AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene58863

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene58863.t1 MTR_3g099570 72.189 169 45 1 1 169 17 183 5.78e-73 217
MS.gene58863.t1 MTR_3g099580 72.189 169 47 0 1 169 17 185 3.68e-65 197
MS.gene58863.t1 MTR_3g099680 57.282 206 44 4 1 165 17 219 1.17e-60 187
MS.gene58863.t1 MTR_3g099980 57.843 204 44 4 1 165 17 217 1.93e-60 187
MS.gene58863.t1 MTR_3g099540 64.912 114 40 0 1 114 18 131 3.75e-45 145
MS.gene58863.t1 MTR_8g007020 44.944 178 76 5 1 164 14 183 2.98e-38 129
MS.gene58863.t1 MTR_8g007035 55.455 110 46 2 1 107 14 123 1.08e-35 123
MS.gene58863.t1 MTR_1g090190 37.226 137 81 1 7 143 20 151 7.28e-29 105
MS.gene58863.t1 MTR_5g006040 41.912 136 76 3 7 139 23 158 7.00e-28 102
MS.gene58863.t1 MTR_4g114870 46.552 116 57 2 8 118 27 142 5.98e-26 101
MS.gene58863.t1 MTR_4g114870 49.000 100 46 2 10 104 191 290 3.96e-25 99.8
MS.gene58863.t1 MTR_6g080660 44.554 101 56 0 10 110 28 128 4.25e-24 94.0
MS.gene58863.t1 MTR_2g088990 41.667 108 62 1 6 112 21 128 2.16e-23 92.4
MS.gene58863.t1 MTR_0334s0010 45.283 106 53 3 5 106 23 127 1.59e-22 89.4
MS.gene58863.t1 MTR_1g104800 41.748 103 57 3 5 104 20 122 7.50e-22 87.4
MS.gene58863.t1 MTR_6g023760 42.000 100 57 1 6 104 22 121 8.19e-21 84.7
MS.gene58863.t1 MTR_1g112700 37.383 107 65 2 7 111 30 136 1.51e-20 84.0
MS.gene58863.t1 MTR_6g083240 35.928 167 82 7 7 165 24 173 1.72e-20 83.6
MS.gene58863.t1 MTR_2g043730 43.137 102 54 3 5 105 27 125 2.30e-19 79.3
MS.gene58863.t1 MTR_7g086140 41.748 103 58 2 7 107 23 125 4.66e-19 79.3
MS.gene58863.t1 MTR_7g086190 41.748 103 58 2 7 107 23 125 4.66e-19 79.3
MS.gene58863.t1 MTR_4g067200 39.130 115 63 3 1 108 19 133 6.30e-19 79.3
MS.gene58863.t1 MTR_4g066110 39.130 115 63 3 1 108 19 133 6.30e-19 79.3
MS.gene58863.t1 MTR_3g089035 45.361 97 49 3 7 102 30 123 1.36e-18 77.4
MS.gene58863.t1 MTR_8g099220 39.806 103 58 2 7 105 26 128 4.16e-18 76.3
MS.gene58863.t1 MTR_1g105130 39.175 97 57 2 10 104 25 121 4.80e-18 76.6
MS.gene58863.t1 MTR_1g105120 39.175 97 57 2 10 104 25 121 4.80e-18 76.6
MS.gene58863.t1 MTR_7g086160 40.777 103 59 2 7 107 24 126 5.63e-18 76.6
MS.gene58863.t1 MTR_4g007250 40.196 102 59 2 4 104 23 123 1.88e-16 72.8
MS.gene58863.t1 MTR_7g086220 38.372 86 52 1 10 94 25 110 3.59e-16 72.0
MS.gene58863.t1 MTR_2g025580 28.313 166 103 4 1 164 18 169 8.41e-16 71.2
MS.gene58863.t1 MTR_7g086100 39.362 94 56 1 12 104 28 121 1.20e-15 72.0
MS.gene58863.t1 MTR_3g089005 39.806 103 58 3 1 102 24 123 1.85e-15 69.3
MS.gene58863.t1 MTR_2g083250 39.623 106 57 2 12 110 28 133 1.96e-15 72.0
MS.gene58863.t1 MTR_7g086090 40.000 95 56 1 12 105 28 122 4.27e-15 70.9
MS.gene58863.t1 MTR_1g090420 26.752 157 105 3 7 153 25 181 4.34e-15 70.5
MS.gene58863.t1 MTR_8g089110 40.206 97 54 3 7 102 25 118 5.57e-15 67.8
MS.gene58863.t1 MTR_2g043790 42.308 104 54 4 5 107 2 100 8.41e-15 66.6
MS.gene58863.t1 MTR_7g086230 38.776 98 59 1 12 108 28 125 1.19e-14 68.2
MS.gene58863.t1 MTR_7g086280 38.776 98 59 1 12 108 28 125 1.35e-14 68.2
MS.gene58863.t1 MTR_4g081100 38.776 98 55 2 12 104 34 131 5.15e-14 67.4
MS.gene58863.t1 MTR_8g088830 38.776 98 55 4 7 102 25 119 1.07e-13 64.7
MS.gene58863.t1 MTR_8g463180 33.913 115 70 3 12 123 26 137 1.08e-13 67.8
MS.gene58863.t1 MTR_2g090580 33.103 145 93 3 12 152 29 173 2.00e-13 65.5
MS.gene58863.t1 MTR_2g101300 34.074 135 77 4 1 124 13 146 2.03e-13 65.5
MS.gene58863.t1 MTR_8g086360 32.609 138 82 4 12 139 26 162 4.54e-13 64.3
MS.gene58863.t1 MTR_2g090575 37.500 96 57 2 12 104 27 122 7.42e-13 65.5
MS.gene58863.t1 MTR_4g111640 27.333 150 98 3 8 151 30 174 1.28e-12 63.2
MS.gene58863.t1 MTR_6g022170 34.951 103 61 3 7 104 31 132 2.18e-12 62.0
MS.gene58863.t1 MTR_6g013200 37.500 96 56 3 12 104 37 131 3.09e-12 62.0
MS.gene58863.t1 MTR_3g105930 30.075 133 85 3 13 137 31 163 3.10e-12 62.0
MS.gene58863.t1 MTR_4g130800 38.272 81 49 1 25 104 49 129 3.61e-12 63.2
MS.gene58863.t1 MTR_4g130800 38.272 81 49 1 25 104 48 128 3.77e-12 63.2
MS.gene58863.t1 MTR_4g114830 37.234 94 52 3 13 99 32 125 6.41e-12 60.8
MS.gene58863.t1 MTR_1g014120 33.962 106 65 2 13 113 29 134 8.38e-12 60.8
MS.gene58863.t1 MTR_4g077787 31.068 103 64 2 8 104 30 131 1.42e-11 60.1
MS.gene58863.t1 MTR_4g112310 28.125 128 87 2 24 151 2 124 1.48e-11 58.9
MS.gene58863.t1 MTR_8g094990 34.821 112 69 2 11 118 26 137 1.61e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene58863.t1 AT1G72230 65.217 92 32 0 18 109 31 122 4.75e-40 134
MS.gene58863.t1 AT1G22480 57.292 96 41 0 15 110 24 119 1.12e-32 115
MS.gene58863.t1 AT5G07475 38.298 141 82 1 7 147 27 162 1.78e-27 102
MS.gene58863.t1 AT2G32300 43.478 115 64 1 5 118 21 135 2.70e-27 103
MS.gene58863.t1 AT3G60270 47.059 102 54 0 6 107 22 123 5.23e-27 100
MS.gene58863.t1 AT2G32300 43.478 115 64 1 5 118 51 165 6.42e-27 103
MS.gene58863.t1 AT2G26720 35.503 169 96 4 7 163 26 193 3.32e-24 94.0
MS.gene58863.t1 AT2G44790 52.688 93 42 1 18 108 36 128 3.97e-24 94.0
MS.gene58863.t1 AT2G31050 44.737 114 59 3 8 117 27 140 2.50e-23 91.7
MS.gene58863.t1 AT5G26330 43.564 101 54 2 7 104 21 121 3.12e-22 88.6
MS.gene58863.t1 AT3G27200 41.000 100 58 1 6 104 22 121 8.58e-22 87.0
MS.gene58863.t1 AT3G60280 43.137 102 58 0 6 107 20 121 1.96e-21 87.4
MS.gene58863.t1 AT3G17675 38.095 105 64 1 1 104 23 127 6.91e-20 80.9
MS.gene58863.t1 AT5G20230 34.756 164 90 4 10 156 25 188 7.04e-16 72.0
MS.gene58863.t1 AT5G15350 35.398 113 69 3 7 117 26 136 9.28e-15 68.6
MS.gene58863.t1 AT5G53870 32.353 136 80 3 1 124 13 148 1.22e-14 70.9
MS.gene58863.t1 AT1G64640 35.537 121 73 3 7 123 30 149 1.40e-14 68.6
MS.gene58863.t1 AT5G53870 32.353 136 80 3 1 124 13 148 1.69e-14 70.5
MS.gene58863.t1 AT2G25060 38.710 124 69 5 11 127 32 155 5.90e-14 66.6
MS.gene58863.t1 AT4G12880 36.634 101 60 3 7 104 26 125 1.05e-13 65.1
MS.gene58863.t1 AT1G45063 35.294 119 67 5 9 121 148 262 1.19e-13 67.4
MS.gene58863.t1 AT1G45063 35.294 119 67 5 9 121 148 262 1.78e-13 67.4
MS.gene58863.t1 AT3G18590 35.577 104 60 2 7 104 24 126 6.44e-13 63.9
MS.gene58863.t1 AT4G28365 33.913 115 67 3 12 117 31 145 9.91e-13 63.5
MS.gene58863.t1 AT3G53330 31.496 127 82 4 3 125 182 307 1.71e-12 64.3
MS.gene58863.t1 AT4G31840 32.716 162 83 7 11 158 28 177 1.92e-12 62.4
MS.gene58863.t1 AT2G02850 38.144 97 56 3 7 102 33 126 3.79e-12 60.8
MS.gene58863.t1 AT2G27035 28.758 153 87 6 7 156 25 158 5.16e-12 61.2
MS.gene58863.t1 AT4G27520 33.663 101 64 2 7 104 28 128 9.05e-12 62.4
MS.gene58863.t1 AT4G30590 33.333 99 58 2 27 117 50 148 9.43e-12 60.8
MS.gene58863.t1 AT4G01380 28.571 119 75 4 15 125 77 193 1.61e-11 60.5
MS.gene58863.t1 AT3G20570 31.579 152 82 3 6 135 26 177 2.10e-11 60.1
MS.gene58863.t1 AT4G32490 33.333 96 61 2 12 104 33 128 8.05e-11 58.9

Find 40 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTTCATATGCGCTGTTCC+TGG 0.318286 6.2:-78802283 MS.gene58863:CDS
ATTATGACAGTGTTCAACTA+TGG 0.324971 6.2:-78802427 MS.gene58863:intron
GCTCCTTCTGCAACACCATC+AGG 0.341751 6.2:-78802202 MS.gene58863:CDS
ACAGTGTTCAACTATGGAAT+TGG 0.345697 6.2:-78802421 MS.gene58863:intron
GATCTTGATAGGTCATATAT+TGG 0.384007 6.2:-78802050 MS.gene58863:CDS
AATGACAAAACCTTTGTAGT+TGG 0.413140 6.2:-78802598 MS.gene58863:CDS
ACAGTTTCATGGATCTTGAT+AGG 0.419018 6.2:-78802061 MS.gene58863:CDS
CACACCGTTGGAGATACTTC+AGG 0.449866 6.2:-78802655 MS.gene58863:CDS
GATACTTCAGGTTGGACAAT+CGG 0.457701 6.2:-78802643 MS.gene58863:CDS
GGTAGGAGTGGTGGTGGTCG+TGG 0.462242 6.2:+78802138 None:intergenic
CAGTGTTCAACTATGGAATT+GGG 0.499419 6.2:-78802420 MS.gene58863:CDS
TGGCATGAAACTCTCTGTTA+AGG 0.505412 6.2:-78802248 MS.gene58863:CDS
TTTGCAACTGTCCACACCGT+TGG 0.509170 6.2:-78802667 MS.gene58863:CDS
TTTGTAGTTGGAGACAGTCT+TGG 0.511925 6.2:-78802586 MS.gene58863:intron
ACACCATCAGGGAAAGTTGA+TGG 0.512811 6.2:-78802190 MS.gene58863:CDS
TTCCCTGATGGTGTTGCAGA+AGG 0.516823 6.2:+78802199 None:intergenic
GAAGTTGCACTTTGCGTGGT+AGG 0.529660 6.2:+78802121 None:intergenic
ATGCCACCTACGCAATGTCC+AGG 0.545019 6.2:+78802265 None:intergenic
GTGTGGTAGTTGTTGCGGCA+AGG 0.547471 6.2:+78802164 None:intergenic
GTGTGGACAGTTGCAAAAGT+TGG 0.551081 6.2:+78802673 None:intergenic
AGCTGAAGTTGCACTTTGCG+TGG 0.552340 6.2:+78802117 None:intergenic
GTTCCTGGACATTGCGTAGG+TGG 0.555389 6.2:-78802268 MS.gene58863:CDS
TGTGGTAGTTGTTGCGGCAA+GGG 0.558068 6.2:+78802165 None:intergenic
CTCCTTCTGCAACACCATCA+GGG 0.584013 6.2:-78802201 MS.gene58863:CDS
GTGCCATCAACTTTCCCTGA+TGG 0.588940 6.2:+78802187 None:intergenic
TCGGTTCTGATTATAGCACA+TGG 0.592715 6.2:-78802624 MS.gene58863:CDS
CAACTATGGAATTGGGCACA+CGG 0.599601 6.2:-78802413 MS.gene58863:CDS
TGCACTTTGCGTGGTAGGAG+TGG 0.601900 6.2:+78802126 None:intergenic
GGTGGTGGTCGTGGAATGTG+TGG 0.616937 6.2:+78802147 None:intergenic
TTGCGTGGTAGGAGTGGTGG+TGG 0.624187 6.2:+78802132 None:intergenic
GGAATGTGTGGTAGTTGTTG+CGG 0.631513 6.2:+78802159 None:intergenic
AAGACTGTCTCCAACTACAA+AGG 0.647672 6.2:+78802588 None:intergenic
CCAACCTGAAGTATCTCCAA+CGG 0.658901 6.2:+78802651 None:intergenic
CCGTTGGAGATACTTCAGGT+TGG 0.662766 6.2:-78802651 MS.gene58863:CDS
GCTGTTCCTGGACATTGCGT+AGG 0.662871 6.2:-78802271 MS.gene58863:CDS
CGGTTCTGATTATAGCACAT+GGG 0.665310 6.2:-78802623 MS.gene58863:CDS
ACTTTGCGTGGTAGGAGTGG+TGG 0.668649 6.2:+78802129 None:intergenic
CTGAAGTATCTCCAACGGTG+TGG 0.674320 6.2:+78802656 None:intergenic
TCAATTAGTACAGACAGTAG+CGG 0.713968 6.2:-78802343 MS.gene58863:CDS
CTATGGAATTGGGCACACGG+TGG 0.733563 6.2:-78802410 MS.gene58863:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACATTAGTTTTTTAAATTA+TGG + chr6.2:78802267-78802286 None:intergenic 10.0%
! GTGAAAAAGAAAGCAAAAAT+TGG + chr6.2:78802648-78802667 None:intergenic 25.0%
AATGACAAAACCTTTGTAGT+TGG - chr6.2:78802129-78802148 MS.gene58863:CDS 30.0%
ATTATGACAGTGTTCAACTA+TGG - chr6.2:78802300-78802319 MS.gene58863:CDS 30.0%
GATCTTGATAGGTCATATAT+TGG - chr6.2:78802677-78802696 MS.gene58863:CDS 30.0%
!! CTTTCTTTTTCACAGTTTCA+TGG - chr6.2:78802655-78802674 MS.gene58863:CDS 30.0%
ACAGTGTTCAACTATGGAAT+TGG - chr6.2:78802306-78802325 MS.gene58863:CDS 35.0%
ACAGTTTCATGGATCTTGAT+AGG - chr6.2:78802666-78802685 MS.gene58863:CDS 35.0%
CAGTGTTCAACTATGGAATT+GGG - chr6.2:78802307-78802326 MS.gene58863:CDS 35.0%
TCAATTAGTACAGACAGTAG+CGG - chr6.2:78802384-78802403 MS.gene58863:CDS 35.0%
!!! TTTTTTGAAGGGAATGGTTG+TGG + chr6.2:78802412-78802431 None:intergenic 35.0%
AAGACTGTCTCCAACTACAA+AGG + chr6.2:78802142-78802161 None:intergenic 40.0%
ACCATTCCCTTCAAAAAAGC+AGG - chr6.2:78802414-78802433 MS.gene58863:CDS 40.0%
TGGCATGAAACTCTCTGTTA+AGG - chr6.2:78802479-78802498 MS.gene58863:intron 40.0%
TTTGTAGTTGGAGACAGTCT+TGG - chr6.2:78802141-78802160 MS.gene58863:CDS 40.0%
! CGGTTCTGATTATAGCACAT+GGG - chr6.2:78802104-78802123 MS.gene58863:CDS 40.0%
! TCGGTTCTGATTATAGCACA+TGG - chr6.2:78802103-78802122 MS.gene58863:CDS 40.0%
!! GATACTTCAGGTTGGACAAT+CGG - chr6.2:78802084-78802103 MS.gene58863:CDS 40.0%
!!! ATGCGTTCCTGCTTTTTTGA+AGG + chr6.2:78802424-78802443 None:intergenic 40.0%
!!! TCCTGCTTTTTTGAAGGGAA+TGG + chr6.2:78802418-78802437 None:intergenic 40.0%
!!! TGCGTTCCTGCTTTTTTGAA+GGG + chr6.2:78802423-78802442 None:intergenic 40.0%
ACACCATCAGGGAAAGTTGA+TGG - chr6.2:78802537-78802556 MS.gene58863:intron 45.0%
CAACTATGGAATTGGGCACA+CGG - chr6.2:78802314-78802333 MS.gene58863:CDS 45.0%
GGAATGTGTGGTAGTTGTTG+CGG + chr6.2:78802571-78802590 None:intergenic 45.0%
GTGTGGACAGTTGCAAAAGT+TGG + chr6.2:78802057-78802076 None:intergenic 45.0%
TACTTCATATGCGCTGTTCC+TGG - chr6.2:78802444-78802463 MS.gene58863:intron 45.0%
! CCAACCTGAAGTATCTCCAA+CGG + chr6.2:78802079-78802098 None:intergenic 45.0%
AGCTGAAGTTGCACTTTGCG+TGG + chr6.2:78802613-78802632 None:intergenic 50.0%
CACACCGTTGGAGATACTTC+AGG - chr6.2:78802072-78802091 MS.gene58863:CDS 50.0%
CCGTTGGAGATACTTCAGGT+TGG - chr6.2:78802076-78802095 MS.gene58863:CDS 50.0%
CTCCTTCTGCAACACCATCA+GGG - chr6.2:78802526-78802545 MS.gene58863:intron 50.0%
GAAGTTGCACTTTGCGTGGT+AGG + chr6.2:78802609-78802628 None:intergenic 50.0%
GTGCCATCAACTTTCCCTGA+TGG + chr6.2:78802543-78802562 None:intergenic 50.0%
TGTGGTAGTTGTTGCGGCAA+GGG + chr6.2:78802565-78802584 None:intergenic 50.0%
TTTGCAACTGTCCACACCGT+TGG - chr6.2:78802060-78802079 MS.gene58863:CDS 50.0%
! CTGAAGTATCTCCAACGGTG+TGG + chr6.2:78802074-78802093 None:intergenic 50.0%
!! TTCCCTGATGGTGTTGCAGA+AGG + chr6.2:78802531-78802550 None:intergenic 50.0%
ACTTTGCGTGGTAGGAGTGG+TGG + chr6.2:78802601-78802620 None:intergenic 55.0%
ATGCCACCTACGCAATGTCC+AGG + chr6.2:78802465-78802484 None:intergenic 55.0%
CTATGGAATTGGGCACACGG+TGG - chr6.2:78802317-78802336 MS.gene58863:CDS 55.0%
GCTCCTTCTGCAACACCATC+AGG - chr6.2:78802525-78802544 MS.gene58863:intron 55.0%
GCTGTTCCTGGACATTGCGT+AGG - chr6.2:78802456-78802475 MS.gene58863:intron 55.0%
GTGTGGTAGTTGTTGCGGCA+AGG + chr6.2:78802566-78802585 None:intergenic 55.0%
GTTCCTGGACATTGCGTAGG+TGG - chr6.2:78802459-78802478 MS.gene58863:intron 55.0%
TGCACTTTGCGTGGTAGGAG+TGG + chr6.2:78802604-78802623 None:intergenic 55.0%
TTGCGTGGTAGGAGTGGTGG+TGG + chr6.2:78802598-78802617 None:intergenic 60.0%
! GGTGGTGGTCGTGGAATGTG+TGG + chr6.2:78802583-78802602 None:intergenic 60.0%
!! GGTAGGAGTGGTGGTGGTCG+TGG + chr6.2:78802592-78802611 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 78802045 78802704 78802045 ID=MS.gene58863
chr6.2 mRNA 78802045 78802704 78802045 ID=MS.gene58863.t1;Parent=MS.gene58863
chr6.2 exon 78802587 78802704 78802587 ID=MS.gene58863.t1.exon1;Parent=MS.gene58863.t1
chr6.2 CDS 78802587 78802704 78802587 ID=cds.MS.gene58863.t1;Parent=MS.gene58863.t1
chr6.2 exon 78802045 78802439 78802045 ID=MS.gene58863.t1.exon2;Parent=MS.gene58863.t1
chr6.2 CDS 78802045 78802439 78802045 ID=cds.MS.gene58863.t1;Parent=MS.gene58863.t1
Gene Sequence

>MS.gene58863

ATGGCACTGCCAACTTTTGCAACTGTCCACACCGTTGGAGATACTTCAGGTTGGACAATCGGTTCTGATTATAGCACATGGGCTAATGACAAAACCTTTGTAGTTGGAGACAGTCTTGGTAAGTATGAACTATAAACTTTCTTTATTAAACACAACTCAATAATGAGAAGAAAATTGAATTTTTCTCAATTTGATTATTTGTATAGTTTTAAATTGCAACCATAATTTAAAAAACTAATGTATGTATGTGACTTTATTATGACAGTGTTCAACTATGGAATTGGGCACACGGTGGATGAAGTTCAAGAAAGTGACTATAAATCATGCATAACTAGAAATTCAATTAGTACAGACAGTAGCGGTGCCACAACCATTCCCTTCAAAAAAGCAGGAACGCATTACTTCATATGCGCTGTTCCTGGACATTGCGTAGGTGGCATGAAACTCTCTGTTAAGGTTAACGCTTCTTCTACTTCTGCTGCTCCTTCTGCAACACCATCAGGGAAAGTTGATGGCACCCTTGCCGCAACAACTACCACACATTCCACGACCACCACCACTCCTACCACGCAAAGTGCAACTTCAGCTACTAGTATCTCACCAATTTTTGCTTTCTTTTTCACAGTTTCATGGATCTTGATAGGTCATATATTGGAGTGA
Protein sequence

>MS.gene58863.t1

MALPTFATVHTVGDTSGWTIGSDYSTWANDKTFVVGDSLVFNYGIGHTVDEVQESDYKSCITRNSISTDSSGATTIPFKKAGTHYFICAVPGHCVGGMKLSVKVNASSTSAAPSATPSGKVDGTLAATTTTHSTTTTTPTTQSATSATSISPIFAFFFTVSWILIGHILE