AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76531

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76531.t1 MTR_2g101300 97.368 190 5 0 1 190 1 190 1.19e-138 384
MS.gene76531.t1 MTR_4g077787 35.000 180 102 3 8 186 15 180 4.51e-36 124
MS.gene76531.t1 MTR_2g079030 45.963 161 74 5 8 164 8 159 9.81e-36 131
MS.gene76531.t1 MTR_8g463180 47.727 132 61 3 9 135 3 131 1.50e-33 121
MS.gene76531.t1 MTR_4g111640 37.589 141 83 3 6 143 13 151 3.50e-32 114
MS.gene76531.t1 MTR_3g105930 44.526 137 68 5 24 155 24 157 1.56e-31 112
MS.gene76531.t1 MTR_2g090580 40.625 160 70 5 24 161 24 180 1.75e-30 110
MS.gene76531.t1 MTR_6g022170 46.226 106 57 0 21 126 28 133 3.14e-30 108
MS.gene76531.t1 MTR_4g078410 40.223 179 90 6 9 177 7 178 3.61e-29 107
MS.gene76531.t1 MTR_4g081100 41.791 134 70 3 1 127 1 133 1.41e-28 106
MS.gene76531.t1 MTR_1g014120 40.157 127 68 4 18 137 16 141 4.66e-27 101
MS.gene76531.t1 MTR_2g090575 44.355 124 63 3 9 129 6 126 2.75e-26 103
MS.gene76531.t1 MTR_4g112310 41.000 100 57 1 46 143 2 101 6.70e-26 97.1
MS.gene76531.t1 MTR_2g083250 45.794 107 55 2 24 127 23 129 9.96e-26 100
MS.gene76531.t1 MTR_8g086360 38.298 141 73 4 9 138 5 142 7.57e-25 95.9
MS.gene76531.t1 MTR_8g094990 41.463 123 67 3 9 128 6 126 6.99e-24 95.5
MS.gene76531.t1 MTR_8g095020 44.444 108 48 4 27 129 25 125 1.09e-22 92.8
MS.gene76531.t1 MTR_7g090170 37.037 135 64 5 24 155 24 140 4.46e-22 87.8
MS.gene76531.t1 MTR_8g095013 43.119 109 58 2 19 125 17 123 1.60e-21 89.7
MS.gene76531.t1 MTR_4g124280 38.849 139 74 3 24 152 22 159 1.96e-21 88.2
MS.gene76531.t1 MTR_0334s0010 38.333 120 70 3 9 127 11 127 1.50e-19 82.4
MS.gene76531.t1 MTR_2g088990 34.848 132 77 3 29 155 27 154 9.15e-19 80.9
MS.gene76531.t1 MTR_4g114870 40.777 103 54 3 27 125 191 290 1.30e-18 82.4
MS.gene76531.t1 MTR_4g114870 35.766 137 82 3 6 137 5 140 1.47e-18 82.4
MS.gene76531.t1 MTR_5g006040 29.299 157 103 4 4 155 3 156 2.28e-18 79.0
MS.gene76531.t1 MTR_1g077790 37.255 102 62 1 26 125 28 129 5.84e-18 78.2
MS.gene76531.t1 MTR_4g130780 36.893 103 62 2 35 135 38 139 1.00e-17 77.0
MS.gene76531.t1 MTR_1g090420 32.278 158 97 5 7 159 6 158 2.42e-17 77.0
MS.gene76531.t1 MTR_3g092170 36.000 125 74 3 8 129 5 126 3.78e-17 77.4
MS.gene76531.t1 MTR_8g099220 34.783 115 71 2 13 125 15 127 7.99e-17 73.6
MS.gene76531.t1 MTR_1g104800 35.238 105 63 2 24 126 22 123 8.62e-17 74.7
MS.gene76531.t1 MTR_6g013420 38.843 121 62 5 21 136 32 145 5.53e-16 72.4
MS.gene76531.t1 MTR_4g114830 35.200 125 72 4 22 142 23 142 1.15e-15 71.2
MS.gene76531.t1 MTR_7g086090 33.333 123 75 2 9 129 8 125 2.81e-15 72.0
MS.gene76531.t1 MTR_6g083240 32.530 166 102 5 1 157 1 165 4.17e-15 70.1
MS.gene76531.t1 MTR_3g099540 37.143 105 60 2 24 127 24 123 4.45e-15 68.9
MS.gene76531.t1 MTR_8g007020 29.442 197 116 6 1 185 1 186 6.20e-15 69.7
MS.gene76531.t1 MTR_3g099570 35.385 130 75 5 8 136 10 131 1.40e-14 68.9
MS.gene76531.t1 MTR_8g007035 38.318 107 58 3 24 127 21 122 1.70e-14 68.9
MS.gene76531.t1 MTR_6g023760 35.577 104 60 4 24 125 23 121 1.94e-14 68.6
MS.gene76531.t1 MTR_7g086100 32.500 120 74 2 9 126 8 122 2.28e-14 69.3
MS.gene76531.t1 MTR_6g080660 35.000 120 71 4 9 127 11 124 3.01e-14 68.6
MS.gene76531.t1 MTR_2g025580 29.730 148 90 5 9 147 9 151 3.05e-14 67.8
MS.gene76531.t1 MTR_3g099580 36.893 103 59 2 24 125 23 120 1.63e-13 66.2
MS.gene76531.t1 MTR_4g130800 36.842 95 57 2 35 127 38 131 9.96e-13 65.1
MS.gene76531.t1 MTR_7g086280 30.833 120 74 3 9 125 8 121 1.00e-12 63.5
MS.gene76531.t1 MTR_3g099980 38.843 121 63 5 8 125 10 122 1.45e-12 63.9
MS.gene76531.t1 MTR_1g090190 30.657 137 77 4 17 142 15 144 1.50e-12 63.2
MS.gene76531.t1 MTR_3g099680 38.843 121 63 5 8 125 10 122 1.54e-12 63.9
MS.gene76531.t1 MTR_7g086230 30.833 120 74 3 9 125 8 121 1.61e-12 63.2
MS.gene76531.t1 MTR_4g130800 36.842 95 57 2 35 127 37 130 2.02e-12 64.3
MS.gene76531.t1 MTR_4g067200 33.333 126 78 4 9 130 11 134 5.02e-12 61.6
MS.gene76531.t1 MTR_4g066110 33.333 126 78 4 9 130 11 134 5.02e-12 61.6
MS.gene76531.t1 MTR_6g013170 31.783 129 78 5 25 150 29 150 3.35e-11 59.7
MS.gene76531.t1 MTR_6g013200 31.818 132 78 5 9 134 15 140 6.12e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76531.t1 AT1G79800 52.101 119 54 1 25 140 32 150 5.61e-40 135
MS.gene76531.t1 AT5G53870 43.258 178 85 6 1 167 5 177 1.31e-34 125
MS.gene76531.t1 AT5G53870 43.182 176 84 6 1 165 5 175 2.18e-34 125
MS.gene76531.t1 AT5G57920 47.706 109 53 3 24 129 20 127 6.28e-31 111
MS.gene76531.t1 AT5G57920 42.553 141 72 5 23 155 18 157 6.59e-31 111
MS.gene76531.t1 AT5G57920 42.857 140 71 5 24 155 52 190 9.79e-31 112
MS.gene76531.t1 AT2G25060 43.284 134 70 4 23 153 27 157 1.39e-30 110
MS.gene76531.t1 AT3G20570 48.113 106 51 2 24 127 27 130 9.26e-30 108
MS.gene76531.t1 AT4G31840 38.411 151 81 5 5 152 10 151 5.62e-29 106
MS.gene76531.t1 AT3G18590 45.455 110 58 2 18 126 19 127 8.50e-29 106
MS.gene76531.t1 AT4G27520 43.802 121 63 2 9 127 13 130 9.69e-29 109
MS.gene76531.t1 AT1G48940 39.024 123 67 2 5 126 11 126 1.87e-28 105
MS.gene76531.t1 AT2G23990 40.940 149 82 5 1 144 1 148 2.10e-28 105
MS.gene76531.t1 AT5G25090 38.710 124 69 4 9 129 11 130 3.60e-26 99.4
MS.gene76531.t1 AT4G28365 35.928 167 95 5 6 168 7 165 6.11e-26 99.0
MS.gene76531.t1 AT4G30590 33.133 166 105 4 25 186 26 189 2.87e-25 97.1
MS.gene76531.t1 AT4G32490 40.984 122 66 3 9 127 12 130 7.01e-25 97.1
MS.gene76531.t1 AT5G14345 39.640 111 65 1 32 140 21 131 1.31e-24 94.0
MS.gene76531.t1 AT2G23990 36.310 168 82 6 1 144 1 167 9.11e-24 94.0
MS.gene76531.t1 AT5G07475 31.414 191 114 6 4 190 9 186 5.17e-19 80.9
MS.gene76531.t1 AT2G32300 37.500 120 68 2 9 126 8 122 1.18e-17 78.6
MS.gene76531.t1 AT2G26720 29.534 193 109 6 6 180 10 193 2.84e-17 76.6
MS.gene76531.t1 AT3G60270 38.095 105 59 2 24 127 23 122 3.19e-17 75.9
MS.gene76531.t1 AT2G32300 37.500 120 68 2 9 126 38 152 3.26e-17 77.8
MS.gene76531.t1 AT5G26330 35.514 107 64 2 24 128 21 124 3.16e-16 73.2
MS.gene76531.t1 AT5G20230 32.283 127 80 3 25 148 23 146 5.57e-16 72.8
MS.gene76531.t1 AT1G64640 34.906 106 65 2 22 125 28 131 7.70e-16 72.4
MS.gene76531.t1 AT3G17675 34.375 128 73 5 6 128 8 129 3.10e-15 69.3
MS.gene76531.t1 AT2G31050 32.609 138 85 3 2 137 6 137 1.25e-14 69.3
MS.gene76531.t1 AT1G45063 31.624 117 74 2 23 136 145 258 4.12e-13 66.2
MS.gene76531.t1 AT1G45063 31.405 121 75 3 9 126 12 127 6.32e-13 65.9
MS.gene76531.t1 AT3G60280 35.849 106 62 2 24 128 21 121 4.51e-13 65.5
MS.gene76531.t1 AT1G45063 31.624 117 74 2 23 136 145 258 8.72e-13 66.2
MS.gene76531.t1 AT1G45063 31.405 121 75 3 9 126 12 127 1.14e-12 65.9
MS.gene76531.t1 AT3G27200 28.333 120 78 4 9 126 9 122 2.81e-12 62.4
MS.gene76531.t1 AT4G01380 35.897 117 64 6 31 139 76 189 3.59e-12 62.8
MS.gene76531.t1 AT1G72230 27.397 146 101 2 46 190 37 178 7.44e-12 61.6
MS.gene76531.t1 AT5G15350 33.058 121 71 5 22 138 24 138 9.85e-12 60.8

Find 40 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCAGTGTTGTTTGGTTC+AGG 0.328897 2.3:+2714777 None:intergenic
TTTCAAGTTGGTGGTCGTTT+AGG 0.332074 2.3:-2714810 MS.gene76531:CDS
GGAGGAGGATGAAGCCTCTA+TGG 0.371580 2.3:+2714321 None:intergenic
GAAGAATAAGGTGAATTTGC+AGG 0.374650 2.3:+2714349 None:intergenic
TACCGAGAGAATCTCCGATT+TGG 0.380988 2.3:+2714724 None:intergenic
GATAAAGCAGTTGAATATAA+AGG 0.398175 2.3:+2714881 None:intergenic
ATGTTAACTTTGGTCACATT+CGG 0.414548 2.3:-2714277 MS.gene76531:CDS
ATCGAGGTTGGTGGAGATGC+TGG 0.424568 2.3:+2714409 None:intergenic
CCATTGGTAAAAGTAGTGAT+AGG 0.426491 2.3:+2714547 None:intergenic
TCTATGGAATCAGAAGAATA+AGG 0.432060 2.3:+2714337 None:intergenic
GGACCTTTCTACTTTATAAG+TGG 0.443327 2.3:-2714496 MS.gene76531:CDS
GTTGGTGGAGATGCTGGAAT+TGG 0.443709 2.3:+2714415 None:intergenic
ATTAAGAGTGCTCTTTCCAT+TGG 0.479225 2.3:+2714531 None:intergenic
AAAGTTGCTTGTCGAAGTTA+TGG 0.482445 2.3:-2714446 MS.gene76531:CDS
GAGAATCTCCGATTTGGAAT+CGG 0.483821 2.3:+2714730 None:intergenic
AGAAGGTTCATCACCGATCA+TGG 0.499745 2.3:-2714374 MS.gene76531:CDS
GCAAGACAATTTCAAGTTGG+TGG 0.502423 2.3:-2714819 MS.gene76531:CDS
ACTCTTAATCTTGACAGATC+TGG 0.516660 2.3:-2714517 MS.gene76531:CDS
GAAAGAAACCGATTCCAAAT+CGG 0.517550 2.3:-2714738 MS.gene76531:CDS
GTTCCACTTATAAAGTAGAA+AGG 0.533810 2.3:+2714493 None:intergenic
TTATTCTTCTGATTCCATAG+AGG 0.542969 2.3:-2714335 MS.gene76531:CDS
AGAGGCTTCATCCTCCTCCA+TGG 0.543862 2.3:-2714317 MS.gene76531:CDS
AAGTTGGTGGTCGTTTAGGT+TGG 0.547472 2.3:-2714806 MS.gene76531:CDS
GGTGGATTCGAAATCGAGGT+TGG 0.556684 2.3:+2714397 None:intergenic
ATGATCGGTGATGAACCTTC+TGG 0.564349 2.3:+2714376 None:intergenic
TCTGCAAGACAATTTCAAGT+TGG 0.564753 2.3:-2714822 MS.gene76531:CDS
ACTGATGAGCATTGCAGTCA+TGG 0.567850 2.3:-2714472 MS.gene76531:CDS
GGAGATGCTGGAATTGGATG+TGG 0.574757 2.3:+2714421 None:intergenic
GGATTCGAAATCGAGGTTGG+TGG 0.585966 2.3:+2714400 None:intergenic
TGAAGTAACCACCATGGAGG+AGG 0.590177 2.3:+2714306 None:intergenic
TAGAACACAAGTAAAAGTAG+TGG 0.595484 2.3:+2714845 None:intergenic
GAATTTGCAGGAGCCATGAT+CGG 0.605477 2.3:+2714361 None:intergenic
TTCCAAATCGGAGATTCTCT+CGG 0.606612 2.3:-2714726 MS.gene76531:intron
TTCTGGTGGATTCGAAATCG+AGG 0.625163 2.3:+2714393 None:intergenic
ATCGGTGATGAACCTTCTGG+TGG 0.631559 2.3:+2714379 None:intergenic
GGCTTCATCCTCCTCCATGG+TGG 0.643939 2.3:-2714314 MS.gene76531:CDS
TCGATTTCGAATCCACCAGA+AGG 0.653741 2.3:-2714391 MS.gene76531:CDS
GAATGATTCAGTTCTTACTG+TGG 0.664101 2.3:-2714605 MS.gene76531:CDS
AAAACTTGAAGTAACCACCA+TGG 0.678888 2.3:+2714300 None:intergenic
ACTTGAAGTAACCACCATGG+AGG 0.733661 2.3:+2714303 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATGTGAATCATAACTT+GGG + chr2.3:2714492-2714511 None:intergenic 20.0%
!!! TTCAAGTTTTATGTTAACTT+TGG - chr2.3:2714853-2714872 MS.gene76531:CDS 20.0%
! CAAAAATGTGAATCATAACT+TGG + chr2.3:2714493-2714512 None:intergenic 25.0%
! GATAAAGCAGTTGAATATAA+AGG + chr2.3:2714262-2714281 None:intergenic 25.0%
ATGTTAACTTTGGTCACATT+CGG - chr2.3:2714863-2714882 MS.gene76531:CDS 30.0%
GTTCCACTTATAAAGTAGAA+AGG + chr2.3:2714650-2714669 None:intergenic 30.0%
TAGAACACAAGTAAAAGTAG+TGG + chr2.3:2714298-2714317 None:intergenic 30.0%
TCTATGGAATCAGAAGAATA+AGG + chr2.3:2714806-2714825 None:intergenic 30.0%
TTATTCTTCTGATTCCATAG+AGG - chr2.3:2714805-2714824 MS.gene76531:CDS 30.0%
! CAACTGCTTTATCATTTTCT+TGG - chr2.3:2714269-2714288 MS.gene76531:CDS 30.0%
AAAACTTGAAGTAACCACCA+TGG + chr2.3:2714843-2714862 None:intergenic 35.0%
AAAGTTGCTTGTCGAAGTTA+TGG - chr2.3:2714694-2714713 MS.gene76531:intron 35.0%
ACTCTTAATCTTGACAGATC+TGG - chr2.3:2714623-2714642 MS.gene76531:intron 35.0%
CCATTGGTAAAAGTAGTGAT+AGG + chr2.3:2714596-2714615 None:intergenic 35.0%
GAAGAATAAGGTGAATTTGC+AGG + chr2.3:2714794-2714813 None:intergenic 35.0%
GAATGATTCAGTTCTTACTG+TGG - chr2.3:2714535-2714554 MS.gene76531:CDS 35.0%
GGACCTTTCTACTTTATAAG+TGG - chr2.3:2714644-2714663 MS.gene76531:intron 35.0%
! GAAAGAAACCGATTCCAAAT+CGG - chr2.3:2714402-2714421 MS.gene76531:CDS 35.0%
! GTGTAAAAAGCAGTGTTGTT+TGG + chr2.3:2714372-2714391 None:intergenic 35.0%
! TCTGCAAGACAATTTCAAGT+TGG - chr2.3:2714318-2714337 MS.gene76531:CDS 35.0%
!! ATTAAGAGTGCTCTTTCCAT+TGG + chr2.3:2714612-2714631 None:intergenic 35.0%
!! CCTATCACTACTTTTACCAA+TGG - chr2.3:2714593-2714612 MS.gene76531:CDS 35.0%
!!! ACACTGCTTTTTACACTCAA+TGG - chr2.3:2714376-2714395 MS.gene76531:CDS 35.0%
!!! CACTGCTTTTTACACTCAAT+GGG - chr2.3:2714377-2714396 MS.gene76531:CDS 35.0%
TGGGCTGCAAGAAAAAGAAA+TGG + chr2.3:2714473-2714492 None:intergenic 40.0%
TTCCAAATCGGAGATTCTCT+CGG - chr2.3:2714414-2714433 MS.gene76531:CDS 40.0%
!! AAAGCAGTGTTGTTTGGTTC+AGG + chr2.3:2714366-2714385 None:intergenic 40.0%
!! GAGAATCTCCGATTTGGAAT+CGG + chr2.3:2714413-2714432 None:intergenic 40.0%
!! GCAAGACAATTTCAAGTTGG+TGG - chr2.3:2714321-2714340 MS.gene76531:CDS 40.0%
!! TTTCAAGTTGGTGGTCGTTT+AGG - chr2.3:2714330-2714349 MS.gene76531:CDS 40.0%
ACTTGAAGTAACCACCATGG+AGG + chr2.3:2714840-2714859 None:intergenic 45.0%
AGAAGGTTCATCACCGATCA+TGG - chr2.3:2714766-2714785 MS.gene76531:CDS 45.0%
ATGATCGGTGATGAACCTTC+TGG + chr2.3:2714767-2714786 None:intergenic 45.0%
GAATTTGCAGGAGCCATGAT+CGG + chr2.3:2714782-2714801 None:intergenic 45.0%
TACCGAGAGAATCTCCGATT+TGG + chr2.3:2714419-2714438 None:intergenic 45.0%
TCGATTTCGAATCCACCAGA+AGG - chr2.3:2714749-2714768 MS.gene76531:CDS 45.0%
! ACTGATGAGCATTGCAGTCA+TGG - chr2.3:2714668-2714687 MS.gene76531:intron 45.0%
!! AAGTTGGTGGTCGTTTAGGT+TGG - chr2.3:2714334-2714353 MS.gene76531:CDS 45.0%
!! TTCTGGTGGATTCGAAATCG+AGG + chr2.3:2714750-2714769 None:intergenic 45.0%
ATCGGTGATGAACCTTCTGG+TGG + chr2.3:2714764-2714783 None:intergenic 50.0%
GGAGATGCTGGAATTGGATG+TGG + chr2.3:2714722-2714741 None:intergenic 50.0%
GGATTCGAAATCGAGGTTGG+TGG + chr2.3:2714743-2714762 None:intergenic 50.0%
TGAAGTAACCACCATGGAGG+AGG + chr2.3:2714837-2714856 None:intergenic 50.0%
! GGTGGATTCGAAATCGAGGT+TGG + chr2.3:2714746-2714765 None:intergenic 50.0%
! GTTGGTGGAGATGCTGGAAT+TGG + chr2.3:2714728-2714747 None:intergenic 50.0%
AGAGGCTTCATCCTCCTCCA+TGG - chr2.3:2714823-2714842 MS.gene76531:CDS 55.0%
GGAGGAGGATGAAGCCTCTA+TGG + chr2.3:2714822-2714841 None:intergenic 55.0%
!! ATCGAGGTTGGTGGAGATGC+TGG + chr2.3:2714734-2714753 None:intergenic 55.0%
GGCTTCATCCTCCTCCATGG+TGG - chr2.3:2714826-2714845 MS.gene76531:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 2714252 2714910 2714252 ID=MS.gene76531
chr2.3 mRNA 2714252 2714910 2714252 ID=MS.gene76531.t1;Parent=MS.gene76531
chr2.3 exon 2714727 2714910 2714727 ID=MS.gene76531.t1.exon1;Parent=MS.gene76531.t1
chr2.3 CDS 2714727 2714910 2714727 ID=cds.MS.gene76531.t1;Parent=MS.gene76531.t1
chr2.3 exon 2714252 2714640 2714252 ID=MS.gene76531.t1.exon2;Parent=MS.gene76531.t1
chr2.3 CDS 2714252 2714640 2714252 ID=cds.MS.gene76531.t1;Parent=MS.gene76531.t1
Gene Sequence

>MS.gene76531

ATGTCATCCTTTATATTCAACTGCTTTATCATTTTCTTGGCTGCCACTACTTTTACTTGTGTTCTATCTGCAAGACAATTTCAAGTTGGTGGTCGTTTAGGTTGGCATGAACCTGAACCAAACAACACTGCTTTTTACACTCAATGGGCTGAAAGAAACCGATTCCAAATCGGAGATTCTCTCGGTATATAATGCTTTTTTTAATTCATTATTCACTTCCATTTCTTTTTCTTGCAGCCCAAGTTATGATTCACATTTTTGTTTATGCAGTTTTTGAGTACGAGAATGATTCAGTTCTTACTGTGGAGAAGTTTGATTACTTCAATTGTGATGCAAGTCAACCTATCACTACTTTTACCAATGGAAAGAGCACTCTTAATCTTGACAGATCTGGACCTTTCTACTTTATAAGTGGAACTGATGAGCATTGCAGTCATGGTCAAAAGTTGCTTGTCGAAGTTATGGCGCCACATCCAATTCCAGCATCTCCACCAACCTCGATTTCGAATCCACCAGAAGGTTCATCACCGATCATGGCTCCTGCAAATTCACCTTATTCTTCTGATTCCATAGAGGCTTCATCCTCCTCCATGGTGGTTACTTCAAGTTTTATGTTAACTTTGGTCACATTCGGAATTGTGATGATGTTAGCACTCTAG
Protein sequence

>MS.gene76531.t1

MSSFIFNCFIIFLAATTFTCVLSARQFQVGGRLGWHEPEPNNTAFYTQWAERNRFQIGDSLVFEYENDSVLTVEKFDYFNCDASQPITTFTNGKSTLNLDRSGPFYFISGTDEHCSHGQKLLVEVMAPHPIPASPPTSISNPPEGSSPIMAPANSPYSSDSIEASSSSMVVTSSFMLTLVTFGIVMMLAL