AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24971

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24971.t1 MTR_4g013335 95.918 196 8 0 1 196 1 196 5.10e-133 371
MS.gene24971.t1 MTR_4g013350 77.778 198 41 2 1 196 1 197 5.33e-110 313
MS.gene24971.t1 MTR_4g013345 79.781 183 34 2 16 196 15 196 1.00e-106 304
MS.gene24971.t1 MTR_4g013330 74.457 184 43 2 17 196 16 199 8.50e-103 295
MS.gene24971.t1 MTR_4g013325 83.085 201 27 4 1 196 1 199 1.29e-101 291
MS.gene24971.t1 MTR_4g013320 73.913 184 44 2 17 196 16 199 8.55e-100 287
MS.gene24971.t1 MTR_4g013310 67.000 200 59 5 1 196 1 197 1.21e-88 259
MS.gene24971.t1 MTR_7g070390 71.765 170 46 2 29 196 23 192 1.40e-79 236
MS.gene24971.t1 MTR_4g013385 56.915 188 75 3 10 196 8 190 5.93e-72 216
MS.gene24971.t1 MTR_0433s0040 56.915 188 75 3 10 196 8 190 5.93e-72 216
MS.gene24971.t1 MTR_1g054525 54.592 196 77 3 3 196 7 192 4.96e-70 211
MS.gene24971.t1 MTR_4g013770 60.588 170 62 2 30 196 24 191 7.49e-66 201
MS.gene24971.t1 MTR_4g013355 50.794 189 76 4 10 196 6 179 3.39e-60 186
MS.gene24971.t1 MTR_7g093870 53.846 156 65 2 48 196 38 193 8.45e-57 179
MS.gene24971.t1 MTR_7g093820 46.774 186 94 4 14 196 11 194 1.16e-54 172
MS.gene24971.t1 MTR_7g093850 45.699 186 96 4 14 196 11 194 2.39e-54 171
MS.gene24971.t1 MTR_7g093790 45.783 166 86 3 34 196 27 191 1.65e-53 169
MS.gene24971.t1 MTR_7g093830 44.624 186 98 4 14 196 10 193 6.08e-53 168
MS.gene24971.t1 MTR_4g073950 49.342 152 74 1 48 196 41 192 3.23e-51 164
MS.gene24971.t1 MTR_1g056370 46.000 150 79 2 48 195 36 185 1.91e-43 144
MS.gene24971.t1 MTR_4g078885 43.537 147 83 0 50 196 39 185 5.35e-43 142
MS.gene24971.t1 MTR_3g034030 43.537 147 83 0 50 196 39 185 2.01e-42 141
MS.gene24971.t1 MTR_3g105640 43.478 161 87 2 40 196 28 188 2.30e-42 141
MS.gene24971.t1 MTR_3g105630 38.614 202 105 5 1 196 1 189 2.66e-41 138
MS.gene24971.t1 MTR_5g096120 43.421 152 80 2 51 196 38 189 1.06e-38 131
MS.gene24971.t1 MTR_4g122130 37.762 143 85 2 57 196 39 180 6.16e-28 103
MS.gene24971.t1 MTR_4g122110 36.986 146 90 1 53 196 35 180 7.47e-28 103
MS.gene24971.t1 MTR_4g049570 31.469 143 96 1 51 191 31 173 9.43e-19 80.1
MS.gene24971.t1 MTR_4g049550 29.252 147 102 1 47 191 27 173 1.08e-17 77.0
MS.gene24971.t1 MTR_8g099115 34.286 140 81 3 50 179 34 172 2.37e-17 76.6
MS.gene24971.t1 MTR_8g099135 33.333 132 77 3 58 179 38 168 2.78e-14 68.2
MS.gene24971.t1 MTR_1g046490 35.556 90 57 1 83 172 121 209 2.30e-12 63.9
MS.gene24971.t1 MTR_1g046800 37.778 90 55 1 83 172 135 223 4.03e-12 63.5
MS.gene24971.t1 MTR_1g046500 37.778 90 55 1 83 172 135 223 5.44e-12 63.2
MS.gene24971.t1 MTR_1g115510 33.884 121 69 4 84 195 235 353 3.08e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24971.t1 AT1G55210 59.474 190 74 2 7 196 1 187 2.81e-78 232
MS.gene24971.t1 AT1G55210 59.474 190 74 2 7 196 1 187 2.81e-78 232
MS.gene24971.t1 AT5G49040 55.102 196 80 2 3 196 2 191 1.33e-73 220
MS.gene24971.t1 AT1G58170 56.383 188 69 3 13 196 7 185 1.92e-71 214
MS.gene24971.t1 AT3G13650 55.155 194 78 4 3 196 2 186 3.66e-67 204
MS.gene24971.t1 AT3G13662 59.589 146 58 1 37 182 27 171 1.66e-60 186
MS.gene24971.t1 AT5G49030 55.738 183 73 2 3 183 2 178 2.20e-60 203
MS.gene24971.t1 AT1G65870 52.980 151 69 1 47 195 39 189 6.35e-53 168
MS.gene24971.t1 AT3G13660 64.407 118 42 0 79 196 8 125 7.35e-51 160
MS.gene24971.t1 AT2G21100 48.993 149 74 1 49 195 39 187 1.69e-48 156
MS.gene24971.t1 AT2G21100 48.993 149 74 1 49 195 39 187 1.69e-48 156
MS.gene24971.t1 AT1G22900 50.331 151 71 2 47 195 45 193 3.00e-47 154
MS.gene24971.t1 AT5G42510 48.667 150 73 2 48 195 35 182 1.24e-46 151
MS.gene24971.t1 AT5G42500 48.000 150 74 2 48 195 38 185 5.22e-46 150
MS.gene24971.t1 AT4G38700 40.000 195 99 7 10 196 6 190 1.16e-42 142
MS.gene24971.t1 AT2G21110 40.000 170 90 2 33 196 23 186 7.34e-40 134
MS.gene24971.t1 AT3G58090 51.376 109 53 0 87 195 163 271 3.49e-37 130
MS.gene24971.t1 AT4G11210 28.409 176 108 3 8 179 5 166 2.27e-16 73.9
MS.gene24971.t1 AT4G23690 33.588 131 80 4 46 171 34 162 2.43e-16 73.9
MS.gene24971.t1 AT1G64160 30.000 130 86 2 54 179 37 165 1.19e-14 69.3
MS.gene24971.t1 AT4G11190 25.137 183 116 4 1 179 1 166 2.35e-14 68.6
MS.gene24971.t1 AT4G11180 29.474 190 112 6 12 195 10 183 1.07e-13 66.6

Find 32 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAAGTACTATTACTATTT+TGG 0.077749 4.1:+82375448 MS.gene24971:CDS
AACTGTGGTCCTAAAGTTAA+AGG 0.173169 4.1:-82375317 None:intergenic
ATCGACAACCCTTTAACTTT+AGG 0.310884 4.1:+82375308 MS.gene24971:CDS
TTTACTGAAGGAAAGTATAA+TGG 0.333494 4.1:+82375428 MS.gene24971:CDS
CCTAACAACTTGCGATCTAT+TGG 0.340385 4.1:-82375152 None:intergenic
AGATGAAGTTGATTTGCTTA+TGG 0.369472 4.1:+82375391 MS.gene24971:CDS
CAAAGTGATGAGGAAATGTT+TGG 0.371335 4.1:-82375048 None:intergenic
CCAATAGATCGCAAGTTGTT+AGG 0.388446 4.1:+82375152 MS.gene24971:CDS
TTAAACTCTACCACTGCCTT+TGG 0.391230 4.1:+82375272 MS.gene24971:CDS
GGAATAACTATGATAGAAGT+AGG 0.416983 4.1:-82375242 None:intergenic
ACTGTGGTCCTAAAGTTAAA+GGG 0.432091 4.1:-82375316 None:intergenic
CAGTTGAATTCTAAGATTGT+TGG 0.460772 4.1:+82375335 MS.gene24971:CDS
AAGATTGTTGGAAAAGCTCA+AGG 0.501113 4.1:+82375347 MS.gene24971:CDS
ATGCCTGTGATTGGTGGTAG+TGG 0.523186 4.1:+82375503 MS.gene24971:CDS
AGAGTGTGTTGCAAGATATG+AGG 0.539071 4.1:-82375082 None:intergenic
GTGGTAGAGTTTAATGATGG+TGG 0.541569 4.1:-82375263 None:intergenic
GTTAGAGAGATGCCTGTGAT+TGG 0.567283 4.1:+82375494 MS.gene24971:CDS
GGAAGAAGAACAAAGTGATG+AGG 0.576295 4.1:-82375058 None:intergenic
TATTGGCATGACATAGTGAG+TGG 0.584607 4.1:+82375212 MS.gene24971:CDS
TTCGATTGATCTCAAATCTG+AGG 0.584967 4.1:+82375568 MS.gene24971:CDS
GAATAACTATGATAGAAGTA+GGG 0.585056 4.1:-82375241 None:intergenic
GTGTGTTGCAAGATATGAGG+AGG 0.585643 4.1:-82375079 None:intergenic
GTGATGAGGAAATGTTTGGA+AGG 0.586936 4.1:-82375044 None:intergenic
GTTGTTAGGCCTAAACAAGA+AGG 0.591926 4.1:+82375166 MS.gene24971:CDS
GCGGACTGAACCAAAGGCAG+TGG 0.603551 4.1:-82375282 None:intergenic
GATCATGCGGACTGAACCAA+AGG 0.606989 4.1:-82375288 None:intergenic
GCAGTGGTAGAGTTTAATGA+TGG 0.613743 4.1:-82375266 None:intergenic
AGTCCACTACCACCAATCAC+AGG 0.616685 4.1:-82375506 None:intergenic
AGAGAGATGCCTGTGATTGG+TGG 0.627082 4.1:+82375497 MS.gene24971:CDS
AGATTGTTGGAAAAGCTCAA+GGG 0.648311 4.1:+82375348 MS.gene24971:CDS
TTAAAGGGTTGTCGATCATG+CGG 0.659792 4.1:-82375301 None:intergenic
ACAATCTTAGAATTCAACTG+TGG 0.718096 4.1:-82375332 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAGTCATTTCAAATTTTAT+TGG + chr4.1:82375195-82375214 MS.gene24971:CDS 15.0%
! GAATAACTATGATAGAAGTA+GGG - chr4.1:82375244-82375263 None:intergenic 25.0%
!! TTTACTGAAGGAAAGTATAA+TGG + chr4.1:82375428-82375447 MS.gene24971:CDS 25.0%
!!! ATGAATTTTGCTTTTACTGA+AGG + chr4.1:82375416-82375435 MS.gene24971:CDS 25.0%
!!! GGAAGTACTATTACTATTTT+GGG + chr4.1:82375449-82375468 MS.gene24971:CDS 25.0%
!!! TGGAAGTACTATTACTATTT+TGG + chr4.1:82375448-82375467 MS.gene24971:CDS 25.0%
ACAATCTTAGAATTCAACTG+TGG - chr4.1:82375335-82375354 None:intergenic 30.0%
GGAATAACTATGATAGAAGT+AGG - chr4.1:82375245-82375264 None:intergenic 30.0%
!! AGATGAAGTTGATTTGCTTA+TGG + chr4.1:82375391-82375410 MS.gene24971:CDS 30.0%
!! CAGTTGAATTCTAAGATTGT+TGG + chr4.1:82375335-82375354 MS.gene24971:CDS 30.0%
!! GTACTATTACTATTTTGGGA+AGG + chr4.1:82375453-82375472 MS.gene24971:CDS 30.0%
!! TTAGCTTTTCCTTCTTGTTT+AGG - chr4.1:82375178-82375197 None:intergenic 30.0%
AACTGTGGTCCTAAAGTTAA+AGG - chr4.1:82375320-82375339 None:intergenic 35.0%
AAGATTGTTGGAAAAGCTCA+AGG + chr4.1:82375347-82375366 MS.gene24971:CDS 35.0%
ACTGTGGTCCTAAAGTTAAA+GGG - chr4.1:82375319-82375338 None:intergenic 35.0%
AGATTGTTGGAAAAGCTCAA+GGG + chr4.1:82375348-82375367 MS.gene24971:CDS 35.0%
CAAAGTGATGAGGAAATGTT+TGG - chr4.1:82375051-82375070 None:intergenic 35.0%
TTCGATTGATCTCAAATCTG+AGG + chr4.1:82375568-82375587 MS.gene24971:CDS 35.0%
! ATCGACAACCCTTTAACTTT+AGG + chr4.1:82375308-82375327 MS.gene24971:CDS 35.0%
! GACTTTTCAGATTTGCAAGA+GGG + chr4.1:82375525-82375544 MS.gene24971:CDS 35.0%
AGAGTGTGTTGCAAGATATG+AGG - chr4.1:82375085-82375104 None:intergenic 40.0%
CCAATAGATCGCAAGTTGTT+AGG + chr4.1:82375152-82375171 MS.gene24971:CDS 40.0%
CCTAACAACTTGCGATCTAT+TGG - chr4.1:82375155-82375174 None:intergenic 40.0%
GCAGTGGTAGAGTTTAATGA+TGG - chr4.1:82375269-82375288 None:intergenic 40.0%
GGAAGAAGAACAAAGTGATG+AGG - chr4.1:82375061-82375080 None:intergenic 40.0%
GTGATGAGGAAATGTTTGGA+AGG - chr4.1:82375047-82375066 None:intergenic 40.0%
GTGGTAGAGTTTAATGATGG+TGG - chr4.1:82375266-82375285 None:intergenic 40.0%
GTTGTTAGGCCTAAACAAGA+AGG + chr4.1:82375166-82375185 MS.gene24971:CDS 40.0%
TATTGGCATGACATAGTGAG+TGG + chr4.1:82375212-82375231 MS.gene24971:CDS 40.0%
TTAAACTCTACCACTGCCTT+TGG + chr4.1:82375272-82375291 MS.gene24971:CDS 40.0%
TTAAAGGGTTGTCGATCATG+CGG - chr4.1:82375304-82375323 None:intergenic 40.0%
! GGACTTTTCAGATTTGCAAG+AGG + chr4.1:82375524-82375543 MS.gene24971:CDS 40.0%
GTGTGTTGCAAGATATGAGG+AGG - chr4.1:82375082-82375101 None:intergenic 45.0%
GTTAGAGAGATGCCTGTGAT+TGG + chr4.1:82375494-82375513 MS.gene24971:CDS 45.0%
AGAGAGATGCCTGTGATTGG+TGG + chr4.1:82375497-82375516 MS.gene24971:CDS 50.0%
AGTCCACTACCACCAATCAC+AGG - chr4.1:82375509-82375528 None:intergenic 50.0%
! ATGCCTGTGATTGGTGGTAG+TGG + chr4.1:82375503-82375522 MS.gene24971:CDS 50.0%
! GATCATGCGGACTGAACCAA+AGG - chr4.1:82375291-82375310 None:intergenic 50.0%
! GCGGACTGAACCAAAGGCAG+TGG - chr4.1:82375285-82375304 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 82375041 82375631 82375041 ID=MS.gene24971
chr4.1 mRNA 82375041 82375631 82375041 ID=MS.gene24971.t1;Parent=MS.gene24971
chr4.1 exon 82375041 82375631 82375041 ID=MS.gene24971.t1.exon1;Parent=MS.gene24971.t1
chr4.1 CDS 82375041 82375631 82375041 ID=cds.MS.gene24971.t1;Parent=MS.gene24971.t1
Gene Sequence

>MS.gene24971

ATGCCTTCCAAACATTTCCTCATCACTTTGTTCTTCTTCCTCCTCATATCTTGCAACACACTCTCTGCTTCAACTTCATCAGAAAAAGAAGACACTTTTGATTTTGTTCGTCCAATAGATCGCAAGTTGTTAGGCCTAAACAAGAAGGAAAAGCTAAGTCATTTCAAATTTTATTGGCATGACATAGTGAGTGGAAAAAACCCTACTTCTATCATAGTTATTCCACCATCATTAAACTCTACCACTGCCTTTGGTTCAGTCCGCATGATCGACAACCCTTTAACTTTAGGACCACAGTTGAATTCTAAGATTGTTGGAAAAGCTCAAGGGTTCTATGCATCTGCATGCAAAGATGAAGTTGATTTGCTTATGGCTATGAATTTTGCTTTTACTGAAGGAAAGTATAATGGAAGTACTATTACTATTTTGGGAAGGAATGTTGTTTTTCATAAAGTTAGAGAGATGCCTGTGATTGGTGGTAGTGGACTTTTCAGATTTGCAAGAGGGTATGCTGAAGCTAATACTCATTCGATTGATCTCAAATCTGAGGATGCTTGTGTAGAGTACAATGTTCATGTTTTTCACTATTAA
Protein sequence

>MS.gene24971.t1

MPSKHFLITLFFFLLISCNTLSASTSSEKEDTFDFVRPIDRKLLGLNKKEKLSHFKFYWHDIVSGKNPTSIIVIPPSLNSTTAFGSVRMIDNPLTLGPQLNSKIVGKAQGFYASACKDEVDLLMAMNFAFTEGKYNGSTITILGRNVVFHKVREMPVIGGSGLFRFARGYAEANTHSIDLKSEDACVEYNVHVFHY