AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040011

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040011.t1 MTR_3g071590 98.113 159 3 0 1 159 1 159 3.84e-116 325
MS.gene040011.t1 MTR_5g083230 74.534 161 32 4 1 156 1 157 5.41e-80 234
MS.gene040011.t1 MTR_3g031660 65.359 153 40 1 3 142 2 154 3.97e-70 209
MS.gene040011.t1 MTR_2g068760 75.455 110 27 0 4 113 9 118 8.86e-58 177
MS.gene040011.t1 MTR_4g083680 70.339 118 31 1 2 115 5 122 1.68e-56 175
MS.gene040011.t1 MTR_2g093310 63.063 111 41 0 7 117 32 142 1.10e-50 161
MS.gene040011.t1 MTR_4g060950 59.848 132 42 2 7 137 23 144 5.55e-50 159
MS.gene040011.t1 MTR_1g095850 71.287 101 29 0 9 109 73 173 1.33e-48 157
MS.gene040011.t1 MTR_5g083960 67.619 105 34 0 4 108 35 139 5.73e-48 154
MS.gene040011.t1 MTR_3g094690 63.393 112 41 0 4 115 43 154 4.81e-47 153
MS.gene040011.t1 MTR_7g033800 59.829 117 43 1 5 117 8 124 2.80e-46 149
MS.gene040011.t1 MTR_3g077240 66.346 104 35 0 6 109 8 111 5.99e-46 149
MS.gene040011.t1 MTR_4g105170 66.019 103 35 0 7 109 10 112 8.05e-46 148
MS.gene040011.t1 MTR_3g073690 61.111 108 42 0 1 108 2 109 1.92e-45 147
MS.gene040011.t1 MTR_6g005080 51.408 142 60 3 3 144 5 137 2.36e-45 145
MS.gene040011.t1 MTR_6g005070 61.261 111 41 1 5 115 6 114 3.48e-45 145
MS.gene040011.t1 MTR_3g094690 63.063 111 40 1 4 114 43 152 1.73e-44 146
MS.gene040011.t1 MTR_3g071420 63.366 101 37 0 5 105 11 111 1.71e-42 139
MS.gene040011.t1 MTR_5g075020 66.038 106 36 0 4 109 39 144 1.82e-42 141
MS.gene040011.t1 MTR_3g452660 53.175 126 58 1 4 128 3 128 2.14e-42 142
MS.gene040011.t1 MTR_5g075020 66.038 106 36 0 4 109 43 148 2.69e-42 140
MS.gene040011.t1 MTR_5g017950 58.333 108 45 0 1 108 1 108 8.29e-42 142
MS.gene040011.t1 MTR_5g083010 60.577 104 41 0 5 108 8 111 1.99e-41 137
MS.gene040011.t1 MTR_7g096530 57.143 105 44 1 5 108 11 115 2.25e-37 127
MS.gene040011.t1 MTR_8g040900 59.615 104 42 0 5 108 4 107 5.89e-37 127
MS.gene040011.t1 MTR_1g070220 50.413 121 59 1 8 127 15 135 9.16e-37 125
MS.gene040011.t1 MTR_5g093010 46.094 128 61 1 9 136 6 125 1.56e-36 123
MS.gene040011.t1 MTR_7g074990 56.863 102 43 1 8 108 20 121 6.34e-36 124
MS.gene040011.t1 MTR_7g028905 52.941 102 48 0 7 108 4 105 1.11e-35 120
MS.gene040011.t1 MTR_7g075230 48.092 131 65 2 2 129 6 136 2.28e-35 122
MS.gene040011.t1 MTR_8g036105 56.075 107 46 1 7 112 17 123 7.29e-35 121
MS.gene040011.t1 MTR_7g096610 48.413 126 62 2 1 123 1 126 1.62e-34 120
MS.gene040011.t1 MTR_8g036085 54.369 103 46 1 7 108 22 124 3.32e-34 120
MS.gene040011.t1 MTR_5g080470 44.275 131 67 2 7 131 6 136 4.71e-34 118
MS.gene040011.t1 MTR_6g027710 45.299 117 63 1 7 122 39 155 1.37e-33 118
MS.gene040011.t1 MTR_1g070205 55.670 97 40 2 8 102 12 107 6.50e-33 117
MS.gene040011.t1 MTR_8g079660 47.525 101 53 0 8 108 8 108 1.41e-29 108
MS.gene040011.t1 MTR_8g079620 44.554 101 56 0 8 108 8 108 1.56e-28 105
MS.gene040011.t1 MTR_6g027700 46.535 101 53 1 8 107 7 107 2.57e-28 104
MS.gene040011.t1 MTR_8g079580 44.545 110 60 1 1 109 1 110 1.16e-27 103
MS.gene040011.t1 MTR_6g011250 38.971 136 77 3 9 143 10 140 3.73e-26 98.2
MS.gene040011.t1 MTR_4g107450 42.742 124 64 2 1 117 3 126 3.86e-26 100
MS.gene040011.t1 MTR_6g011230 40.404 99 59 0 3 101 6 104 5.00e-26 98.2
MS.gene040011.t1 MTR_2g100020 38.462 104 64 0 5 108 16 119 2.14e-22 90.5
MS.gene040011.t1 MTR_6g011200 43.750 80 44 1 9 87 10 89 5.37e-22 89.0
MS.gene040011.t1 MTR_8g017090 37.500 104 65 0 5 108 9 112 5.93e-22 89.7
MS.gene040011.t1 MTR_4g088035 39.080 87 53 0 9 95 7 93 3.49e-19 81.6
MS.gene040011.t1 MTR_4g099230 38.947 95 53 2 9 98 3 97 1.14e-18 78.2
MS.gene040011.t1 MTR_5g085390 31.973 147 91 4 9 146 10 156 7.24e-18 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040011.t1 AT2G30130 79.259 135 22 2 1 131 1 133 7.19e-73 217
MS.gene040011.t1 AT1G16530 67.544 114 36 1 3 115 9 122 2.53e-52 164
MS.gene040011.t1 AT1G07900 64.865 111 39 0 7 117 32 142 1.77e-50 160
MS.gene040011.t1 AT1G31320 71.171 111 32 0 4 114 9 119 6.00e-50 158
MS.gene040011.t1 AT2G28500 65.138 109 38 0 7 115 54 162 6.62e-50 160
MS.gene040011.t1 AT2G30340 64.151 106 38 0 4 109 48 153 2.62e-46 152
MS.gene040011.t1 AT2G30340 64.151 106 38 0 4 109 49 154 2.77e-46 152
MS.gene040011.t1 AT3G27650 62.385 109 41 0 1 109 32 140 4.30e-46 148
MS.gene040011.t1 AT5G63090 66.990 103 34 0 6 108 9 111 6.82e-46 148
MS.gene040011.t1 AT5G63090 66.990 103 34 0 6 108 9 111 6.82e-46 148
MS.gene040011.t1 AT5G63090 66.990 103 34 0 6 108 9 111 6.82e-46 148
MS.gene040011.t1 AT5G63090 66.990 103 34 0 6 108 9 111 6.82e-46 148
MS.gene040011.t1 AT3G26660 62.264 106 40 0 9 114 6 111 4.76e-45 144
MS.gene040011.t1 AT3G26620 62.264 106 40 0 9 114 6 111 5.79e-45 144
MS.gene040011.t1 AT2G40470 68.868 106 33 0 4 109 16 121 8.07e-45 146
MS.gene040011.t1 AT2G40470 68.868 106 33 0 4 109 41 146 1.23e-44 146
MS.gene040011.t1 AT2G23660 56.731 104 45 0 6 109 3 106 2.30e-42 143
MS.gene040011.t1 AT2G23660 56.731 104 45 0 6 109 3 106 2.30e-42 143
MS.gene040011.t1 AT2G23660 56.731 104 45 0 6 109 3 106 2.30e-42 143
MS.gene040011.t1 AT5G66870 49.306 144 66 1 4 147 3 139 8.35e-42 142
MS.gene040011.t1 AT3G11090 56.000 125 53 1 5 127 8 132 1.00e-41 137
MS.gene040011.t1 AT1G65620 61.905 105 40 0 4 108 5 109 6.15e-39 131
MS.gene040011.t1 AT1G65620 61.905 105 40 0 4 108 5 109 6.15e-39 131
MS.gene040011.t1 AT1G65620 61.905 105 40 0 4 108 5 109 6.15e-39 131
MS.gene040011.t1 AT1G65620 61.905 105 40 0 4 108 5 109 6.15e-39 131
MS.gene040011.t1 AT1G65620 61.905 105 40 0 4 108 5 109 6.15e-39 131
MS.gene040011.t1 AT4G00210 54.310 116 49 2 1 112 1 116 2.68e-37 127
MS.gene040011.t1 AT3G03760 45.517 145 76 2 7 148 50 194 7.50e-37 128
MS.gene040011.t1 AT2G42430 57.547 106 44 1 4 108 11 116 1.00e-36 127
MS.gene040011.t1 AT2G45410 57.282 103 43 1 11 112 19 121 2.09e-34 119
MS.gene040011.t1 AT2G42440 45.255 137 69 3 4 139 3 134 5.59e-34 120
MS.gene040011.t1 AT3G58190 54.639 97 43 1 8 103 11 107 4.21e-33 117
MS.gene040011.t1 AT2G31310 50.926 108 51 2 1 107 1 107 1.70e-32 114
MS.gene040011.t1 AT2G45420 51.923 104 49 1 11 113 40 143 1.92e-32 116
MS.gene040011.t1 AT4G00220 52.885 104 48 1 11 113 20 123 5.34e-32 114
MS.gene040011.t1 AT3G50510 44.262 122 66 1 6 125 10 131 4.00e-30 108
MS.gene040011.t1 AT3G50510 44.262 122 66 1 6 125 10 131 4.00e-30 108
MS.gene040011.t1 AT5G06080 51.376 109 47 2 7 114 6 109 8.40e-30 107
MS.gene040011.t1 AT5G35900 42.718 103 59 0 9 111 6 108 1.81e-25 97.1
MS.gene040011.t1 AT1G72980 38.525 122 74 1 3 123 8 129 5.26e-25 95.9
MS.gene040011.t1 AT3G47870 37.037 108 68 0 1 108 29 136 3.17e-24 96.3
MS.gene040011.t1 AT3G13850 35.537 121 74 1 9 125 37 157 2.55e-23 92.8
MS.gene040011.t1 AT1G06280 49.351 77 39 0 9 85 25 101 9.72e-21 84.7
MS.gene040011.t1 AT4G22700 35.821 134 72 4 9 141 6 126 6.62e-19 79.7
MS.gene040011.t1 AT2G19820 40.449 89 52 1 7 94 11 99 8.03e-17 72.4
MS.gene040011.t1 AT5G15060 40.000 80 44 2 3 79 12 90 6.38e-14 65.5
MS.gene040011.t1 AT1G36000 29.885 87 61 0 8 94 9 95 2.09e-12 60.8
MS.gene040011.t1 AT3G27940 36.364 66 42 0 7 72 4 69 3.58e-11 58.5
MS.gene040011.t1 AT3G27940 36.364 66 42 0 7 72 4 69 3.58e-11 58.5
MS.gene040011.t1 AT3G27940 36.364 66 42 0 7 72 4 69 3.58e-11 58.5

Find 21 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTAGCACAACGGCGTCTA+AGG 0.285930 3.2:-64931629 None:intergenic
GGATCATGTGAAGGGAAATA+AGG 0.350330 3.2:-64931666 None:intergenic
TGCATCAGCTCTTTGTTGAA+TGG 0.382757 3.2:-64932284 None:intergenic
GTTGATCATCATGTTTCATC+TGG 0.388561 3.2:-64932447 None:intergenic
AGAGTGAAAGATCCTGTTTA+TGG 0.398409 3.2:+64932337 MS.gene040011:CDS
GCATTTGAAGCTCAGAAACT+TGG 0.418459 3.2:-64932390 None:intergenic
GTTCATAAAATTTATGATCA+AGG 0.420987 3.2:-64932495 None:intergenic
GCATCAGCTCTTTGTTGAAT+GGG 0.433832 3.2:-64932283 None:intergenic
TGAATTACATTGCTTGAAGA+AGG 0.450118 3.2:-64932538 None:intergenic
GCTCCAACACAACCATAAAC+AGG 0.455574 3.2:-64932349 None:intergenic
GATCCTGTTTATGGTTGTGT+TGG 0.509317 3.2:+64932346 MS.gene040011:CDS
TTCATAAAATTTATGATCAA+GGG 0.510028 3.2:-64932494 None:intergenic
GAAGGAAAGTTGAAGTACTG+AGG 0.516426 3.2:-64932520 None:intergenic
CCTTAGACGCCGTTGTGCTA+AGG 0.517412 3.2:+64931629 MS.gene040011:CDS
AAGGAAAGTTGAAGTACTGA+GGG 0.536387 3.2:-64932519 None:intergenic
CAATGTTAGCAAAATGCTCC+AGG 0.562470 3.2:+64931728 MS.gene040011:CDS
AAAATTTGCAATTGTTCACA+AGG 0.564865 3.2:+64931692 MS.gene040011:CDS
AGGAGTTTGCATGAAGCACA+AGG 0.592427 3.2:-64931609 None:intergenic
GAGTTTGCATGAAGCACAAG+GGG 0.629954 3.2:-64931607 None:intergenic
GGAGTTTGCATGAAGCACAA+GGG 0.671143 3.2:-64931608 None:intergenic
AGATACAATCCTTAGCACAA+CGG 0.718268 3.2:-64931638 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGATTTTATTTTTTAAGAA+AGG + chr3.2:64932221-64932240 MS.gene040011:intron 10.0%
!! ATGTCATATCATTTAAAAAT+TGG + chr3.2:64932045-64932064 MS.gene040011:intron 15.0%
!! TTCATAAAATTTATGATCAA+GGG - chr3.2:64932497-64932516 None:intergenic 15.0%
!!! TCGTTTTTAAAATAGAATAT+TGG - chr3.2:64932107-64932126 None:intergenic 15.0%
!!! TTATTTTTTAAGAAAGGAAA+TGG + chr3.2:64932227-64932246 MS.gene040011:intron 15.0%
!! AAATGATATGACATTAAACA+TGG - chr3.2:64932039-64932058 None:intergenic 20.0%
!! GTTCATAAAATTTATGATCA+AGG - chr3.2:64932498-64932517 None:intergenic 20.0%
!!! AAAACTTCGATTTTAAAATG+TGG - chr3.2:64931903-64931922 None:intergenic 20.0%
!!! AAAAGTGCAATTTTCTTATT+AGG + chr3.2:64932163-64932182 MS.gene040011:intron 20.0%
!!! AAGTTTTTCTTTTTCTTTCA+AGG - chr3.2:64931779-64931798 None:intergenic 20.0%
!!! TATTAGGTTTTGAGTTTTAA+CGG + chr3.2:64932179-64932198 MS.gene040011:intron 20.0%
!!! TGAACAATTGCAAATTTTTT+AGG - chr3.2:64931690-64931709 None:intergenic 20.0%
! AAAATTTGCAATTGTTCACA+AGG + chr3.2:64931692-64931711 MS.gene040011:CDS 25.0%
!! AGAACAAAAGTACAATTAAG+CGG - chr3.2:64931851-64931870 None:intergenic 25.0%
!!! AATTTTTTAGGATCATGTGA+AGG - chr3.2:64931678-64931697 None:intergenic 25.0%
!!! ATTTTTTAGGATCATGTGAA+GGG - chr3.2:64931677-64931696 None:intergenic 25.0%
!!! TTTTGAGTTTTAACGGTTTT+GGG + chr3.2:64932186-64932205 MS.gene040011:intron 25.0%
GACTTATTGTACAATGCTAT+AGG + chr3.2:64932255-64932274 MS.gene040011:intron 30.0%
TGAATTACATTGCTTGAAGA+AGG - chr3.2:64932541-64932560 None:intergenic 30.0%
! GTTTCTTGATTTTGCATTAG+AGG - chr3.2:64932472-64932491 None:intergenic 30.0%
!! ATTTGTTTCAAAAAGTGTCG+TGG - chr3.2:64932071-64932090 None:intergenic 30.0%
!!! GTATAAGAGAGCGTTATTTT+AGG + chr3.2:64931807-64931826 MS.gene040011:intron 30.0%
!!! GTTTTGAGTTTTAACGGTTT+TGG + chr3.2:64932185-64932204 MS.gene040011:intron 30.0%
AGAGTGAAAGATCCTGTTTA+TGG + chr3.2:64932337-64932356 MS.gene040011:CDS 35.0%
AGATACAATCCTTAGCACAA+CGG - chr3.2:64931641-64931660 None:intergenic 35.0%
CACCATTAGAGCAAAAATCT+GGG - chr3.2:64931965-64931984 None:intergenic 35.0%
GTTGATCATCATGTTTCATC+TGG - chr3.2:64932450-64932469 None:intergenic 35.0%
TTAGAGCAAAAATCTGGGTT+AGG - chr3.2:64931960-64931979 None:intergenic 35.0%
! AACCCAGATTTTTGCTCTAA+TGG + chr3.2:64931960-64931979 MS.gene040011:intron 35.0%
! GCAATTGTTCACAAGGTTTT+TGG + chr3.2:64931699-64931718 MS.gene040011:CDS 35.0%
! TATCAAACTCGTTGCAGTTT+TGG + chr3.2:64931933-64931952 MS.gene040011:intron 35.0%
!! AAGGAAAGTTGAAGTACTGA+GGG - chr3.2:64932522-64932541 None:intergenic 35.0%
!!! AGAAACTTGGTTTTGAAGGT+AGG - chr3.2:64932380-64932399 None:intergenic 35.0%
!!! TTAACGGTTTTGGGTGAAAA+TGG + chr3.2:64932195-64932214 MS.gene040011:intron 35.0%
CAATGTTAGCAAAATGCTCC+AGG + chr3.2:64931728-64931747 MS.gene040011:CDS 40.0%
CCACCATTAGAGCAAAAATC+TGG - chr3.2:64931966-64931985 None:intergenic 40.0%
GATCCTGTTTATGGTTGTGT+TGG + chr3.2:64932346-64932365 MS.gene040011:CDS 40.0%
GCATCAGCTCTTTGTTGAAT+GGG - chr3.2:64932286-64932305 None:intergenic 40.0%
GGATCATGTGAAGGGAAATA+AGG - chr3.2:64931669-64931688 None:intergenic 40.0%
TGCATCAGCTCTTTGTTGAA+TGG - chr3.2:64932287-64932306 None:intergenic 40.0%
! CCAGATTTTTGCTCTAATGG+TGG + chr3.2:64931963-64931982 MS.gene040011:intron 40.0%
! GAGCATTTTGCTAACATTGC+TGG - chr3.2:64931727-64931746 None:intergenic 40.0%
! GCATTTGAAGCTCAGAAACT+TGG - chr3.2:64932393-64932412 None:intergenic 40.0%
! TCAAGGAAGCATAGAAAGTG+TGG - chr3.2:64931762-64931781 None:intergenic 40.0%
!! GAAGGAAAGTTGAAGTACTG+AGG - chr3.2:64932523-64932542 None:intergenic 40.0%
!! TTTTTGCTCTAATGGTGGTG+TGG + chr3.2:64931968-64931987 MS.gene040011:intron 40.0%
!!! GCTCAGAAACTTGGTTTTGA+AGG - chr3.2:64932384-64932403 None:intergenic 40.0%
AGGAGTTTGCATGAAGCACA+AGG - chr3.2:64931612-64931631 None:intergenic 45.0%
GAGTTTGCATGAAGCACAAG+GGG - chr3.2:64931610-64931629 None:intergenic 45.0%
GCTCCAACACAACCATAAAC+AGG - chr3.2:64932352-64932371 None:intergenic 45.0%
GGAGTTTGCATGAAGCACAA+GGG - chr3.2:64931611-64931630 None:intergenic 45.0%
! GAAAGTGTGGATGAAGTACC+TGG - chr3.2:64931749-64931768 None:intergenic 45.0%
CCTTAGACGCCGTTGTGCTA+AGG + chr3.2:64931629-64931648 MS.gene040011:CDS 55.0%
CCTTAGCACAACGGCGTCTA+AGG - chr3.2:64931632-64931651 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 64931588 64932594 64931588 ID=MS.gene040011
chr3.2 mRNA 64931588 64932594 64931588 ID=MS.gene040011.t1;Parent=MS.gene040011
chr3.2 exon 64931588 64931749 64931588 ID=MS.gene040011.t1.exon1;Parent=MS.gene040011.t1
chr3.2 CDS 64931588 64931749 64931588 ID=cds.MS.gene040011.t1;Parent=MS.gene040011.t1
chr3.2 exon 64932277 64932594 64932277 ID=MS.gene040011.t1.exon2;Parent=MS.gene040011.t1
chr3.2 CDS 64932277 64932594 64932277 ID=cds.MS.gene040011.t1;Parent=MS.gene040011.t1
Gene Sequence

>MS.gene040011

ATGGGTGGTAATACTACTTCCCCTTGTGCTTCATGCAAACTCCTTAGACGCCGTTGTGCTAAGGATTGTATCTTTGCTCCTTATTTCCCTTCACATGATCCTAAAAAATTTGCAATTGTTCACAAGGTTTTTGGTGCCAGCAATGTTAGCAAAATGCTCCAGGTACTTCATCCACACTTTCTATGCTTCCTTGAAAGAAAAAGAAAAACTTCATAGTGTGTATAAGAGAGCGTTATTTTAGGTTTAGTTTTATTATCTTTCCGCTTAATTGTACTTTTGTTCTTCTTATTTTATCATGTTCACGAAAATAGTCCACATTTTAAAATCGAAGTTTTTGTCTTCAAGTATCAAACTCGTTGCAGTTTTGGTCCTAACCCAGATTTTTGCTCTAATGGTGGTGTGGCTTGTTTATAATTTCAACTATTTGTAATTTATTTTTGTTACGACACCATGTTTAATGTCATATCATTTAAAAATTGGCCACGACACTTTTTGAAACAAATATCTGCGTTTAAACCAATATTCTATTTTAAAAACGACGACTATTTTTGTGAACGCAGTAAAATAGAAAGATCAAAAGTGCAATTTTCTTATTAGGTTTTGAGTTTTAACGGTTTTGGGTGAAAATGGTTATTGATTTTATTTTTTAAGAAAGGAAATGGTTATTGACTTATTGTACAATGCTATAGGAACTTCCCATTCAACAAAGAGCTGATGCAGTAAGCAGCTTAGTATATGAAGCAAATGCAAGAGTGAAAGATCCTGTTTATGGTTGTGTTGGAGCAATATCCTACCTTCAAAACCAAGTTTCTGAGCTTCAAATGCAGCTTGCAGTAGCACAAGCAGAGATACTTTGCATCCAGATGAAACATGATGATCAACCTCTAATGCAAAATCAAGAAACAGCCCTTGATCATAAATTTTATGAACTCCCTCAGTACTTCAACTTTCCTTCTTCAAGCAATGTAATTCATCATGATTCTTTCTCAAGAGAGAGAATTTTTTGA
Protein sequence

>MS.gene040011.t1

MGGNTTSPCASCKLLRRRCAKDCIFAPYFPSHDPKKFAIVHKVFGASNVSKMLQELPIQQRADAVSSLVYEANARVKDPVYGCVGAISYLQNQVSELQMQLAVAQAEILCIQMKHDDQPLMQNQETALDHKFYELPQYFNFPSSSNVIHHDSFSRERIF