AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene67536

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67536.t1 MTR_5g023340 88.732 284 32 0 1 284 1 284 6.07e-180 497
MS.gene67536.t1 MTR_5g023350 88.732 284 32 0 1 284 1 284 2.36e-179 495
MS.gene67536.t1 MTR_5g023320 87.413 286 32 2 1 285 1 283 4.67e-178 492
MS.gene67536.t1 MTR_5g023600 87.676 284 35 0 1 284 1 284 3.79e-177 490
MS.gene67536.t1 MTR_5g023390 86.268 284 39 0 1 284 1 284 1.41e-176 488
MS.gene67536.t1 MTR_5g023370 86.268 284 39 0 1 284 1 284 3.35e-176 488
MS.gene67536.t1 MTR_5g023520 84.615 286 42 2 1 285 1 285 2.10e-171 475
MS.gene67536.t1 MTR_5g023530 84.561 285 43 1 1 284 1 285 9.10e-171 474
MS.gene67536.t1 MTR_5g023550 84.211 285 44 1 1 285 1 284 2.39e-170 473
MS.gene67536.t1 MTR_5g023470 83.509 285 46 1 1 284 1 285 2.13e-168 468
MS.gene67536.t1 MTR_5g023580 83.916 286 42 2 1 282 1 286 1.71e-164 461
MS.gene67536.t1 MTR_8g074450 69.097 288 83 2 4 285 3 290 1.15e-138 392
MS.gene67536.t1 MTR_8g074510 66.899 287 87 3 5 285 4 288 4.60e-134 381
MS.gene67536.t1 MTR_8g074420 67.474 289 88 2 3 285 2 290 1.72e-131 374
MS.gene67536.t1 MTR_5g023460 81.720 186 30 1 100 285 11 192 3.32e-108 311
MS.gene67536.t1 MTR_8g074530 45.172 290 149 6 3 284 17 304 5.81e-69 216
MS.gene67536.t1 MTR_5g023290 37.667 300 169 4 3 284 9 308 3.25e-58 189
MS.gene67536.t1 MTR_5g023410 89.899 99 10 0 3 101 2 100 2.81e-53 172
MS.gene67536.t1 MTR_8g074380 36.027 297 154 7 1 283 7 281 3.27e-46 158
MS.gene67536.t1 MTR_4g070530 34.386 285 180 4 7 285 13 296 1.17e-45 155
MS.gene67536.t1 MTR_5g023650 35.836 293 172 5 8 285 14 305 2.42e-45 155
MS.gene67536.t1 MTR_4g070590 35.135 296 175 7 3 285 10 301 4.13e-41 144
MS.gene67536.t1 MTR_3g116950 34.602 289 176 7 6 285 12 296 4.77e-41 144
MS.gene67536.t1 MTR_4g070540 33.684 285 182 4 7 285 13 296 5.48e-41 144
MS.gene67536.t1 MTR_4g070570 30.068 296 192 6 2 285 11 303 2.26e-39 139
MS.gene67536.t1 MTR_3g116920 32.192 292 181 7 6 285 12 298 7.06e-34 125
MS.gene67536.t1 MTR_1g037820 32.479 234 140 6 52 284 9 225 5.66e-26 102
MS.gene67536.t1 MTR_3g115150 27.575 301 184 8 6 284 27 315 7.85e-23 96.3
MS.gene67536.t1 MTR_5g023540 57.353 68 26 1 163 230 1 65 1.79e-18 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67536.t1 AT4G35690 38.621 290 157 7 5 285 7 284 1.24e-56 184
MS.gene67536.t1 AT2G17680 37.627 295 161 9 5 285 7 292 2.91e-47 160
MS.gene67536.t1 AT2G17080 37.276 279 152 6 6 283 5 261 2.44e-46 157
MS.gene67536.t1 AT4G35710 36.054 294 158 7 5 285 7 283 2.28e-43 149
MS.gene67536.t1 AT2G17070 36.101 277 154 6 6 281 5 259 2.28e-43 149
MS.gene67536.t1 AT4G35200 34.532 278 152 8 6 282 5 253 1.05e-41 144
MS.gene67536.t1 AT4G35210 33.571 280 149 8 6 282 5 250 1.05e-38 136
MS.gene67536.t1 AT4G35720 31.746 315 175 8 6 284 14 324 6.28e-27 107
MS.gene67536.t1 AT4G35680 33.333 300 169 9 8 284 18 309 8.49e-27 107
MS.gene67536.t1 AT4G35660 30.363 303 168 10 1 284 9 287 9.35e-25 100
MS.gene67536.t1 AT1G76240 30.508 295 175 11 6 285 29 308 2.71e-23 97.4
MS.gene67536.t1 AT3G51400 30.640 297 170 11 1 284 1 274 4.87e-19 85.1
MS.gene67536.t1 AT1G76210 28.631 241 145 8 48 284 8 225 1.23e-16 77.4
MS.gene67536.t1 AT3G51410 32.624 282 144 9 8 284 39 279 3.04e-16 77.4
MS.gene67536.t1 AT1G20520 25.714 245 147 7 48 284 8 225 9.36e-13 66.6
MS.gene67536.t1 AT1G76220 27.027 296 158 11 2 284 5 255 3.23e-11 62.8

Find 48 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACGAATGGAAACTAAATT+TGG 0.155287 5.4:-15077442 MS.gene67536:CDS
GGCTTCCCATGTCTTGATTT+TGG 0.206130 5.4:+15077807 None:intergenic
GCAATTGAAATGATAGAAAA+TGG 0.225171 5.4:-15077124 MS.gene67536:CDS
TGAAGATTTGTATATTTCTT+TGG 0.280108 5.4:-15077737 MS.gene67536:CDS
TGTTCTATTCTTGTGGAGTT+AGG 0.282747 5.4:+15077838 None:intergenic
CCACAAATTTCTCACCTTGA+TGG 0.298231 5.4:+15077671 None:intergenic
GGATGGTTCAGTGAGAATTT+TGG 0.305843 5.4:-15077638 MS.gene67536:CDS
CTTTGTGAAGAATTTATATT+CGG 0.312307 5.4:+15077504 None:intergenic
CACTTCACTCTTCTCTTAGA+AGG 0.337508 5.4:-15077561 MS.gene67536:CDS
CTTTGTTACTTTCAACCATT+TGG 0.343326 5.4:+15077282 None:intergenic
GAAATTTGTGGAAGAGTTGT+TGG 0.365610 5.4:-15077659 MS.gene67536:CDS
AGATAATGTATTTAGGCGTT+TGG 0.399736 5.4:-15077098 MS.gene67536:CDS
ATGGTTTAGATAATGTATTT+AGG 0.405059 5.4:-15077105 MS.gene67536:CDS
CTCACCTTGATGGTTAGAAA+TGG 0.407617 5.4:+15077681 None:intergenic
ACATGAAAGATTTGAGGCTT+TGG 0.411831 5.4:-15077152 MS.gene67536:CDS
TAACAAAGTTGATGCATAAG+AGG 0.418308 5.4:-15077267 MS.gene67536:CDS
ATTAGAACCTTCACTTGAAA+GGG 0.443245 5.4:+15077180 None:intergenic
TATTGCACATGAAAGATTTG+AGG 0.451858 5.4:-15077158 MS.gene67536:CDS
CCATCAAGGTGAGAAATTTG+TGG 0.454188 5.4:-15077671 MS.gene67536:CDS
TATTAGAACCTTCACTTGAA+AGG 0.455803 5.4:+15077179 None:intergenic
TAGGTCTTGTTCTATTCTTG+TGG 0.483171 5.4:+15077831 None:intergenic
CTCTTCTCTTAGAAGGAGAA+GGG 0.490473 5.4:-15077554 MS.gene67536:CDS
ACTCTTCTCTTAGAAGGAGA+AGG 0.492722 5.4:-15077555 MS.gene67536:CDS
GATCACATCTTTAAAACGAA+TGG 0.501269 5.4:-15077455 MS.gene67536:CDS
TTAAGAACCCTTTCAAGTGA+AGG 0.514521 5.4:-15077187 MS.gene67536:CDS
GTTAATATGTGAAGGGAACA+TGG 0.515021 5.4:-15077245 MS.gene67536:CDS
AAACAGATTGAAAGATAGAC+AGG 0.517586 5.4:+15077344 None:intergenic
CATAAGAGGTTAATATGTGA+AGG 0.524385 5.4:-15077253 MS.gene67536:CDS
TGGATATATGTGGCATCACA+AGG 0.534307 5.4:-15077618 MS.gene67536:CDS
GAGTTAGGATGAGATTGAGA+AGG 0.554693 5.4:+15077853 None:intergenic
TTCAAGAAATGAAAGGCCAT+TGG 0.560471 5.4:+15077756 None:intergenic
CAAAGTCAAAGGCAACCAAA+TGG 0.562903 5.4:-15077297 MS.gene67536:CDS
GAAAACTATTTGAGCGAACA+TGG 0.586233 5.4:+15077875 None:intergenic
ACAAATCTTCAAGAAATGAA+AGG 0.588246 5.4:+15077749 None:intergenic
TGGATCTTCATCAAAGTCAA+AGG 0.588491 5.4:-15077308 MS.gene67536:CDS
AAAGCCATTTCTAACCATCA+AGG 0.589581 5.4:-15077685 MS.gene67536:CDS
ACCTAACCAAAATCAAGACA+TGG 0.597023 5.4:-15077813 MS.gene67536:CDS
TTGATCTTGATTCAAAAGTG+AGG 0.609457 5.4:+15077414 None:intergenic
TTTGTGGAAGAGTTGTTGGA+TGG 0.615570 5.4:-15077655 MS.gene67536:CDS
ATAAGAGGTTAATATGTGAA+GGG 0.619250 5.4:-15077252 MS.gene67536:CDS
ACATCTGATTCAATTACCAA+TGG 0.619749 5.4:-15077772 MS.gene67536:CDS
AGTGATTACAGTTCTTAGAG+AGG 0.623623 5.4:-15077380 MS.gene67536:CDS
ATTGGTAATTGAATCAGATG+TGG 0.626315 5.4:+15077774 None:intergenic
ATCAGATGTGGATGTTGATG+CGG 0.638432 5.4:+15077786 None:intergenic
CCTAACCAAAATCAAGACAT+GGG 0.643436 5.4:-15077812 MS.gene67536:CDS
TCTTCTCTTAGAAGGAGAAG+GGG 0.654023 5.4:-15077553 MS.gene67536:CDS
GAACTGTAATCACTGCAACA+AGG 0.656672 5.4:+15077389 None:intergenic
GGATATATGTGGCATCACAA+GGG 0.664791 5.4:-15077617 MS.gene67536:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTCTTTAATTTGTAACA+CGG + chr5.4:15077361-15077380 None:intergenic 15.0%
!! ATGGTTTAGATAATGTATTT+AGG - chr5.4:15077844-15077863 MS.gene67536:CDS 20.0%
!! CTTTGTGAAGAATTTATATT+CGG + chr5.4:15077448-15077467 None:intergenic 20.0%
!! TGAAGATTTGTATATTTCTT+TGG - chr5.4:15077212-15077231 MS.gene67536:CDS 20.0%
! AAACGAATGGAAACTAAATT+TGG - chr5.4:15077507-15077526 MS.gene67536:CDS 25.0%
! ACAAATCTTCAAGAAATGAA+AGG + chr5.4:15077203-15077222 None:intergenic 25.0%
! ATAAGAGGTTAATATGTGAA+GGG - chr5.4:15077697-15077716 MS.gene67536:CDS 25.0%
! GCAATTGAAATGATAGAAAA+TGG - chr5.4:15077825-15077844 MS.gene67536:CDS 25.0%
AAACAGATTGAAAGATAGAC+AGG + chr5.4:15077608-15077627 None:intergenic 30.0%
ACATCTGATTCAATTACCAA+TGG - chr5.4:15077177-15077196 MS.gene67536:CDS 30.0%
AGATAATGTATTTAGGCGTT+TGG - chr5.4:15077851-15077870 MS.gene67536:CDS 30.0%
ATTAGAACCTTCACTTGAAA+GGG + chr5.4:15077772-15077791 None:intergenic 30.0%
CATAAGAGGTTAATATGTGA+AGG - chr5.4:15077696-15077715 MS.gene67536:CDS 30.0%
TATTAGAACCTTCACTTGAA+AGG + chr5.4:15077773-15077792 None:intergenic 30.0%
TATTGCACATGAAAGATTTG+AGG - chr5.4:15077791-15077810 MS.gene67536:CDS 30.0%
TTGATCTTGATTCAAAAGTG+AGG + chr5.4:15077538-15077557 None:intergenic 30.0%
! ATTGGTAATTGAATCAGATG+TGG + chr5.4:15077178-15077197 None:intergenic 30.0%
! GTGAGAATTTTGGATATATG+TGG - chr5.4:15077321-15077340 MS.gene67536:CDS 30.0%
! TCAATCTGTTTTGTCTTTCT+TGG - chr5.4:15077617-15077636 MS.gene67536:CDS 30.0%
!! CTTTGTTACTTTCAACCATT+TGG + chr5.4:15077670-15077689 None:intergenic 30.0%
!! GATCACATCTTTAAAACGAA+TGG - chr5.4:15077494-15077513 MS.gene67536:CDS 30.0%
!! TAACAAAGTTGATGCATAAG+AGG - chr5.4:15077682-15077701 MS.gene67536:CDS 30.0%
AAAGCCATTTCTAACCATCA+AGG - chr5.4:15077264-15077283 MS.gene67536:CDS 35.0%
ACCTAACCAAAATCAAGACA+TGG - chr5.4:15077136-15077155 MS.gene67536:CDS 35.0%
AGTGATTACAGTTCTTAGAG+AGG - chr5.4:15077569-15077588 MS.gene67536:CDS 35.0%
CCTAACCAAAATCAAGACAT+GGG - chr5.4:15077137-15077156 MS.gene67536:CDS 35.0%
GAAAACTATTTGAGCGAACA+TGG + chr5.4:15077077-15077096 None:intergenic 35.0%
GAAATTTGTGGAAGAGTTGT+TGG - chr5.4:15077290-15077309 MS.gene67536:CDS 35.0%
GTTAATATGTGAAGGGAACA+TGG - chr5.4:15077704-15077723 MS.gene67536:CDS 35.0%
TGGATCTTCATCAAAGTCAA+AGG - chr5.4:15077641-15077660 MS.gene67536:CDS 35.0%
TGTTCTATTCTTGTGGAGTT+AGG + chr5.4:15077114-15077133 None:intergenic 35.0%
TTCAAGAAATGAAAGGCCAT+TGG + chr5.4:15077196-15077215 None:intergenic 35.0%
! ACATGAAAGATTTGAGGCTT+TGG - chr5.4:15077797-15077816 MS.gene67536:CDS 35.0%
! TCTGTTTTGTCTTTCTTGGT+TGG - chr5.4:15077621-15077640 MS.gene67536:CDS 35.0%
! TTAAGAACCCTTTCAAGTGA+AGG - chr5.4:15077762-15077781 MS.gene67536:CDS 35.0%
!! TAGGTCTTGTTCTATTCTTG+TGG + chr5.4:15077121-15077140 None:intergenic 35.0%
ACTCTTCTCTTAGAAGGAGA+AGG - chr5.4:15077394-15077413 MS.gene67536:CDS 40.0%
ATCAGATGTGGATGTTGATG+CGG + chr5.4:15077166-15077185 None:intergenic 40.0%
CAAAGTCAAAGGCAACCAAA+TGG - chr5.4:15077652-15077671 MS.gene67536:CDS 40.0%
CACTTCACTCTTCTCTTAGA+AGG - chr5.4:15077388-15077407 MS.gene67536:CDS 40.0%
CCACAAATTTCTCACCTTGA+TGG + chr5.4:15077281-15077300 None:intergenic 40.0%
CCATCAAGGTGAGAAATTTG+TGG - chr5.4:15077278-15077297 MS.gene67536:CDS 40.0%
CTCTTCTCTTAGAAGGAGAA+GGG - chr5.4:15077395-15077414 MS.gene67536:CDS 40.0%
GAACTGTAATCACTGCAACA+AGG + chr5.4:15077563-15077582 None:intergenic 40.0%
GAGTTAGGATGAGATTGAGA+AGG + chr5.4:15077099-15077118 None:intergenic 40.0%
GGATATATGTGGCATCACAA+GGG - chr5.4:15077332-15077351 MS.gene67536:CDS 40.0%
TCTTCTCTTAGAAGGAGAAG+GGG - chr5.4:15077396-15077415 MS.gene67536:CDS 40.0%
TGGATATATGTGGCATCACA+AGG - chr5.4:15077331-15077350 MS.gene67536:CDS 40.0%
TTTGTGGAAGAGTTGTTGGA+TGG - chr5.4:15077294-15077313 MS.gene67536:CDS 40.0%
! CTCACCTTGATGGTTAGAAA+TGG + chr5.4:15077271-15077290 None:intergenic 40.0%
! GGATGGTTCAGTGAGAATTT+TGG - chr5.4:15077311-15077330 MS.gene67536:CDS 40.0%
!!! CCCATGTCTTGATTTTGGTT+AGG + chr5.4:15077140-15077159 None:intergenic 40.0%
! GGCTTCCCATGTCTTGATTT+TGG + chr5.4:15077145-15077164 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 15077057 15077914 15077057 ID=MS.gene67536
chr5.4 mRNA 15077057 15077914 15077057 ID=MS.gene67536.t1;Parent=MS.gene67536
chr5.4 exon 15077057 15077914 15077057 ID=MS.gene67536.t1.exon1;Parent=MS.gene67536.t1
chr5.4 CDS 15077057 15077914 15077057 ID=cds.MS.gene67536.t1;Parent=MS.gene67536.t1
Gene Sequence

>MS.gene67536

ATGGCAAGCAACAAGTACCATGTTCGCTCAAATAGTTTTCCTTCTCAATCTCATCCTAACTCCACAAGAATAGAACAAGACCTAACCAAAATCAAGACATGGGAAGCCGCATCAACATCCACATCTGATTCAATTACCAATGGCCTTTCATTTCTTGAAGATTTGTATATTTCTTTGGAAGATCTTCTCAATATGTCATCAACACAAAAAGCCATTTCTAACCATCAAGGTGAGAAATTTGTGGAAGAGTTGTTGGATGGTTCAGTGAGAATTTTGGATATATGTGGCATCACAAGGGACACCGTGTTACAAATTAAAGAAAATGTTCAATCACTTCACTCTTCTCTTAGAAGGAGAAGGGGAGATTCAAGCATTGAAAAAAGTGTAGCCGAATATAAATTCTTCACAAAGAAGATGAAGAAGAATATCACAAATTTGATCACATCTTTAAAACGAATGGAAACTAAATTTGGATCTTCCTCACTTTTGAATCAAGATCAAGACCTTGTTGCAGTGATTACAGTTCTTAGAGAGGTCATTGCAATGAACCTGTCTATCTTTCAATCTGTTTTGTCTTTCTTGGTTGGATCTTCATCAAAGTCAAAGGCAACCAAATGGTTGAAAGTAACAAAGTTGATGCATAAGAGGTTAATATGTGAAGGGAACATGGAGAATTTCAATGAATTGCAGTGTGTTGAAGCATCTTTAAGAACCCTTTCAAGTGAAGGTTCTAATATTGCACATGAAAGATTTGAGGCTTTGGAGAATGCAATTGAAATGATAGAAAATGGTTTAGATAATGTATTTAGGCGTTTGGTTAAAACTAGAGTCAGTCTTTTGAACATAATAAGTCAATAG
Protein sequence

>MS.gene67536.t1

MASNKYHVRSNSFPSQSHPNSTRIEQDLTKIKTWEAASTSTSDSITNGLSFLEDLYISLEDLLNMSSTQKAISNHQGEKFVEELLDGSVRILDICGITRDTVLQIKENVQSLHSSLRRRRGDSSIEKSVAEYKFFTKKMKKNITNLITSLKRMETKFGSSSLLNQDQDLVAVITVLREVIAMNLSIFQSVLSFLVGSSSKSKATKWLKVTKLMHKRLICEGNMENFNELQCVEASLRTLSSEGSNIAHERFEALENAIEMIENGLDNVFRRLVKTRVSLLNIISQ