AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene67541

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67541.t1 MTR_5g023390 93.357 286 19 0 1 286 1 286 0.0 523
MS.gene67541.t1 MTR_5g023370 92.308 286 22 0 1 286 1 286 0.0 516
MS.gene67541.t1 MTR_5g023340 90.909 286 26 0 1 286 1 286 0.0 506
MS.gene67541.t1 MTR_5g023600 90.559 286 27 0 1 286 1 286 0.0 504
MS.gene67541.t1 MTR_5g023350 89.860 286 29 0 1 286 1 286 0.0 500
MS.gene67541.t1 MTR_5g023530 88.502 287 32 1 1 286 1 287 7.39e-178 492
MS.gene67541.t1 MTR_5g023470 87.456 287 35 1 1 286 1 287 1.00e-175 486
MS.gene67541.t1 MTR_5g023520 86.667 285 36 2 1 284 1 284 4.47e-172 477
MS.gene67541.t1 MTR_5g023550 86.620 284 37 1 1 284 1 283 1.21e-170 473
MS.gene67541.t1 MTR_5g023320 85.965 285 36 2 1 284 1 282 2.89e-170 472
MS.gene67541.t1 MTR_5g023580 83.217 286 44 2 1 282 1 286 3.46e-161 452
MS.gene67541.t1 MTR_8g074450 69.338 287 82 2 4 284 3 289 2.28e-139 394
MS.gene67541.t1 MTR_8g074510 66.667 285 87 3 6 284 5 287 1.72e-133 379
MS.gene67541.t1 MTR_8g074420 66.319 288 91 2 3 284 2 289 5.58e-129 368
MS.gene67541.t1 MTR_5g023460 88.108 185 18 1 100 284 11 191 2.75e-114 327
MS.gene67541.t1 MTR_8g074530 42.561 289 158 5 3 284 17 304 3.30e-64 204
MS.gene67541.t1 MTR_5g023290 36.333 300 173 4 3 284 9 308 1.51e-55 182
MS.gene67541.t1 MTR_5g023410 85.859 99 14 0 3 101 2 100 1.26e-48 160
MS.gene67541.t1 MTR_8g074380 34.694 294 166 6 1 285 7 283 5.47e-45 155
MS.gene67541.t1 MTR_5g023650 34.589 292 175 4 8 284 14 304 2.68e-44 152
MS.gene67541.t1 MTR_3g116950 35.959 292 172 8 2 283 8 294 2.27e-42 147
MS.gene67541.t1 MTR_4g070530 33.333 282 183 3 7 283 13 294 4.23e-41 144
MS.gene67541.t1 MTR_3g116920 34.694 294 175 9 2 283 8 296 2.80e-38 137
MS.gene67541.t1 MTR_4g070570 30.303 297 186 9 2 283 11 301 3.14e-38 137
MS.gene67541.t1 MTR_4g070540 33.569 283 181 4 7 283 13 294 3.52e-38 136
MS.gene67541.t1 MTR_4g070590 35.034 294 174 8 3 283 10 299 6.91e-38 135
MS.gene67541.t1 MTR_3g115150 29.180 305 180 10 5 286 26 317 6.29e-28 110
MS.gene67541.t1 MTR_1g037820 30.769 234 144 4 52 284 9 225 7.75e-26 102
MS.gene67541.t1 MTR_5g023540 51.471 68 30 1 163 230 1 65 6.48e-15 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67541.t1 AT4G35690 38.542 288 154 7 7 284 9 283 1.86e-57 186
MS.gene67541.t1 AT2G17680 38.356 292 157 9 7 284 9 291 3.52e-48 162
MS.gene67541.t1 AT4G35710 36.426 291 155 8 7 284 9 282 1.28e-43 150
MS.gene67541.t1 AT2G17080 36.071 280 156 6 5 283 4 261 2.94e-43 149
MS.gene67541.t1 AT2G17070 35.971 278 155 6 5 281 4 259 1.04e-41 144
MS.gene67541.t1 AT4G35200 33.692 279 155 7 5 282 4 253 9.96e-40 139
MS.gene67541.t1 AT4G35210 32.616 279 155 7 5 282 4 250 4.24e-37 132
MS.gene67541.t1 AT1G76240 29.352 293 181 9 5 284 28 307 7.64e-26 104
MS.gene67541.t1 AT4G35720 29.393 313 185 5 6 284 14 324 1.33e-25 103
MS.gene67541.t1 AT4G35680 31.773 299 175 9 8 284 18 309 6.77e-24 99.0
MS.gene67541.t1 AT4G35660 30.449 312 158 12 1 285 9 288 2.40e-23 97.1
MS.gene67541.t1 AT3G51400 30.612 294 169 10 5 285 4 275 1.31e-19 86.7
MS.gene67541.t1 AT1G76210 29.646 226 124 6 68 284 26 225 6.50e-18 80.9
MS.gene67541.t1 AT1G20520 31.982 222 111 10 75 284 32 225 8.04e-15 72.4
MS.gene67541.t1 AT3G51410 31.071 280 151 9 8 284 39 279 2.38e-14 72.0
MS.gene67541.t1 AT1G76220 27.119 295 161 10 2 285 5 256 2.63e-12 65.9

Find 45 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACATCATGACTCTATCTT+AGG 0.153901 5.4:-15118400 None:intergenic
AAACATATGGAAACTAAATT+TGG 0.157953 5.4:-15118789 MS.gene67541:CDS
GGACGGTTCAATGAAAATTT+TGG 0.167155 5.4:-15118985 MS.gene67541:CDS
GGCTTCCCATGTCTTCATTT+TGG 0.197889 5.4:+15119154 None:intergenic
GCAATTGAAAATATAGAAAA+TGG 0.213595 5.4:-15118471 MS.gene67541:CDS
TGAAGATTTGTATATATCTT+TGG 0.284754 5.4:-15119084 MS.gene67541:CDS
CTTTGTGAAGAATTTATATT+CGG 0.312307 5.4:+15118851 None:intergenic
CCACAAAATTCTCACCTTGA+TGG 0.319695 5.4:+15119018 None:intergenic
TTCTTCAATTCTTGTGGAGT+TGG 0.333799 5.4:+15119184 None:intergenic
CACTTCACTCTTCTCTTAGA+AGG 0.337508 5.4:-15118908 MS.gene67541:CDS
TCTTCAATTCTTGTGGAGTT+GGG 0.358306 5.4:+15119185 None:intergenic
GATCACATCTTTAAAACATA+TGG 0.374642 5.4:-15118802 MS.gene67541:CDS
ACATGAAAGATTTGAGGCTT+TGG 0.411831 5.4:-15118499 MS.gene67541:CDS
TAGCTCTTCTTCAATTCTTG+TGG 0.429253 5.4:+15119178 None:intergenic
CATTAGAACCTTCACTTGAA+AGG 0.429263 5.4:+15118526 None:intergenic
TCTTCTCTTAGAAGGAGAAA+TGG 0.439819 5.4:-15118900 MS.gene67541:CDS
ATTAGAACCTTCACTTGAAA+GGG 0.442145 5.4:+15118527 None:intergenic
ATGGTTTAGAGAATATATTT+AGG 0.442461 5.4:-15118452 MS.gene67541:CDS
TGTTGCACATGAAAGATTTG+AGG 0.445316 5.4:-15118505 MS.gene67541:CDS
CTTTGCTACTTTCAACCATT+CGG 0.449655 5.4:+15118629 None:intergenic
AACATCATGACTCTATCTTA+GGG 0.475458 5.4:-15118399 None:intergenic
ACAAATCTTCAAGCAAGAAA+AGG 0.492126 5.4:+15119096 None:intergenic
GATGAAGAACCAACCAAGAA+AGG 0.493357 5.4:+15118666 None:intergenic
TAGCAAAGTTGATGCAAAAG+AGG 0.512951 5.4:-15118614 MS.gene67541:CDS
TTGAGAACCCTTTCAAGTGA+AGG 0.518841 5.4:-15118534 MS.gene67541:CDS
TGGATATATGTGGCATCACA+AGG 0.534307 5.4:-15118965 MS.gene67541:CDS
AAGCTTGTTTCTCACCATCA+AGG 0.549955 5.4:-15119032 MS.gene67541:CDS
AGCTAACCAAAATGAAGACA+TGG 0.554329 5.4:-15119160 MS.gene67541:CDS
TGGTTCTTCATCAAAGTCAA+AGG 0.557929 5.4:-15118655 MS.gene67541:CDS
TTCAAGCAAGAAAAGGCCAT+TGG 0.559275 5.4:+15119103 None:intergenic
GGTAACATGTGAAGAGAACA+TGG 0.580064 5.4:-15118592 MS.gene67541:CDS
AGCAAAGTTGATGCAAAAGA+GGG 0.593646 5.4:-15118613 MS.gene67541:CDS
TTGATCTTGATTCAAAAGTG+AGG 0.609457 5.4:+15118761 None:intergenic
TTTCAATGAATTGCAGTGTG+TGG 0.611573 5.4:-15118565 MS.gene67541:CDS
ATCAGATGTGGATGTTGATG+TGG 0.611639 5.4:+15119133 None:intergenic
ACATCTGATTCAATTACCAA+TGG 0.619749 5.4:-15119119 MS.gene67541:CDS
GAAAACTGATTGAACGAACA+TGG 0.620639 5.4:+15119222 None:intergenic
TTTGTGGAAGAGTTGTTGGA+CGG 0.621043 5.4:-15119002 MS.gene67541:CDS
AGTGATTACAGTTCTTAGAG+AGG 0.623623 5.4:-15118727 MS.gene67541:CDS
ATTGGTAATTGAATCAGATG+TGG 0.626315 5.4:+15119121 None:intergenic
GCTAACCAAAATGAAGACAT+GGG 0.637923 5.4:-15119159 MS.gene67541:CDS
CAAAGTCAAAGGCAACCGAA+TGG 0.643365 5.4:-15118644 MS.gene67541:CDS
GAACTGTAATCACTGCAACA+AGG 0.656672 5.4:+15118736 None:intergenic
GGATATATGTGGCATCACAA+GGG 0.664791 5.4:-15118964 MS.gene67541:CDS
GAGTTGGGATGAGATTGAGA+AGG 0.749032 5.4:+15119200 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAACTAAATT+TGG - chr5.4:15118851-15118870 MS.gene67541:CDS 20.0%
!! ATGGTTTAGAGAATATATTT+AGG - chr5.4:15119188-15119207 MS.gene67541:CDS 20.0%
!! CTTTGTGAAGAATTTATATT+CGG + chr5.4:15118792-15118811 None:intergenic 20.0%
!! GCAATTGAAAATATAGAAAA+TGG - chr5.4:15119169-15119188 MS.gene67541:CDS 20.0%
!! TGAAGATTTGTATATATCTT+TGG - chr5.4:15118556-15118575 MS.gene67541:CDS 20.0%
!!! ATGAAAATTTTGGATATATG+TGG - chr5.4:15118665-15118684 MS.gene67541:CDS 20.0%
!!! ATTTTCTTTAATCTGTAACA+TGG + chr5.4:15118705-15118724 None:intergenic 20.0%
!!! GATCACATCTTTAAAACATA+TGG - chr5.4:15118838-15118857 MS.gene67541:CDS 25.0%
ACAAATCTTCAAGCAAGAAA+AGG + chr5.4:15118547-15118566 None:intergenic 30.0%
ACATCTGATTCAATTACCAA+TGG - chr5.4:15118521-15118540 MS.gene67541:CDS 30.0%
ATTAGAACCTTCACTTGAAA+GGG + chr5.4:15119116-15119135 None:intergenic 30.0%
TTGATCTTGATTCAAAAGTG+AGG + chr5.4:15118882-15118901 None:intergenic 30.0%
! ATTGGTAATTGAATCAGATG+TGG + chr5.4:15118522-15118541 None:intergenic 30.0%
AGCTAACCAAAATGAAGACA+TGG - chr5.4:15118480-15118499 MS.gene67541:CDS 35.0%
AGTGATTACAGTTCTTAGAG+AGG - chr5.4:15118913-15118932 MS.gene67541:CDS 35.0%
CATTAGAACCTTCACTTGAA+AGG + chr5.4:15119117-15119136 None:intergenic 35.0%
GAAAACTGATTGAACGAACA+TGG + chr5.4:15118421-15118440 None:intergenic 35.0%
GCTAACCAAAATGAAGACAT+GGG - chr5.4:15118481-15118500 MS.gene67541:CDS 35.0%
TAGCTCTTCTTCAATTCTTG+TGG + chr5.4:15118465-15118484 None:intergenic 35.0%
TCTTCAATTCTTGTGGAGTT+GGG + chr5.4:15118458-15118477 None:intergenic 35.0%
TCTTCTCTTAGAAGGAGAAA+TGG - chr5.4:15118740-15118759 MS.gene67541:CDS 35.0%
TGGTTCTTCATCAAAGTCAA+AGG - chr5.4:15118985-15119004 MS.gene67541:CDS 35.0%
TGTTGCACATGAAAGATTTG+AGG - chr5.4:15119135-15119154 MS.gene67541:CDS 35.0%
TTCTTCAATTCTTGTGGAGT+TGG + chr5.4:15118459-15118478 None:intergenic 35.0%
TTTCAATGAATTGCAGTGTG+TGG - chr5.4:15119075-15119094 MS.gene67541:CDS 35.0%
! ACATGAAAGATTTGAGGCTT+TGG - chr5.4:15119141-15119160 MS.gene67541:CDS 35.0%
! GAATTTTGTGGAAGAGTTGT+TGG - chr5.4:15118634-15118653 MS.gene67541:CDS 35.0%
! GGACGGTTCAATGAAAATTT+TGG - chr5.4:15118655-15118674 MS.gene67541:CDS 35.0%
! TCAATCAGTTTTGCCTTTCT+TGG - chr5.4:15118961-15118980 MS.gene67541:CDS 35.0%
!! AGCAAAGTTGATGCAAAAGA+GGG - chr5.4:15119027-15119046 MS.gene67541:CDS 35.0%
!! CTTTGCTACTTTCAACCATT+CGG + chr5.4:15119014-15119033 None:intergenic 35.0%
!! TAGCAAAGTTGATGCAAAAG+AGG - chr5.4:15119026-15119045 MS.gene67541:CDS 35.0%
ATCAGATGTGGATGTTGATG+TGG + chr5.4:15118510-15118529 None:intergenic 40.0%
CACTTCACTCTTCTCTTAGA+AGG - chr5.4:15118732-15118751 MS.gene67541:CDS 40.0%
CCACAAAATTCTCACCTTGA+TGG + chr5.4:15118625-15118644 None:intergenic 40.0%
GAACTGTAATCACTGCAACA+AGG + chr5.4:15118907-15118926 None:intergenic 40.0%
GATGAAGAACCAACCAAGAA+AGG + chr5.4:15118977-15118996 None:intergenic 40.0%
GGATATATGTGGCATCACAA+GGG - chr5.4:15118676-15118695 MS.gene67541:CDS 40.0%
GGTAACATGTGAAGAGAACA+TGG - chr5.4:15119048-15119067 MS.gene67541:CDS 40.0%
TGGATATATGTGGCATCACA+AGG - chr5.4:15118675-15118694 MS.gene67541:CDS 40.0%
TTCAAGCAAGAAAAGGCCAT+TGG + chr5.4:15118540-15118559 None:intergenic 40.0%
TTTGTGGAAGAGTTGTTGGA+CGG - chr5.4:15118638-15118657 MS.gene67541:CDS 40.0%
! AAGCTTGTTTCTCACCATCA+AGG - chr5.4:15118608-15118627 MS.gene67541:CDS 40.0%
! CCATCAAGGTGAGAATTTTG+TGG - chr5.4:15118622-15118641 MS.gene67541:CDS 40.0%
! TCAGTTTTGCCTTTCTTGGT+TGG - chr5.4:15118965-15118984 MS.gene67541:CDS 40.0%
! TTGAGAACCCTTTCAAGTGA+AGG - chr5.4:15119106-15119125 MS.gene67541:CDS 40.0%
CAAAGTCAAAGGCAACCGAA+TGG - chr5.4:15118996-15119015 MS.gene67541:CDS 45.0%
GAGTTGGGATGAGATTGAGA+AGG + chr5.4:15118443-15118462 None:intergenic 45.0%
! GGCTTCCCATGTCTTCATTT+TGG + chr5.4:15118489-15118508 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 15118401 15119261 15118401 ID=MS.gene67541
chr5.4 mRNA 15118401 15119261 15118401 ID=MS.gene67541.t1;Parent=MS.gene67541
chr5.4 exon 15118401 15119261 15118401 ID=MS.gene67541.t1.exon1;Parent=MS.gene67541.t1
chr5.4 CDS 15118401 15119261 15118401 ID=cds.MS.gene67541.t1;Parent=MS.gene67541.t1
Gene Sequence

>MS.gene67541

ATGGCAAGCAACAATTACCATGTTCGTTCAATCAGTTTTCCTTCTCAATCTCATCCCAACTCCACAAGAATTGAAGAAGAGCTAACCAAAATGAAGACATGGGAAGCCACATCAACATCCACATCTGATTCAATTACCAATGGCCTTTTCTTGCTTGAAGATTTGTATATATCTTTGGAAGATCTTCTCAATATGTCATCAACACAGAAGCTTGTTTCTCACCATCAAGGTGAGAATTTTGTGGAAGAGTTGTTGGACGGTTCAATGAAAATTTTGGATATATGTGGCATCACAAGGGACACCATGTTACAGATTAAAGAAAATGTTCAATCACTTCACTCTTCTCTTAGAAGGAGAAATGGAGAATCAAGCATTGAAAAAAGTGTAGCCGAATATAAATTCTTCACAAAGAAGATGAAGAAGAATGTCAGAAAGTTGATCACATCTTTAAAACATATGGAAACTAAATTTGGAGCTTCCTCACTTTTGAATCAAGATCAAGACCTTGTTGCAGTGATTACAGTTCTTAGAGAGGTCATTGCAATGAACTTGTCTATCTTTCAATCAGTTTTGCCTTTCTTGGTTGGTTCTTCATCAAAGTCAAAGGCAACCGAATGGTTGAAAGTAGCAAAGTTGATGCAAAAGAGGGTAACATGTGAAGAGAACATGGAGAATTTCAATGAATTGCAGTGTGTGGAAGCATCTTTGAGAACCCTTTCAAGTGAAGGTTCTAATGTTGCACATGAAAGATTTGAGGCTTTGGAGAATGCAATTGAAAATATAGAAAATGGTTTAGAGAATATATTTAGGCGTTTAGTTAAAACTAGAGTCTGTCTTTTGAACATCATGACTCTATCTTAG
Protein sequence

>MS.gene67541.t1

MASNNYHVRSISFPSQSHPNSTRIEEELTKMKTWEATSTSTSDSITNGLFLLEDLYISLEDLLNMSSTQKLVSHHQGENFVEELLDGSMKILDICGITRDTMLQIKENVQSLHSSLRRRNGESSIEKSVAEYKFFTKKMKKNVRKLITSLKHMETKFGASSLLNQDQDLVAVITVLREVIAMNLSIFQSVLPFLVGSSSKSKATEWLKVAKLMQKRVTCEENMENFNELQCVEASLRTLSSEGSNVAHERFEALENAIENIENGLENIFRRLVKTRVCLLNIMTLS