973120 AT4G00220.1 57.576 99 41 1 13 110 20 118 1.18e-32 115
Msa0973120 AT2G45420.1 57.576 99 41 1 13 110 40 138 6.42e-32 114
Msa0973120 AT2G45410.1 46.667 135 65 3 13 140 19 153 8.22e-31 109
Msa0973120 AT3G58190.1 53.125 96 44 1 10 104 11 106 1.30e-30 110
Msa0973120 AT2G31310.1 51.546 97 46 1 8 103 5 101 1.54e-30 108
Msa0973120 AT3G50510.1 45.283 106 58 0 8 113 10 115 7.01e-30 107
Msa0973120 AT3G50510.2 45.283 106 58 0 8 113 10 115 7.01e-30 107
Msa0973120 AT2G42440.1 49.495 99 49 1 7 104 4 102 1.46e-29 107
Msa0973120 AT3G47870.1 38.182 110 68 0 1 110 27 136 1.48e-25 99.4
Msa0973120 AT3G13850.1 40.777 103 61 0 11 113 37 139 1.94e-25 97.8
Msa0973120 AT5G35900.1 36.719 128 74 1 11 138 6 126 9.09e-25 94.7
Msa0973120 AT1G72980.1 40.187 107 64 0 4 110 7 113 9.61e-23 89.4
Msa0973120 AT1G06280.1 48.052 77 40 0 11 87 25 101 3.51e-20 82.8
Msa0973120 AT4G22700.1 34.586 133 71 4 11 135 6 130 7.07e-18 76.3
Msa0973120 AT2G19820.1 36.264 91 57 1 7 96 9 99 4.25e-16 70.1
Msa0973120 AT5G15060.1 36.986 73 44 1 11 81 18 90 2.08e-12 60.8
Msa0973120 AT3G27940.3 29.245 106 75 0 10 115 5 110 8.92e-12 59.3
Msa0973120 AT3G27940.1 29.245 106 75 0 10 115 5 110 8.92e-12 59.3
Msa0973120 AT3G27940.2 29.245 106 75 0 10 115 5 110 8.92e-12 59.3

Find 24 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAATGTTCACAAAGTATT+TGG 0.212072 6_4:+5478927 Msa0973120:CDS
GCAAACTTATGAGGCTCTTC+TGG 0.277156 6_4:-5478906 None:intergenic
GTTTCTTCTTCTCTTGGTCT+TGG 0.291584 6_4:+5479158 Msa0973120:CDS
AATCCTTGCTTCAGCTTCAT+AGG 0.299183 6_4:-5479021 None:intergenic
CATGAAGTTTCTTCTTCTCT+TGG 0.303347 6_4:+5479152 Msa0973120:CDS
GGCTCTTCTGGTGGGAAATA+AGG 0.304156 6_4:-5478894 None:intergenic
TTGTAGCATCAAGTTCCTTT+TGG 0.323860 6_4:-5479106 None:intergenic
CGCTTCAAGGACAACTCTTT+AGG 0.341714 6_4:+5479081 Msa0973120:CDS
TGAACATTTGCAAACTTATG+AGG 0.383834 6_4:-5478915 None:intergenic
ATGTCATTGCTGAAATTTGA+AGG 0.464467 6_4:-5479212 None:intergenic
GGAGCTATTTCAGCGCTTCA+AGG 0.465943 6_4:+5479068 Msa0973120:CDS
ATGAAGTCTTACCTCATCAA+AGG 0.530030 6_4:+5478976 Msa0973120:CDS
ACAACTCTTTAGGCTCCAAA+AGG 0.536437 6_4:+5479091 Msa0973120:CDS
AACTTATGAGGCTCTTCTGG+TGG 0.540828 6_4:-5478903 None:intergenic
TGAAGTCTTACCTCATCAAA+GGG 0.542775 6_4:+5478977 Msa0973120:CDS
AATCCAGTGTATGGTTGTGT+TGG 0.555823 6_4:+5479047 Msa0973120:CDS
TGTCATTGCTGAAATTTGAA+GGG 0.589927 6_4:-5479211 None:intergenic
AGAAACTTGCAAGCAGCACA+TGG 0.591215 6_4:-5478837 None:intergenic
ACTTATGAGGCTCTTCTGGT+GGG 0.610191 6_4:-5478902 None:intergenic
ACTGTATCCTCCCTTTGATG+AGG 0.610482 6_4:-5478987 None:intergenic
GCTCCAACACAACCATACAC+TGG 0.615806 6_4:-5479050 None:intergenic
TTGCCTATGAAGCTGAAGCA+AGG 0.624248 6_4:+5479018 Msa0973120:CDS
TGGAGAATTTGAGTAGCTTG+AGG 0.626001 6_4:-5478817 None:intergenic
AGTCTTACCTCATCAAAGGG+AGG 0.699522 6_4:+5478980 Msa0973120:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGAACATTTGCAAACTTATG+AGG - chr6_4:5478918-5478937 None:intergenic 30.0%
! GCAAATGTTCACAAAGTATT+TGG + chr6_4:5478927-5478946 Msa0973120:CDS 30.0%
AGGATTAAAAATCCAGTGTA+TGG + chr6_4:5479038-5479057 Msa0973120:CDS 30.0%
TGTCATTGCTGAAATTTGAA+GGG - chr6_4:5479214-5479233 None:intergenic 30.0%
ATGTCATTGCTGAAATTTGA+AGG - chr6_4:5479215-5479234 None:intergenic 30.0%
AAGGTGCAAAAATGCAATCT+TGG - chr6_4:5478878-5478897 None:intergenic 35.0%
ATGAAGTCTTACCTCATCAA+AGG + chr6_4:5478976-5478995 Msa0973120:CDS 35.0%
TGAAGTCTTACCTCATCAAA+GGG + chr6_4:5478977-5478996 Msa0973120:CDS 35.0%
! TTGTAGCATCAAGTTCCTTT+TGG - chr6_4:5479109-5479128 None:intergenic 35.0%
CATGAAGTTTCTTCTTCTCT+TGG + chr6_4:5479152-5479171 Msa0973120:CDS 35.0%
TGGAGAATTTGAGTAGCTTG+AGG - chr6_4:5478820-5478839 None:intergenic 40.0%
AATCCTTGCTTCAGCTTCAT+AGG - chr6_4:5479024-5479043 None:intergenic 40.0%
AATCCAGTGTATGGTTGTGT+TGG + chr6_4:5479047-5479066 Msa0973120:CDS 40.0%
ACAACTCTTTAGGCTCCAAA+AGG + chr6_4:5479091-5479110 Msa0973120:CDS 40.0%
GTTTCTTCTTCTCTTGGTCT+TGG + chr6_4:5479158-5479177 Msa0973120:CDS 40.0%
AGAAACTTGCAAGCAGCACA+TGG - chr6_4:5478840-5478859 None:intergenic 45.0%
ACTTATGAGGCTCTTCTGGT+GGG - chr6_4:5478905-5478924 None:intergenic 45.0%
AACTTATGAGGCTCTTCTGG+TGG - chr6_4:5478906-5478925 None:intergenic 45.0%
GCAAACTTATGAGGCTCTTC+TGG - chr6_4:5478909-5478928 None:intergenic 45.0%
AGTCTTACCTCATCAAAGGG+AGG + chr6_4:5478980-5478999 Msa0973120:CDS 45.0%
ACTGTATCCTCCCTTTGATG+AGG - chr6_4:5478990-5479009 None:intergenic 45.0%
TTGCCTATGAAGCTGAAGCA+AGG + chr6_4:5479018-5479037 Msa0973120:CDS 45.0%
CGCTTCAAGGACAACTCTTT+AGG + chr6_4:5479081-5479100 Msa0973120:CDS 45.0%
GGCTCTTCTGGTGGGAAATA+AGG - chr6_4:5478897-5478916 None:intergenic 50.0%
GCTCCAACACAACCATACAC+TGG - chr6_4:5479053-5479072 None:intergenic 50.0%
! GGAGCTATTTCAGCGCTTCA+AGG + chr6_4:5479068-5479087 Msa0973120:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 5478810 5479238 5478810 ID=Msa0973120;Name=Msa0973120
chr6_4 mRNA 5478810 5479238 5478810 ID=Msa0973120-mRNA-1;Parent=Msa0973120;Name=Msa0973120-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|142
chr6_4 exon 5478810 5479238 5478810 ID=Msa0973120-mRNA-1:exon:2313;Parent=Msa0973120-mRNA-1
chr6_4 CDS 5478810 5479238 5478810 ID=Msa0973120-mRNA-1:cds;Parent=Msa0973120-mRNA-1
Gene Sequence

>Msa0973120

ATGATGGCCTCAAGCTACTCAAATTCTCCATGTGCTGCTTGCAAGTTTCTAAGAAGAAAATGCAACCAAGATTGCATTTTTGCACCTTATTTCCCACCAGAAGAGCCTCATAAGTTTGCAAATGTTCACAAAGTATTTGGTGCAAGCAATGTTAGCAAAATTCTTAATGAAGTCTTACCTCATCAAAGGGAGGATACAGTGAATTCTCTTGCCTATGAAGCTGAAGCAAGGATTAAAAATCCAGTGTATGGTTGTGTTGGAGCTATTTCAGCGCTTCAAGGACAACTCTTTAGGCTCCAAAAGGAACTTGATGCTACAAATGCTGATTTGATTCGTTTTACTCATGAAGTTTCTTCTTCTCTTGGTCTTGGACAATTTCACTCTGATGACTTTTTAAATTACCCTTCAAATTTCAGCAATGACATGTGA
Protein sequence

>Msa0973120

MMASSYSNSPCAACKFLRRKCNQDCIFAPYFPPEEPHKFANVHKVFGASNVSKILNEVLPHQREDTVNSLAYEAEARIKNPVYGCVGAISALQGQLFRLQKELDATNADLIRFTHEVSSSLGLGQFHSDDFLNYPSNFSNDM*