AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0868740

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0868740 MtrunA17_Chr6g0449651 94.326 141 8 0 1 141 59 199 5.98e-100 285
Msa0868740 MtrunA17_Chr6g0449641 89.286 140 15 0 1 140 1 140 5.05e-92 263
Msa0868740 MtrunA17_Chr7g0227511 86.607 112 15 0 2 113 4 115 1.04e-69 207
Msa0868740 MtrunA17_Chr3g0117121 80.870 115 21 1 1 114 1 115 1.52e-64 195
Msa0868740 MtrunA17_Chr4g0058651 80.374 107 21 0 7 113 9 115 5.58e-63 191
Msa0868740 MtrunA17_Chr5g0437571 52.055 146 59 1 7 141 4 149 2.67e-49 155
Msa0868740 MtrunA17_Chr4g0043421 63.810 105 38 0 8 112 14 118 1.80e-48 153
Msa0868740 MtrunA17_Chr2g0311601 57.025 121 44 1 8 128 12 124 4.40e-48 152
Msa0868740 MtrunA17_Chr3g0115431 64.602 113 40 0 1 113 1 113 6.19e-48 154
Msa0868740 MtrunA17_Chr5g0402611 65.455 110 38 0 3 112 2 111 1.15e-47 156
Msa0868740 MtrunA17_Chr8g0353981 68.750 112 33 1 1 112 1 110 1.22e-47 153
Msa0868740 MtrunA17_Chr3g0106101 53.600 125 56 1 7 129 5 129 1.27e-45 146
Msa0868740 MtrunA17_Chr3g0097221 65.138 109 38 0 4 112 2 110 2.43e-45 149
Msa0868740 MtrunA17_Chr3g0114061 60.714 112 42 1 6 115 5 116 7.80e-45 144
Msa0868740 MtrunA17_Chr3g0129071 60.000 105 42 0 8 112 46 150 1.29e-42 140
Msa0868740 MtrunA17_Chr5g0438091 58.879 107 44 0 6 112 36 142 1.31e-42 139
Msa0868740 MtrunA17_Chr3g0113891 67.010 97 32 0 6 102 11 107 2.83e-42 138
Msa0868740 MtrunA17_Chr5g0437401 63.208 106 39 0 6 111 8 113 3.24e-42 137
Msa0868740 MtrunA17_Chr4g0030001 45.070 142 65 2 8 136 23 164 5.48e-40 132
Msa0868740 MtrunA17_Chr5g0432451 57.143 112 48 0 8 119 42 153 4.94e-38 129
Msa0868740 MtrunA17_Chr7g0260971 58.333 108 44 1 3 109 8 115 2.27e-37 127
Msa0868740 MtrunA17_Chr1g0200201 50.442 113 56 0 10 122 73 185 5.08e-37 126
Msa0868740 MtrunA17_Chr1g0184281 55.085 118 50 2 6 120 12 129 2.74e-36 124
Msa0868740 MtrunA17_Chr7g0245871 60.000 95 37 1 9 102 27 121 8.25e-34 118
Msa0868740 MtrunA17_Chr8g0351721 56.731 104 44 1 7 109 16 119 1.34e-33 117
Msa0868740 MtrunA17_Chr8g0351701 54.286 105 47 1 9 112 23 127 1.48e-33 117
Msa0868740 MtrunA17_Chr6g0460951 48.276 116 57 2 8 120 39 154 9.39e-33 115
Msa0868740 MtrunA17_Chr5g0435641 53.608 97 44 1 8 103 6 102 9.19e-32 111
Msa0868740 MtrunA17_Chr5g0444351 49.000 100 51 0 10 109 6 105 1.29e-31 110
Msa0868740 MtrunA17_Chr7g0225111 46.078 102 55 0 8 109 4 105 1.82e-31 108
Msa0868740 MtrunA17_Chr7g0261031 55.102 98 43 1 6 102 5 102 1.13e-30 109
Msa0868740 MtrunA17_Chr8g0374601 47.115 104 55 0 9 112 26 129 1.18e-30 111
Msa0868740 MtrunA17_Chr8g0374591 44.231 104 58 0 9 112 8 111 6.93e-30 105
Msa0868740 MtrunA17_Chr1g0184271 52.632 95 44 1 9 102 12 106 1.32e-29 107
Msa0868740 MtrunA17_Chr6g0452661 45.918 98 52 1 7 103 7 104 5.37e-29 106
Msa0868740 MtrunA17_Chr4g0059901 47.000 100 53 0 10 109 11 110 1.18e-28 105
Msa0868740 MtrunA17_Chr7g0245861 54.839 93 39 2 6 95 9 101 9.67e-28 100
Msa0868740 MtrunA17_Chr6g0452671 42.000 100 58 0 6 105 8 107 9.03e-27 99.4
Msa0868740 MtrunA17_Chr6g0452691 43.689 103 57 1 6 107 6 108 1.65e-26 98.2
Msa0868740 MtrunA17_Chr8g0374581 46.667 105 55 1 9 112 8 112 4.64e-26 98.2
Msa0868740 MtrunA17_Chr6g0460941 50.000 88 43 1 9 95 7 94 9.71e-26 93.6
Msa0868740 MtrunA17_Chr8g0342351 40.777 103 61 0 10 112 13 115 5.13e-24 93.6
Msa0868740 MtrunA17_Chr2g0330201 41.000 100 59 0 6 105 16 115 1.79e-23 92.8
Msa0868740 MtrunA17_Chr5g0439111 42.857 98 55 1 7 103 7 104 3.70e-22 88.2
Msa0868740 MtrunA17_Chr4g0040831 43.011 93 53 0 10 102 16 108 6.91e-22 86.7
Msa0868740 MtrunA17_Chr4g0055441 40.000 95 56 1 10 103 3 97 9.14e-22 85.1
Msa0868740 MtrunA17_Chr2g0326041 60.345 58 23 0 1 58 25 82 2.26e-21 82.0
Msa0868740 MtrunA17_Chr4g0046201 32.222 90 61 0 8 97 5 94 2.59e-15 70.5
Msa0868740 MtrunA17_Chr2g0326051 47.826 69 36 0 54 122 5 73 5.71e-15 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0868740 AT3G27650.1 80.000 110 22 0 3 112 33 142 1.49e-65 196
Msa0868740 AT5G63090.4 74.400 125 30 1 1 123 1 125 2.89e-63 192
Msa0868740 AT5G63090.3 74.400 125 30 1 1 123 1 125 2.89e-63 192
Msa0868740 AT5G63090.2 74.400 125 30 1 1 123 1 125 2.89e-63 192
Msa0868740 AT5G63090.1 74.400 125 30 1 1 123 1 125 2.89e-63 192
Msa0868740 AT1G65620.1 66.379 116 39 0 1 116 1 116 1.18e-48 155
Msa0868740 AT1G65620.4 66.379 116 39 0 1 116 1 116 1.18e-48 155
Msa0868740 AT1G65620.3 66.379 116 39 0 1 116 1 116 1.18e-48 155
Msa0868740 AT1G65620.5 66.379 116 39 0 1 116 1 116 1.18e-48 155
Msa0868740 AT1G65620.2 66.379 116 39 0 1 116 1 116 1.18e-48 155
Msa0868740 AT2G30130.1 60.526 114 45 0 7 120 6 119 2.46e-48 154
Msa0868740 AT5G66870.1 63.717 113 39 1 1 113 1 111 1.50e-46 153
Msa0868740 AT2G23660.2 62.617 107 40 0 6 112 2 108 2.58e-46 152
Msa0868740 AT2G23660.3 62.617 107 40 0 6 112 2 108 2.58e-46 152
Msa0868740 AT2G23660.1 62.617 107 40 0 6 112 2 108 2.58e-46 152
Msa0868740 AT1G31320.1 69.318 88 27 0 8 95 12 99 1.14e-43 141
Msa0868740 AT2G30340.1 55.752 113 50 0 8 120 51 163 7.03e-43 142
Msa0868740 AT2G30340.2 55.752 113 50 0 8 120 52 164 7.69e-43 142
Msa0868740 AT1G16530.1 61.538 104 39 1 8 110 13 116 1.33e-41 136
Msa0868740 AT1G07900.1 48.148 135 64 1 8 136 32 166 2.90e-41 136
Msa0868740 AT3G11090.1 57.658 111 45 1 6 116 8 116 5.41e-41 134
Msa0868740 AT2G28500.1 45.860 157 62 3 8 141 54 210 9.76e-41 136
Msa0868740 AT2G40470.2 62.857 105 39 0 8 112 19 123 1.81e-40 134
Msa0868740 AT2G40470.1 62.857 105 39 0 8 112 44 148 3.83e-40 134
Msa0868740 AT3G26620.1 46.721 122 59 1 10 131 6 121 7.58e-39 127
Msa0868740 AT3G26660.1 45.902 122 60 1 10 131 6 121 3.82e-38 126
Msa0868740 AT3G03760.1 55.769 104 45 1 8 110 50 153 4.15e-35 122
Msa0868740 AT2G42430.1 47.287 129 67 1 6 133 12 140 2.22e-34 120
Msa0868740 AT5G06080.1 50.926 108 52 1 8 114 6 113 3.68e-33 115
Msa0868740 AT4G00210.1 56.863 102 43 1 9 109 11 112 7.64e-33 115
Msa0868740 AT4G00220.1 57.576 99 41 1 12 109 20 118 1.06e-32 115
Msa0868740 AT2G45420.1 57.576 99 41 1 12 109 40 138 5.34e-32 114
Msa0868740 AT2G45410.1 46.667 135 65 3 12 139 19 153 3.68e-31 110
Msa0868740 AT3G58190.1 53.125 96 44 1 9 103 11 106 1.38e-30 109
Msa0868740 AT2G31310.1 52.083 96 45 1 8 102 6 101 1.78e-30 108
Msa0868740 AT3G50510.1 45.283 106 58 0 7 112 10 115 7.07e-30 107
Msa0868740 AT3G50510.2 45.283 106 58 0 7 112 10 115 7.07e-30 107
Msa0868740 AT2G42440.1 49.495 99 49 1 6 103 4 102 1.41e-29 107
Msa0868740 AT3G47870.1 39.423 104 63 0 6 109 33 136 1.50e-25 99.0
Msa0868740 AT3G13850.1 40.777 103 61 0 10 112 37 139 1.93e-25 97.8
Msa0868740 AT5G35900.1 43.000 100 57 0 10 109 6 105 1.47e-24 94.0
Msa0868740 AT1G72980.1 40.187 107 64 0 3 109 7 113 1.15e-22 89.4
Msa0868740 AT1G06280.1 48.052 77 40 0 10 86 25 101 3.29e-20 82.8
Msa0868740 AT4G22700.1 34.921 126 80 2 10 134 6 130 5.43e-18 76.6
Msa0868740 AT2G19820.1 36.264 91 57 1 6 95 9 99 4.35e-16 70.1
Msa0868740 AT5G15060.1 36.986 73 44 1 10 80 18 90 2.25e-12 60.8
Msa0868740 AT3G27940.3 29.245 106 75 0 9 114 5 110 8.24e-12 59.7
Msa0868740 AT3G27940.1 29.245 106 75 0 9 114 5 110 8.24e-12 59.7
Msa0868740 AT3G27940.2 29.245 106 75 0 9 114 5 110 8.24e-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
GCAAATGTTCACAAAGTATT+TGG 0.212072 6_1:+2487739 Msa0868740:CDS
GCAAACTTATGAGGCTCTTC+TGG 0.277156 6_1:-2487718 None:intergenic
AATCCTTGCTTCAGCTTCAT+AGG 0.299183 6_1:-2487833 None:intergenic
GGCTCTTCTGGTGGGAAATA+AGG 0.304156 6_1:-2487706 None:intergenic
GGTTCTTCTTCTCTTGGTCT+TGG 0.305065 6_1:+2487970 Msa0868740:CDS
CATGAAGGTTCTTCTTCTCT+TGG 0.312102 6_1:+2487964 Msa0868740:CDS
TTGTAGCATCAAGTTCCTTT+TGG 0.323860 6_1:-2487918 None:intergenic
CGCTTCAAGGACAACTCTTT+AGG 0.341714 6_1:+2487893 Msa0868740:CDS
TGAACATTTGCAAACTTATG+AGG 0.383834 6_1:-2487727 None:intergenic
ATGTCATTGCTGAAATTTGA+AGG 0.464467 6_1:-2488024 None:intergenic
GGAGCTATTTCAGCGCTTCA+AGG 0.465943 6_1:+2487880 Msa0868740:CDS
ATGAAGTCTTACCTCATCAA+AGG 0.530030 6_1:+2487788 Msa0868740:CDS
ACAACTCTTTAGGCTCCAAA+AGG 0.536437 6_1:+2487903 Msa0868740:CDS
AACTTATGAGGCTCTTCTGG+TGG 0.540828 6_1:-2487715 None:intergenic
TGAAGTCTTACCTCATCAAA+GGG 0.542775 6_1:+2487789 Msa0868740:CDS
AATCCAGTGTATGGTTGTGT+TGG 0.555823 6_1:+2487859 Msa0868740:CDS
TGTCATTGCTGAAATTTGAA+GGG 0.589927 6_1:-2488023 None:intergenic
AGAAACTTGCAAGCAGCACA+TGG 0.591215 6_1:-2487649 None:intergenic
ACTTATGAGGCTCTTCTGGT+GGG 0.610191 6_1:-2487714 None:intergenic
ACTGTATCCTCCCTTTGATG+AGG 0.610482 6_1:-2487799 None:intergenic
GCTCCAACACAACCATACAC+TGG 0.615806 6_1:-2487862 None:intergenic
TTGCCTATGAAGCTGAAGCA+AGG 0.624248 6_1:+2487830 Msa0868740:CDS
TGGAGAATTTGAGTAGCTTG+AGG 0.626001 6_1:-2487629 None:intergenic
AGTCTTACCTCATCAAAGGG+AGG 0.699522 6_1:+2487792 Msa0868740:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGAACATTTGCAAACTTATG+AGG - chr6_1:2487730-2487749 None:intergenic 30.0%
! GCAAATGTTCACAAAGTATT+TGG + chr6_1:2487739-2487758 Msa0868740:CDS 30.0%
AGGATTAAAAATCCAGTGTA+TGG + chr6_1:2487850-2487869 Msa0868740:CDS 30.0%
!! TTGATTCGTTTTACTCATGA+AGG + chr6_1:2487949-2487968 Msa0868740:CDS 30.0%
TGTCATTGCTGAAATTTGAA+GGG - chr6_1:2488026-2488045 None:intergenic 30.0%
ATGTCATTGCTGAAATTTGA+AGG - chr6_1:2488027-2488046 None:intergenic 30.0%
AAGGTGCAAAAATGCAATCT+TGG - chr6_1:2487690-2487709 None:intergenic 35.0%
ATGAAGTCTTACCTCATCAA+AGG + chr6_1:2487788-2487807 Msa0868740:CDS 35.0%
TGAAGTCTTACCTCATCAAA+GGG + chr6_1:2487789-2487808 Msa0868740:CDS 35.0%
! TTGTAGCATCAAGTTCCTTT+TGG - chr6_1:2487921-2487940 None:intergenic 35.0%
TGGAGAATTTGAGTAGCTTG+AGG - chr6_1:2487632-2487651 None:intergenic 40.0%
AATCCTTGCTTCAGCTTCAT+AGG - chr6_1:2487836-2487855 None:intergenic 40.0%
AATCCAGTGTATGGTTGTGT+TGG + chr6_1:2487859-2487878 Msa0868740:CDS 40.0%
ACAACTCTTTAGGCTCCAAA+AGG + chr6_1:2487903-2487922 Msa0868740:CDS 40.0%
CATGAAGGTTCTTCTTCTCT+TGG + chr6_1:2487964-2487983 Msa0868740:CDS 40.0%
AGAAACTTGCAAGCAGCACA+TGG - chr6_1:2487652-2487671 None:intergenic 45.0%
ACTTATGAGGCTCTTCTGGT+GGG - chr6_1:2487717-2487736 None:intergenic 45.0%
AACTTATGAGGCTCTTCTGG+TGG - chr6_1:2487718-2487737 None:intergenic 45.0%
GCAAACTTATGAGGCTCTTC+TGG - chr6_1:2487721-2487740 None:intergenic 45.0%
AGTCTTACCTCATCAAAGGG+AGG + chr6_1:2487792-2487811 Msa0868740:CDS 45.0%
ACTGTATCCTCCCTTTGATG+AGG - chr6_1:2487802-2487821 None:intergenic 45.0%
TTGCCTATGAAGCTGAAGCA+AGG + chr6_1:2487830-2487849 Msa0868740:CDS 45.0%
CGCTTCAAGGACAACTCTTT+AGG + chr6_1:2487893-2487912 Msa0868740:CDS 45.0%
GGTTCTTCTTCTCTTGGTCT+TGG + chr6_1:2487970-2487989 Msa0868740:CDS 45.0%
GGCTCTTCTGGTGGGAAATA+AGG - chr6_1:2487709-2487728 None:intergenic 50.0%
GCTCCAACACAACCATACAC+TGG - chr6_1:2487865-2487884 None:intergenic 50.0%
! GGAGCTATTTCAGCGCTTCA+AGG + chr6_1:2487880-2487899 Msa0868740:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 2487625 2488050 2487625 ID=Msa0868740;Name=Msa0868740
chr6_1 mRNA 2487625 2488050 2487625 ID=Msa0868740-mRNA-1;Parent=Msa0868740;Name=Msa0868740-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|141
chr6_1 exon 2487625 2488050 2487625 ID=Msa0868740-mRNA-1:exon:693;Parent=Msa0868740-mRNA-1
chr6_1 CDS 2487625 2488050 2487625 ID=Msa0868740-mRNA-1:cds;Parent=Msa0868740-mRNA-1
Gene Sequence

>Msa0868740

ATGGCCTCAAGCTACTCAAATTCTCCATGTGCTGCTTGCAAGTTTCTAAGAAGAAAATGCAACCAAGATTGCATTTTTGCACCTTATTTCCCACCAGAAGAGCCTCATAAGTTTGCAAATGTTCACAAAGTATTTGGTGCAAGCAATGTTAGCAAAATTCTTAATGAAGTCTTACCTCATCAAAGGGAGGATACAGTGAATTCTCTTGCCTATGAAGCTGAAGCAAGGATTAAAAATCCAGTGTATGGTTGTGTTGGAGCTATTTCAGCGCTTCAAGGACAACTCTTTAGGCTCCAAAAGGAACTTGATGCTACAAATGCTGATTTGATTCGTTTTACTCATGAAGGTTCTTCTTCTCTTGGTCTTGGACAATTTCACTCTGATGACTTTTTAAATTACCCTTCAAATTTCAGCAATGACATGTGA
Protein sequence

>Msa0868740

MASSYSNSPCAACKFLRRKCNQDCIFAPYFPPEEPHKFANVHKVFGASNVSKILNEVLPHQREDTVNSLAYEAEARIKNPVYGCVGAISALQGQLFRLQKELDATNADLIRFTHEGSSSLGLGQFHSDDFLNYPSNFSNDM*