AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043112

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043112.t1 MTR_4g032620 90.476 231 22 0 1 231 1 231 1.20e-161 446
MS.gene043112.t1 MTR_8g036130 58.300 247 87 3 1 231 1 247 2.58e-93 274
MS.gene043112.t1 MTR_4g031910 53.361 238 95 2 1 231 1 229 3.63e-77 232
MS.gene043112.t1 MTR_4g032290 54.918 244 84 4 1 231 1 231 5.30e-75 227
MS.gene043112.t1 MTR_3g065100 48.750 240 109 4 1 228 1 238 5.37e-67 207
MS.gene043112.t1 MTR_3g466980 52.564 156 73 1 1 156 1 155 5.24e-56 178
MS.gene043112.t1 MTR_4g032260 60.645 155 61 0 1 155 1 155 1.79e-54 172
MS.gene043112.t1 MTR_2g035610 68.595 121 38 0 1 121 1 121 1.59e-50 160
MS.gene043112.t1 MTR_3g466830 43.210 162 89 2 3 163 2 161 1.02e-44 147
MS.gene043112.t1 MTR_3g031100 43.871 155 87 0 1 155 1 155 7.21e-41 140
MS.gene043112.t1 MTR_4g063790 40.000 165 99 0 1 165 1 165 9.35e-41 137
MS.gene043112.t1 MTR_3g466890 42.138 159 89 2 3 160 2 158 1.97e-39 134
MS.gene043112.t1 MTR_5g047580 40.645 155 90 2 1 155 1 153 3.18e-39 133
MS.gene043112.t1 MTR_3g467080 38.961 154 94 0 1 154 1 154 5.50e-39 132
MS.gene043112.t1 MTR_5g075380 40.909 154 90 1 1 154 1 153 5.78e-38 130
MS.gene043112.t1 MTR_7g011950 42.208 154 87 2 1 154 1 152 3.04e-37 128
MS.gene043112.t1 MTR_1g090697 37.975 158 96 2 1 158 1 156 3.86e-35 122
MS.gene043112.t1 MTR_2g016210 33.040 227 130 4 1 219 1 213 5.24e-35 125
MS.gene043112.t1 MTR_1g084950 40.000 155 91 2 1 155 1 153 1.99e-34 120
MS.gene043112.t1 MTR_1g090783 40.816 147 85 2 3 149 2 146 3.33e-34 120
MS.gene043112.t1 MTR_3g031240 35.802 162 104 0 1 162 1 162 1.15e-33 119
MS.gene043112.t1 MTR_4g028720 38.961 154 92 2 1 154 1 152 2.84e-33 118
MS.gene043112.t1 MTR_1g077390 37.013 154 95 2 1 154 1 152 5.82e-33 117
MS.gene043112.t1 MTR_4g028800 76.389 72 15 1 1 72 1 70 1.29e-32 113
MS.gene043112.t1 MTR_1g090710 35.443 158 101 1 1 158 1 157 1.38e-32 116
MS.gene043112.t1 MTR_1g077320 37.662 154 94 2 1 154 1 152 4.68e-31 112
MS.gene043112.t1 MTR_2g035580 38.710 155 94 1 1 155 1 154 3.54e-29 107
MS.gene043112.t1 MTR_3g465410 37.956 137 85 0 29 165 1 137 4.85e-29 106
MS.gene043112.t1 MTR_1g077300 39.490 157 85 3 1 154 1 150 1.74e-28 105
MS.gene043112.t1 MTR_7g055800 48.739 119 33 2 1 119 1 91 4.54e-28 102
MS.gene043112.t1 MTR_3g466900 36.923 130 79 2 32 160 2 129 6.11e-28 103
MS.gene043112.t1 MTR_3g466930 39.695 131 74 4 32 160 2 129 8.16e-28 103
MS.gene043112.t1 MTR_5g047560 38.843 121 57 2 1 121 1 104 3.18e-25 96.7
MS.gene043112.t1 MTR_7g055790 49.550 111 38 1 1 111 59 151 3.62e-24 94.4
MS.gene043112.t1 MTR_4g032270 46.018 113 52 4 125 231 22 131 2.48e-22 89.0
MS.gene043112.t1 MTR_7g055940 46.667 105 28 2 1 105 1 77 6.93e-22 86.3
MS.gene043112.t1 MTR_4g019670 32.911 158 102 2 3 157 6 162 4.57e-21 91.7
MS.gene043112.t1 MTR_7g106510 36.066 122 78 0 3 124 6 127 6.17e-21 90.9
MS.gene043112.t1 MTR_3g093900 33.766 154 99 3 3 155 6 157 1.31e-19 87.4
MS.gene043112.t1 MTR_2g035590 47.191 89 47 0 74 162 1 89 4.49e-15 68.9
MS.gene043112.t1 MTR_6g018920 37.500 104 58 4 1 98 1 103 7.01e-13 67.4
MS.gene043112.t1 MTR_1g114730 34.188 117 62 4 1 103 1 116 9.84e-13 66.6
MS.gene043112.t1 MTR_6g005450 34.746 118 62 4 1 104 1 117 8.51e-12 63.9
MS.gene043112.t1 MTR_4g084780 56.250 48 21 0 74 121 1 48 1.56e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043112.t1 AT5G48670 52.174 161 76 1 1 161 1 160 1.17e-49 165
MS.gene043112.t1 AT1G65300 39.560 182 105 2 3 184 2 178 1.01e-37 133
MS.gene043112.t1 AT3G05860 40.000 150 89 1 1 150 1 149 1.55e-37 130
MS.gene043112.t1 AT3G05860 40.000 150 89 1 1 150 1 149 4.62e-37 130
MS.gene043112.t1 AT3G05860 40.000 150 89 1 1 150 1 149 5.81e-37 130
MS.gene043112.t1 AT5G26650 39.306 173 102 2 4 176 2 171 3.61e-36 131
MS.gene043112.t1 AT5G26630 38.947 190 114 2 1 189 1 189 1.95e-35 125
MS.gene043112.t1 AT5G27960 38.150 173 104 2 4 176 2 171 2.39e-35 128
MS.gene043112.t1 AT1G65330 39.181 171 101 2 3 173 2 169 6.98e-34 123
MS.gene043112.t1 AT5G27810 47.863 117 61 0 29 145 1 117 7.25e-33 115
MS.gene043112.t1 AT1G31630 33.918 171 109 3 3 173 2 168 6.60e-30 114
MS.gene043112.t1 AT1G31640 32.450 151 100 2 3 153 2 150 1.80e-26 106
MS.gene043112.t1 AT2G28700 30.500 200 133 2 1 195 1 199 1.55e-25 102
MS.gene043112.t1 AT5G26580 33.523 176 99 3 1 176 1 158 2.49e-25 102
MS.gene043112.t1 AT1G22590 33.125 160 91 3 1 154 1 150 9.19e-22 88.6
MS.gene043112.t1 AT2G40210 40.833 120 71 0 1 120 1 120 1.92e-19 86.3
MS.gene043112.t1 AT5G06500 29.221 154 107 1 1 154 1 152 1.35e-17 79.3
MS.gene043112.t1 AT5G55690 32.500 160 91 6 1 145 1 158 3.17e-13 67.8
MS.gene043112.t1 AT5G55690 32.500 160 91 6 1 145 1 158 3.17e-13 67.8
MS.gene043112.t1 AT5G58890 38.384 99 53 3 1 92 1 98 6.57e-13 67.0

Find 58 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTGCCATTTCCTCATTCC+TGG 0.183624 4.2:-72504384 None:intergenic
TTCATTCAAGGTAGTATATT+GGG 0.290202 4.2:-72504539 None:intergenic
AATGATGTCACCATTATTCA+TGG 0.300939 4.2:-72504432 None:intergenic
TTGTATCTTCAGTTTCTCTT+TGG 0.302597 4.2:-72504150 None:intergenic
ATTCATTCAAGGTAGTATAT+TGG 0.310144 4.2:-72504540 None:intergenic
ATCTCTGGTTGAGGCTTGTA+TGG 0.342107 4.2:-72504008 None:intergenic
GAAGCATGTGCCATAGTCTA+TGG 0.364353 4.2:+72503984 MS.gene043112:CDS
GGAAAGCAACATACAATAAC+AGG 0.369187 4.2:+72503910 MS.gene043112:CDS
ATGTTTCAATTTCTTTATGA+AGG 0.411623 4.2:+72504209 MS.gene043112:CDS
ATGGCAATGGTGGTGCCATT+TGG 0.414280 4.2:-72504361 None:intergenic
ACAAGCCTCAACCAGAGATA+TGG 0.424604 4.2:+72504012 MS.gene043112:CDS
CATGCAGAGTAATATGTCAT+TGG 0.426918 4.2:+72504238 MS.gene043112:CDS
TTATTGTAAATGATGCATCT+AGG 0.431822 4.2:+72503889 MS.gene043112:CDS
AGGATGGGTCATGGCCATGC+TGG 0.433216 4.2:+72504404 MS.gene043112:CDS
AAGAGACATATATGAAAGAA+AGG 0.443744 4.2:+72504117 MS.gene043112:CDS
GAAGATGAGACGGTGCCATT+TGG 0.449628 4.2:+72504494 MS.gene043112:CDS
AAATGAAGGAGGTTGGTAGA+AGG 0.451827 4.2:+72504297 MS.gene043112:CDS
GCCATCCAGGAATGAGGAAA+TGG 0.456661 4.2:+72504379 MS.gene043112:CDS
TGGCACCACCATTGCCATCC+AGG 0.461702 4.2:+72504366 MS.gene043112:CDS
TATGAAAGAAAGGGTTCTAA+AGG 0.463711 4.2:+72504127 MS.gene043112:CDS
GCCATTTCCTCATTCCTGGA+TGG 0.469646 4.2:-72504380 None:intergenic
TTGATTCAAAACATCTTTGT+TGG 0.470119 4.2:+72504261 MS.gene043112:CDS
ACATGAAATTCAACTCCAAA+TGG 0.474248 4.2:+72504346 MS.gene043112:CDS
TGTGATGACGGCCATATCTC+TGG 0.481006 4.2:-72504023 None:intergenic
TTGATGGGCTTGATGATGAA+TGG 0.481425 4.2:+72504467 MS.gene043112:CDS
GAATGAGGAAATGGCAAGGA+TGG 0.482915 4.2:+72504388 MS.gene043112:CDS
GAAGGAGGTTGGTAGAAGGT+TGG 0.483853 4.2:+72504301 MS.gene043112:CDS
TCCTCATTCCTGGATGGCAA+TGG 0.486555 4.2:-72504374 None:intergenic
GTTGATTGACGAGAAAATGA+AGG 0.491460 4.2:+72504283 MS.gene043112:CDS
ATTCAGAACAATGACTGAAA+GGG 0.494087 4.2:+72504070 MS.gene043112:CDS
CTAGGATCAACCTCGCCAAA+TGG 0.499555 4.2:-72504509 None:intergenic
GACGAGAAAATGAAGGAGGT+TGG 0.500356 4.2:+72504290 MS.gene043112:CDS
CTTGTATGGTCCATAGACTA+TGG 0.514753 4.2:-72503994 None:intergenic
GCTGGGATGACCATGAATAA+TGG 0.515101 4.2:+72504422 MS.gene043112:CDS
TTGGACGAAGAGGATAATAA+TGG 0.522146 4.2:+72504320 MS.gene043112:CDS
GTTTGGACTCCTTGTGATGA+CGG 0.522277 4.2:-72504035 None:intergenic
GGATGGGTCATGGCCATGCT+GGG 0.533577 4.2:+72504405 MS.gene043112:CDS
TGGTAGAAGGTTGGACGAAG+AGG 0.541273 4.2:+72504310 MS.gene043112:CDS
AGAGACATATATGAAAGAAA+GGG 0.542993 4.2:+72504118 MS.gene043112:CDS
AATTCAGAACAATGACTGAA+AGG 0.545022 4.2:+72504069 MS.gene043112:CDS
ACCATTGCCATCCAGGAATG+AGG 0.549091 4.2:+72504373 MS.gene043112:CDS
GACGGCCATATCTCTGGTTG+AGG 0.560463 4.2:-72504017 None:intergenic
AACATACAATAACAGGTGGA+AGG 0.581713 4.2:+72503917 MS.gene043112:CDS
GTGGAAGGGTCTACTAAAGA+AGG 0.591594 4.2:+72503932 MS.gene043112:CDS
AAGAGAAACTGAAGATACAA+AGG 0.595097 4.2:+72504153 MS.gene043112:CDS
GATTGACGAGAAAATGAAGG+AGG 0.595622 4.2:+72504286 MS.gene043112:CDS
GAGATATGGCCGTCATCACA+AGG 0.597681 4.2:+72504026 MS.gene043112:CDS
TCATTCCTGGATGGCAATGG+TGG 0.602855 4.2:-72504371 None:intergenic
AATGAGGAAATGGCAAGGAT+GGG 0.613705 4.2:+72504389 MS.gene043112:CDS
GATACAAAGGCATGACAACA+AGG 0.619432 4.2:+72504166 MS.gene043112:CDS
ACATACAATAACAGGTGGAA+GGG 0.624477 4.2:+72503918 MS.gene043112:CDS
GAAATGGCAAGGATGGGTCA+TGG 0.626584 4.2:+72504395 MS.gene043112:CDS
TGAGACGGTGCCATTTGGCG+AGG 0.635055 4.2:+72504499 MS.gene043112:CDS
AAGCAACATACAATAACAGG+TGG 0.643203 4.2:+72503913 MS.gene043112:CDS
TATTCATGGTCATCCCAGCA+TGG 0.650127 4.2:-72504418 None:intergenic
CCAGGAATGAGGAAATGGCA+AGG 0.651946 4.2:+72504384 MS.gene043112:CDS
TATGAACTAAGCACTCTGTG+TGG 0.701795 4.2:+72503957 MS.gene043112:CDS
GAATGGTTATGAAGATGAGA+CGG 0.707575 4.2:+72504484 MS.gene043112:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGAAAATCAATTTTTGAT+GGG + chr4.2:72504452-72504471 MS.gene043112:CDS 15.0%
!! ATGTTTCAATTTCTTTATGA+AGG + chr4.2:72504209-72504228 MS.gene043112:CDS 20.0%
!!! CATTGAAAATCAATTTTTGA+TGG + chr4.2:72504451-72504470 MS.gene043112:CDS 20.0%
! AAGAGACATATATGAAAGAA+AGG + chr4.2:72504117-72504136 MS.gene043112:CDS 25.0%
! AGAGACATATATGAAAGAAA+GGG + chr4.2:72504118-72504137 MS.gene043112:CDS 25.0%
! TTATTGTAAATGATGCATCT+AGG + chr4.2:72503889-72503908 MS.gene043112:CDS 25.0%
! TTGATTCAAAACATCTTTGT+TGG + chr4.2:72504261-72504280 MS.gene043112:CDS 25.0%
AAGAGAAACTGAAGATACAA+AGG + chr4.2:72504153-72504172 MS.gene043112:CDS 30.0%
AATGATGTCACCATTATTCA+TGG - chr4.2:72504435-72504454 None:intergenic 30.0%
AATTCAGAACAATGACTGAA+AGG + chr4.2:72504069-72504088 MS.gene043112:CDS 30.0%
ACATGAAATTCAACTCCAAA+TGG + chr4.2:72504346-72504365 MS.gene043112:CDS 30.0%
AGTATATTGGGCAAAAATCT+AGG - chr4.2:72504530-72504549 None:intergenic 30.0%
ATTCAGAACAATGACTGAAA+GGG + chr4.2:72504070-72504089 MS.gene043112:CDS 30.0%
TTGTATCTTCAGTTTCTCTT+TGG - chr4.2:72504153-72504172 None:intergenic 30.0%
! TATGAAAGAAAGGGTTCTAA+AGG + chr4.2:72504127-72504146 MS.gene043112:CDS 30.0%
AACATACAATAACAGGTGGA+AGG + chr4.2:72503917-72503936 MS.gene043112:CDS 35.0%
AAGCAACATACAATAACAGG+TGG + chr4.2:72503913-72503932 MS.gene043112:CDS 35.0%
ACATACAATAACAGGTGGAA+GGG + chr4.2:72503918-72503937 MS.gene043112:CDS 35.0%
CATGCAGAGTAATATGTCAT+TGG + chr4.2:72504238-72504257 MS.gene043112:CDS 35.0%
GAATGGTTATGAAGATGAGA+CGG + chr4.2:72504484-72504503 MS.gene043112:CDS 35.0%
GGAAAGCAACATACAATAAC+AGG + chr4.2:72503910-72503929 MS.gene043112:CDS 35.0%
GTTGATTGACGAGAAAATGA+AGG + chr4.2:72504283-72504302 MS.gene043112:CDS 35.0%
TTGGACGAAGAGGATAATAA+TGG + chr4.2:72504320-72504339 MS.gene043112:CDS 35.0%
!!! TGAATTTTGAGAGCACTGTT+TGG - chr4.2:72504055-72504074 None:intergenic 35.0%
AATGAGGAAATGGCAAGGAT+GGG + chr4.2:72504389-72504408 MS.gene043112:CDS 40.0%
CTTGTATGGTCCATAGACTA+TGG - chr4.2:72503997-72504016 None:intergenic 40.0%
GATTGACGAGAAAATGAAGG+AGG + chr4.2:72504286-72504305 MS.gene043112:CDS 40.0%
TATGAACTAAGCACTCTGTG+TGG + chr4.2:72503957-72503976 MS.gene043112:CDS 40.0%
! GATACAAAGGCATGACAACA+AGG + chr4.2:72504166-72504185 MS.gene043112:CDS 40.0%
!! AAATGAAGGAGGTTGGTAGA+AGG + chr4.2:72504297-72504316 MS.gene043112:CDS 40.0%
!! TTGATGGGCTTGATGATGAA+TGG + chr4.2:72504467-72504486 MS.gene043112:CDS 40.0%
ACAAGCCTCAACCAGAGATA+TGG + chr4.2:72504012-72504031 MS.gene043112:CDS 45.0%
ATCTCTGGTTGAGGCTTGTA+TGG - chr4.2:72504011-72504030 None:intergenic 45.0%
GAAGCATGTGCCATAGTCTA+TGG + chr4.2:72503984-72504003 MS.gene043112:CDS 45.0%
GAATGAGGAAATGGCAAGGA+TGG + chr4.2:72504388-72504407 MS.gene043112:CDS 45.0%
GACGAGAAAATGAAGGAGGT+TGG + chr4.2:72504290-72504309 MS.gene043112:CDS 45.0%
GCTGGGATGACCATGAATAA+TGG + chr4.2:72504422-72504441 MS.gene043112:CDS 45.0%
GTGGAAGGGTCTACTAAAGA+AGG + chr4.2:72503932-72503951 MS.gene043112:CDS 45.0%
GTTTGGACTCCTTGTGATGA+CGG - chr4.2:72504038-72504057 None:intergenic 45.0%
TATTCATGGTCATCCCAGCA+TGG - chr4.2:72504421-72504440 None:intergenic 45.0%
ACCATTGCCATCCAGGAATG+AGG + chr4.2:72504373-72504392 MS.gene043112:CDS 50.0%
CCAGGAATGAGGAAATGGCA+AGG + chr4.2:72504384-72504403 MS.gene043112:CDS 50.0%
CTAGGATCAACCTCGCCAAA+TGG - chr4.2:72504512-72504531 None:intergenic 50.0%
GAAATGGCAAGGATGGGTCA+TGG + chr4.2:72504395-72504414 MS.gene043112:CDS 50.0%
GAGATATGGCCGTCATCACA+AGG + chr4.2:72504026-72504045 MS.gene043112:CDS 50.0%
GCCATCCAGGAATGAGGAAA+TGG + chr4.2:72504379-72504398 MS.gene043112:CDS 50.0%
GCCATTTCCTCATTCCTGGA+TGG - chr4.2:72504383-72504402 None:intergenic 50.0%
TCATTCCTGGATGGCAATGG+TGG - chr4.2:72504374-72504393 None:intergenic 50.0%
TCCTCATTCCTGGATGGCAA+TGG - chr4.2:72504377-72504396 None:intergenic 50.0%
TGGTAGAAGGTTGGACGAAG+AGG + chr4.2:72504310-72504329 MS.gene043112:CDS 50.0%
! CCTTGCCATTTCCTCATTCC+TGG - chr4.2:72504387-72504406 None:intergenic 50.0%
!! ATGGCAATGGTGGTGCCATT+TGG - chr4.2:72504364-72504383 None:intergenic 50.0%
!! GAAGATGAGACGGTGCCATT+TGG + chr4.2:72504494-72504513 MS.gene043112:CDS 50.0%
!! GAAGGAGGTTGGTAGAAGGT+TGG + chr4.2:72504301-72504320 MS.gene043112:CDS 50.0%
!! TGTGATGACGGCCATATCTC+TGG - chr4.2:72504026-72504045 None:intergenic 50.0%
GACGGCCATATCTCTGGTTG+AGG - chr4.2:72504020-72504039 None:intergenic 55.0%
AGGATGGGTCATGGCCATGC+TGG + chr4.2:72504404-72504423 MS.gene043112:CDS 60.0%
GGATGGGTCATGGCCATGCT+GGG + chr4.2:72504405-72504424 MS.gene043112:CDS 60.0%
TGGCACCACCATTGCCATCC+AGG + chr4.2:72504366-72504385 MS.gene043112:CDS 60.0%
!! TGAGACGGTGCCATTTGGCG+AGG + chr4.2:72504499-72504518 MS.gene043112:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 72503861 72504556 72503861 ID=MS.gene043112
chr4.2 mRNA 72503861 72504556 72503861 ID=MS.gene043112.t1;Parent=MS.gene043112
chr4.2 exon 72503861 72504556 72503861 ID=MS.gene043112.t1.exon1;Parent=MS.gene043112.t1
chr4.2 CDS 72503861 72504556 72503861 ID=cds.MS.gene043112.t1;Parent=MS.gene043112.t1
Gene Sequence

>MS.gene043112

ATGACTAGGAAAAAGATGAAAATTGCTTTTATTGTAAATGATGCATCTAGGAAAGCAACATACAATAACAGGTGGAAGGGTCTACTAAAGAAGGTTTATGAACTAAGCACTCTGTGTGGAGTTGAAGCATGTGCCATAGTCTATGGACCATACAAGCCTCAACCAGAGATATGGCCGTCATCACAAGGAGTCCAAACAGTGCTCTCAAAATTCAGAACAATGACTGAAAGGGATAAGAGCAAGAGAATGTTGAATCAAGAGACATATATGAAAGAAAGGGTTCTAAAGGCCAAAGAGAAACTGAAGATACAAAGGCATGACAACAAGGAGAAAGAGATGACAATGCTCATGTTTCAATTTCTTTATGAAGGTAACTTCATGCAGAGTAATATGTCATTGGTTGATTCAAAACATCTTTGTTGGTTGATTGACGAGAAAATGAAGGAGGTTGGTAGAAGGTTGGACGAAGAGGATAATAATGGTCAACATGAAATTCAACTCCAAATGGCACCACCATTGCCATCCAGGAATGAGGAAATGGCAAGGATGGGTCATGGCCATGCTGGGATGACCATGAATAATGGTGACATCATTGAAAATCAATTTTTGATGGGCTTGATGATGAATGGTTATGAAGATGAGACGGTGCCATTTGGCGAGGTTGATCCTAGATTTTTGCCCAATATACTACCTTGA
Protein sequence

>MS.gene043112.t1

MTRKKMKIAFIVNDASRKATYNNRWKGLLKKVYELSTLCGVEACAIVYGPYKPQPEIWPSSQGVQTVLSKFRTMTERDKSKRMLNQETYMKERVLKAKEKLKIQRHDNKEKEMTMLMFQFLYEGNFMQSNMSLVDSKHLCWLIDEKMKEVGRRLDEEDNNGQHEIQLQMAPPLPSRNEEMARMGHGHAGMTMNNGDIIENQFLMGLMMNGYEDETVPFGEVDPRFLPNILP