AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene012169

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene012169.t1 MTR_8g074510 94.444 288 16 0 1 288 1 288 0.0 547
MS.gene012169.t1 MTR_8g074450 86.207 290 38 1 1 288 1 290 0.0 501
MS.gene012169.t1 MTR_8g074420 82.759 290 48 1 1 288 1 290 2.07e-165 460
MS.gene012169.t1 MTR_5g023550 65.744 289 91 3 1 287 1 283 1.07e-126 362
MS.gene012169.t1 MTR_5g023370 66.316 285 88 3 5 287 6 284 1.04e-125 360
MS.gene012169.t1 MTR_5g023600 66.434 286 88 3 4 287 5 284 1.62e-125 359
MS.gene012169.t1 MTR_5g023390 65.965 285 89 3 5 287 6 284 1.83e-125 359
MS.gene012169.t1 MTR_5g023520 64.138 290 97 2 1 288 1 285 1.97e-125 359
MS.gene012169.t1 MTR_5g023320 66.551 287 84 5 5 288 6 283 2.11e-124 356
MS.gene012169.t1 MTR_5g023340 65.614 285 90 3 5 287 6 284 4.32e-124 356
MS.gene012169.t1 MTR_5g023350 65.385 286 91 3 4 287 5 284 1.60e-123 354
MS.gene012169.t1 MTR_5g023530 64.111 287 94 4 4 287 5 285 3.02e-121 348
MS.gene012169.t1 MTR_5g023470 63.066 287 97 4 4 287 5 285 4.42e-119 343
MS.gene012169.t1 MTR_5g023580 63.604 283 99 2 5 285 6 286 1.94e-115 337
MS.gene012169.t1 MTR_8g074530 46.528 288 148 4 4 287 19 304 9.21e-75 231
MS.gene012169.t1 MTR_5g023460 62.500 192 62 3 97 288 11 192 1.28e-73 224
MS.gene012169.t1 MTR_5g023290 39.933 298 165 4 4 287 11 308 1.83e-63 202
MS.gene012169.t1 MTR_5g023650 33.788 293 180 4 7 287 14 304 5.16e-44 152
MS.gene012169.t1 MTR_4g070530 34.266 286 181 4 6 287 13 295 7.10e-44 151
MS.gene012169.t1 MTR_8g074380 32.302 291 163 6 7 286 14 281 1.82e-40 143
MS.gene012169.t1 MTR_5g023410 67.000 100 31 1 1 98 1 100 1.30e-39 137
MS.gene012169.t1 MTR_4g070540 32.292 288 186 5 6 288 13 296 4.94e-37 133
MS.gene012169.t1 MTR_4g070570 28.374 289 200 3 5 287 15 302 2.17e-36 132
MS.gene012169.t1 MTR_4g070590 33.106 293 179 7 6 287 14 300 1.55e-35 129
MS.gene012169.t1 MTR_3g116920 32.526 289 186 7 5 287 12 297 7.56e-35 127
MS.gene012169.t1 MTR_3g116950 33.562 292 177 9 5 287 12 295 5.56e-34 125
MS.gene012169.t1 MTR_3g115150 27.273 308 184 9 3 287 25 315 2.53e-26 105
MS.gene012169.t1 MTR_1g037820 30.290 241 142 5 49 287 9 225 2.60e-26 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene012169.t1 AT4G35690 35.906 298 162 6 1 287 4 283 3.14e-54 177
MS.gene012169.t1 AT2G17680 38.111 307 153 7 1 288 4 292 1.55e-50 168
MS.gene012169.t1 AT4G35710 36.860 293 165 7 1 287 4 282 1.14e-45 155
MS.gene012169.t1 AT2G17080 37.847 288 150 8 1 286 1 261 7.57e-43 147
MS.gene012169.t1 AT4G35200 37.544 285 146 11 1 285 1 253 6.38e-40 140
MS.gene012169.t1 AT2G17070 37.413 286 150 9 1 284 1 259 1.02e-38 137
MS.gene012169.t1 AT4G35210 35.088 285 150 9 1 285 1 250 1.24e-35 129
MS.gene012169.t1 AT4G35660 32.180 289 171 8 7 287 16 287 2.10e-28 110
MS.gene012169.t1 AT4G35720 31.746 315 179 10 5 287 14 324 9.72e-25 101
MS.gene012169.t1 AT1G76240 27.551 294 193 6 3 288 27 308 8.55e-21 90.5
MS.gene012169.t1 AT3G51400 30.717 293 178 10 1 287 1 274 5.34e-19 85.1
MS.gene012169.t1 AT4G35680 29.568 301 183 10 7 287 18 309 1.69e-18 84.3
MS.gene012169.t1 AT3G51410 30.142 282 155 6 7 287 39 279 9.74e-17 79.0
MS.gene012169.t1 AT1G76210 26.754 228 138 5 63 287 24 225 5.78e-16 75.5

Find 42 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTAGTACCTTCACTTAAA+AGG 0.153684 8.4:+30266345 None:intergenic
GGATAGTTCAATGAGAATTT+TGG 0.221029 8.4:-30266807 MS.gene012169:CDS
AATATATAAATCATCTATTA+AGG 0.302191 8.4:+30266913 None:intergenic
CAATGCATTTCTCACCTCTA+TGG 0.309012 8.4:+30266840 None:intergenic
AATTTGCATGTCTTCAACTT+TGG 0.327447 8.4:-30266594 MS.gene012169:CDS
AAGCCCTTCACTCTTGTCTA+AGG 0.365459 8.4:-30266733 MS.gene012169:CDS
AGATGATTTATATATTTCAT+TGG 0.368321 8.4:-30266906 MS.gene012169:CDS
TGAAAGTATTGAGAATGGTT+TGG 0.376420 8.4:-30266270 MS.gene012169:CDS
ATGGTTTGGAGAACTTATTT+AGG 0.391036 8.4:-30266256 MS.gene012169:CDS
ACACTCTAATCAAAGAATAA+AGG 0.396201 8.4:+30266558 None:intergenic
ACATGAAAGATTGGAGGCTT+TGG 0.416323 8.4:-30266303 MS.gene012169:CDS
ATTAGTACCTTCACTTAAAA+GGG 0.427283 8.4:+30266346 None:intergenic
GATCACATCTTTGAAGCAAA+TGG 0.443039 8.4:-30266624 MS.gene012169:CDS
TGGATATTTGTGGCATCACT+AGG 0.456088 8.4:-30266787 MS.gene012169:CDS
GCAATTGAAAGTATTGAGAA+TGG 0.456284 8.4:-30266275 MS.gene012169:CDS
TCTTCTACTCTAATTGTGCT+AGG 0.472883 8.4:+30267001 None:intergenic
ATGGTGAGAAATCACTTGTT+GGG 0.479630 8.4:+30266859 None:intergenic
GCAGGCTGCACATGAAAGAT+TGG 0.481060 8.4:-30266312 MS.gene012169:CDS
TATGGTGAGAAATCACTTGT+TGG 0.484011 8.4:+30266858 None:intergenic
TAAGGAAAGACCACTATGAA+TGG 0.495456 8.4:+30266931 None:intergenic
GGATACAATTCTTCAAATCA+AGG 0.500801 8.4:-30266765 MS.gene012169:CDS
TCTTGTCTAAGGAGAAGAAA+AGG 0.505857 8.4:-30266722 MS.gene012169:CDS
GTGCTAGGATGAGATCTAGA+AGG 0.513144 8.4:+30267016 None:intergenic
TAGCACAATTAGAGTAGAAG+AGG 0.522386 8.4:-30266999 MS.gene012169:CDS
TTCTCCTTAGACAAGAGTGA+AGG 0.531189 8.4:+30266729 None:intergenic
GAAATGCATTGAAGAGGTGT+TGG 0.557821 8.4:-30266828 MS.gene012169:CDS
GGCTGCACATGAAAGATTGG+AGG 0.562732 8.4:-30266309 MS.gene012169:CDS
TCTCCTTAGACAAGAGTGAA+GGG 0.564139 8.4:+30266730 None:intergenic
TTTAGCAACAAATTTCCGCT+TGG 0.567854 8.4:+30266451 None:intergenic
GGATATTTGTGGCATCACTA+GGG 0.577026 8.4:-30266786 MS.gene012169:CDS
AACAAGCTCAAGACATGGGA+AGG 0.580057 8.4:-30266971 MS.gene012169:CDS
AGGTGAGAAATGCATTGAAG+AGG 0.582191 8.4:-30266834 MS.gene012169:CDS
TACTAATGGAGAAAACATGC+AGG 0.606065 8.4:-30266330 MS.gene012169:CDS
ATTGGATGATCTTCTCAACA+TGG 0.611714 8.4:-30266888 MS.gene012169:CDS
AATTGAACAAGCTCAAGACA+TGG 0.618716 8.4:-30266976 MS.gene012169:CDS
ACATCATGTTCCATTCATAG+TGG 0.619690 8.4:-30266941 MS.gene012169:CDS
CAAGTGATTTCTCACCATAG+AGG 0.629127 8.4:-30266854 MS.gene012169:CDS
ATTGAACAAGCTCAAGACAT+GGG 0.630590 8.4:-30266975 MS.gene012169:CDS
GTTGCTAAAATGATGCACAA+AGG 0.639952 8.4:-30266437 MS.gene012169:CDS
TTCAAGTGTTGAAAGAAGTG+TGG 0.668403 8.4:-30266696 MS.gene012169:CDS
AACATGATATTTGATTGCCA+TGG 0.672115 8.4:+30267054 None:intergenic
CAAAGTCAAAGACAACCAAG+CGG 0.727642 8.4:-30266466 MS.gene012169:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATAAATCATCTATTA+AGG + chr8.4:30266350-30266369 None:intergenic 10.0%
!! AGATGATTTATATATTTCAT+TGG - chr8.4:30266354-30266373 MS.gene012169:CDS 15.0%
! ACACTCTAATCAAAGAATAA+AGG + chr8.4:30266705-30266724 None:intergenic 25.0%
! ATTAGTACCTTCACTTAAAA+GGG + chr8.4:30266917-30266936 None:intergenic 25.0%
!! ATGAGAATTTTGGATATTTG+TGG - chr8.4:30266463-30266482 MS.gene012169:CDS 25.0%
AATTTGCATGTCTTCAACTT+TGG - chr8.4:30266666-30266685 MS.gene012169:CDS 30.0%
CATTAGTACCTTCACTTAAA+AGG + chr8.4:30266918-30266937 None:intergenic 30.0%
GGATACAATTCTTCAAATCA+AGG - chr8.4:30266495-30266514 MS.gene012169:CDS 30.0%
! ATGGTTTGGAGAACTTATTT+AGG - chr8.4:30267004-30267023 MS.gene012169:CDS 30.0%
! GGATAGTTCAATGAGAATTT+TGG - chr8.4:30266453-30266472 MS.gene012169:CDS 30.0%
!! GCAATTGAAAGTATTGAGAA+TGG - chr8.4:30266985-30267004 MS.gene012169:CDS 30.0%
!! TGAAAGTATTGAGAATGGTT+TGG - chr8.4:30266990-30267009 MS.gene012169:CDS 30.0%
!! TTAAACACCCTTTTAAGTGA+AGG - chr8.4:30266907-30266926 MS.gene012169:CDS 30.0%
!!! CTTTTAAGTGAAGGTACTAA+TGG - chr8.4:30266916-30266935 MS.gene012169:CDS 30.0%
AATTGAACAAGCTCAAGACA+TGG - chr8.4:30266284-30266303 MS.gene012169:CDS 35.0%
ACATCATGTTCCATTCATAG+TGG - chr8.4:30266319-30266338 MS.gene012169:CDS 35.0%
ATGGTGAGAAATCACTTGTT+GGG + chr8.4:30266404-30266423 None:intergenic 35.0%
ATTGAACAAGCTCAAGACAT+GGG - chr8.4:30266285-30266304 MS.gene012169:CDS 35.0%
ATTGGATGATCTTCTCAACA+TGG - chr8.4:30266372-30266391 MS.gene012169:CDS 35.0%
GTTGCTAAAATGATGCACAA+AGG - chr8.4:30266823-30266842 MS.gene012169:CDS 35.0%
TAAGGAAAGACCACTATGAA+TGG + chr8.4:30266332-30266351 None:intergenic 35.0%
TACTAATGGAGAAAACATGC+AGG - chr8.4:30266930-30266949 MS.gene012169:CDS 35.0%
TAGCACAATTAGAGTAGAAG+AGG - chr8.4:30266261-30266280 MS.gene012169:CDS 35.0%
TATGGTGAGAAATCACTTGT+TGG + chr8.4:30266405-30266424 None:intergenic 35.0%
TCTTCTACTCTAATTGTGCT+AGG + chr8.4:30266262-30266281 None:intergenic 35.0%
TCTTGTCTAAGGAGAAGAAA+AGG - chr8.4:30266538-30266557 MS.gene012169:CDS 35.0%
TTTAGCAACAAATTTCCGCT+TGG + chr8.4:30266812-30266831 None:intergenic 35.0%
!! GATCACATCTTTGAAGCAAA+TGG - chr8.4:30266636-30266655 MS.gene012169:CDS 35.0%
!! TTCAAGTGTTGAAAGAAGTG+TGG - chr8.4:30266564-30266583 MS.gene012169:CDS 35.0%
ACATGAAAGATTGGAGGCTT+TGG - chr8.4:30266957-30266976 MS.gene012169:CDS 40.0%
AGGTGAGAAATGCATTGAAG+AGG - chr8.4:30266426-30266445 MS.gene012169:CDS 40.0%
CAAAGTCAAAGACAACCAAG+CGG - chr8.4:30266794-30266813 MS.gene012169:CDS 40.0%
CAAGTGATTTCTCACCATAG+AGG - chr8.4:30266406-30266425 MS.gene012169:CDS 40.0%
CAATGCATTTCTCACCTCTA+TGG + chr8.4:30266423-30266442 None:intergenic 40.0%
GGATATTTGTGGCATCACTA+GGG - chr8.4:30266474-30266493 MS.gene012169:CDS 40.0%
TCTCCTTAGACAAGAGTGAA+GGG + chr8.4:30266533-30266552 None:intergenic 40.0%
TGGATATTTGTGGCATCACT+AGG - chr8.4:30266473-30266492 MS.gene012169:CDS 40.0%
TTCTCCTTAGACAAGAGTGA+AGG + chr8.4:30266534-30266553 None:intergenic 40.0%
! GAAATGCATTGAAGAGGTGT+TGG - chr8.4:30266432-30266451 MS.gene012169:CDS 40.0%
AACAAGCTCAAGACATGGGA+AGG - chr8.4:30266289-30266308 MS.gene012169:CDS 45.0%
AAGCCCTTCACTCTTGTCTA+AGG - chr8.4:30266527-30266546 MS.gene012169:CDS 45.0%
GTGCTAGGATGAGATCTAGA+AGG + chr8.4:30266247-30266266 None:intergenic 45.0%
GCAGGCTGCACATGAAAGAT+TGG - chr8.4:30266948-30266967 MS.gene012169:CDS 50.0%
GGCTGCACATGAAAGATTGG+AGG - chr8.4:30266951-30266970 MS.gene012169:CDS 50.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 30266208 30267074 30266208 ID=MS.gene012169
chr8.4 mRNA 30266208 30267074 30266208 ID=MS.gene012169.t1;Parent=MS.gene012169
chr8.4 exon 30266208 30267074 30266208 ID=MS.gene012169.t1.exon1;Parent=MS.gene012169.t1
chr8.4 CDS 30266208 30267074 30266208 ID=cds.MS.gene012169.t1;Parent=MS.gene012169.t1
Gene Sequence

>MS.gene012169

ATGGCAATCAAATATCATGTTCGTTCAATTAGTTTGCCTTCTAGATCTCATCCTAGCACAATTAGAGTAGAAGAGGAATTGAACAAGCTCAAGACATGGGAAGGAACATCTACATCATGTTCCATTCATAGTGGTCTTTCCTTAATAGATGATTTATATATTTCATTGGATGATCTTCTCAACATGGCATCAACCCAACAAGTGATTTCTCACCATAGAGGTGAGAAATGCATTGAAGAGGTGTTGGATAGTTCAATGAGAATTTTGGATATTTGTGGCATCACTAGGGATACAATTCTTCAAATCAAGGAAAATGTTCAAGCCCTTCACTCTTGTCTAAGGAGAAGAAAAGGTGATTCAAGTGTTGAAAGAAGTGTGGTAGAATACAAATTCTTCACAAAAAAGATGAAAAAAAATGTCAACAAGTTGATCACATCTTTGAAGCAAATGGATAGTAAAATTTGCATGTCTTCAACTTTGGAACTTGATCATCACCTTTATTCTTTGATTAGAGTGTTTAAAGAAGTCATTGCAATGAATTTGTCTATTTTTCAAATCATTTTGTCATTCTTGACTATGTCTTCATCAAAGTCAAAGACAACCAAGCGGAAATTTGTTGCTAAAATGATGCACAAAGGAGTCATAACATGTGAAGATAACTCAGATAATGTCAATGAGTTTTTGTGTGTTGAAACTACTTTAAACACCCTTTTAAGTGAAGGTACTAATGGAGAAAACATGCAGGCTGCACATGAAAGATTGGAGGCTTTGGAGAATGCAATTGAAAGTATTGAGAATGGTTTGGAGAACTTATTTAGGCGCTTGATTAAATCTAGAGCTTCTCTCTTGAATATAATTTCTCAATAG
Protein sequence

>MS.gene012169.t1

MAIKYHVRSISLPSRSHPSTIRVEEELNKLKTWEGTSTSCSIHSGLSLIDDLYISLDDLLNMASTQQVISHHRGEKCIEEVLDSSMRILDICGITRDTILQIKENVQALHSCLRRRKGDSSVERSVVEYKFFTKKMKKNVNKLITSLKQMDSKICMSSTLELDHHLYSLIRVFKEVIAMNLSIFQIILSFLTMSSSKSKTTKRKFVAKMMHKGVITCEDNSDNVNEFLCVETTLNTLLSEGTNGENMQAAHERLEALENAIESIENGLENLFRRLIKSRASLLNIISQ