AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64840.t1 MTR_5g023390 93.007 286 20 0 1 286 1 286 0.0 527
MS.gene64840.t1 MTR_5g023370 93.357 286 19 0 1 286 1 286 0.0 527
MS.gene64840.t1 MTR_5g023340 91.259 286 25 0 1 286 1 286 0.0 514
MS.gene64840.t1 MTR_5g023600 91.608 286 24 0 1 286 1 286 0.0 514
MS.gene64840.t1 MTR_5g023350 90.559 286 27 0 1 286 1 286 0.0 508
MS.gene64840.t1 MTR_5g023530 89.895 287 28 1 1 286 1 287 0.0 506
MS.gene64840.t1 MTR_5g023470 88.850 287 31 1 1 286 1 287 0.0 499
MS.gene64840.t1 MTR_5g023520 87.719 285 33 2 1 284 1 284 5.34e-176 487
MS.gene64840.t1 MTR_5g023550 87.676 284 34 1 1 284 1 283 9.19e-175 484
MS.gene64840.t1 MTR_5g023320 86.667 285 34 2 1 284 1 282 2.35e-173 480
MS.gene64840.t1 MTR_5g023580 84.266 286 41 2 1 282 1 286 1.21e-164 461
MS.gene64840.t1 MTR_8g074450 68.641 287 84 2 4 284 3 289 6.29e-138 391
MS.gene64840.t1 MTR_8g074510 65.965 285 89 3 6 284 5 287 7.33e-132 375
MS.gene64840.t1 MTR_8g074420 66.667 288 90 2 3 284 2 289 4.76e-130 371
MS.gene64840.t1 MTR_5g023460 87.027 185 20 1 100 284 11 191 1.35e-113 325
MS.gene64840.t1 MTR_8g074530 42.907 289 157 5 3 284 17 304 3.19e-65 206
MS.gene64840.t1 MTR_5g023290 36.333 300 173 4 3 284 9 308 8.12e-56 182
MS.gene64840.t1 MTR_5g023410 87.879 99 12 0 3 101 2 100 8.51e-51 166
MS.gene64840.t1 MTR_8g074380 35.714 294 163 6 1 285 7 283 2.18e-46 159
MS.gene64840.t1 MTR_5g023650 35.274 292 173 4 8 284 14 304 2.76e-46 157
MS.gene64840.t1 MTR_4g070530 34.397 282 180 3 7 283 13 294 1.73e-44 153
MS.gene64840.t1 MTR_3g116950 35.986 289 170 8 5 283 11 294 6.76e-43 149
MS.gene64840.t1 MTR_4g070590 36.395 294 170 8 3 283 10 299 2.66e-41 144
MS.gene64840.t1 MTR_4g070570 29.630 297 188 8 2 283 11 301 1.84e-39 140
MS.gene64840.t1 MTR_4g070540 33.688 282 180 4 7 282 13 293 2.08e-39 139
MS.gene64840.t1 MTR_3g116920 34.483 290 175 9 5 283 11 296 1.42e-36 132
MS.gene64840.t1 MTR_1g037820 31.276 243 131 5 52 284 9 225 1.88e-27 106
MS.gene64840.t1 MTR_3g115150 28.947 304 180 10 6 286 27 317 7.02e-26 104
MS.gene64840.t1 MTR_5g023540 53.731 67 28 1 164 230 2 65 5.91e-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.gene64840.t1 AT4G35690 38.732 284 159 7 7 284 9 283 3.72e-56 182
MS.gene64840.t1 AT2G17680 37.671 292 159 9 7 284 9 291 1.63e-47 160
MS.gene64840.t1 AT2G17080 35.714 280 157 6 5 283 4 261 8.63e-45 152
MS.gene64840.t1 AT2G17070 35.612 278 156 6 5 281 4 259 1.28e-43 149
MS.gene64840.t1 AT4G35710 35.294 289 161 7 7 284 9 282 2.42e-43 149
MS.gene64840.t1 AT4G35200 33.692 279 155 7 5 282 4 253 6.43e-41 142
MS.gene64840.t1 AT4G35210 33.096 281 151 8 5 282 4 250 4.54e-38 135
MS.gene64840.t1 AT4G35720 31.310 313 179 6 6 284 14 324 2.22e-26 105
MS.gene64840.t1 AT4G35680 32.000 300 173 9 8 284 18 309 1.74e-25 103
MS.gene64840.t1 AT1G76240 29.352 293 181 9 5 284 28 307 2.86e-25 102
MS.gene64840.t1 AT4G35660 30.645 310 160 11 1 285 9 288 2.19e-24 99.8
MS.gene64840.t1 AT3G51400 30.952 294 168 10 5 285 4 275 1.32e-20 89.4
MS.gene64840.t1 AT1G76210 31.222 221 127 7 68 284 26 225 2.49e-19 84.7
MS.gene64840.t1 AT3G51410 31.786 280 149 9 8 284 39 279 2.27e-14 72.0
MS.gene64840.t1 AT1G20520 28.767 219 122 7 75 284 32 225 4.08e-14 70.5
MS.gene64840.t1 AT1G76220 28.283 198 115 5 2 191 5 183 1.39e-11 63.9

Find 47 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACATCATGACTCTATCTT+AGG 0.153901 5.1:-14150784 None:intergenic
AAACATATGGAAACTAAATT+TGG 0.157953 5.1:-14151173 MS.gene64840:CDS
GGCTTCCCATGTCTTCATTT+TGG 0.197889 5.1:+14151538 None:intergenic
GGATGGTTCAATGAAAATTT+TGG 0.216087 5.1:-14151369 MS.gene64840:CDS
GCAATTGAAAGTATAGAAAA+TGG 0.264764 5.1:-14150855 MS.gene64840:CDS
CCACAAATTTCTCACCTTGA+TGG 0.264918 5.1:+14151402 None:intergenic
TGAAGATTTGTATATATCTT+TGG 0.284754 5.1:-14151468 MS.gene64840:CDS
CATTAGAACCTTCACTTGTA+AGG 0.311738 5.1:+14150910 None:intergenic
CTTTGTGAAGAATTTATATT+CGG 0.312307 5.1:+14151235 None:intergenic
CACTTCACTCTTCTCTTAGA+AGG 0.323794 5.1:-14151292 MS.gene64840:CDS
CTTTGTCACTTTCAACCATT+TGG 0.324091 5.1:+14151013 None:intergenic
TTCTTCAATTCTTGTGGAGT+TGG 0.333799 5.1:+14151568 None:intergenic
TCTTCAATTCTTGTGGAGTT+GGG 0.358306 5.1:+14151569 None:intergenic
GAAATTTGTGGAAGAGTTGT+TGG 0.365610 5.1:-14151390 MS.gene64840:CDS
GATCACATCTTTAAAACATA+TGG 0.374642 5.1:-14151186 MS.gene64840:CDS
ACATGAAAGATTTGAGGCTT+TGG 0.411831 5.1:-14150883 MS.gene64840:CDS
CTCTTCTCTTAGAAGGAGAA+AGG 0.427476 5.1:-14151285 MS.gene64840:CDS
TAGCTCTTCTTCAATTCTTG+TGG 0.429253 5.1:+14151562 None:intergenic
ATGGTTTAGAGAATATATTT+AGG 0.442461 5.1:-14150836 MS.gene64840:CDS
TGTTGCACATGAAAGATTTG+AGG 0.445316 5.1:-14150889 MS.gene64840:CDS
CCATCAAGGTGAGAAATTTG+TGG 0.460090 5.1:-14151402 MS.gene64840:CDS
AACATCATGACTCTATCTTA+GGG 0.475458 5.1:-14150783 None:intergenic
ACAAATCTTCAAGCAAGAAA+AGG 0.492126 5.1:+14151480 None:intergenic
TGACAAAGTTGATGCAAAAG+AGG 0.510512 5.1:-14150998 MS.gene64840:CDS
TTAAGAACCCTTACAAGTGA+AGG 0.516626 5.1:-14150918 MS.gene64840:CDS
ATTAGAACCTTCACTTGTAA+GGG 0.520773 5.1:+14150911 None:intergenic
TGGATATATGTGGCATCACA+AGG 0.534307 5.1:-14151349 MS.gene64840:CDS
TCTTCTCTTAGAAGGAGAAA+GGG 0.543836 5.1:-14151284 MS.gene64840:CDS
AAGCTTGTTTCTCACCATCA+AGG 0.549955 5.1:-14151416 MS.gene64840:CDS
AGCTAACCAAAATGAAGACA+TGG 0.554329 5.1:-14151544 MS.gene64840:CDS
TGGTTCTTCATCAAAGTCAA+AGG 0.557929 5.1:-14151039 MS.gene64840:CDS
TTCAAGCAAGAAAAGGCCAT+TGG 0.559275 5.1:+14151487 None:intergenic
GGTATCATGTGAAGAGAACA+TGG 0.559553 5.1:-14150976 MS.gene64840:CDS
CAAAGTCAAAGGCAACCAAA+TGG 0.562903 5.1:-14151028 MS.gene64840:CDS
GACAAAGTTGATGCAAAAGA+GGG 0.591207 5.1:-14150997 MS.gene64840:CDS
ATCAGATGTGGATGTTGATG+TGG 0.611639 5.1:+14151517 None:intergenic
GAAAACTGTTTGAACGAACA+TGG 0.612401 5.1:+14151606 None:intergenic
TTTGTGGAAGAGTTGTTGGA+TGG 0.615570 5.1:-14151386 MS.gene64840:CDS
ACATCTGATTCAATTACCAA+TGG 0.619749 5.1:-14151503 MS.gene64840:CDS
TTTCAATGAATTGCAGTGTG+TGG 0.620631 5.1:-14150949 MS.gene64840:CDS
TTGATCTTGATTCGAAAGTG+AGG 0.621821 5.1:+14151145 None:intergenic
AGTGATTACAGTTCTTAGAG+AGG 0.623623 5.1:-14151111 MS.gene64840:CDS
ATTGGTAATTGAATCAGATG+TGG 0.626315 5.1:+14151505 None:intergenic
GCTAACCAAAATGAAGACAT+GGG 0.637923 5.1:-14151543 MS.gene64840:CDS
GAACTGTAATCACTGCAACA+AGG 0.656672 5.1:+14151120 None:intergenic
GGATATATGTGGCATCACAA+GGG 0.664791 5.1:-14151348 MS.gene64840:CDS
GAGTTGGGATGAGATTGAGA+AGG 0.749032 5.1:+14151584 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAACTAAATT+TGG - chr5.1:14151235-14151254 MS.gene64840:CDS 20.0%
!! ATGGTTTAGAGAATATATTT+AGG - chr5.1:14151572-14151591 MS.gene64840:CDS 20.0%
!! CTTTGTGAAGAATTTATATT+CGG + chr5.1:14151176-14151195 None:intergenic 20.0%
!! TGAAGATTTGTATATATCTT+TGG - chr5.1:14150940-14150959 MS.gene64840:CDS 20.0%
!!! ATGAAAATTTTGGATATATG+TGG - chr5.1:14151049-14151068 MS.gene64840:CDS 20.0%
!! GCAATTGAAAGTATAGAAAA+TGG - chr5.1:14151553-14151572 MS.gene64840:CDS 25.0%
!!! GATCACATCTTTAAAACATA+TGG - chr5.1:14151222-14151241 MS.gene64840:CDS 25.0%
ACAAATCTTCAAGCAAGAAA+AGG + chr5.1:14150931-14150950 None:intergenic 30.0%
ACATCTGATTCAATTACCAA+TGG - chr5.1:14150905-14150924 MS.gene64840:CDS 30.0%
ATTAGAACCTTCACTTGTAA+GGG + chr5.1:14151500-14151519 None:intergenic 30.0%
! ATTGGTAATTGAATCAGATG+TGG + chr5.1:14150906-14150925 None:intergenic 30.0%
! GGATGGTTCAATGAAAATTT+TGG - chr5.1:14151039-14151058 MS.gene64840:CDS 30.0%
! TCAATCTGTTTTGTCTTTCT+TGG - chr5.1:14151345-14151364 MS.gene64840:CDS 30.0%
AGCTAACCAAAATGAAGACA+TGG - chr5.1:14150864-14150883 MS.gene64840:CDS 35.0%
AGTGATTACAGTTCTTAGAG+AGG - chr5.1:14151297-14151316 MS.gene64840:CDS 35.0%
CATTAGAACCTTCACTTGTA+AGG + chr5.1:14151501-14151520 None:intergenic 35.0%
GAAAACTGTTTGAACGAACA+TGG + chr5.1:14150805-14150824 None:intergenic 35.0%
GAAATTTGTGGAAGAGTTGT+TGG - chr5.1:14151018-14151037 MS.gene64840:CDS 35.0%
GCTAACCAAAATGAAGACAT+GGG - chr5.1:14150865-14150884 MS.gene64840:CDS 35.0%
TAGCTCTTCTTCAATTCTTG+TGG + chr5.1:14150849-14150868 None:intergenic 35.0%
TCTTCAATTCTTGTGGAGTT+GGG + chr5.1:14150842-14150861 None:intergenic 35.0%
TCTTCTCTTAGAAGGAGAAA+GGG - chr5.1:14151124-14151143 MS.gene64840:CDS 35.0%
TGGTTCTTCATCAAAGTCAA+AGG - chr5.1:14151369-14151388 MS.gene64840:CDS 35.0%
TGTTGCACATGAAAGATTTG+AGG - chr5.1:14151519-14151538 MS.gene64840:CDS 35.0%
TTAAGAACCCTTACAAGTGA+AGG - chr5.1:14151490-14151509 MS.gene64840:CDS 35.0%
TTCTTCAATTCTTGTGGAGT+TGG + chr5.1:14150843-14150862 None:intergenic 35.0%
TTTCAATGAATTGCAGTGTG+TGG - chr5.1:14151459-14151478 MS.gene64840:CDS 35.0%
! ACATGAAAGATTTGAGGCTT+TGG - chr5.1:14151525-14151544 MS.gene64840:CDS 35.0%
! TCTGTTTTGTCTTTCTTGGT+TGG - chr5.1:14151349-14151368 MS.gene64840:CDS 35.0%
! TTGATCTTGATTCGAAAGTG+AGG + chr5.1:14151266-14151285 None:intergenic 35.0%
!! CTTTGTCACTTTCAACCATT+TGG + chr5.1:14151398-14151417 None:intergenic 35.0%
!! GACAAAGTTGATGCAAAAGA+GGG - chr5.1:14151411-14151430 MS.gene64840:CDS 35.0%
!! TGACAAAGTTGATGCAAAAG+AGG - chr5.1:14151410-14151429 MS.gene64840:CDS 35.0%
ATCAGATGTGGATGTTGATG+TGG + chr5.1:14150894-14150913 None:intergenic 40.0%
CAAAGTCAAAGGCAACCAAA+TGG - chr5.1:14151380-14151399 MS.gene64840:CDS 40.0%
CACTTCACTCTTCTCTTAGA+AGG - chr5.1:14151116-14151135 MS.gene64840:CDS 40.0%
CCACAAATTTCTCACCTTGA+TGG + chr5.1:14151009-14151028 None:intergenic 40.0%
CCATCAAGGTGAGAAATTTG+TGG - chr5.1:14151006-14151025 MS.gene64840:CDS 40.0%
CTCTTCTCTTAGAAGGAGAA+AGG - chr5.1:14151123-14151142 MS.gene64840:CDS 40.0%
GAACTGTAATCACTGCAACA+AGG + chr5.1:14151291-14151310 None:intergenic 40.0%
GGATATATGTGGCATCACAA+GGG - chr5.1:14151060-14151079 MS.gene64840:CDS 40.0%
GGTATCATGTGAAGAGAACA+TGG - chr5.1:14151432-14151451 MS.gene64840:CDS 40.0%
TGGATATATGTGGCATCACA+AGG - chr5.1:14151059-14151078 MS.gene64840:CDS 40.0%
TTCAAGCAAGAAAAGGCCAT+TGG + chr5.1:14150924-14150943 None:intergenic 40.0%
TTTGTGGAAGAGTTGTTGGA+TGG - chr5.1:14151022-14151041 MS.gene64840:CDS 40.0%
! AAGCTTGTTTCTCACCATCA+AGG - chr5.1:14150992-14151011 MS.gene64840:CDS 40.0%
GAGTTGGGATGAGATTGAGA+AGG + chr5.1:14150827-14150846 None:intergenic 45.0%
! GGCTTCCCATGTCTTCATTT+TGG + chr5.1:14150873-14150892 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14150785 14151645 14150785 ID=MS.gene64840
chr5.1 mRNA 14150785 14151645 14150785 ID=MS.gene64840.t1;Parent=MS.gene64840
chr5.1 exon 14150785 14151645 14150785 ID=MS.gene64840.t1.exon1;Parent=MS.gene64840.t1
chr5.1 CDS 14150785 14151645 14150785 ID=cds.MS.gene64840.t1;Parent=MS.gene64840.t1
Gene Sequence

>MS.gene64840

ATGGCAAGCAACAATTACCATGTTCGTTCAAACAGTTTTCCTTCTCAATCTCATCCCAACTCCACAAGAATTGAAGAAGAGCTAACCAAAATGAAGACATGGGAAGCCACATCAACATCCACATCTGATTCAATTACCAATGGCCTTTTCTTGCTTGAAGATTTGTATATATCTTTGGAAGATCTTCTCAATATGTCATCAACACAGAAGCTTGTTTCTCACCATCAAGGTGAGAAATTTGTGGAAGAGTTGTTGGATGGTTCAATGAAAATTTTGGATATATGTGGCATCACAAGGGACACAATGTTACAGATTAAAGAAAATGTTCAAACACTTCACTCTTCTCTTAGAAGGAGAAAGGGAGAATCAAGCATTGAAAAAAGTATAGCCGAATATAAATTCTTCACAAAGAAGATGAAGAAGAATGTCACAAAGTTGATCACATCTTTAAAACATATGGAAACTAAATTTGGAGCTTCCTCACTTTCGAATCAAGATCAAGACCTTGTTGCAGTGATTACAGTTCTTAGAGAGGTCATTGCAATGAACGTGTCTATCTTTCAATCTGTTTTGTCTTTCTTGGTTGGTTCTTCATCAAAGTCAAAGGCAACCAAATGGTTGAAAGTGACAAAGTTGATGCAAAAGAGGGTATCATGTGAAGAGAACATGGAGAGTTTCAATGAATTGCAGTGTGTGGAAGCATCTTTAAGAACCCTTACAAGTGAAGGTTCTAATGTTGCACATGAAAGATTTGAGGCTTTGGAGAATGCAATTGAAAGTATAGAAAATGGTTTAGAGAATATATTTAGGCGTTTAGTTAAAACTAGAGTCTGTCTTTTGAACATCATGACTCTATCTTAG
Protein sequence

>MS.gene64840.t1

MASNNYHVRSNSFPSQSHPNSTRIEEELTKMKTWEATSTSTSDSITNGLFLLEDLYISLEDLLNMSSTQKLVSHHQGEKFVEELLDGSMKILDICGITRDTMLQIKENVQTLHSSLRRRKGESSIEKSIAEYKFFTKKMKKNVTKLITSLKHMETKFGASSLSNQDQDLVAVITVLREVIAMNVSIFQSVLSFLVGSSSKSKATKWLKVTKLMQKRVSCEENMESFNELQCVEASLRTLTSEGSNVAHERFEALENAIESIENGLENIFRRLVKTRVCLLNIMTLS