AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64838

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64838.t1 MTR_5g023340 94.056 286 17 0 1 286 1 286 0.0 518
MS.gene64838.t1 MTR_5g023350 93.357 286 19 0 1 286 1 286 0.0 513
MS.gene64838.t1 MTR_5g023390 90.210 286 28 0 1 286 1 286 0.0 504
MS.gene64838.t1 MTR_5g023370 90.210 286 28 0 1 286 1 286 0.0 504
MS.gene64838.t1 MTR_5g023600 90.909 286 26 0 1 286 1 286 0.0 501
MS.gene64838.t1 MTR_5g023530 88.850 287 31 1 1 286 1 287 7.98e-177 489
MS.gene64838.t1 MTR_5g023320 88.070 285 30 2 1 284 1 282 7.04e-175 484
MS.gene64838.t1 MTR_5g023470 87.805 287 34 1 1 286 1 287 1.47e-174 483
MS.gene64838.t1 MTR_5g023520 88.421 285 31 2 1 284 1 284 4.14e-174 482
MS.gene64838.t1 MTR_5g023550 87.324 284 35 1 1 284 1 283 9.07e-172 476
MS.gene64838.t1 MTR_5g023580 84.266 286 41 2 1 282 1 286 5.48e-164 459
MS.gene64838.t1 MTR_8g074450 67.596 287 87 2 4 284 3 289 2.12e-135 384
MS.gene64838.t1 MTR_8g074510 64.561 285 93 3 6 284 5 287 1.49e-127 364
MS.gene64838.t1 MTR_8g074420 65.625 288 93 2 3 284 2 289 1.66e-126 362
MS.gene64838.t1 MTR_5g023460 87.568 185 19 1 100 284 11 191 5.68e-112 321
MS.gene64838.t1 MTR_8g074530 42.759 290 156 6 3 284 17 304 1.13e-62 200
MS.gene64838.t1 MTR_5g023290 36.333 300 173 4 3 284 9 308 9.95e-53 174
MS.gene64838.t1 MTR_5g023410 91.919 99 8 0 3 101 2 100 3.16e-52 170
MS.gene64838.t1 MTR_8g074380 35.374 294 164 6 1 285 7 283 1.79e-45 156
MS.gene64838.t1 MTR_5g023650 34.247 292 176 5 8 284 14 304 8.56e-42 146
MS.gene64838.t1 MTR_4g070530 32.979 282 184 3 7 283 13 294 1.53e-41 145
MS.gene64838.t1 MTR_3g116950 35.294 289 172 9 5 283 11 294 2.09e-38 137
MS.gene64838.t1 MTR_4g070570 30.508 295 188 8 2 283 11 301 1.85e-36 132
MS.gene64838.t1 MTR_4g070540 32.155 283 185 4 7 283 13 294 3.07e-36 131
MS.gene64838.t1 MTR_4g070590 33.788 293 179 7 3 283 10 299 7.42e-35 127
MS.gene64838.t1 MTR_3g116920 32.534 292 178 8 5 283 11 296 4.31e-33 123
MS.gene64838.t1 MTR_1g037820 30.041 243 134 5 52 284 9 225 3.47e-25 100
MS.gene64838.t1 MTR_3g115150 27.213 305 186 10 5 286 26 317 9.78e-22 93.2
MS.gene64838.t1 MTR_5g023540 52.174 69 30 1 163 231 1 66 5.97e-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.gene64838.t1 AT4G35690 37.282 287 159 8 7 284 9 283 4.61e-51 169
MS.gene64838.t1 AT2G17680 37.329 292 160 9 7 284 9 291 3.30e-45 154
MS.gene64838.t1 AT2G17080 34.286 280 161 6 5 283 4 261 1.42e-42 147
MS.gene64838.t1 AT2G17070 33.813 278 161 6 5 281 4 259 8.33e-40 140
MS.gene64838.t1 AT4G35710 34.256 289 164 7 7 284 9 282 1.87e-39 139
MS.gene64838.t1 AT4G35200 32.258 279 159 8 5 282 4 253 1.13e-38 136
MS.gene64838.t1 AT4G35210 31.900 279 157 8 5 282 4 250 3.66e-36 130
MS.gene64838.t1 AT4G35680 31.333 300 175 9 8 284 18 309 1.14e-25 103
MS.gene64838.t1 AT4G35720 30.794 315 178 8 6 284 14 324 3.93e-23 97.1
MS.gene64838.t1 AT1G76240 28.328 293 184 9 5 284 28 307 4.45e-23 96.7
MS.gene64838.t1 AT4G35660 29.605 304 171 10 1 285 9 288 9.96e-22 92.8
MS.gene64838.t1 AT3G51400 30.612 294 169 10 5 285 4 275 2.41e-18 83.2
MS.gene64838.t1 AT1G76210 29.091 220 131 7 69 284 27 225 1.35e-15 74.7
MS.gene64838.t1 AT3G51410 31.071 280 151 9 8 284 39 279 1.16e-13 70.1
MS.gene64838.t1 AT1G20520 27.755 245 142 8 48 284 8 225 1.75e-12 65.9
MS.gene64838.t1 AT1G76220 26.014 296 163 9 2 285 5 256 2.27e-11 63.2

Find 44 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACATATGGAAACTAAATT+TGG 0.157953 5.1:-14141426 MS.gene64838:CDS
GGCTTCCCATGTCTTGATTT+TGG 0.226979 5.1:+14141791 None:intergenic
TGAAGATTTGTATATTTCTT+TGG 0.280108 5.1:-14141721 MS.gene64838:CDS
GCAACTGAAATGATAGAAAA+TGG 0.294687 5.1:-14141108 MS.gene64838:CDS
TGTTCAATTCTAGTGGAGTT+AGG 0.328618 5.1:+14141822 None:intergenic
CTTTGTGAAGAGTTTATATT+CGG 0.333272 5.1:+14141488 None:intergenic
CACTTCACTCTTCTCTTAGA+AGG 0.337508 5.1:-14141545 MS.gene64838:CDS
GATCACATCTTTAAAACATA+TGG 0.374642 5.1:-14141439 MS.gene64838:CDS
GGATGGTTCGGTGAAAGTTT+TGG 0.395778 5.1:-14141622 MS.gene64838:CDS
ATGGTTTAGAGAATATATTT+AGG 0.402535 5.1:-14141089 MS.gene64838:CDS
CAAAGTCAAAGGCAACAAAA+TGG 0.408302 5.1:-14141281 MS.gene64838:CDS
ACATGAAAGATTTGAGGCTT+TGG 0.411831 5.1:-14141136 MS.gene64838:CDS
CATTTGAACCTTCACTTGAA+AGG 0.414722 5.1:+14141163 None:intergenic
CTCTTCTCTTAGAAGGAGAA+AGG 0.427476 5.1:-14141538 MS.gene64838:CDS
ATTTGAACCTTCACTTGAAA+GGG 0.433756 5.1:+14141164 None:intergenic
TGTTGCACATGAAAGATTTG+AGG 0.457835 5.1:-14141142 MS.gene64838:CDS
CAATATGTCATCAATACAAA+AGG 0.468624 5.1:-14141688 MS.gene64838:CDS
TAACTCTTGTTCAATTCTAG+TGG 0.471339 5.1:+14141815 None:intergenic
GGAAGAATTGTTGGATGGTT+CGG 0.474552 5.1:-14141634 MS.gene64838:CDS
AATATACAAATCTTCAAGAA+AGG 0.505581 5.1:+14141728 None:intergenic
TGACAAAGTTGATGCAAAAG+AGG 0.510512 5.1:-14141251 MS.gene64838:CDS
TTAAGAACCCTTTCAAGTGA+AGG 0.514521 5.1:-14141171 MS.gene64838:CDS
TGGATATATGTGGCATCACA+AGG 0.532845 5.1:-14141602 MS.gene64838:CDS
GAGTTAGGATGAGATTGAGA+AGG 0.535434 5.1:+14141837 None:intergenic
TCTTCTCTTAGAAGGAGAAA+GGG 0.543836 5.1:-14141537 MS.gene64838:CDS
GAAAACTGTTTGAGCGGACA+TGG 0.545024 5.1:+14141859 None:intergenic
ACATCTGATTCAATTACCAC+TGG 0.584960 5.1:-14141756 MS.gene64838:CDS
TGGATCTTCATCAAAGTCAA+AGG 0.588491 5.1:-14141292 MS.gene64838:CDS
GACAAAGTTGATGCAAAAGA+GGG 0.591207 5.1:-14141250 MS.gene64838:CDS
ATTCTCTTTAATCTGTAACA+TGG 0.595297 5.1:+14141575 None:intergenic
ACAAATCTTCAAGAAAGGAA+AGG 0.601275 5.1:+14141733 None:intergenic
TTGATCTTGATTCAAAAGTG+AGG 0.609457 5.1:+14141398 None:intergenic
ATCAGATGTGGATGTTGATG+TGG 0.611639 5.1:+14141770 None:intergenic
ATTGTGGAAGAATTGTTGGA+TGG 0.613251 5.1:-14141639 MS.gene64838:CDS
AAGGCTATATCTCACCATCA+AGG 0.613728 5.1:-14141669 MS.gene64838:CDS
AGTTAACCAAAATCAAGACA+TGG 0.616346 5.1:-14141797 MS.gene64838:CDS
GGTAACATGTGAAGAGAACA+TGG 0.618682 5.1:-14141229 MS.gene64838:CDS
GAGAAGGAAAACTGTTTGAG+CGG 0.618730 5.1:+14141853 None:intergenic
GTTAACCAAAATCAAGACAT+GGG 0.625458 5.1:-14141796 MS.gene64838:CDS
AGTCATTACAGTTCTTCGAG+AGG 0.646301 5.1:-14141364 MS.gene64838:CDS
TTCAAGAAAGGAAAGGCCAG+TGG 0.658882 5.1:+14141740 None:intergenic
AGTGGTAATTGAATCAGATG+TGG 0.659124 5.1:+14141758 None:intergenic
GAACTGTAATGACTGCAACA+AGG 0.668339 5.1:+14141373 None:intergenic
GGATATATGTGGCATCACAA+GGG 0.671330 5.1:-14141601 MS.gene64838:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAACTAAATT+TGG - chr5.1:14141488-14141507 MS.gene64838:CDS 20.0%
!! AATATACAAATCTTCAAGAA+AGG + chr5.1:14141189-14141208 None:intergenic 20.0%
!! ATGGTTTAGAGAATATATTT+AGG - chr5.1:14141825-14141844 MS.gene64838:CDS 20.0%
!! TGAAGATTTGTATATTTCTT+TGG - chr5.1:14141193-14141212 MS.gene64838:CDS 20.0%
! AAAAATTGTGGAAGAATTGT+TGG - chr5.1:14141271-14141290 MS.gene64838:CDS 25.0%
! ATTCTCTTTAATCTGTAACA+TGG + chr5.1:14141342-14141361 None:intergenic 25.0%
! CAATATGTCATCAATACAAA+AGG - chr5.1:14141226-14141245 MS.gene64838:CDS 25.0%
! CTTTGTGAAGAGTTTATATT+CGG + chr5.1:14141429-14141448 None:intergenic 25.0%
!!! GATCACATCTTTAAAACATA+TGG - chr5.1:14141475-14141494 MS.gene64838:CDS 25.0%
ACAAATCTTCAAGAAAGGAA+AGG + chr5.1:14141184-14141203 None:intergenic 30.0%
AGTTAACCAAAATCAAGACA+TGG - chr5.1:14141117-14141136 MS.gene64838:CDS 30.0%
ATTTGAACCTTCACTTGAAA+GGG + chr5.1:14141753-14141772 None:intergenic 30.0%
GCAACTGAAATGATAGAAAA+TGG - chr5.1:14141806-14141825 MS.gene64838:CDS 30.0%
GTTAACCAAAATCAAGACAT+GGG - chr5.1:14141118-14141137 MS.gene64838:CDS 30.0%
TAACTCTTGTTCAATTCTAG+TGG + chr5.1:14141102-14141121 None:intergenic 30.0%
TTGATCTTGATTCAAAAGTG+AGG + chr5.1:14141519-14141538 None:intergenic 30.0%
! TCAATCTGTTTTGTCTTTCT+TGG - chr5.1:14141598-14141617 MS.gene64838:CDS 30.0%
!!! GTGAAAGTTTTGGATATATG+TGG - chr5.1:14141302-14141321 MS.gene64838:CDS 30.0%
ACATCTGATTCAATTACCAC+TGG - chr5.1:14141158-14141177 MS.gene64838:CDS 35.0%
AGTGGTAATTGAATCAGATG+TGG + chr5.1:14141159-14141178 None:intergenic 35.0%
ATTGTGGAAGAATTGTTGGA+TGG - chr5.1:14141275-14141294 MS.gene64838:CDS 35.0%
CAAAGTCAAAGGCAACAAAA+TGG - chr5.1:14141633-14141652 MS.gene64838:CDS 35.0%
CATTTGAACCTTCACTTGAA+AGG + chr5.1:14141754-14141773 None:intergenic 35.0%
CCATCAAGGTGAAAAAATTG+TGG - chr5.1:14141259-14141278 MS.gene64838:CDS 35.0%
TCTTCTCTTAGAAGGAGAAA+GGG - chr5.1:14141377-14141396 MS.gene64838:CDS 35.0%
TGGATCTTCATCAAAGTCAA+AGG - chr5.1:14141622-14141641 MS.gene64838:CDS 35.0%
TGTTCAATTCTAGTGGAGTT+AGG + chr5.1:14141095-14141114 None:intergenic 35.0%
TGTTGCACATGAAAGATTTG+AGG - chr5.1:14141772-14141791 MS.gene64838:CDS 35.0%
! ACATGAAAGATTTGAGGCTT+TGG - chr5.1:14141778-14141797 MS.gene64838:CDS 35.0%
! TCTGTTTTGTCTTTCTTGGT+TGG - chr5.1:14141602-14141621 MS.gene64838:CDS 35.0%
! TTAAGAACCCTTTCAAGTGA+AGG - chr5.1:14141743-14141762 MS.gene64838:CDS 35.0%
!! GACAAAGTTGATGCAAAAGA+GGG - chr5.1:14141664-14141683 MS.gene64838:CDS 35.0%
!! TGACAAAGTTGATGCAAAAG+AGG - chr5.1:14141663-14141682 MS.gene64838:CDS 35.0%
!!! CCACAATTTTTTCACCTTGA+TGG + chr5.1:14141262-14141281 None:intergenic 35.0%
AAGGCTATATCTCACCATCA+AGG - chr5.1:14141245-14141264 MS.gene64838:CDS 40.0%
AGTCATTACAGTTCTTCGAG+AGG - chr5.1:14141550-14141569 MS.gene64838:CDS 40.0%
ATCAGATGTGGATGTTGATG+TGG + chr5.1:14141147-14141166 None:intergenic 40.0%
CACTTCACTCTTCTCTTAGA+AGG - chr5.1:14141369-14141388 MS.gene64838:CDS 40.0%
CTCTTCTCTTAGAAGGAGAA+AGG - chr5.1:14141376-14141395 MS.gene64838:CDS 40.0%
GAACTGTAATGACTGCAACA+AGG + chr5.1:14141544-14141563 None:intergenic 40.0%
GAGAAGGAAAACTGTTTGAG+CGG + chr5.1:14141064-14141083 None:intergenic 40.0%
GAGTTAGGATGAGATTGAGA+AGG + chr5.1:14141080-14141099 None:intergenic 40.0%
GGAAGAATTGTTGGATGGTT+CGG - chr5.1:14141280-14141299 MS.gene64838:CDS 40.0%
GGATATATGTGGCATCACAA+GGG - chr5.1:14141313-14141332 MS.gene64838:CDS 40.0%
GGTAACATGTGAAGAGAACA+TGG - chr5.1:14141685-14141704 MS.gene64838:CDS 40.0%
TGGATATATGTGGCATCACA+AGG - chr5.1:14141312-14141331 MS.gene64838:CDS 40.0%
GAAAACTGTTTGAGCGGACA+TGG + chr5.1:14141058-14141077 None:intergenic 45.0%
TTCAAGAAAGGAAAGGCCAG+TGG + chr5.1:14141177-14141196 None:intergenic 45.0%
! GGCTTCCCATGTCTTGATTT+TGG + chr5.1:14141126-14141145 None:intergenic 45.0%
!!! GGATGGTTCGGTGAAAGTTT+TGG - chr5.1:14141292-14141311 MS.gene64838:CDS 45.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14141038 14141898 14141038 ID=MS.gene64838
chr5.1 mRNA 14141038 14141898 14141038 ID=MS.gene64838.t1;Parent=MS.gene64838
chr5.1 exon 14141038 14141898 14141038 ID=MS.gene64838.t1.exon1;Parent=MS.gene64838.t1
chr5.1 CDS 14141038 14141898 14141038 ID=cds.MS.gene64838.t1;Parent=MS.gene64838.t1
Gene Sequence

>MS.gene64838

ATGGCAAGCAACAATTACCATGTCCGCTCAAACAGTTTTCCTTCTCAATCTCATCCTAACTCCACTAGAATTGAACAAGAGTTAACCAAAATCAAGACATGGGAAGCCACATCAACATCCACATCTGATTCAATTACCACTGGCCTTTCCTTTCTTGAAGATTTGTATATTTCTTTGGAAGATCTTCTCAATATGTCATCAATACAAAAGGCTATATCTCACCATCAAGGTGAAAAAATTGTGGAAGAATTGTTGGATGGTTCGGTGAAAGTTTTGGATATATGTGGCATCACAAGGGAAACCATGTTACAGATTAAAGAGAATGTTCAATCACTTCACTCTTCTCTTAGAAGGAGAAAGGGAGAATCATGCATTGAAAAAAGTGTAGCCGAATATAAACTCTTCACAAAGAAGATGAAGAAGAATGTCACAAAGTTGATCACATCTTTAAAACATATGGAAACTAAATTTGGAGCTTCCTCACTTTTGAATCAAGATCAAGACCTTGTTGCAGTCATTACAGTTCTTCGAGAGGTCATTAAAATGAACTTGTCTATCTTTCAATCTGTTTTGTCTTTCTTGGTTGGATCTTCATCAAAGTCAAAGGCAACAAAATGGTTGAAAGTGACAAAGTTGATGCAAAAGAGGGTAACATGTGAAGAGAACATGGTGAATTTCAATGAATTGCAGTGTGTCGAAGCATCTTTAAGAACCCTTTCAAGTGAAGGTTCAAATGTTGCACATGAAAGATTTGAGGCTTTGGAGAATGCAACTGAAATGATAGAAAATGGTTTAGAGAATATATTTAGGAGATTAGTTAAAACTAGAGTTTGTCTTTTGAACATTATGACTCTATCTTAG
Protein sequence

>MS.gene64838.t1

MASNNYHVRSNSFPSQSHPNSTRIEQELTKIKTWEATSTSTSDSITTGLSFLEDLYISLEDLLNMSSIQKAISHHQGEKIVEELLDGSVKVLDICGITRETMLQIKENVQSLHSSLRRRKGESCIEKSVAEYKLFTKKMKKNVTKLITSLKHMETKFGASSLLNQDQDLVAVITVLREVIKMNLSIFQSVLSFLVGSSSKSKATKWLKVTKLMQKRVTCEENMVNFNELQCVEASLRTLSSEGSNVAHERFEALENATEMIENGLENIFRRLVKTRVCLLNIMTLS