AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64848

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64848.t1 MTR_5g023350 92.308 286 21 1 1 285 1 286 0.0 514
MS.gene64848.t1 MTR_5g023340 91.608 286 23 1 1 285 1 286 0.0 511
MS.gene64848.t1 MTR_5g023550 90.106 283 28 0 1 283 1 283 0.0 503
MS.gene64848.t1 MTR_5g023530 89.789 284 28 1 3 285 4 287 0.0 501
MS.gene64848.t1 MTR_5g023390 89.161 286 30 1 1 285 1 286 0.0 500
MS.gene64848.t1 MTR_5g023370 89.510 286 29 1 1 285 1 286 0.0 499
MS.gene64848.t1 MTR_5g023520 88.732 284 31 1 1 283 1 284 5.31e-180 497
MS.gene64848.t1 MTR_5g023600 89.510 286 29 1 1 285 1 286 5.81e-180 497
MS.gene64848.t1 MTR_5g023470 89.085 284 30 1 3 285 4 287 1.73e-179 496
MS.gene64848.t1 MTR_5g023320 86.316 285 34 3 1 283 1 282 6.83e-173 479
MS.gene64848.t1 MTR_5g023580 83.217 286 43 3 1 281 1 286 3.11e-161 452
MS.gene64848.t1 MTR_8g074450 69.204 289 83 2 1 283 1 289 2.18e-140 397
MS.gene64848.t1 MTR_8g074510 66.782 289 88 3 1 283 1 287 2.80e-136 387
MS.gene64848.t1 MTR_8g074420 67.474 289 88 2 1 283 1 289 4.33e-132 376
MS.gene64848.t1 MTR_5g023460 85.405 185 23 1 99 283 11 191 9.36e-112 321
MS.gene64848.t1 MTR_8g074530 43.945 289 154 5 2 283 17 304 1.44e-68 215
MS.gene64848.t1 MTR_5g023290 37.333 300 170 5 2 283 9 308 1.30e-58 189
MS.gene64848.t1 MTR_5g023410 92.929 99 7 0 1 99 1 99 7.93e-55 177
MS.gene64848.t1 MTR_8g074380 36.934 287 155 6 7 284 14 283 4.93e-49 166
MS.gene64848.t1 MTR_5g023650 35.959 292 171 4 7 283 14 304 6.60e-49 164
MS.gene64848.t1 MTR_4g070530 34.266 286 183 3 1 281 8 293 1.35e-46 158
MS.gene64848.t1 MTR_3g116950 36.897 290 168 8 3 282 10 294 1.27e-44 153
MS.gene64848.t1 MTR_4g070540 34.737 285 179 4 3 281 10 293 7.39e-44 151
MS.gene64848.t1 MTR_4g070570 32.765 293 180 8 3 282 13 301 5.07e-42 146
MS.gene64848.t1 MTR_4g070590 34.948 289 173 8 6 282 14 299 6.45e-40 141
MS.gene64848.t1 MTR_3g116920 35.154 293 171 9 3 282 10 296 9.75e-39 138
MS.gene64848.t1 MTR_1g037820 31.624 234 142 5 51 283 9 225 7.95e-27 105
MS.gene64848.t1 MTR_3g115150 29.703 303 179 10 5 285 27 317 3.87e-26 105
MS.gene64848.t1 MTR_5g023540 50.000 68 31 1 162 229 1 65 4.62e-15 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64848.t1 AT4G35690 37.370 289 166 6 1 283 4 283 4.86e-57 185
MS.gene64848.t1 AT2G17680 36.877 301 159 10 1 283 4 291 6.22e-48 161
MS.gene64848.t1 AT2G17080 37.456 283 154 7 1 282 1 261 1.49e-47 160
MS.gene64848.t1 AT2G17070 37.367 281 153 7 1 280 1 259 3.37e-45 154
MS.gene64848.t1 AT4G35200 35.816 282 151 8 1 281 1 253 1.24e-44 152
MS.gene64848.t1 AT4G35710 35.714 294 163 7 1 283 4 282 5.52e-43 148
MS.gene64848.t1 AT4G35210 34.397 282 152 8 1 281 1 250 4.61e-41 142
MS.gene64848.t1 AT4G35720 32.698 315 172 9 5 283 14 324 1.24e-27 109
MS.gene64848.t1 AT4G35680 31.667 300 174 9 7 283 18 309 2.68e-27 108
MS.gene64848.t1 AT4G35660 31.667 300 160 10 6 284 13 288 8.78e-27 106
MS.gene64848.t1 AT1G76240 29.452 292 180 9 5 283 29 307 1.02e-24 101
MS.gene64848.t1 AT3G51400 31.650 297 168 10 1 284 1 275 3.07e-24 99.4
MS.gene64848.t1 AT1G76210 28.959 221 132 7 67 283 26 225 1.42e-17 80.1
MS.gene64848.t1 AT3G51410 30.357 280 153 9 7 283 39 279 1.94e-14 72.4
MS.gene64848.t1 AT1G20520 26.939 245 144 7 47 283 8 225 1.11e-13 69.3
MS.gene64848.t1 AT1G76220 27.365 296 157 10 2 284 6 256 1.55e-11 63.5

Find 49 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATATCATGACTCTATCTT+AGG 0.152475 5.1:+14221956 MS.gene64848:CDS
AAACATATGGAAACTAAATT+TGG 0.157953 5.1:+14221567 MS.gene64848:CDS
CATTAGAACCTTCATTTATA+AGG 0.192529 5.1:-14221830 None:intergenic
GGATGGTTCAGTCAAAATTT+TGG 0.207335 5.1:+14221371 MS.gene64848:CDS
GCAATTGAAAGTATAGAAAA+TGG 0.264764 5.1:+14221885 MS.gene64848:CDS
CCACAAATTTCTCACCTTGA+TGG 0.264918 5.1:-14221338 None:intergenic
CTTTGTGAAGAATTTATATT+CGG 0.312307 5.1:-14221505 None:intergenic
AGAGAATATATTTAGGCGTT+TGG 0.352912 5.1:+14221911 MS.gene64848:CDS
GAAATTTGTGGAAGAGTTGT+TGG 0.365610 5.1:+14221350 MS.gene64848:CDS
ATTAGAACCTTCATTTATAA+GGG 0.372347 5.1:-14221829 None:intergenic
CTCACCTTGATGGTGAGAAA+TGG 0.372930 5.1:-14221328 None:intergenic
GATCACATCTTTAAAACATA+TGG 0.374642 5.1:+14221554 MS.gene64848:CDS
TTGTTCTATTCTTGTGGAGT+TGG 0.376848 5.1:-14221172 None:intergenic
TGTTCTATTCTTGTGGAGTT+GGG 0.378838 5.1:-14221171 None:intergenic
TGAAGATTTGTATATTTCAT+TGG 0.381582 5.1:+14221272 MS.gene64848:CDS
CCCTTCACTCTGCTCTTAGA+AGG 0.394926 5.1:+14221448 MS.gene64848:CDS
CAAAGTCAAAGGCAACAAAA+TGG 0.408302 5.1:+14221712 MS.gene64848:CDS
ACATGAAAGATTTGAGGCTT+TGG 0.411831 5.1:+14221857 MS.gene64848:CDS
TTAAGAACCCTTATAAATGA+AGG 0.417998 5.1:+14221822 MS.gene64848:CDS
TAGCTCTTGTTCTATTCTTG+TGG 0.426456 5.1:-14221178 None:intergenic
AATATCATGACTCTATCTTA+GGG 0.426644 5.1:+14221957 MS.gene64848:CDS
ATGGTTTAGAGAATATATTT+AGG 0.442461 5.1:+14221904 MS.gene64848:CDS
TGTTGCACATGAAAGATTTG+AGG 0.445316 5.1:+14221851 MS.gene64848:CDS
CCATCAAGGTGAGAAATTTG+TGG 0.460090 5.1:+14221338 MS.gene64848:CDS
CTCTGCTCTTAGAAGGAGAA+AGG 0.467785 5.1:+14221455 MS.gene64848:CDS
TGACAAAGTTGATGCAAAAG+AGG 0.510512 5.1:+14221742 MS.gene64848:CDS
AATATACAAATCTTCAAGAA+AGG 0.521593 5.1:-14221265 None:intergenic
TCCTTCTAAGAGCAGAGTGA+AGG 0.531554 5.1:-14221449 None:intergenic
TGGATATCTGTGGCATCACA+AGG 0.539961 5.1:+14221391 MS.gene64848:CDS
AGCTAACTAAAATGAAGACA+TGG 0.559596 5.1:+14221196 MS.gene64848:CDS
TCTGCTCTTAGAAGGAGAAA+GGG 0.566127 5.1:+14221456 MS.gene64848:CDS
TCATCTGATTCAATTACCAC+TGG 0.572076 5.1:+14221237 MS.gene64848:CDS
CCTTCTAAGAGCAGAGTGAA+GGG 0.572703 5.1:-14221448 None:intergenic
GAAAACTATTTGAGCGAACA+TGG 0.573814 5.1:-14221134 None:intergenic
TTAAAGATGCTTCCACACAC+TGG 0.576028 5.1:-14221803 None:intergenic
TGGATCTTCATCAAAGTCAA+AGG 0.588491 5.1:+14221701 MS.gene64848:CDS
GACAAAGTTGATGCAAAAGA+GGG 0.591207 5.1:+14221743 MS.gene64848:CDS
CTTCAATGAATTCCAGTGTG+TGG 0.596892 5.1:+14221791 MS.gene64848:CDS
AAAGCCATTTCTCACCATCA+AGG 0.600487 5.1:+14221324 MS.gene64848:CDS
ACAAATCTTCAAGAAAGGAA+AGG 0.601275 5.1:-14221260 None:intergenic
TTTGTGGAAGAGTTGTTGGA+TGG 0.615570 5.1:+14221354 MS.gene64848:CDS
GCTAACTAAAATGAAGACAT+GGG 0.621213 5.1:+14221197 MS.gene64848:CDS
AGTGATTACAGTTCTTAGAG+AGG 0.623623 5.1:+14221629 MS.gene64848:CDS
GGATATCTGTGGCATCACAA+GGG 0.651501 5.1:+14221392 MS.gene64848:CDS
ATCAGATGAGGATGTTGATG+TGG 0.655798 5.1:-14221223 None:intergenic
GAACTGTAATCACTGCAACA+AGG 0.656672 5.1:-14221620 None:intergenic
TTCAAGAAAGGAAAGGCCAG+TGG 0.658882 5.1:-14221253 None:intergenic
AGTGGTAATTGAATCAGATG+AGG 0.670222 5.1:-14221235 None:intergenic
GAGTTGGGATGTGATTGAGA+AGG 0.736915 5.1:-14221156 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAACTAAATT+TGG + chr5.1:14221567-14221586 MS.gene64848:CDS 20.0%
!! AATATACAAATCTTCAAGAA+AGG - chr5.1:14221268-14221287 None:intergenic 20.0%
!! ATGGTTTAGAGAATATATTT+AGG + chr5.1:14221904-14221923 MS.gene64848:CDS 20.0%
!! ATTAGAACCTTCATTTATAA+GGG - chr5.1:14221832-14221851 None:intergenic 20.0%
!! CTTTGTGAAGAATTTATATT+CGG - chr5.1:14221508-14221527 None:intergenic 20.0%
!! TGAAGATTTGTATATTTCAT+TGG + chr5.1:14221272-14221291 MS.gene64848:CDS 20.0%
! CATTAGAACCTTCATTTATA+AGG - chr5.1:14221833-14221852 None:intergenic 25.0%
! TTAAGAACCCTTATAAATGA+AGG + chr5.1:14221822-14221841 MS.gene64848:CDS 25.0%
!! GCAATTGAAAGTATAGAAAA+TGG + chr5.1:14221885-14221904 MS.gene64848:CDS 25.0%
!!! GATCACATCTTTAAAACATA+TGG + chr5.1:14221554-14221573 MS.gene64848:CDS 25.0%
ACAAATCTTCAAGAAAGGAA+AGG - chr5.1:14221263-14221282 None:intergenic 30.0%
AGAGAATATATTTAGGCGTT+TGG + chr5.1:14221911-14221930 MS.gene64848:CDS 30.0%
AGCTAACTAAAATGAAGACA+TGG + chr5.1:14221196-14221215 MS.gene64848:CDS 30.0%
GCTAACTAAAATGAAGACAT+GGG + chr5.1:14221197-14221216 MS.gene64848:CDS 30.0%
! GTCAAAATTTTGGATATCTG+TGG + chr5.1:14221381-14221400 MS.gene64848:CDS 30.0%
! TCAATCTGTTTTGTCTTTCT+TGG + chr5.1:14221677-14221696 MS.gene64848:CDS 30.0%
AGTGATTACAGTTCTTAGAG+AGG + chr5.1:14221629-14221648 MS.gene64848:CDS 35.0%
AGTGGTAATTGAATCAGATG+AGG - chr5.1:14221238-14221257 None:intergenic 35.0%
CAAAGTCAAAGGCAACAAAA+TGG + chr5.1:14221712-14221731 MS.gene64848:CDS 35.0%
GAAAACTATTTGAGCGAACA+TGG - chr5.1:14221137-14221156 None:intergenic 35.0%
GAAATTTGTGGAAGAGTTGT+TGG + chr5.1:14221350-14221369 MS.gene64848:CDS 35.0%
TAGCTCTTGTTCTATTCTTG+TGG - chr5.1:14221181-14221200 None:intergenic 35.0%
TCATCTGATTCAATTACCAC+TGG + chr5.1:14221237-14221256 MS.gene64848:CDS 35.0%
TGGATCTTCATCAAAGTCAA+AGG + chr5.1:14221701-14221720 MS.gene64848:CDS 35.0%
TGTTCTATTCTTGTGGAGTT+GGG - chr5.1:14221174-14221193 None:intergenic 35.0%
TGTTGCACATGAAAGATTTG+AGG + chr5.1:14221851-14221870 MS.gene64848:CDS 35.0%
TTGTTCTATTCTTGTGGAGT+TGG - chr5.1:14221175-14221194 None:intergenic 35.0%
! ACATGAAAGATTTGAGGCTT+TGG + chr5.1:14221857-14221876 MS.gene64848:CDS 35.0%
! GGATGGTTCAGTCAAAATTT+TGG + chr5.1:14221371-14221390 MS.gene64848:CDS 35.0%
! TCTGTTTTGTCTTTCTTGGT+TGG + chr5.1:14221681-14221700 MS.gene64848:CDS 35.0%
!! GACAAAGTTGATGCAAAAGA+GGG + chr5.1:14221743-14221762 MS.gene64848:CDS 35.0%
!! TGACAAAGTTGATGCAAAAG+AGG + chr5.1:14221742-14221761 MS.gene64848:CDS 35.0%
AAAGCCATTTCTCACCATCA+AGG + chr5.1:14221324-14221343 MS.gene64848:CDS 40.0%
ATCAGATGAGGATGTTGATG+TGG - chr5.1:14221226-14221245 None:intergenic 40.0%
CCACAAATTTCTCACCTTGA+TGG - chr5.1:14221341-14221360 None:intergenic 40.0%
CCATCAAGGTGAGAAATTTG+TGG + chr5.1:14221338-14221357 MS.gene64848:CDS 40.0%
CTTCAATGAATTCCAGTGTG+TGG + chr5.1:14221791-14221810 MS.gene64848:CDS 40.0%
GAACTGTAATCACTGCAACA+AGG - chr5.1:14221623-14221642 None:intergenic 40.0%
TCTGCTCTTAGAAGGAGAAA+GGG + chr5.1:14221456-14221475 MS.gene64848:CDS 40.0%
TTAAAGATGCTTCCACACAC+TGG - chr5.1:14221806-14221825 None:intergenic 40.0%
TTTGTGGAAGAGTTGTTGGA+TGG + chr5.1:14221354-14221373 MS.gene64848:CDS 40.0%
CTCTGCTCTTAGAAGGAGAA+AGG + chr5.1:14221455-14221474 MS.gene64848:CDS 45.0%
GAGTTGGGATGTGATTGAGA+AGG - chr5.1:14221159-14221178 None:intergenic 45.0%
GGATATCTGTGGCATCACAA+GGG + chr5.1:14221392-14221411 MS.gene64848:CDS 45.0%
TGGATATCTGTGGCATCACA+AGG + chr5.1:14221391-14221410 MS.gene64848:CDS 45.0%
TTCAAGAAAGGAAAGGCCAG+TGG - chr5.1:14221256-14221275 None:intergenic 45.0%
! CCTTCTAAGAGCAGAGTGAA+GGG - chr5.1:14221451-14221470 None:intergenic 45.0%
! TCCTTCTAAGAGCAGAGTGA+AGG - chr5.1:14221452-14221471 None:intergenic 45.0%
!! CTCACCTTGATGGTGAGAAA+TGG - chr5.1:14221331-14221350 None:intergenic 45.0%
CCCTTCACTCTGCTCTTAGA+AGG + chr5.1:14221448-14221467 MS.gene64848:CDS 50.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14221120 14221977 14221120 ID=MS.gene64848
chr5.1 mRNA 14221120 14221977 14221120 ID=MS.gene64848.t1;Parent=MS.gene64848
chr5.1 exon 14221120 14221977 14221120 ID=MS.gene64848.t1.exon1;Parent=MS.gene64848.t1
chr5.1 CDS 14221120 14221977 14221120 ID=cds.MS.gene64848.t1;Parent=MS.gene64848.t1
Gene Sequence

>MS.gene64848

ATGGCAAGCAAATACCATGTTCGCTCAAATAGTTTTCCTTCTCAATCACATCCCAACTCCACAAGAATAGAACAAGAGCTAACTAAAATGAAGACATGGGAAGCCACATCAACATCCTCATCTGATTCAATTACCACTGGCCTTTCCTTTCTTGAAGATTTGTATATTTCATTGGAAGATCTTCTCAATCTGAAATCAACACAAAAAGCCATTTCTCACCATCAAGGTGAGAAATTTGTGGAAGAGTTGTTGGATGGTTCAGTCAAAATTTTGGATATCTGTGGCATCACAAGGGACATCATTTTACAAATTAAAGAAAATGTTCAATCCCTTCACTCTGCTCTTAGAAGGAGAAAGGGAGAATCAAGCATTGAAACAAGTGTAGCCGAATATAAATTCTTCACAAAGAAGATGAAGAAGAATGTCACAAAGTTGATCACATCTTTAAAACATATGGAAACTAAATTTGGAGCTTCTTCACTTTTGAATCAAGATCAAGACCTTGTTGCAGTGATTACAGTTCTTAGAGAGGTCATTGCAATGAACTTGTCTGTCTTTCAATCTGTTTTGTCTTTCTTGGTTGGATCTTCATCAAAGTCAAAGGCAACAAAATGGTTGAAAGTGACAAAGTTGATGCAAAAGAGGGTAACATGTGAAGAGAACATGAAGAACTTCAATGAATTCCAGTGTGTGGAAGCATCTTTAAGAACCCTTATAAATGAAGGTTCTAATGTTGCACATGAAAGATTTGAGGCTTTGGAGAATGCAATTGAAAGTATAGAAAATGGTTTAGAGAATATATTTAGGCGTTTGGTTAAAACTAGAGTCTGTCTTTTGAATATCATGACTCTATCTTAG
Protein sequence

>MS.gene64848.t1

MASKYHVRSNSFPSQSHPNSTRIEQELTKMKTWEATSTSSSDSITTGLSFLEDLYISLEDLLNLKSTQKAISHHQGEKFVEELLDGSVKILDICGITRDIILQIKENVQSLHSALRRRKGESSIETSVAEYKFFTKKMKKNVTKLITSLKHMETKFGASSLLNQDQDLVAVITVLREVIAMNLSVFQSVLSFLVGSSSKSKATKWLKVTKLMQKRVTCEENMKNFNEFQCVEASLRTLINEGSNVAHERFEALENAIESIENGLENIFRRLVKTRVCLLNIMTLS