AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64839

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64839.t1 MTR_5g023350 94.755 286 15 0 1 286 1 286 0.0 526
MS.gene64839.t1 MTR_5g023600 92.308 286 22 0 1 286 1 286 0.0 516
MS.gene64839.t1 MTR_5g023340 92.657 286 21 0 1 286 1 286 0.0 514
MS.gene64839.t1 MTR_5g023370 91.259 286 25 0 1 286 1 286 0.0 511
MS.gene64839.t1 MTR_5g023390 90.559 286 27 0 1 286 1 286 0.0 507
MS.gene64839.t1 MTR_5g023530 90.592 287 26 1 1 286 1 287 0.0 505
MS.gene64839.t1 MTR_5g023470 89.547 287 29 1 1 286 1 287 1.15e-180 499
MS.gene64839.t1 MTR_5g023550 90.141 284 27 1 1 284 1 283 2.70e-180 498
MS.gene64839.t1 MTR_5g023520 90.175 285 26 2 1 284 1 284 2.04e-179 496
MS.gene64839.t1 MTR_5g023320 88.070 285 30 2 1 284 1 282 6.67e-175 484
MS.gene64839.t1 MTR_5g023580 85.315 286 38 2 1 282 1 286 1.87e-167 468
MS.gene64839.t1 MTR_8g074450 69.338 287 82 2 4 284 3 289 2.46e-139 394
MS.gene64839.t1 MTR_8g074420 68.403 288 85 2 3 284 2 289 1.69e-133 380
MS.gene64839.t1 MTR_8g074510 66.434 286 88 3 5 284 4 287 1.13e-132 377
MS.gene64839.t1 MTR_5g023460 86.486 185 21 1 100 284 11 191 6.55e-112 321
MS.gene64839.t1 MTR_8g074530 43.793 290 153 5 3 284 17 304 4.61e-67 211
MS.gene64839.t1 MTR_5g023290 36.667 300 172 5 3 284 9 308 2.12e-56 184
MS.gene64839.t1 MTR_5g023410 91.919 99 8 0 3 101 2 100 8.28e-53 171
MS.gene64839.t1 MTR_5g023650 36.301 292 170 4 8 284 14 304 1.19e-49 166
MS.gene64839.t1 MTR_8g074380 36.395 294 161 6 1 285 7 283 9.04e-48 162
MS.gene64839.t1 MTR_4g070530 32.979 282 184 3 7 283 13 294 4.08e-42 147
MS.gene64839.t1 MTR_3g116950 34.722 288 173 9 6 283 12 294 8.69e-39 138
MS.gene64839.t1 MTR_4g070540 32.270 282 184 4 7 282 13 293 1.39e-37 135
MS.gene64839.t1 MTR_4g070590 34.812 293 176 8 3 283 10 299 1.45e-37 135
MS.gene64839.t1 MTR_4g070570 30.405 296 187 9 2 283 11 301 2.60e-37 134
MS.gene64839.t1 MTR_3g116920 33.333 291 175 9 6 283 12 296 4.61e-34 125
MS.gene64839.t1 MTR_1g037820 31.624 234 142 5 52 284 9 225 9.34e-26 102
MS.gene64839.t1 MTR_3g115150 27.961 304 183 10 6 286 27 317 8.20e-24 99.0
MS.gene64839.t1 MTR_5g023540 55.072 69 28 1 163 231 1 66 1.18e-16 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64839.t1 AT4G35690 37.413 286 164 7 5 284 7 283 2.89e-53 175
MS.gene64839.t1 AT2G17680 38.591 298 152 10 5 284 7 291 7.61e-48 161
MS.gene64839.t1 AT2G17080 36.201 279 155 6 6 283 5 261 1.27e-45 155
MS.gene64839.t1 AT4G35710 35.739 291 161 7 5 284 7 282 1.24e-41 145
MS.gene64839.t1 AT2G17070 35.018 277 157 6 6 281 5 259 2.61e-41 144
MS.gene64839.t1 AT4G35200 33.813 278 154 7 6 282 5 253 5.03e-41 142
MS.gene64839.t1 AT4G35210 32.734 278 154 7 6 282 5 250 5.93e-38 134
MS.gene64839.t1 AT4G35680 31.773 299 175 9 8 284 18 309 4.85e-28 110
MS.gene64839.t1 AT4G35720 30.032 313 183 5 6 284 14 324 8.06e-26 104
MS.gene64839.t1 AT4G35660 29.934 304 170 9 1 285 9 288 1.23e-24 100
MS.gene64839.t1 AT1G76240 26.621 293 187 7 6 284 29 307 3.57e-21 91.7
MS.gene64839.t1 AT3G51400 30.872 298 170 11 1 285 1 275 1.73e-19 86.3
MS.gene64839.t1 AT1G76210 28.696 230 121 6 68 284 26 225 8.04e-18 80.9
MS.gene64839.t1 AT3G51410 31.429 280 150 9 8 284 39 279 1.27e-14 72.8
MS.gene64839.t1 AT1G20520 26.721 247 142 8 48 284 8 225 1.88e-13 68.6
MS.gene64839.t1 AT1G76220 30.808 198 110 6 2 191 5 183 1.81e-12 66.2

Find 49 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACATATGGAAAGTAAATT+TGG 0.150071 5.1:-14146547 MS.gene64839:CDS
GAACATCATGACTCTATCTT+AGG 0.153901 5.1:-14146158 None:intergenic
CGTTAGAACCTTCACTTATA+AGG 0.174479 5.1:+14146284 None:intergenic
ATTTGGAGCTTCCTCACTTT+TGG 0.231167 5.1:-14146530 MS.gene64839:CDS
GCAATTGAAAGTATAGAAAA+TGG 0.264764 5.1:-14146229 MS.gene64839:CDS
CCACAAATTTCTCACCTTGA+TGG 0.264918 5.1:+14146776 None:intergenic
TGAAGATTTGTATATTTCTT+TGG 0.280108 5.1:-14146842 MS.gene64839:CDS
TGTTCAATTCTTGTGGAGTT+TGG 0.281712 5.1:+14146943 None:intergenic
CTTTGTGAAGAATTTATATT+CGG 0.312307 5.1:+14146609 None:intergenic
CACTTCACTCTTCTCTTAGA+AGG 0.337508 5.1:-14146666 MS.gene64839:CDS
AGAGAATATATTTAGGTGTT+TGG 0.341972 5.1:-14146203 MS.gene64839:CDS
GTTAGAACCTTCACTTATAA+GGG 0.365747 5.1:+14146285 None:intergenic
TTGATGTGGCTTCCCATGTC+TGG 0.370632 5.1:+14146905 None:intergenic
GATCACATCTTTAAAACATA+TGG 0.374642 5.1:-14146560 MS.gene64839:CDS
CAAAGTCAAAGGCAACAAAA+TGG 0.408302 5.1:-14146402 MS.gene64839:CDS
ATGGTTTAGAGAATATATTT+AGG 0.411004 5.1:-14146210 MS.gene64839:CDS
ACATGAAAGATTTGAGGCTT+TGG 0.411831 5.1:-14146257 MS.gene64839:CDS
CGTTGCACATGAAAGATTTG+AGG 0.421906 5.1:-14146263 MS.gene64839:CDS
GGATGGTTCAGTGAAAGTTT+TGG 0.423908 5.1:-14146743 MS.gene64839:CDS
CTCTTCTCTTAGAAGGAGAA+AGG 0.427476 5.1:-14146659 MS.gene64839:CDS
GAAATTTGTGGAAGAGATGT+TGG 0.427536 5.1:-14146764 MS.gene64839:CDS
TAGCTCTTGTTCAATTCTTG+TGG 0.437588 5.1:+14146936 None:intergenic
CCATCAAGGTGAGAAATTTG+TGG 0.460090 5.1:-14146776 MS.gene64839:CDS
AACATCATGACTCTATCTTA+GGG 0.475458 5.1:-14146157 None:intergenic
AATATACAAATCTTCAAGAA+AGG 0.505581 5.1:+14146849 None:intergenic
TGACAAAGTTGATGCAAAAG+AGG 0.510512 5.1:-14146372 MS.gene64839:CDS
CAATATGTCATCAACACAAA+CGG 0.511974 5.1:-14146809 MS.gene64839:CDS
TTAAGAACCCTTATAAGTGA+AGG 0.516729 5.1:-14146292 MS.gene64839:CDS
TGGATATCTGTGGCATCACA+AGG 0.538499 5.1:-14146723 MS.gene64839:CDS
TCTTCTCTTAGAAGGAGAAA+GGG 0.543836 5.1:-14146658 MS.gene64839:CDS
GGTATCATGTGAAGAGAACA+TGG 0.559553 5.1:-14146350 MS.gene64839:CDS
GAAAACTGTTTGAGCGAACA+TGG 0.580551 5.1:+14146980 None:intergenic
ACATCTGATTCAATTACCAC+TGG 0.584960 5.1:-14146877 MS.gene64839:CDS
TGGATCTTCATCAAAGTCAA+AGG 0.588491 5.1:-14146413 MS.gene64839:CDS
GACAAAGTTGATGCAAAAGA+GGG 0.591207 5.1:-14146371 MS.gene64839:CDS
GAGTTTGGATGTGATTGAGA+TGG 0.592244 5.1:+14146958 None:intergenic
AGCTATGCAAAATCCAGACA+TGG 0.600165 5.1:-14146918 MS.gene64839:CDS
ATCAGATGTGGATGTTGATG+TGG 0.611639 5.1:+14146891 None:intergenic
TTTGTGGAAGAGATGTTGGA+TGG 0.615570 5.1:-14146760 MS.gene64839:CDS
ACGGCTATTTCTCACCATCA+AGG 0.616806 5.1:-14146790 MS.gene64839:CDS
AGTGATTACAGTTCTTAGAG+AGG 0.623623 5.1:-14146485 MS.gene64839:CDS
CTTCAATGAACTGCAGTGTG+TGG 0.642952 5.1:-14146323 MS.gene64839:CDS
TTGATCTTGATCCAAAAGTG+AGG 0.652915 5.1:+14146519 None:intergenic
GAACTGTAATCACTGCAACA+AGG 0.656672 5.1:+14146494 None:intergenic
ACAAATCTTCAAGAAAGGAG+AGG 0.657674 5.1:+14146854 None:intergenic
AGTGGTAATTGAATCAGATG+TGG 0.659124 5.1:+14146879 None:intergenic
GCTATGCAAAATCCAGACAT+GGG 0.663981 5.1:-14146917 MS.gene64839:CDS
GGATATCTGTGGCATCACAA+GGG 0.673626 5.1:-14146722 MS.gene64839:CDS
TTCAAGAAAGGAGAGGCCAG+TGG 0.677549 5.1:+14146861 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTCTTTAATTTGTAACA+TGG + chr5.1:14146463-14146482 None:intergenic 15.0%
!! AAACATATGGAAAGTAAATT+TGG - chr5.1:14146609-14146628 MS.gene64839:CDS 20.0%
!! AATATACAAATCTTCAAGAA+AGG + chr5.1:14146310-14146329 None:intergenic 20.0%
!! ATGGTTTAGAGAATATATTT+AGG - chr5.1:14146946-14146965 MS.gene64839:CDS 20.0%
!! CTTTGTGAAGAATTTATATT+CGG + chr5.1:14146550-14146569 None:intergenic 20.0%
!! TGAAGATTTGTATATTTCTT+TGG - chr5.1:14146314-14146333 MS.gene64839:CDS 20.0%
! AGAGAATATATTTAGGTGTT+TGG - chr5.1:14146953-14146972 MS.gene64839:CDS 25.0%
!! GCAATTGAAAGTATAGAAAA+TGG - chr5.1:14146927-14146946 MS.gene64839:CDS 25.0%
!!! GATCACATCTTTAAAACATA+TGG - chr5.1:14146596-14146615 MS.gene64839:CDS 25.0%
CAATATGTCATCAACACAAA+CGG - chr5.1:14146347-14146366 MS.gene64839:CDS 30.0%
GTTAGAACCTTCACTTATAA+GGG + chr5.1:14146874-14146893 None:intergenic 30.0%
TTAAGAACCCTTATAAGTGA+AGG - chr5.1:14146864-14146883 MS.gene64839:CDS 30.0%
!! TCAATCAGTTTTGTCTTTCT+TGG - chr5.1:14146719-14146738 MS.gene64839:CDS 30.0%
ACAAATCTTCAAGAAAGGAG+AGG + chr5.1:14146305-14146324 None:intergenic 35.0%
ACATCTGATTCAATTACCAC+TGG - chr5.1:14146279-14146298 MS.gene64839:CDS 35.0%
AGTGATTACAGTTCTTAGAG+AGG - chr5.1:14146671-14146690 MS.gene64839:CDS 35.0%
AGTGGTAATTGAATCAGATG+TGG + chr5.1:14146280-14146299 None:intergenic 35.0%
CAAAGTCAAAGGCAACAAAA+TGG - chr5.1:14146754-14146773 MS.gene64839:CDS 35.0%
CGTTAGAACCTTCACTTATA+AGG + chr5.1:14146875-14146894 None:intergenic 35.0%
GAAATTTGTGGAAGAGATGT+TGG - chr5.1:14146392-14146411 MS.gene64839:CDS 35.0%
TAGCTCTTGTTCAATTCTTG+TGG + chr5.1:14146223-14146242 None:intergenic 35.0%
TCTTCTCTTAGAAGGAGAAA+GGG - chr5.1:14146498-14146517 MS.gene64839:CDS 35.0%
TGGATCTTCATCAAAGTCAA+AGG - chr5.1:14146743-14146762 MS.gene64839:CDS 35.0%
TGTTCAATTCTTGTGGAGTT+TGG + chr5.1:14146216-14146235 None:intergenic 35.0%
TTGATCTTGATCCAAAAGTG+AGG + chr5.1:14146640-14146659 None:intergenic 35.0%
! ACATGAAAGATTTGAGGCTT+TGG - chr5.1:14146899-14146918 MS.gene64839:CDS 35.0%
!! GACAAAGTTGATGCAAAAGA+GGG - chr5.1:14146785-14146804 MS.gene64839:CDS 35.0%
!! TCAGTTTTGTCTTTCTTGGT+TGG - chr5.1:14146723-14146742 MS.gene64839:CDS 35.0%
!! TGACAAAGTTGATGCAAAAG+AGG - chr5.1:14146784-14146803 MS.gene64839:CDS 35.0%
!!! GTGAAAGTTTTGGATATCTG+TGG - chr5.1:14146423-14146442 MS.gene64839:CDS 35.0%
AGCTATGCAAAATCCAGACA+TGG - chr5.1:14146238-14146257 MS.gene64839:CDS 40.0%
ATCAGATGTGGATGTTGATG+TGG + chr5.1:14146268-14146287 None:intergenic 40.0%
CACTTCACTCTTCTCTTAGA+AGG - chr5.1:14146490-14146509 MS.gene64839:CDS 40.0%
CCACAAATTTCTCACCTTGA+TGG + chr5.1:14146383-14146402 None:intergenic 40.0%
CCATCAAGGTGAGAAATTTG+TGG - chr5.1:14146380-14146399 MS.gene64839:CDS 40.0%
CGTTGCACATGAAAGATTTG+AGG - chr5.1:14146893-14146912 MS.gene64839:CDS 40.0%
CTCTTCTCTTAGAAGGAGAA+AGG - chr5.1:14146497-14146516 MS.gene64839:CDS 40.0%
GAAAACTGTTTGAGCGAACA+TGG + chr5.1:14146179-14146198 None:intergenic 40.0%
GAACTGTAATCACTGCAACA+AGG + chr5.1:14146665-14146684 None:intergenic 40.0%
GAGTTTGGATGTGATTGAGA+TGG + chr5.1:14146201-14146220 None:intergenic 40.0%
GCTATGCAAAATCCAGACAT+GGG - chr5.1:14146239-14146258 MS.gene64839:CDS 40.0%
GGTATCATGTGAAGAGAACA+TGG - chr5.1:14146806-14146825 MS.gene64839:CDS 40.0%
TTTGTGGAAGAGATGTTGGA+TGG - chr5.1:14146396-14146415 MS.gene64839:CDS 40.0%
! GGATGGTTCAGTGAAAGTTT+TGG - chr5.1:14146413-14146432 MS.gene64839:CDS 40.0%
!! ATTTGGAGCTTCCTCACTTT+TGG - chr5.1:14146626-14146645 MS.gene64839:CDS 40.0%
CTTCAATGAACTGCAGTGTG+TGG - chr5.1:14146833-14146852 MS.gene64839:CDS 45.0%
GGATATCTGTGGCATCACAA+GGG - chr5.1:14146434-14146453 MS.gene64839:CDS 45.0%
TGGATATCTGTGGCATCACA+AGG - chr5.1:14146433-14146452 MS.gene64839:CDS 45.0%
!! ACGGCTATTTCTCACCATCA+AGG - chr5.1:14146366-14146385 MS.gene64839:CDS 45.0%
TTCAAGAAAGGAGAGGCCAG+TGG + chr5.1:14146298-14146317 None:intergenic 50.0%
TTGATGTGGCTTCCCATGTC+TGG + chr5.1:14146254-14146273 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14146159 14147019 14146159 ID=MS.gene64839
chr5.1 mRNA 14146159 14147019 14146159 ID=MS.gene64839.t1;Parent=MS.gene64839
chr5.1 exon 14146159 14147019 14146159 ID=MS.gene64839.t1.exon1;Parent=MS.gene64839.t1
chr5.1 CDS 14146159 14147019 14146159 ID=cds.MS.gene64839.t1;Parent=MS.gene64839.t1
Gene Sequence

>MS.gene64839

ATGGCAAGCAACAAGTACCATGTTCGCTCAAACAGTTTTCCATCTCAATCACATCCAAACTCCACAAGAATTGAACAAGAGCTATGCAAAATCCAGACATGGGAAGCCACATCAACATCCACATCTGATTCAATTACCACTGGCCTCTCCTTTCTTGAAGATTTGTATATTTCTTTGGAAGATCTTCTCAATATGTCATCAACACAAACGGCTATTTCTCACCATCAAGGTGAGAAATTTGTGGAAGAGATGTTGGATGGTTCAGTGAAAGTTTTGGATATCTGTGGCATCACAAGGGATACCATGTTACAAATTAAAGAAAATGTTCAATCACTTCACTCTTCTCTTAGAAGGAGAAAGGGAGATTCAAGCATTGAAAAAAGTGTAGCCGAATATAAATTCTTCACAAAGAAGATGAAGAAAAATGTCACAAAGTTGATCACATCTTTAAAACATATGGAAAGTAAATTTGGAGCTTCCTCACTTTTGGATCAAGATCAAGACCTTGTTGCAGTGATTACAGTTCTTAGAGAGGTCATTAAAATGAACTTGTCTATCTTTCAATCAGTTTTGTCTTTCTTGGTTGGATCTTCATCAAAGTCAAAGGCAACAAAATGGTTGAAAGTGACAAAGTTGATGCAAAAGAGGGTATCATGTGAAGAGAACATGGAGAACTTCAATGAACTGCAGTGTGTGGAAGCATCTTTAAGAACCCTTATAAGTGAAGGTTCTAACGTTGCACATGAAAGATTTGAGGCTTTGGAGAATGCAATTGAAAGTATAGAAAATGGTTTAGAGAATATATTTAGGTGTTTGGTTAAAACTAGAGTCTGTCTTTTGAACATCATGACTCTATCTTAG
Protein sequence

>MS.gene64839.t1

MASNKYHVRSNSFPSQSHPNSTRIEQELCKIQTWEATSTSTSDSITTGLSFLEDLYISLEDLLNMSSTQTAISHHQGEKFVEEMLDGSVKVLDICGITRDTMLQIKENVQSLHSSLRRRKGDSSIEKSVAEYKFFTKKMKKNVTKLITSLKHMESKFGASSLLDQDQDLVAVITVLREVIKMNLSIFQSVLSFLVGSSSKSKATKWLKVTKLMQKRVSCEENMENFNELQCVEASLRTLISEGSNVAHERFEALENAIESIENGLENIFRCLVKTRVCLLNIMTLS