AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64846

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64846.t1 MTR_5g023350 87.762 286 31 1 1 282 1 286 1.29e-177 491
MS.gene64846.t1 MTR_5g023600 86.364 286 35 1 1 282 1 286 6.69e-175 484
MS.gene64846.t1 MTR_5g023390 84.615 286 40 1 1 282 1 286 1.05e-173 481
MS.gene64846.t1 MTR_5g023340 85.315 286 38 1 1 282 1 286 7.30e-173 479
MS.gene64846.t1 MTR_5g023320 86.316 285 31 3 1 280 1 282 2.84e-172 477
MS.gene64846.t1 MTR_5g023370 83.566 286 43 1 1 282 1 286 2.33e-171 475
MS.gene64846.t1 MTR_5g023530 84.321 287 40 2 1 282 1 287 9.20e-170 471
MS.gene64846.t1 MTR_5g023580 87.413 286 28 3 1 278 1 286 3.82e-169 473
MS.gene64846.t1 MTR_5g023520 84.698 281 38 2 5 280 4 284 1.63e-168 468
MS.gene64846.t1 MTR_5g023550 84.643 280 39 1 5 280 4 283 2.14e-168 468
MS.gene64846.t1 MTR_5g023470 83.275 287 43 2 1 282 1 287 1.39e-167 466
MS.gene64846.t1 MTR_8g074450 68.403 288 81 3 3 280 2 289 2.74e-134 381
MS.gene64846.t1 MTR_8g074510 67.361 288 85 4 1 280 1 287 5.36e-133 378
MS.gene64846.t1 MTR_8g074420 66.783 286 85 3 5 280 4 289 2.92e-125 358
MS.gene64846.t1 MTR_5g023460 83.511 188 27 1 93 280 8 191 8.89e-111 318
MS.gene64846.t1 MTR_8g074530 41.812 287 155 5 5 280 19 304 1.82e-61 197
MS.gene64846.t1 MTR_5g023290 35.235 298 171 5 5 280 11 308 1.60e-52 174
MS.gene64846.t1 MTR_5g023410 83.505 97 12 1 5 97 4 100 8.30e-47 156
MS.gene64846.t1 MTR_4g070530 34.386 285 172 5 7 279 13 294 2.25e-45 155
MS.gene64846.t1 MTR_8g074380 36.111 288 152 7 8 281 14 283 9.79e-43 149
MS.gene64846.t1 MTR_5g023650 33.904 292 173 4 8 280 14 304 4.09e-41 144
MS.gene64846.t1 MTR_4g070540 34.386 285 170 6 7 278 13 293 3.67e-39 139
MS.gene64846.t1 MTR_4g070570 31.724 290 179 9 6 279 15 301 7.26e-39 138
MS.gene64846.t1 MTR_3g116950 33.793 290 169 9 6 279 12 294 2.53e-37 134
MS.gene64846.t1 MTR_4g070590 32.526 289 176 7 7 279 14 299 9.16e-37 132
MS.gene64846.t1 MTR_3g116920 31.741 293 173 10 6 279 12 296 7.15e-32 120
MS.gene64846.t1 MTR_1g037820 29.915 234 146 5 48 280 9 225 3.24e-23 95.1
MS.gene64846.t1 MTR_3g115150 26.316 304 184 9 6 282 27 317 1.10e-19 87.4
MS.gene64846.t1 MTR_5g023540 58.209 67 25 1 159 225 1 64 2.27e-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.gene64846.t1 AT4G35690 35.764 288 162 7 5 280 7 283 8.30e-52 171
MS.gene64846.t1 AT2G17680 35.855 304 156 10 1 280 3 291 9.52e-43 148
MS.gene64846.t1 AT2G17080 35.563 284 155 8 1 279 1 261 8.01e-42 145
MS.gene64846.t1 AT4G35710 34.932 292 162 7 3 280 5 282 4.89e-41 143
MS.gene64846.t1 AT4G35200 33.929 280 156 8 1 278 1 253 3.13e-40 140
MS.gene64846.t1 AT2G17070 35.461 282 154 8 1 277 1 259 6.62e-40 140
MS.gene64846.t1 AT4G35210 32.143 280 158 8 1 278 1 250 1.45e-36 130
MS.gene64846.t1 AT4G35720 30.794 315 178 6 4 280 12 324 1.70e-25 103
MS.gene64846.t1 AT4G35660 29.097 299 165 10 7 281 13 288 4.00e-22 93.6
MS.gene64846.t1 AT4G35680 31.438 299 172 9 8 280 18 309 7.68e-21 90.5
MS.gene64846.t1 AT1G76240 28.082 292 180 10 6 280 29 307 9.73e-20 87.4
MS.gene64846.t1 AT3G51400 29.758 289 172 10 6 281 5 275 4.15e-17 79.7
MS.gene64846.t1 AT1G76210 27.984 243 146 6 43 280 7 225 8.34e-17 77.8
MS.gene64846.t1 AT1G20520 28.311 219 123 7 71 280 32 225 1.14e-12 66.6
MS.gene64846.t1 AT3G51410 29.137 278 155 7 8 280 39 279 9.69e-12 64.3

Find 45 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACATCATGACTCTATCTT+AGG 0.153901 5.1:+14197635 MS.gene64846:CDS
CATTAGAACCTTCACTTATA+AGG 0.159224 5.1:-14197509 None:intergenic
AAACATATGGAAAGTAAATT+TGG 0.179089 5.1:+14197246 MS.gene64846:CDS
GGCTTCCCATGTCTTAATTT+TGG 0.204721 5.1:-14196893 None:intergenic
TGAAGATTTGTATATTTCTT+TGG 0.249422 5.1:+14196951 MS.gene64846:CDS
GCAATTGAAAGTATAGAAAA+TGG 0.264764 5.1:+14197564 MS.gene64846:CDS
CATGGAGAATTTCAATGAAT+TGG 0.288433 5.1:+14197461 MS.gene64846:CDS
TGTTCTAATCTTGAGGTGTT+AGG 0.291169 5.1:-14196862 None:intergenic
TAGAAAAGTTGATGCATAAG+AGG 0.298421 5.1:+14197421 MS.gene64846:CDS
TCCAACCAAGAAAGACAAAA+TGG 0.347485 5.1:-14197361 None:intergenic
ATTAGAACCTTCACTTATAA+GGG 0.348108 5.1:-14197508 None:intergenic
AGAGAATATATTTAGGCGTT+TGG 0.352912 5.1:+14197590 MS.gene64846:CDS
TAACTGTAATCACTGCAATA+AGG 0.362390 5.1:-14197299 None:intergenic
GAAATTTGTTGAAGAGTTGT+TGG 0.385629 5.1:+14197029 MS.gene64846:CDS
CACTTCACTCTGCTCTTAGA+AGG 0.386439 5.1:+14197127 MS.gene64846:CDS
CAACAAATTTCTCACCTTGA+CGG 0.400296 5.1:-14197017 None:intergenic
CAAAGTCAAAGGCAACAAAA+TGG 0.408302 5.1:+14197391 MS.gene64846:CDS
ACATGAAAGATTTGAGGCTT+TGG 0.411831 5.1:+14197536 MS.gene64846:CDS
ATGGTTTAGAGAATATATTT+AGG 0.442461 5.1:+14197583 MS.gene64846:CDS
TGTTGCACATGAAAGATTTG+AGG 0.445316 5.1:+14197530 MS.gene64846:CDS
TAACTCTTGTTCTAATCTTG+AGG 0.452697 5.1:-14196869 None:intergenic
GATCACATCATTAAAACATA+TGG 0.453290 5.1:+14197233 MS.gene64846:CDS
AACATCATGACTCTATCTTA+GGG 0.475458 5.1:+14197636 MS.gene64846:CDS
GGTAATATGTGAAGAGAACA+TGG 0.486514 5.1:+14197443 MS.gene64846:CDS
CAATATGTCATCAACACAAA+AGG 0.488097 5.1:+14196984 MS.gene64846:CDS
AATATACAAATCTTCAAGAA+AGG 0.505581 5.1:-14196944 None:intergenic
TTAAGAACCCTTATAAGTGA+AGG 0.516729 5.1:+14197501 MS.gene64846:CDS
CTCTGCTCTTAGAAGGAGAA+AGG 0.522599 5.1:+14197134 MS.gene64846:CDS
AGAAAAGTTGATGCATAAGA+GGG 0.530100 5.1:+14197422 MS.gene64846:CDS
GGATGGTTCAGTGAAAACTT+TGG 0.547383 5.1:+14197050 MS.gene64846:CDS
TTTCAATGAATTGGAGTGTG+TGG 0.567119 5.1:+14197470 MS.gene64846:CDS
ATCAGATGTGGATGTTGATG+TGG 0.573031 5.1:-14196914 None:intergenic
AAAGGAAAGGCCATCAGATG+TGG 0.574463 5.1:-14196926 None:intergenic
GAAAACTGTTTGAGCGAACA+TGG 0.580551 5.1:-14196825 None:intergenic
TGGATCTTCATCAAAGTCAA+AGG 0.588491 5.1:+14197380 MS.gene64846:CDS
GTGTTAGGATGAGATTGAGA+TGG 0.593460 5.1:-14196847 None:intergenic
ACATCAACATCCACATCTGA+TGG 0.599081 5.1:+14196916 MS.gene64846:CDS
TTTGTTGAAGAGTTGTTGGA+TGG 0.600565 5.1:+14197033 MS.gene64846:CDS
ACAAATCTTCAAGAAAGGAA+AGG 0.601275 5.1:-14196939 None:intergenic
AGTGATTACAGTTATTAGAG+AGG 0.603135 5.1:+14197308 MS.gene64846:CDS
AAGGTCATTGCTCACCGTCA+AGG 0.605239 5.1:+14197003 MS.gene64846:CDS
GTTAACCAAAATTAAGACAT+GGG 0.608808 5.1:+14196888 MS.gene64846:CDS
AGTTAACCAAAATTAAGACA+TGG 0.616346 5.1:+14196887 MS.gene64846:CDS
GTGAAAACTTTGGATATCTG+CGG 0.626495 5.1:+14197060 MS.gene64846:CDS
TTGATCTTGATTCAAAAGCG+AGG 0.637937 5.1:-14197274 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAAGTAAATT+TGG + chr5.1:14197246-14197265 MS.gene64846:CDS 20.0%
!! AATATACAAATCTTCAAGAA+AGG - chr5.1:14196947-14196966 None:intergenic 20.0%
!! ATGGTTTAGAGAATATATTT+AGG + chr5.1:14197583-14197602 MS.gene64846:CDS 20.0%
!! TGAAGATTTGTATATTTCTT+TGG + chr5.1:14196951-14196970 MS.gene64846:CDS 20.0%
!!! ATTTTCTTTAATTTGTGACA+CGG - chr5.1:14197100-14197119 None:intergenic 20.0%
! AGTTAACCAAAATTAAGACA+TGG + chr5.1:14196887-14196906 MS.gene64846:CDS 25.0%
! ATTAGAACCTTCACTTATAA+GGG - chr5.1:14197511-14197530 None:intergenic 25.0%
! GATCACATCATTAAAACATA+TGG + chr5.1:14197233-14197252 MS.gene64846:CDS 25.0%
! GTTAACCAAAATTAAGACAT+GGG + chr5.1:14196888-14196907 MS.gene64846:CDS 25.0%
!! GCAATTGAAAGTATAGAAAA+TGG + chr5.1:14197564-14197583 MS.gene64846:CDS 25.0%
ACAAATCTTCAAGAAAGGAA+AGG - chr5.1:14196942-14196961 None:intergenic 30.0%
AGAGAATATATTTAGGCGTT+TGG + chr5.1:14197590-14197609 MS.gene64846:CDS 30.0%
AGTGATTACAGTTATTAGAG+AGG + chr5.1:14197308-14197327 MS.gene64846:CDS 30.0%
CAATATGTCATCAACACAAA+AGG + chr5.1:14196984-14197003 MS.gene64846:CDS 30.0%
CATGGAGAATTTCAATGAAT+TGG + chr5.1:14197461-14197480 MS.gene64846:CDS 30.0%
CATTAGAACCTTCACTTATA+AGG - chr5.1:14197512-14197531 None:intergenic 30.0%
TAACTCTTGTTCTAATCTTG+AGG - chr5.1:14196872-14196891 None:intergenic 30.0%
TAACTGTAATCACTGCAATA+AGG - chr5.1:14197302-14197321 None:intergenic 30.0%
TTAAGAACCCTTATAAGTGA+AGG + chr5.1:14197501-14197520 MS.gene64846:CDS 30.0%
! TCAATCCATTTTGTCTTTCT+TGG + chr5.1:14197356-14197375 MS.gene64846:CDS 30.0%
!! AGAAAAGTTGATGCATAAGA+GGG + chr5.1:14197422-14197441 MS.gene64846:CDS 30.0%
!! GAAATTTGTTGAAGAGTTGT+TGG + chr5.1:14197029-14197048 MS.gene64846:CDS 30.0%
!! TAGAAAAGTTGATGCATAAG+AGG + chr5.1:14197421-14197440 MS.gene64846:CDS 30.0%
CAAAGTCAAAGGCAACAAAA+TGG + chr5.1:14197391-14197410 MS.gene64846:CDS 35.0%
CAACAAATTTCTCACCTTGA+CGG - chr5.1:14197020-14197039 None:intergenic 35.0%
GGTAATATGTGAAGAGAACA+TGG + chr5.1:14197443-14197462 MS.gene64846:CDS 35.0%
GTGAAAACTTTGGATATCTG+CGG + chr5.1:14197060-14197079 MS.gene64846:CDS 35.0%
TCCAACCAAGAAAGACAAAA+TGG - chr5.1:14197364-14197383 None:intergenic 35.0%
TGGATCTTCATCAAAGTCAA+AGG + chr5.1:14197380-14197399 MS.gene64846:CDS 35.0%
TGTTGCACATGAAAGATTTG+AGG + chr5.1:14197530-14197549 MS.gene64846:CDS 35.0%
TTGATCTTGATTCAAAAGCG+AGG - chr5.1:14197277-14197296 None:intergenic 35.0%
TTTCAATGAATTGGAGTGTG+TGG + chr5.1:14197470-14197489 MS.gene64846:CDS 35.0%
TTTGTTGAAGAGTTGTTGGA+TGG + chr5.1:14197033-14197052 MS.gene64846:CDS 35.0%
! ACATGAAAGATTTGAGGCTT+TGG + chr5.1:14197536-14197555 MS.gene64846:CDS 35.0%
! TCCATTTTGTCTTTCTTGGT+TGG + chr5.1:14197360-14197379 MS.gene64846:CDS 35.0%
! TGTTCTAATCTTGAGGTGTT+AGG - chr5.1:14196865-14196884 None:intergenic 35.0%
ACATCAACATCCACATCTGA+TGG + chr5.1:14196916-14196935 MS.gene64846:CDS 40.0%
ATCAGATGTGGATGTTGATG+TGG - chr5.1:14196917-14196936 None:intergenic 40.0%
GAAAACTGTTTGAGCGAACA+TGG - chr5.1:14196828-14196847 None:intergenic 40.0%
GGATGGTTCAGTGAAAACTT+TGG + chr5.1:14197050-14197069 MS.gene64846:CDS 40.0%
GTGTTAGGATGAGATTGAGA+TGG - chr5.1:14196850-14196869 None:intergenic 40.0%
! GGCTTCCCATGTCTTAATTT+TGG - chr5.1:14196896-14196915 None:intergenic 40.0%
AAAGGAAAGGCCATCAGATG+TGG - chr5.1:14196929-14196948 None:intergenic 45.0%
CACTTCACTCTGCTCTTAGA+AGG + chr5.1:14197127-14197146 MS.gene64846:CDS 45.0%
CTCTGCTCTTAGAAGGAGAA+AGG + chr5.1:14197134-14197153 MS.gene64846:CDS 45.0%
AAGGTCATTGCTCACCGTCA+AGG + chr5.1:14197003-14197022 MS.gene64846:CDS 50.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14196808 14197656 14196808 ID=MS.gene64846
chr5.1 mRNA 14196808 14197656 14196808 ID=MS.gene64846.t1;Parent=MS.gene64846
chr5.1 exon 14196808 14197656 14196808 ID=MS.gene64846.t1.exon1;Parent=MS.gene64846.t1
chr5.1 CDS 14196808 14197656 14196808 ID=cds.MS.gene64846.t1;Parent=MS.gene64846.t1
Gene Sequence

>MS.gene64846

ATGGCAATCAGAAAGTACCATGTTCGCTCAAACAGTTTTCCATCTCAATCTCATCCTAACACCTCAAGATTAGAACAAGAGTTAACCAAAATTAAGACATGGGAAGCCACATCAACATCCACATCTGATGGCCTTTCCTTTCTTGAAGATTTGTATATTTCTTTGGAAAATCTTCTCAATATGTCATCAACACAAAAGGTCATTGCTCACCGTCAAGGTGAGAAATTTGTTGAAGAGTTGTTGGATGGTTCAGTGAAAACTTTGGATATCTGCGGCATCACAAGCGACACCGTGTCACAAATTAAAGAAAATGTTCAAACACTTCACTCTGCTCTTAGAAGGAGAAAGGCAGATTCAAGCATTGAAACAAGTGTAGCAGAATATAAATTCTTCACAAAGAAGATGAAGAAGAATGTCACAAAGTTGATCACATCATTAAAACATATGGAAAGTAAATTTGGAGCTTCCTCGCTTTTGAATCAAGATCAAAACCTTATTGCAGTGATTACAGTTATTAGAGAGGTCATTGCAATGAACTTGTCTATCTTTCAATCCATTTTGTCTTTCTTGGTTGGATCTTCATCAAAGTCAAAGGCAACAAAATGGTTGAAAGTAGAAAAGTTGATGCATAAGAGGGTAATATGTGAAGAGAACATGGAGAATTTCAATGAATTGGAGTGTGTGGAAGCATCTTTAAGAACCCTTATAAGTGAAGGTTCTAATGTTGCACATGAAAGATTTGAGGCTTTGGAGAATGCAATTGAAAGTATAGAAAATGGTTTAGAGAATATATTTAGGCGTTTGGTTAAAACTAGAGTTTGTCTTTTGAACATCATGACTCTATCTTAG
Protein sequence

>MS.gene64846.t1

MAIRKYHVRSNSFPSQSHPNTSRLEQELTKIKTWEATSTSTSDGLSFLEDLYISLENLLNMSSTQKVIAHRQGEKFVEELLDGSVKTLDICGITSDTVSQIKENVQTLHSALRRRKADSSIETSVAEYKFFTKKMKKNVTKLITSLKHMESKFGASSLLNQDQNLIAVITVIREVIAMNLSIFQSILSFLVGSSSKSKATKWLKVEKLMHKRVICEENMENFNELECVEASLRTLISEGSNVAHERFEALENAIESIENGLENIFRRLVKTRVCLLNIMTLS