AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64845

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64845.t1 MTR_5g023350 86.505 289 35 2 1 288 1 286 1.28e-174 484
MS.gene64845.t1 MTR_5g023600 86.505 289 35 2 1 288 1 286 6.90e-173 479
MS.gene64845.t1 MTR_5g023340 85.467 289 38 2 1 288 1 286 8.59e-173 479
MS.gene64845.t1 MTR_5g023550 83.916 286 43 1 1 286 1 283 5.03e-170 472
MS.gene64845.t1 MTR_5g023530 83.275 287 44 2 3 288 4 287 1.17e-168 469
MS.gene64845.t1 MTR_5g023520 83.275 287 44 2 1 286 1 284 3.01e-168 468
MS.gene64845.t1 MTR_5g023370 83.391 289 44 2 1 288 1 286 3.84e-168 467
MS.gene64845.t1 MTR_5g023390 82.699 289 46 2 1 288 1 286 7.91e-168 466
MS.gene64845.t1 MTR_5g023470 82.230 287 47 2 3 288 4 287 2.08e-166 463
MS.gene64845.t1 MTR_5g023320 83.681 288 39 4 1 286 1 282 7.24e-166 461
MS.gene64845.t1 MTR_5g023580 83.916 286 44 2 1 284 1 286 2.38e-163 458
MS.gene64845.t1 MTR_8g074450 69.204 289 86 2 1 286 1 289 3.31e-139 394
MS.gene64845.t1 MTR_8g074510 67.474 289 89 3 1 286 1 287 4.28e-136 386
MS.gene64845.t1 MTR_8g074420 67.820 289 90 2 1 286 1 289 8.59e-130 370
MS.gene64845.t1 MTR_5g023460 81.383 188 28 2 99 286 11 191 2.50e-104 302
MS.gene64845.t1 MTR_8g074530 44.828 290 153 5 2 286 17 304 4.19e-71 221
MS.gene64845.t1 MTR_5g023290 38.333 300 170 5 2 286 9 308 2.68e-61 196
MS.gene64845.t1 MTR_5g023410 88.000 100 12 0 1 100 1 100 3.22e-53 172
MS.gene64845.t1 MTR_8g074380 35.739 291 156 7 7 287 14 283 1.27e-44 154
MS.gene64845.t1 MTR_4g070530 32.292 288 193 2 1 286 8 295 1.83e-44 153
MS.gene64845.t1 MTR_5g023650 34.247 292 179 4 7 286 14 304 1.72e-43 150
MS.gene64845.t1 MTR_4g070570 31.757 296 182 9 3 285 13 301 1.25e-42 148
MS.gene64845.t1 MTR_4g070590 35.294 289 175 7 6 285 14 299 3.75e-42 147
MS.gene64845.t1 MTR_3g116950 35.495 293 171 9 3 285 10 294 7.70e-41 143
MS.gene64845.t1 MTR_4g070540 32.753 287 189 4 3 286 10 295 1.82e-39 140
MS.gene64845.t1 MTR_3g116920 33.673 294 177 10 3 285 10 296 1.07e-36 132
MS.gene64845.t1 MTR_1g037820 31.646 237 141 5 51 286 9 225 2.46e-25 100
MS.gene64845.t1 MTR_3g115150 28.053 303 187 9 5 288 27 317 8.00e-25 101
MS.gene64845.t1 MTR_5g023540 53.731 67 28 1 162 228 1 64 1.79e-14 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64845.t1 AT4G35690 36.986 292 166 6 1 286 4 283 9.22e-58 187
MS.gene64845.t1 AT2G17680 38.411 302 156 10 1 286 4 291 2.99e-48 162
MS.gene64845.t1 AT2G17080 36.014 286 157 6 1 285 1 261 2.76e-46 156
MS.gene64845.t1 AT4G35710 35.714 294 166 7 1 286 4 282 4.39e-45 154
MS.gene64845.t1 AT2G17070 36.620 284 154 6 1 283 1 259 3.83e-44 151
MS.gene64845.t1 AT4G35200 35.088 285 152 7 1 284 1 253 1.87e-43 149
MS.gene64845.t1 AT4G35210 33.333 285 154 7 1 284 1 250 2.62e-39 138
MS.gene64845.t1 AT4G35720 32.698 315 175 9 5 286 14 324 5.27e-28 110
MS.gene64845.t1 AT4G35680 31.104 299 180 7 7 286 18 309 7.76e-26 104
MS.gene64845.t1 AT4G35660 32.459 305 150 13 7 287 16 288 7.94e-26 103
MS.gene64845.t1 AT1G76240 29.110 292 184 7 5 286 29 307 4.50e-25 102
MS.gene64845.t1 AT3G51400 31.313 297 172 10 1 287 1 275 9.69e-21 89.7
MS.gene64845.t1 AT1G76210 27.273 242 155 6 46 286 4 225 1.92e-17 79.7
MS.gene64845.t1 AT3G51410 32.028 281 150 9 7 286 39 279 1.48e-16 78.2
MS.gene64845.t1 AT1G20520 25.403 248 147 7 47 286 8 225 8.05e-13 67.0

Find 50 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATTTGAACCTTCCCTTAAA+AGG 0.143471 5.1:-14188903 None:intergenic
AAACATATGGAAACTAAATT+TGG 0.157953 5.1:+14188640 MS.gene64845:CDS
GGATGGTTCAGTCAAAATTT+TGG 0.207335 5.1:+14188444 MS.gene64845:CDS
GCAATTGAAATGATAGAAAA+TGG 0.225171 5.1:+14188967 MS.gene64845:CDS
CCACAAATTTCTGACCTTGA+TGG 0.274053 5.1:-14188411 None:intergenic
TGTTCTATTCTTGTGGTGTT+AGG 0.282503 5.1:-14188244 None:intergenic
TGAAGATTTGTATATATCTT+TGG 0.284754 5.1:+14188345 MS.gene64845:CDS
CTTTGTGAAGAATTTATATT+CGG 0.312307 5.1:-14188578 None:intergenic
TCCAACCAAGAAAGACAAAA+TGG 0.347485 5.1:-14188755 None:intergenic
GGAGAGTTTATTTAGGAGAT+TGG 0.352571 5.1:+14188993 MS.gene64845:CDS
ACATGAAAGATTTGAGAGTT+TGG 0.364272 5.1:+14188939 MS.gene64845:CDS
CTCTGACAATATCAATGAAT+TGG 0.365005 5.1:+14188855 MS.gene64845:CDS
GATCACATCTTTAAAACATA+TGG 0.374642 5.1:+14188627 MS.gene64845:CDS
GAAATTTGTGGAAGAGTTGT+TGG 0.388764 5.1:+14188423 MS.gene64845:CDS
ATGGTTTGGAGAGTTTATTT+AGG 0.391038 5.1:+14188986 MS.gene64845:CDS
CCCTTCACTCTGCTCTTAGA+AGG 0.394926 5.1:+14188521 MS.gene64845:CDS
TGAAATGATAGAAAATGGTT+TGG 0.414105 5.1:+14188972 MS.gene64845:CDS
ACATCTGATTCAATTATCAT+TGG 0.423183 5.1:+14188310 MS.gene64845:CDS
GAACTGTAATCACTGCAATA+AGG 0.430581 5.1:-14188693 None:intergenic
ATTTGAACCTTCCCTTAAAA+GGG 0.441136 5.1:-14188902 None:intergenic
CAATTTGTCATCAACACAAA+AGG 0.464258 5.1:+14188378 MS.gene64845:CDS
CTCTGCTCTTAGAAGGAGAA+AGG 0.467785 5.1:+14188528 MS.gene64845:CDS
GAACATCATCACACTAACAT+AGG 0.468709 5.1:+14189038 MS.gene64845:CDS
TATCTCTTGTTCTATTCTTG+TGG 0.476617 5.1:-14188251 None:intergenic
TGACAAAATTGATGCAAAAG+AGG 0.490023 5.1:+14188815 MS.gene64845:CDS
CCATCAAGGTCAGAAATTTG+TGG 0.500718 5.1:+14188411 MS.gene64845:CDS
TATATACAAATCTTCAAGAA+AGG 0.505581 5.1:-14188338 None:intergenic
ATTGTCAGAGTTCTCTTCAC+AGG 0.525168 5.1:-14188842 None:intergenic
TCCTTCTAAGAGCAGAGTGA+AGG 0.531554 5.1:-14188522 None:intergenic
TGGATATCTGTGGCATCACA+AGG 0.539961 5.1:+14188464 MS.gene64845:CDS
GGAAGGTTCAAATATTTCAA+AGG 0.540457 5.1:+14188912 MS.gene64845:CDS
GACAAAATTGATGCAAAAGA+GGG 0.552355 5.1:+14188816 MS.gene64845:CDS
CAAAGTCAAAGGCAACCAAA+TGG 0.562903 5.1:+14188785 MS.gene64845:CDS
TCTGCTCTTAGAAGGAGAAA+GGG 0.566127 5.1:+14188529 MS.gene64845:CDS
CCTTCTAAGAGCAGAGTGAA+GGG 0.572703 5.1:-14188521 None:intergenic
AACATCATCACACTAACATA+GGG 0.573655 5.1:+14189039 MS.gene64845:CDS
GATGTTCAATAGATGAACTC+TGG 0.579047 5.1:-14189022 None:intergenic
TGGATCTTCATCAAAGTCAA+AGG 0.588491 5.1:+14188774 MS.gene64845:CDS
TATCAATGAATTGGAGTGTG+TGG 0.598230 5.1:+14188864 MS.gene64845:CDS
AAGGCTATTTCTCACCATCA+AGG 0.605742 5.1:+14188397 MS.gene64845:CDS
TTGATCTTGATTCAAAAGTG+AGG 0.609457 5.1:-14188668 None:intergenic
ATCAGATGTGGATGTTGATG+TGG 0.611639 5.1:-14188296 None:intergenic
GAAAACTGTTTGAACGAACA+TGG 0.612401 5.1:-14188207 None:intergenic
TTTGTGGAAGAGTTGTTGGA+TGG 0.615570 5.1:+14188427 MS.gene64845:CDS
AGTGATTACAGTTCTTAGAG+AGG 0.623623 5.1:+14188702 MS.gene64845:CDS
AATGATAATTGAATCAGATG+TGG 0.626315 5.1:-14188308 None:intergenic
GTGTTAGGATGTGATTGAGA+AGG 0.634141 5.1:-14188229 None:intergenic
AGATATGCAAGATCAAGACA+TGG 0.645800 5.1:+14188269 MS.gene64845:CDS
GGATATCTGTGGCATCACAA+GGG 0.651501 5.1:+14188465 MS.gene64845:CDS
GATATGCAAGATCAAGACAT+GGG 0.662406 5.1:+14188270 MS.gene64845:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAACTAAATT+TGG + chr5.1:14188640-14188659 MS.gene64845:CDS 20.0%
!! CTTTGTGAAGAATTTATATT+CGG - chr5.1:14188581-14188600 None:intergenic 20.0%
!! TATATACAAATCTTCAAGAA+AGG - chr5.1:14188341-14188360 None:intergenic 20.0%
!! TGAAGATTTGTATATATCTT+TGG + chr5.1:14188345-14188364 MS.gene64845:CDS 20.0%
!!! ATTTTCTTTGATTTGTAAGA+TGG - chr5.1:14188494-14188513 None:intergenic 20.0%
! AATGATAATTGAATCAGATG+TGG - chr5.1:14188311-14188330 None:intergenic 25.0%
! ACATCTGATTCAATTATCAT+TGG + chr5.1:14188310-14188329 MS.gene64845:CDS 25.0%
! GCAATTGAAATGATAGAAAA+TGG + chr5.1:14188967-14188986 MS.gene64845:CDS 25.0%
! TGAAATGATAGAAAATGGTT+TGG + chr5.1:14188972-14188991 MS.gene64845:CDS 25.0%
!!! GATCACATCTTTAAAACATA+TGG + chr5.1:14188627-14188646 MS.gene64845:CDS 25.0%
ACATGAAAGATTTGAGAGTT+TGG + chr5.1:14188939-14188958 MS.gene64845:CDS 30.0%
ATTTGAACCTTCCCTTAAAA+GGG - chr5.1:14188905-14188924 None:intergenic 30.0%
CAATTTGTCATCAACACAAA+AGG + chr5.1:14188378-14188397 MS.gene64845:CDS 30.0%
CTCTGACAATATCAATGAAT+TGG + chr5.1:14188855-14188874 MS.gene64845:CDS 30.0%
GACAAAATTGATGCAAAAGA+GGG + chr5.1:14188816-14188835 MS.gene64845:CDS 30.0%
GGAAGGTTCAAATATTTCAA+AGG + chr5.1:14188912-14188931 MS.gene64845:CDS 30.0%
TATCTCTTGTTCTATTCTTG+TGG - chr5.1:14188254-14188273 None:intergenic 30.0%
TATTTGAACCTTCCCTTAAA+AGG - chr5.1:14188906-14188925 None:intergenic 30.0%
TGACAAAATTGATGCAAAAG+AGG + chr5.1:14188815-14188834 MS.gene64845:CDS 30.0%
TTGATCTTGATTCAAAAGTG+AGG - chr5.1:14188671-14188690 None:intergenic 30.0%
! ATGGTTTGGAGAGTTTATTT+AGG + chr5.1:14188986-14189005 MS.gene64845:CDS 30.0%
! GTCAAAATTTTGGATATCTG+TGG + chr5.1:14188454-14188473 MS.gene64845:CDS 30.0%
! TCAATCCATTTTGTCTTTCT+TGG + chr5.1:14188750-14188769 MS.gene64845:CDS 30.0%
!! ATCTTTGAGAACCCTTTTAA+GGG + chr5.1:14188891-14188910 MS.gene64845:CDS 30.0%
!!! TTTTGTCACTTTCAACCATT+TGG - chr5.1:14188803-14188822 None:intergenic 30.0%
AGATATGCAAGATCAAGACA+TGG + chr5.1:14188269-14188288 MS.gene64845:CDS 35.0%
AGTGATTACAGTTCTTAGAG+AGG + chr5.1:14188702-14188721 MS.gene64845:CDS 35.0%
GAAAACTGTTTGAACGAACA+TGG - chr5.1:14188210-14188229 None:intergenic 35.0%
GAAATTTGTGGAAGAGTTGT+TGG + chr5.1:14188423-14188442 MS.gene64845:CDS 35.0%
GAACTGTAATCACTGCAATA+AGG - chr5.1:14188696-14188715 None:intergenic 35.0%
GATATGCAAGATCAAGACAT+GGG + chr5.1:14188270-14188289 MS.gene64845:CDS 35.0%
GATGTTCAATAGATGAACTC+TGG - chr5.1:14189025-14189044 None:intergenic 35.0%
GGAGAGTTTATTTAGGAGAT+TGG + chr5.1:14188993-14189012 MS.gene64845:CDS 35.0%
TATCAATGAATTGGAGTGTG+TGG + chr5.1:14188864-14188883 MS.gene64845:CDS 35.0%
TCCAACCAAGAAAGACAAAA+TGG - chr5.1:14188758-14188777 None:intergenic 35.0%
TGGATCTTCATCAAAGTCAA+AGG + chr5.1:14188774-14188793 MS.gene64845:CDS 35.0%
TGTTCTATTCTTGTGGTGTT+AGG - chr5.1:14188247-14188266 None:intergenic 35.0%
! GGATGGTTCAGTCAAAATTT+TGG + chr5.1:14188444-14188463 MS.gene64845:CDS 35.0%
! TCCATTTTGTCTTTCTTGGT+TGG + chr5.1:14188754-14188773 MS.gene64845:CDS 35.0%
!! CATCTTTGAGAACCCTTTTA+AGG + chr5.1:14188890-14188909 MS.gene64845:CDS 35.0%
ATCAGATGTGGATGTTGATG+TGG - chr5.1:14188299-14188318 None:intergenic 40.0%
ATTGTCAGAGTTCTCTTCAC+AGG - chr5.1:14188845-14188864 None:intergenic 40.0%
CAAAGTCAAAGGCAACCAAA+TGG + chr5.1:14188785-14188804 MS.gene64845:CDS 40.0%
CCACAAATTTCTGACCTTGA+TGG - chr5.1:14188414-14188433 None:intergenic 40.0%
CCATCAAGGTCAGAAATTTG+TGG + chr5.1:14188411-14188430 MS.gene64845:CDS 40.0%
GTGTTAGGATGTGATTGAGA+AGG - chr5.1:14188232-14188251 None:intergenic 40.0%
TCTGCTCTTAGAAGGAGAAA+GGG + chr5.1:14188529-14188548 MS.gene64845:CDS 40.0%
TTTGTGGAAGAGTTGTTGGA+TGG + chr5.1:14188427-14188446 MS.gene64845:CDS 40.0%
!! AAGGCTATTTCTCACCATCA+AGG + chr5.1:14188397-14188416 MS.gene64845:CDS 40.0%
!! TTGAGAACCCTTTTAAGGGA+AGG + chr5.1:14188895-14188914 MS.gene64845:CDS 40.0%
CTCTGCTCTTAGAAGGAGAA+AGG + chr5.1:14188528-14188547 MS.gene64845:CDS 45.0%
GGATATCTGTGGCATCACAA+GGG + chr5.1:14188465-14188484 MS.gene64845:CDS 45.0%
TGGATATCTGTGGCATCACA+AGG + chr5.1:14188464-14188483 MS.gene64845:CDS 45.0%
! CCTTCTAAGAGCAGAGTGAA+GGG - chr5.1:14188524-14188543 None:intergenic 45.0%
! TCCTTCTAAGAGCAGAGTGA+AGG - chr5.1:14188525-14188544 None:intergenic 45.0%
CCCTTCACTCTGCTCTTAGA+AGG + chr5.1:14188521-14188540 MS.gene64845:CDS 50.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14188193 14189059 14188193 ID=MS.gene64845
chr5.1 mRNA 14188193 14189059 14188193 ID=MS.gene64845.t1;Parent=MS.gene64845
chr5.1 exon 14188193 14189059 14188193 ID=MS.gene64845.t1.exon1;Parent=MS.gene64845.t1
chr5.1 CDS 14188193 14189059 14188193 ID=cds.MS.gene64845.t1;Parent=MS.gene64845.t1
Gene Sequence

>MS.gene64845

ATGGCAAGCAAATACCATGTTCGTTCAAACAGTTTTCCTTCTCAATCACATCCTAACACCACAAGAATAGAACAAGAGATATGCAAGATCAAGACATGGGAAGCCACATCAACATCCACATCTGATTCAATTATCATTGGTCTTTCCTTTCTTGAAGATTTGTATATATCTTTGGAAGATCTTCTCAATTTGTCATCAACACAAAAGGCTATTTCTCACCATCAAGGTCAGAAATTTGTGGAAGAGTTGTTGGATGGTTCAGTCAAAATTTTGGATATCTGTGGCATCACAAGGGACACCATCTTACAAATCAAAGAAAATGTTCAATCCCTTCACTCTGCTCTTAGAAGGAGAAAGGGAGAATCAAGCATTGAAACAAGTGTAGCCGAATATAAATTCTTCACAAAGAAGATGAAGAAGAATGTCACAAAGTTGATCACATCTTTAAAACATATGGAAACTAAATTTGGAGCTTCCTCACTTTTGAATCAAGATCAAGACCTTATTGCAGTGATTACAGTTCTTAGAGAGGTCATTGCAATGAACATGTCTATCTTTCAATCCATTTTGTCTTTCTTGGTTGGATCTTCATCAAAGTCAAAGGCAACCAAATGGTTGAAAGTGACAAAATTGATGCAAAAGAGGGTATCCTGTGAAGAGAACTCTGACAATATCAATGAATTGGAGTGTGTGGAAGCATCTTTGAGAACCCTTTTAAGGGAAGGTTCAAATATTTCAAAGGATGCACATGAAAGATTTGAGAGTTTGGAGAATGCAATTGAAATGATAGAAAATGGTTTGGAGAGTTTATTTAGGAGATTGGTTAAAACCAGAGTTCATCTATTGAACATCATCACACTAACATAG
Protein sequence

>MS.gene64845.t1

MASKYHVRSNSFPSQSHPNTTRIEQEICKIKTWEATSTSTSDSIIIGLSFLEDLYISLEDLLNLSSTQKAISHHQGQKFVEELLDGSVKILDICGITRDTILQIKENVQSLHSALRRRKGESSIETSVAEYKFFTKKMKKNVTKLITSLKHMETKFGASSLLNQDQDLIAVITVLREVIAMNMSIFQSILSFLVGSSSKSKATKWLKVTKLMQKRVSCEENSDNINELECVEASLRTLLREGSNISKDAHERFESLENAIEMIENGLESLFRRLVKTRVHLLNIITLT