AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24969

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24969.t1 MTR_4g013320 93.500 200 12 1 1 200 1 199 3.00e-130 364
MS.gene24969.t1 MTR_4g013350 76.000 200 45 2 1 200 1 197 3.19e-107 306
MS.gene24969.t1 MTR_4g013330 77.612 201 42 2 1 200 1 199 1.58e-105 301
MS.gene24969.t1 MTR_4g013345 76.000 200 44 2 1 200 1 196 2.10e-105 301
MS.gene24969.t1 MTR_4g013335 69.730 185 51 2 16 200 17 196 4.11e-96 278
MS.gene24969.t1 MTR_4g013310 71.500 200 54 2 1 200 1 197 9.56e-96 277
MS.gene24969.t1 MTR_4g013325 70.149 201 57 3 1 200 1 199 1.10e-90 264
MS.gene24969.t1 MTR_7g070390 69.767 172 49 2 30 200 23 192 1.67e-77 230
MS.gene24969.t1 MTR_4g013385 57.812 192 72 3 9 200 8 190 2.57e-73 220
MS.gene24969.t1 MTR_0433s0040 57.812 192 72 3 9 200 8 190 2.57e-73 220
MS.gene24969.t1 MTR_4g013770 56.471 170 72 1 31 200 24 191 2.18e-64 197
MS.gene24969.t1 MTR_1g054525 56.627 166 69 2 35 200 30 192 8.42e-64 196
MS.gene24969.t1 MTR_4g013355 51.562 192 75 5 9 200 6 179 3.79e-59 183
MS.gene24969.t1 MTR_4g073950 53.289 152 71 0 49 200 41 192 1.08e-56 177
MS.gene24969.t1 MTR_7g093820 47.619 189 93 5 13 200 11 194 3.42e-52 166
MS.gene24969.t1 MTR_7g093850 47.090 189 94 5 13 200 11 194 5.29e-52 166
MS.gene24969.t1 MTR_7g093790 47.904 167 84 3 35 200 27 191 1.02e-51 165
MS.gene24969.t1 MTR_7g093830 45.503 189 97 5 13 200 10 193 4.33e-51 163
MS.gene24969.t1 MTR_7g093870 51.923 156 71 2 49 200 38 193 5.38e-51 164
MS.gene24969.t1 MTR_1g056370 49.333 150 73 2 51 199 38 185 1.23e-47 154
MS.gene24969.t1 MTR_3g105640 45.342 161 87 1 41 200 28 188 1.21e-44 147
MS.gene24969.t1 MTR_4g078885 45.033 151 80 1 50 200 38 185 1.65e-41 139
MS.gene24969.t1 MTR_3g034030 45.033 151 80 1 50 200 38 185 3.81e-41 138
MS.gene24969.t1 MTR_3g105630 43.396 159 88 2 44 200 31 189 5.13e-40 135
MS.gene24969.t1 MTR_5g096120 40.127 157 81 3 52 200 38 189 2.11e-35 123
MS.gene24969.t1 MTR_4g122110 37.415 147 91 1 54 200 35 180 1.78e-26 100
MS.gene24969.t1 MTR_4g122130 36.364 154 95 2 49 200 28 180 4.68e-25 96.7
MS.gene24969.t1 MTR_4g013340 40.625 96 22 1 105 200 78 138 2.69e-17 75.1
MS.gene24969.t1 MTR_4g049550 30.263 152 97 2 48 195 27 173 3.56e-17 75.9
MS.gene24969.t1 MTR_4g049570 30.405 148 94 2 52 195 31 173 2.09e-16 73.9
MS.gene24969.t1 MTR_8g099135 33.333 132 80 3 59 183 38 168 3.25e-16 73.6
MS.gene24969.t1 MTR_8g099115 31.579 133 83 3 58 183 41 172 3.52e-15 70.9
MS.gene24969.t1 MTR_8g073850 31.293 147 95 4 52 196 39 181 2.30e-13 65.9
MS.gene24969.t1 MTR_8g073770 31.293 147 95 4 52 196 39 181 2.49e-13 65.9
MS.gene24969.t1 MTR_1g115510 33.607 122 68 4 88 199 235 353 2.58e-12 64.7
MS.gene24969.t1 MTR_4g062520 38.889 90 51 3 88 175 187 274 4.77e-11 60.8
MS.gene24969.t1 MTR_4g062470 38.889 90 51 3 88 175 188 275 5.23e-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.gene24969.t1 AT1G55210 62.048 166 59 1 35 200 26 187 3.16e-74 222
MS.gene24969.t1 AT1G55210 62.048 166 59 1 35 200 26 187 3.16e-74 222
MS.gene24969.t1 AT5G49040 53.684 190 86 2 11 200 4 191 4.84e-71 214
MS.gene24969.t1 AT1G58170 61.438 153 58 1 48 200 34 185 9.74e-71 213
MS.gene24969.t1 AT3G13650 52.105 190 84 3 11 200 4 186 6.23e-66 201
MS.gene24969.t1 AT5G49030 52.809 178 80 2 9 186 4 177 1.21e-54 187
MS.gene24969.t1 AT3G13662 55.333 150 63 2 38 187 27 172 2.17e-53 169
MS.gene24969.t1 AT2G21100 53.333 150 69 1 50 199 39 187 1.20e-52 167
MS.gene24969.t1 AT2G21100 53.333 150 69 1 50 199 39 187 1.20e-52 167
MS.gene24969.t1 AT1G65870 48.684 152 77 1 48 199 39 189 1.32e-51 164
MS.gene24969.t1 AT3G13660 65.254 118 41 0 83 200 8 125 1.40e-51 162
MS.gene24969.t1 AT1G22900 48.026 152 76 2 48 199 45 193 1.45e-44 147
MS.gene24969.t1 AT5G42510 48.026 152 74 3 49 199 35 182 3.11e-43 143
MS.gene24969.t1 AT5G42500 47.651 149 75 2 51 199 40 185 3.87e-43 143
MS.gene24969.t1 AT4G38700 45.912 159 80 4 47 200 33 190 1.28e-40 137
MS.gene24969.t1 AT2G21110 40.698 172 93 2 32 200 21 186 6.70e-38 129
MS.gene24969.t1 AT3G58090 53.211 109 51 0 91 199 163 271 1.03e-37 131
MS.gene24969.t1 AT4G23690 33.571 140 85 3 47 182 34 169 1.07e-15 72.4
MS.gene24969.t1 AT4G11210 27.841 176 114 3 8 183 4 166 5.45e-14 67.8
MS.gene24969.t1 AT1G64160 30.216 139 88 4 50 183 31 165 1.03e-13 66.6

Find 41 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGCATCACAAGATGATTT+TGG 0.206837 4.1:+82393252 MS.gene24969:CDS
TTTGATGACCCTTTGACTTT+AGG 0.248779 4.1:+82393180 MS.gene24969:CDS
CAACAAGCTTAGAACTCAAT+TGG 0.313870 4.1:-82393206 None:intergenic
ATAAACACAACCACTTCTTT+TGG 0.334067 4.1:+82393144 MS.gene24969:CDS
CATTGGTTTGATCTCAAAAC+TGG 0.336336 4.1:+82393438 MS.gene24969:CDS
TGAGAGTACTATTACTATCT+TGG 0.339355 4.1:+82393320 MS.gene24969:CDS
ACTATCTTGGGGAGGAATTC+CGG 0.342210 4.1:+82393333 MS.gene24969:CDS
GAGGAATTCCGGTATTAATA+AGG 0.342727 4.1:+82393344 MS.gene24969:CDS
CAATTGAGTTCTAAGCTTGT+TGG 0.346083 4.1:+82393207 MS.gene24969:CDS
CCTAACAACTTGCGGTCTAT+TGG 0.349675 4.1:-82393015 None:intergenic
CCAATAGACCGCAAGTTGTT+AGG 0.362080 4.1:+82393015 MS.gene24969:CDS
CAAGTCACTTCAGATTCTAT+TGG 0.375454 4.1:+82393058 MS.gene24969:CDS
GAGAGTACTATTACTATCTT+GGG 0.382670 4.1:+82393321 MS.gene24969:CDS
AACAAGCTTAGAACTCAATT+GGG 0.402997 4.1:-82393205 None:intergenic
AAGTGAGAGTGTTGCAAGAG+AGG 0.407219 4.1:-82392942 None:intergenic
ATGCCAATAGTTGGTGGTAG+TGG 0.428780 4.1:+82393375 MS.gene24969:CDS
ATGCTAAAGCTACTACTCAT+TGG 0.447261 4.1:+82393421 MS.gene24969:CDS
AGTCCACTACCACCAACTAT+TGG 0.457800 4.1:-82393378 None:intergenic
GAGTGTTGCAAGAGAGGAGA+AGG 0.459092 4.1:-82392936 None:intergenic
CTCTCTAGCCTTATTAATAC+CGG 0.464335 4.1:-82393352 None:intergenic
AGAACAAATTGAGAAAATGA+TGG 0.464684 4.1:-82392909 None:intergenic
CAATAGAATCTGAAGTGACT+TGG 0.507056 4.1:-82393057 None:intergenic
GGAACAATTGTTATTGCAGT+GGG 0.508564 4.1:-82393105 None:intergenic
AAGCTTGTTGGAAAAGCTCA+AGG 0.509980 4.1:+82393219 MS.gene24969:CDS
GTTGTGTTTATAAACTTCAA+TGG 0.515154 4.1:-82393132 None:intergenic
CGTTTAGGCCTAACAACTTG+CGG 0.520020 4.1:-82393023 None:intergenic
TTTATAAACTTCAATGGTGG+TGG 0.522057 4.1:-82393126 None:intergenic
GAACAAATTGAGAAAATGAT+GGG 0.523672 4.1:-82392908 None:intergenic
AATTGGGGTCCTAAAGTCAA+AGG 0.527872 4.1:-82393189 None:intergenic
TGGAACAATTGTTATTGCAG+TGG 0.544715 4.1:-82393106 None:intergenic
TATTGGCATGACATCTTGAG+TGG 0.547551 4.1:+82393075 MS.gene24969:CDS
GCTAGAGAGATGCCAATAGT+TGG 0.553289 4.1:+82393366 MS.gene24969:CDS
ATTGGGGTCCTAAAGTCAAA+GGG 0.594373 4.1:-82393188 None:intergenic
AGAGAGATGCCAATAGTTGG+TGG 0.597518 4.1:+82393369 MS.gene24969:CDS
GTTGATTGAACCAAAAGAAG+TGG 0.598684 4.1:-82393154 None:intergenic
ATAAACATTGTACTCAACAA+TGG 0.615275 4.1:-82393466 None:intergenic
GTGTTTATAAACTTCAATGG+TGG 0.627180 4.1:-82393129 None:intergenic
GTACTATTACTATCTTGGGG+AGG 0.673978 4.1:+82393325 MS.gene24969:CDS
ACAAGCTTAGAACTCAATTG+GGG 0.691901 4.1:-82393204 None:intergenic
GAACAATTGTTATTGCAGTG+GGG 0.694795 4.1:-82393104 None:intergenic
AGAGTACTATTACTATCTTG+GGG 0.700411 4.1:+82393322 MS.gene24969:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAACAAATTGAGAAAATGA+TGG - chr4.1:82392912-82392931 None:intergenic 25.0%
! ATAAACATTGTACTCAACAA+TGG - chr4.1:82393469-82393488 None:intergenic 25.0%
! GAACAAATTGAGAAAATGAT+GGG - chr4.1:82392911-82392930 None:intergenic 25.0%
! GTTGTGTTTATAAACTTCAA+TGG - chr4.1:82393135-82393154 None:intergenic 25.0%
!! ATGAATTTTGCTTTCATTGA+AGG + chr4.1:82393288-82393307 MS.gene24969:CDS 25.0%
AACAAGCTTAGAACTCAATT+GGG - chr4.1:82393208-82393227 None:intergenic 30.0%
GTGTTTATAAACTTCAATGG+TGG - chr4.1:82393132-82393151 None:intergenic 30.0%
TTTATAAACTTCAATGGTGG+TGG - chr4.1:82393129-82393148 None:intergenic 30.0%
! AGAGTACTATTACTATCTTG+GGG + chr4.1:82393322-82393341 MS.gene24969:CDS 30.0%
! ATAAACACAACCACTTCTTT+TGG + chr4.1:82393144-82393163 MS.gene24969:CDS 30.0%
!! GAGAGTACTATTACTATCTT+GGG + chr4.1:82393321-82393340 MS.gene24969:CDS 30.0%
!! TGAGAGTACTATTACTATCT+TGG + chr4.1:82393320-82393339 MS.gene24969:CDS 30.0%
!! TTGGTTTTTCTTTCTCGTTT+AGG - chr4.1:82393041-82393060 None:intergenic 30.0%
!!! AGATGATTTTGGTTTTCTCA+TGG + chr4.1:82393263-82393282 MS.gene24969:CDS 30.0%
ACAAGCTTAGAACTCAATTG+GGG - chr4.1:82393207-82393226 None:intergenic 35.0%
ATGCTAAAGCTACTACTCAT+TGG + chr4.1:82393421-82393440 MS.gene24969:CDS 35.0%
CAACAAGCTTAGAACTCAAT+TGG - chr4.1:82393209-82393228 None:intergenic 35.0%
CAAGTCACTTCAGATTCTAT+TGG + chr4.1:82393058-82393077 MS.gene24969:CDS 35.0%
GAGGAATTCCGGTATTAATA+AGG + chr4.1:82393344-82393363 MS.gene24969:CDS 35.0%
GTTGATTGAACCAAAAGAAG+TGG - chr4.1:82393157-82393176 None:intergenic 35.0%
! CAATAGAATCTGAAGTGACT+TGG - chr4.1:82393060-82393079 None:intergenic 35.0%
! GAACAATTGTTATTGCAGTG+GGG - chr4.1:82393107-82393126 None:intergenic 35.0%
! GGAACAATTGTTATTGCAGT+GGG - chr4.1:82393108-82393127 None:intergenic 35.0%
! TCTGCATCACAAGATGATTT+TGG + chr4.1:82393252-82393271 MS.gene24969:CDS 35.0%
! TGGAACAATTGTTATTGCAG+TGG - chr4.1:82393109-82393128 None:intergenic 35.0%
! TTTGATGACCCTTTGACTTT+AGG + chr4.1:82393180-82393199 MS.gene24969:CDS 35.0%
!! CAATTGAGTTCTAAGCTTGT+TGG + chr4.1:82393207-82393226 MS.gene24969:CDS 35.0%
!! CATTGGTTTGATCTCAAAAC+TGG + chr4.1:82393438-82393457 MS.gene24969:CDS 35.0%
!! CTCTCTAGCCTTATTAATAC+CGG - chr4.1:82393355-82393374 None:intergenic 35.0%
!!! GACTTTTCAGATTTGCTAGA+GGG + chr4.1:82393397-82393416 MS.gene24969:CDS 35.0%
AATTGGGGTCCTAAAGTCAA+AGG - chr4.1:82393192-82393211 None:intergenic 40.0%
ATTGGGGTCCTAAAGTCAAA+GGG - chr4.1:82393191-82393210 None:intergenic 40.0%
GTACTATTACTATCTTGGGG+AGG + chr4.1:82393325-82393344 MS.gene24969:CDS 40.0%
TATTGGCATGACATCTTGAG+TGG + chr4.1:82393075-82393094 MS.gene24969:CDS 40.0%
!! AAGCTTGTTGGAAAAGCTCA+AGG + chr4.1:82393219-82393238 MS.gene24969:CDS 40.0%
!!! GGACTTTTCAGATTTGCTAG+AGG + chr4.1:82393396-82393415 MS.gene24969:CDS 40.0%
ACTATCTTGGGGAGGAATTC+CGG + chr4.1:82393333-82393352 MS.gene24969:CDS 45.0%
AGAGAGATGCCAATAGTTGG+TGG + chr4.1:82393369-82393388 MS.gene24969:CDS 45.0%
AGTCCACTACCACCAACTAT+TGG - chr4.1:82393381-82393400 None:intergenic 45.0%
CCAATAGACCGCAAGTTGTT+AGG + chr4.1:82393015-82393034 MS.gene24969:CDS 45.0%
CCTAACAACTTGCGGTCTAT+TGG - chr4.1:82393018-82393037 None:intergenic 45.0%
CGTTTAGGCCTAACAACTTG+CGG - chr4.1:82393026-82393045 None:intergenic 45.0%
GCTAGAGAGATGCCAATAGT+TGG + chr4.1:82393366-82393385 MS.gene24969:CDS 45.0%
!! AAGTGAGAGTGTTGCAAGAG+AGG - chr4.1:82392945-82392964 None:intergenic 45.0%
!! ATGCCAATAGTTGGTGGTAG+TGG + chr4.1:82393375-82393394 MS.gene24969:CDS 45.0%
! GAGTGTTGCAAGAGAGGAGA+AGG - chr4.1:82392939-82392958 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 82392901 82393503 82392901 ID=MS.gene24969
chr4.1 mRNA 82392901 82393503 82392901 ID=MS.gene24969.t1;Parent=MS.gene24969
chr4.1 exon 82392901 82393503 82392901 ID=MS.gene24969.t1.exon1;Parent=MS.gene24969.t1
chr4.1 CDS 82392901 82393503 82392901 ID=cds.MS.gene24969.t1;Parent=MS.gene24969.t1
Gene Sequence

>MS.gene24969

ATGCTTTCCCATCATTTTCTCAATTTGTTCTTCTTCCTTCTCCTCTCTTGCAACACTCTCACTTCAACTTCATTACAATCTTTAGAAAAACAAGAAACTTTTGATTTTGTTCGTCCAATAGACCGCAAGTTGTTAGGCCTAAACGAGAAAGAAAAACCAAGTCACTTCAGATTCTATTGGCATGACATCTTGAGTGGAAAAAACCCCACTGCAATAACAATTGTTCCACCACCATTGAAGTTTATAAACACAACCACTTCTTTTGGTTCAATCAACATGTTTGATGACCCTTTGACTTTAGGACCCCAATTGAGTTCTAAGCTTGTTGGAAAAGCTCAAGGTTTCTATGCTTCTGCATCACAAGATGATTTTGGTTTTCTCATGGCTATGAATTTTGCTTTCATTGAAGGAAAGTATAATGAGAGTACTATTACTATCTTGGGGAGGAATTCCGGTATTAATAAGGCTAGAGAGATGCCAATAGTTGGTGGTAGTGGACTTTTCAGATTTGCTAGAGGGTATGCTAAAGCTACTACTCATTGGTTTGATCTCAAAACTGGAGATGCCATTGTTGAGTACAATGTTTATGTTTTTCACTATTGA
Protein sequence

>MS.gene24969.t1

MLSHHFLNLFFFLLLSCNTLTSTSLQSLEKQETFDFVRPIDRKLLGLNEKEKPSHFRFYWHDILSGKNPTAITIVPPPLKFINTTTSFGSINMFDDPLTLGPQLSSKLVGKAQGFYASASQDDFGFLMAMNFAFIEGKYNESTITILGRNSGINKAREMPIVGGSGLFRFARGYAKATTHWFDLKTGDAIVEYNVYVFHY