AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene069866

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene069866.t1 MTR_2g101300 97.895 190 4 0 1 190 1 190 8.01e-140 387
MS.gene069866.t1 MTR_2g079030 45.963 161 74 5 8 164 8 159 4.28e-36 132
MS.gene069866.t1 MTR_4g077787 35.000 180 102 3 8 186 15 180 2.54e-35 122
MS.gene069866.t1 MTR_8g463180 44.697 132 68 2 6 135 3 131 2.78e-33 120
MS.gene069866.t1 MTR_4g111640 38.298 141 82 4 6 143 13 151 5.81e-32 114
MS.gene069866.t1 MTR_3g105930 44.526 137 68 5 24 155 24 157 1.59e-31 112
MS.gene069866.t1 MTR_2g090580 37.989 179 86 5 24 180 24 199 1.78e-30 110
MS.gene069866.t1 MTR_6g022170 46.226 106 57 0 21 126 28 133 1.32e-29 107
MS.gene069866.t1 MTR_4g078410 39.665 179 91 6 9 177 7 178 3.57e-29 107
MS.gene069866.t1 MTR_4g081100 41.045 134 71 3 1 127 1 133 7.79e-28 104
MS.gene069866.t1 MTR_1g014120 40.157 127 68 4 18 137 16 141 1.94e-26 99.8
MS.gene069866.t1 MTR_2g090575 40.260 154 79 4 9 159 6 149 3.90e-26 102
MS.gene069866.t1 MTR_4g112310 41.000 100 57 1 46 143 2 101 7.38e-26 97.1
MS.gene069866.t1 MTR_2g083250 45.794 107 55 2 24 127 23 129 9.96e-26 100
MS.gene069866.t1 MTR_8g094990 44.643 112 58 2 19 128 17 126 4.15e-24 95.9
MS.gene069866.t1 MTR_8g086360 37.589 141 74 4 9 138 5 142 5.05e-24 94.0
MS.gene069866.t1 MTR_8g095020 44.444 108 48 4 27 129 25 125 1.02e-22 93.2
MS.gene069866.t1 MTR_7g090170 37.037 135 64 5 24 155 24 140 4.80e-22 87.4
MS.gene069866.t1 MTR_8g095013 43.119 109 58 2 19 125 17 123 8.35e-22 90.5
MS.gene069866.t1 MTR_4g124280 38.849 139 74 3 24 152 22 159 1.90e-21 88.2
MS.gene069866.t1 MTR_0334s0010 38.333 120 70 3 9 127 11 127 2.80e-20 84.3
MS.gene069866.t1 MTR_2g088990 34.848 132 77 3 29 155 27 154 9.34e-19 80.9
MS.gene069866.t1 MTR_5g006040 29.299 157 103 4 4 155 3 156 1.04e-18 79.7
MS.gene069866.t1 MTR_4g114870 40.777 103 54 3 27 125 191 290 1.37e-18 82.4
MS.gene069866.t1 MTR_4g114870 35.766 137 82 3 6 137 5 140 5.78e-18 80.5
MS.gene069866.t1 MTR_1g077790 37.255 102 62 1 26 125 28 129 5.60e-18 78.2
MS.gene069866.t1 MTR_4g130780 36.893 103 62 2 35 135 38 139 1.05e-17 77.0
MS.gene069866.t1 MTR_3g092170 36.000 125 74 3 8 129 5 126 1.69e-17 78.6
MS.gene069866.t1 MTR_8g099220 34.783 115 71 2 13 125 15 127 2.28e-17 74.7
MS.gene069866.t1 MTR_1g090420 32.278 158 97 5 7 159 6 158 4.85e-17 76.3
MS.gene069866.t1 MTR_1g104800 34.259 108 66 2 21 126 19 123 7.84e-17 74.7
MS.gene069866.t1 MTR_6g013420 39.496 119 60 5 23 136 34 145 9.05e-16 72.0
MS.gene069866.t1 MTR_4g114830 35.772 123 70 4 24 142 25 142 1.68e-15 70.9
MS.gene069866.t1 MTR_6g083240 32.530 166 102 5 1 157 1 165 1.70e-15 71.2
MS.gene069866.t1 MTR_7g086090 33.333 123 75 2 9 129 8 125 2.16e-15 72.0
MS.gene069866.t1 MTR_3g099540 37.143 105 60 2 24 127 24 123 4.40e-15 68.9
MS.gene069866.t1 MTR_8g007020 29.442 197 116 6 1 185 1 186 5.25e-15 70.1
MS.gene069866.t1 MTR_3g099570 33.594 128 79 3 10 136 9 131 1.08e-14 69.3
MS.gene069866.t1 MTR_7g086100 32.500 120 74 2 9 126 8 122 1.49e-14 69.7
MS.gene069866.t1 MTR_8g007035 38.318 107 58 3 24 127 21 122 1.79e-14 68.9
MS.gene069866.t1 MTR_6g023760 35.577 104 60 4 24 125 23 121 1.96e-14 68.6
MS.gene069866.t1 MTR_2g025580 29.730 148 90 5 9 147 9 151 2.50e-14 67.8
MS.gene069866.t1 MTR_6g080660 35.000 120 71 4 9 127 11 124 5.03e-14 67.8
MS.gene069866.t1 MTR_3g099580 36.893 103 59 2 24 125 23 120 1.79e-13 65.9
MS.gene069866.t1 MTR_7g086280 30.833 120 74 3 9 125 8 121 7.13e-13 64.3
MS.gene069866.t1 MTR_4g130800 36.842 95 57 2 35 127 38 131 1.09e-12 65.1
MS.gene069866.t1 MTR_3g099980 36.975 119 67 3 10 125 9 122 1.09e-12 64.3
MS.gene069866.t1 MTR_7g086230 30.833 120 74 3 9 125 8 121 1.10e-12 63.5
MS.gene069866.t1 MTR_3g099680 36.975 119 67 3 10 125 9 122 1.22e-12 64.3
MS.gene069866.t1 MTR_4g067200 32.540 126 79 4 9 130 11 134 1.35e-12 63.2
MS.gene069866.t1 MTR_4g066110 32.540 126 79 4 9 130 11 134 1.35e-12 63.2
MS.gene069866.t1 MTR_1g090190 30.657 137 77 4 17 142 15 144 1.37e-12 63.5
MS.gene069866.t1 MTR_4g130800 36.842 95 57 2 35 127 37 130 2.04e-12 64.3
MS.gene069866.t1 MTR_6g013170 31.783 129 78 5 25 150 29 150 4.11e-11 59.3
MS.gene069866.t1 MTR_6g013200 31.818 132 78 5 9 134 15 140 4.79e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene069866.t1 AT1G79800 50.820 122 57 1 22 140 29 150 5.61e-40 135
MS.gene069866.t1 AT5G53870 43.258 178 85 6 1 167 5 177 1.64e-34 125
MS.gene069866.t1 AT5G53870 43.258 178 85 6 1 167 5 177 2.37e-34 125
MS.gene069866.t1 AT5G57920 42.553 141 72 5 23 155 18 157 6.81e-31 111
MS.gene069866.t1 AT5G57920 47.706 109 53 3 24 129 20 127 6.99e-31 111
MS.gene069866.t1 AT5G57920 42.857 140 71 5 24 155 52 190 1.06e-30 111
MS.gene069866.t1 AT2G25060 42.647 136 72 4 21 153 25 157 1.21e-30 110
MS.gene069866.t1 AT3G20570 48.113 106 51 2 24 127 27 130 9.26e-30 108
MS.gene069866.t1 AT4G27520 43.802 121 63 2 9 127 13 130 4.21e-29 110
MS.gene069866.t1 AT3G18590 45.455 110 58 2 18 126 19 127 9.47e-29 105
MS.gene069866.t1 AT2G23990 40.940 149 82 5 1 144 1 148 1.13e-28 106
MS.gene069866.t1 AT4G31840 39.073 151 80 6 5 152 10 151 1.22e-28 105
MS.gene069866.t1 AT1G48940 39.024 123 67 2 5 126 11 126 6.66e-28 103
MS.gene069866.t1 AT4G28365 35.928 167 95 5 6 168 7 165 2.49e-26 100
MS.gene069866.t1 AT5G25090 38.710 124 69 4 9 129 11 130 4.05e-26 99.4
MS.gene069866.t1 AT4G30590 31.319 182 119 4 9 186 10 189 1.83e-25 97.4
MS.gene069866.t1 AT5G14345 39.640 111 65 1 32 140 21 131 1.52e-24 94.0
MS.gene069866.t1 AT4G32490 39.344 122 68 3 9 127 12 130 2.40e-24 95.5
MS.gene069866.t1 AT2G23990 36.310 168 82 6 1 144 1 167 4.68e-24 94.7
MS.gene069866.t1 AT5G07475 31.414 191 114 6 4 190 9 186 4.75e-19 80.9
MS.gene069866.t1 AT2G32300 37.500 120 68 2 9 126 8 122 8.38e-18 79.0
MS.gene069866.t1 AT2G32300 37.500 120 68 2 9 126 38 152 2.02e-17 78.6
MS.gene069866.t1 AT3G60270 38.095 105 59 2 24 127 23 122 3.16e-17 75.9
MS.gene069866.t1 AT2G26720 29.534 193 109 6 6 180 10 193 7.98e-17 75.5
MS.gene069866.t1 AT5G26330 32.520 123 72 3 8 128 11 124 2.10e-16 73.9
MS.gene069866.t1 AT5G20230 32.283 127 80 3 25 148 23 146 5.74e-16 72.8
MS.gene069866.t1 AT1G64640 35.238 105 64 2 23 125 29 131 9.58e-16 72.0
MS.gene069866.t1 AT3G17675 39.216 102 54 4 29 128 34 129 3.79e-15 68.9
MS.gene069866.t1 AT2G31050 32.609 138 85 3 2 137 6 137 3.40e-14 68.2
MS.gene069866.t1 AT1G45063 31.092 119 76 2 21 136 143 258 3.84e-13 66.2
MS.gene069866.t1 AT1G45063 31.405 121 75 3 9 126 12 127 6.99e-13 65.9
MS.gene069866.t1 AT3G60280 35.849 106 62 2 24 128 21 121 4.46e-13 65.5
MS.gene069866.t1 AT1G45063 31.092 119 76 2 21 136 143 258 6.72e-13 66.2
MS.gene069866.t1 AT1G45063 31.405 121 75 3 9 126 12 127 1.06e-12 65.9
MS.gene069866.t1 AT4G01380 35.897 117 64 6 31 139 76 189 3.34e-12 63.2
MS.gene069866.t1 AT1G72230 27.397 146 101 2 46 190 37 178 7.67e-12 61.6
MS.gene069866.t1 AT5G15350 33.083 133 78 6 10 138 13 138 1.25e-11 60.8
MS.gene069866.t1 AT3G27200 27.500 120 79 4 9 126 9 122 2.67e-11 60.1

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 2.1:+3821049 None:intergenic
TTTCAAGTTGGTGGTCGTTT+AGG 0.332074 2.1:-3821082 MS.gene069866:CDS
GGAGGAGGATGAAGCCTCTA+TGG 0.371580 2.1:+3820593 None:intergenic
GAAGAATAAGGTGAATTTGC+AGG 0.374650 2.1:+3820621 None:intergenic
TACCGAGAGAATCTCCGATT+TGG 0.380988 2.1:+3820996 None:intergenic
GATAAAGCAGTTGAATATAA+AGG 0.398175 2.1:+3821153 None:intergenic
ATGTTAACTTTGGTCACATT+CGG 0.414548 2.1:-3820549 MS.gene069866:CDS
ATCGAGGTTGGTGGAGATGC+TGG 0.424568 2.1:+3820681 None:intergenic
CCATTGGTAAAAGTAGTGAT+AGG 0.426491 2.1:+3820819 None:intergenic
TCTATGGAATCAGAAGAATA+AGG 0.432060 2.1:+3820609 None:intergenic
GGACCTTTCTACTTTATAAG+TGG 0.443327 2.1:-3820768 MS.gene069866:CDS
GTTGGTGGAGATGCTGGAAT+TGG 0.443709 2.1:+3820687 None:intergenic
ATTAAGAGTGCTCTTTCCAT+TGG 0.479225 2.1:+3820803 None:intergenic
AAAGTTGCTTGTCGAAGTTA+TGG 0.482445 2.1:-3820718 MS.gene069866:CDS
GAGAATCTCCGATTTGGAAT+CGG 0.483821 2.1:+3821002 None:intergenic
AGAAGGTTCATCACCGATCA+TGG 0.499745 2.1:-3820646 MS.gene069866:CDS
GCAAGACAATTTCAAGTTGG+TGG 0.502423 2.1:-3821091 MS.gene069866:CDS
ACTCTTAATCTTGACAGATC+TGG 0.516660 2.1:-3820789 MS.gene069866:CDS
GAAAGAAACCGATTCCAAAT+CGG 0.517550 2.1:-3821010 MS.gene069866:CDS
GTTCCACTTATAAAGTAGAA+AGG 0.533810 2.1:+3820765 None:intergenic
TTATTCTTCTGATTCCATAG+AGG 0.542969 2.1:-3820607 MS.gene069866:CDS
AGAGGCTTCATCCTCCTCCA+TGG 0.543862 2.1:-3820589 MS.gene069866:CDS
AAGTTGGTGGTCGTTTAGGT+TGG 0.547472 2.1:-3821078 MS.gene069866:CDS
GGTGGATTCGAAATCGAGGT+TGG 0.556684 2.1:+3820669 None:intergenic
ATGATCGGTGATGAACCTTC+TGG 0.564349 2.1:+3820648 None:intergenic
ACTGATGAGCATTGCAGTCA+TGG 0.567850 2.1:-3820744 MS.gene069866:CDS
GGAGATGCTGGAATTGGATG+TGG 0.574757 2.1:+3820693 None:intergenic
TCTGCAAGACAATTTCAAGT+TGG 0.579798 2.1:-3821094 MS.gene069866:CDS
GGATTCGAAATCGAGGTTGG+TGG 0.585966 2.1:+3820672 None:intergenic
TGAAGTAACCACCATGGAGG+AGG 0.590177 2.1:+3820578 None:intergenic
GAATTTGCAGGAGCCATGAT+CGG 0.605477 2.1:+3820633 None:intergenic
TTCCAAATCGGAGATTCTCT+CGG 0.606612 2.1:-3820998 MS.gene069866:intron
TTCTGGTGGATTCGAAATCG+AGG 0.625163 2.1:+3820665 None:intergenic
TTGAACACAAGTAAAAGTAG+TGG 0.625374 2.1:+3821117 None:intergenic
ATCGGTGATGAACCTTCTGG+TGG 0.631559 2.1:+3820651 None:intergenic
GGCTTCATCCTCCTCCATGG+TGG 0.643939 2.1:-3820586 MS.gene069866:CDS
TCGATTTCGAATCCACCAGA+AGG 0.653741 2.1:-3820663 MS.gene069866:CDS
GAATGATTCAGTTCTTACTG+TGG 0.664101 2.1:-3820877 MS.gene069866:CDS
AAAACTTGAAGTAACCACCA+TGG 0.678888 2.1:+3820572 None:intergenic
ACTTGAAGTAACCACCATGG+AGG 0.733661 2.1:+3820575 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATGTGAATCATAACTT+GGG + chr2.1:3820764-3820783 None:intergenic 20.0%
!!! TTCAAGTTTTATGTTAACTT+TGG - chr2.1:3821125-3821144 MS.gene069866:CDS 20.0%
! CAAAAATGTGAATCATAACT+TGG + chr2.1:3820765-3820784 None:intergenic 25.0%
! GATAAAGCAGTTGAATATAA+AGG + chr2.1:3820534-3820553 None:intergenic 25.0%
ATGTTAACTTTGGTCACATT+CGG - chr2.1:3821135-3821154 MS.gene069866:CDS 30.0%
GTTCCACTTATAAAGTAGAA+AGG + chr2.1:3820922-3820941 None:intergenic 30.0%
TCTATGGAATCAGAAGAATA+AGG + chr2.1:3821078-3821097 None:intergenic 30.0%
TTATTCTTCTGATTCCATAG+AGG - chr2.1:3821077-3821096 MS.gene069866:CDS 30.0%
TTGAACACAAGTAAAAGTAG+TGG + chr2.1:3820570-3820589 None:intergenic 30.0%
! CAACTGCTTTATCATTTTCT+TGG - chr2.1:3820541-3820560 MS.gene069866:CDS 30.0%
AAAACTTGAAGTAACCACCA+TGG + chr2.1:3821115-3821134 None:intergenic 35.0%
AAAGTTGCTTGTCGAAGTTA+TGG - chr2.1:3820966-3820985 MS.gene069866:intron 35.0%
ACTCTTAATCTTGACAGATC+TGG - chr2.1:3820895-3820914 MS.gene069866:intron 35.0%
CCATTGGTAAAAGTAGTGAT+AGG + chr2.1:3820868-3820887 None:intergenic 35.0%
GAAGAATAAGGTGAATTTGC+AGG + chr2.1:3821066-3821085 None:intergenic 35.0%
GAATGATTCAGTTCTTACTG+TGG - chr2.1:3820807-3820826 MS.gene069866:CDS 35.0%
GGACCTTTCTACTTTATAAG+TGG - chr2.1:3820916-3820935 MS.gene069866:intron 35.0%
! GAAAGAAACCGATTCCAAAT+CGG - chr2.1:3820674-3820693 MS.gene069866:CDS 35.0%
! GTGTAAAAAGCAGTGTTGTT+TGG + chr2.1:3820644-3820663 None:intergenic 35.0%
! TCTGCAAGACAATTTCAAGT+TGG - chr2.1:3820590-3820609 MS.gene069866:CDS 35.0%
!! ATTAAGAGTGCTCTTTCCAT+TGG + chr2.1:3820884-3820903 None:intergenic 35.0%
!! CCTATCACTACTTTTACCAA+TGG - chr2.1:3820865-3820884 MS.gene069866:CDS 35.0%
!!! ACACTGCTTTTTACACTCAA+TGG - chr2.1:3820648-3820667 MS.gene069866:CDS 35.0%
!!! CACTGCTTTTTACACTCAAT+GGG - chr2.1:3820649-3820668 MS.gene069866:CDS 35.0%
TGGGCTGCAAGAAAAAGAAA+TGG + chr2.1:3820745-3820764 None:intergenic 40.0%
TTCCAAATCGGAGATTCTCT+CGG - chr2.1:3820686-3820705 MS.gene069866:CDS 40.0%
!! AAAGCAGTGTTGTTTGGTTC+AGG + chr2.1:3820638-3820657 None:intergenic 40.0%
!! GAGAATCTCCGATTTGGAAT+CGG + chr2.1:3820685-3820704 None:intergenic 40.0%
!! GCAAGACAATTTCAAGTTGG+TGG - chr2.1:3820593-3820612 MS.gene069866:CDS 40.0%
!! TTTCAAGTTGGTGGTCGTTT+AGG - chr2.1:3820602-3820621 MS.gene069866:CDS 40.0%
ACTTGAAGTAACCACCATGG+AGG + chr2.1:3821112-3821131 None:intergenic 45.0%
AGAAGGTTCATCACCGATCA+TGG - chr2.1:3821038-3821057 MS.gene069866:CDS 45.0%
ATGATCGGTGATGAACCTTC+TGG + chr2.1:3821039-3821058 None:intergenic 45.0%
GAATTTGCAGGAGCCATGAT+CGG + chr2.1:3821054-3821073 None:intergenic 45.0%
TACCGAGAGAATCTCCGATT+TGG + chr2.1:3820691-3820710 None:intergenic 45.0%
TCGATTTCGAATCCACCAGA+AGG - chr2.1:3821021-3821040 MS.gene069866:CDS 45.0%
! ACTGATGAGCATTGCAGTCA+TGG - chr2.1:3820940-3820959 MS.gene069866:intron 45.0%
!! AAGTTGGTGGTCGTTTAGGT+TGG - chr2.1:3820606-3820625 MS.gene069866:CDS 45.0%
!! TTCTGGTGGATTCGAAATCG+AGG + chr2.1:3821022-3821041 None:intergenic 45.0%
ATCGGTGATGAACCTTCTGG+TGG + chr2.1:3821036-3821055 None:intergenic 50.0%
GGAGATGCTGGAATTGGATG+TGG + chr2.1:3820994-3821013 None:intergenic 50.0%
GGATTCGAAATCGAGGTTGG+TGG + chr2.1:3821015-3821034 None:intergenic 50.0%
TGAAGTAACCACCATGGAGG+AGG + chr2.1:3821109-3821128 None:intergenic 50.0%
! GGTGGATTCGAAATCGAGGT+TGG + chr2.1:3821018-3821037 None:intergenic 50.0%
! GTTGGTGGAGATGCTGGAAT+TGG + chr2.1:3821000-3821019 None:intergenic 50.0%
AGAGGCTTCATCCTCCTCCA+TGG - chr2.1:3821095-3821114 MS.gene069866:CDS 55.0%
GGAGGAGGATGAAGCCTCTA+TGG + chr2.1:3821094-3821113 None:intergenic 55.0%
!! ATCGAGGTTGGTGGAGATGC+TGG + chr2.1:3821006-3821025 None:intergenic 55.0%
GGCTTCATCCTCCTCCATGG+TGG - chr2.1:3821098-3821117 MS.gene069866:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 3820524 3821182 3820524 ID=MS.gene069866
chr2.1 mRNA 3820524 3821182 3820524 ID=MS.gene069866.t1;Parent=MS.gene069866
chr2.1 exon 3820999 3821182 3820999 ID=MS.gene069866.t1.exon1;Parent=MS.gene069866.t1
chr2.1 CDS 3820999 3821182 3820999 ID=cds.MS.gene069866.t1;Parent=MS.gene069866.t1
chr2.1 exon 3820524 3820912 3820524 ID=MS.gene069866.t1.exon2;Parent=MS.gene069866.t1
chr2.1 CDS 3820524 3820912 3820524 ID=cds.MS.gene069866.t1;Parent=MS.gene069866.t1
Gene Sequence

>MS.gene069866

ATGTCATCCTTTATATTCAACTGCTTTATCATTTTCTTGGCTGCCACTACTTTTACTTGTGTTCAATCTGCAAGACAATTTCAAGTTGGTGGTCGTTTAGGTTGGCATGAACCTGAACCAAACAACACTGCTTTTTACACTCAATGGGCTGAAAGAAACCGATTCCAAATCGGAGATTCTCTCGGTATATAATGCTTTTTTTAATTCATTATTCACTTCCATTTCTTTTTCTTGCAGCCCAAGTTATGATTCACATTTTTGTTTATGCAGTTTTTGAGTACGAGAATGATTCAGTTCTTACTGTGGAGAAGTTTGATTACTTCAATTGTGATGCAAGTCAACCTATCACTACTTTTACCAATGGAAAGAGCACTCTTAATCTTGACAGATCTGGACCTTTCTACTTTATAAGTGGAACTGATGAGCATTGCAGTCATGGTCAAAAGTTGCTTGTCGAAGTTATGGCGCCACATCCAATTCCAGCATCTCCACCAACCTCGATTTCGAATCCACCAGAAGGTTCATCACCGATCATGGCTCCTGCAAATTCACCTTATTCTTCTGATTCCATAGAGGCTTCATCCTCCTCCATGGTGGTTACTTCAAGTTTTATGTTAACTTTGGTCACATTCGGAATTGTGATGATGTTAGCACTCTAG
Protein sequence

>MS.gene069866.t1

MSSFIFNCFIIFLAATTFTCVQSARQFQVGGRLGWHEPEPNNTAFYTQWAERNRFQIGDSLVFEYENDSVLTVEKFDYFNCDASQPITTFTNGKSTLNLDRSGPFYFISGTDEHCSHGQKLLVEVMAPHPIPASPPTSISNPPEGSSPIMAPANSPYSSDSIEASSSSMVVTSSFMLTLVTFGIVMMLAL