AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27276

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27276.t1 MTR_1g023230 100.000 121 0 0 1 121 108 228 2.19e-85 254
MS.gene27276.t1 MTR_3g112510 61.538 221 68 9 11 226 82 290 2.20e-72 222
MS.gene27276.t1 MTR_8g076620 54.132 242 78 7 1 229 110 331 4.05e-68 213
MS.gene27276.t1 MTR_5g021130 54.661 236 90 6 7 229 92 323 7.09e-68 212
MS.gene27276.t1 MTR_5g089750 45.062 162 82 3 15 169 249 410 3.98e-38 138
MS.gene27276.t1 MTR_3g014660 40.331 181 90 5 1 168 119 294 1.06e-35 129
MS.gene27276.t1 MTR_4g071110 41.611 149 62 2 12 160 14 137 2.65e-34 124
MS.gene27276.t1 MTR_8g039110 39.779 181 96 3 15 182 124 304 1.53e-32 120
MS.gene27276.t1 MTR_0363s0040 75.556 45 11 0 15 59 124 168 2.25e-20 86.7
MS.gene27276.t1 MTR_0105s0070 63.636 33 12 0 17 49 44 76 9.73e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27276.t1 AT1G75520 52.340 235 87 7 11 229 121 346 1.42e-71 222
MS.gene27276.t1 AT3G51060 50.211 237 90 5 13 229 142 370 1.44e-68 215
MS.gene27276.t1 AT1G19790 50.000 244 105 7 1 228 102 344 1.03e-67 212
MS.gene27276.t1 AT1G19790 50.000 244 105 7 1 228 102 344 1.03e-67 212
MS.gene27276.t1 AT5G66350 49.333 225 91 6 15 229 120 331 6.76e-64 202
MS.gene27276.t1 AT5G66350 48.182 220 91 6 15 224 120 326 4.35e-61 194
MS.gene27276.t1 AT5G66350 49.065 214 86 6 15 218 120 320 6.38e-60 191
MS.gene27276.t1 AT2G21400 42.791 215 83 6 12 223 7 184 2.77e-48 157
MS.gene27276.t1 AT2G21400 42.791 215 83 6 12 223 6 183 2.81e-48 157
MS.gene27276.t1 AT4G36260 52.500 160 61 5 13 162 92 246 2.97e-46 156
MS.gene27276.t1 AT2G21400 41.981 212 74 6 12 223 6 168 3.52e-46 151
MS.gene27276.t1 AT2G21400 41.981 212 74 6 12 223 7 169 3.70e-46 151
MS.gene27276.t1 AT2G18120 47.134 157 56 3 13 162 70 206 1.92e-41 140
MS.gene27276.t1 AT2G18120 48.026 152 60 2 13 162 70 204 6.71e-39 134
MS.gene27276.t1 AT5G12330 45.625 160 75 3 15 162 112 271 1.57e-37 133
MS.gene27276.t1 AT5G12330 45.625 160 75 3 15 162 112 271 1.57e-37 133
MS.gene27276.t1 AT5G12330 45.625 160 75 3 15 162 199 358 1.75e-37 135
MS.gene27276.t1 AT5G33210 60.870 92 32 2 13 104 15 102 2.25e-31 111
MS.gene27276.t1 AT5G33210 48.819 127 54 4 13 139 50 165 3.18e-31 113
MS.gene27276.t1 AT3G54430 35.185 162 81 4 11 168 37 178 1.09e-23 94.0
MS.gene27276.t1 AT5G12330 82.609 46 8 0 15 60 112 157 9.83e-22 90.1

Find 60 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGATCCCTCTGGAGCTTC+TGG 0.278538 1.1:+1442705 MS.gene27276:CDS
AGCTCCTCTTAATGCTTTCA+TGG 0.295162 1.1:+1443566 MS.gene27276:CDS
CACTCATGTCTTTAGGATCT+TGG 0.300540 1.1:-1443612 None:intergenic
TGAATTCACCGGCGGTGTTC+AGG 0.312818 1.1:+1443286 MS.gene27276:CDS
TATATACCTGTGGTAGTAAT+AGG 0.332609 1.1:-1442750 None:intergenic
AGGTCTTCAAGTGGTGGTTT+AGG 0.350386 1.1:+1442447 MS.gene27276:CDS
GGTGGTGGCGAGGGTTCTTC+CGG 0.367254 1.1:+1443450 MS.gene27276:CDS
CCACCACCAGCAGCAGCATT+TGG 0.392576 1.1:-1443435 None:intergenic
CGTTCGCGGCGTTTAGCAGC+TGG 0.397352 1.1:-1442597 None:intergenic
CCTCTTAATGCTTTCATGGC+TGG 0.408461 1.1:+1443570 MS.gene27276:CDS
GTGGACAATCTTTCTTAGCT+TGG 0.415642 1.1:-1442503 None:intergenic
TGAGTTGTTGCTGCCGTTCG+CGG 0.429437 1.1:-1442611 None:intergenic
GGCGAGGGTTCTTCCGGTGG+TGG 0.430350 1.1:+1443456 MS.gene27276:CDS
TTGAAATTAGGGTTGGAGTT+GGG 0.437119 1.1:+1443246 MS.gene27276:intron
AGTGGTGGTTTAGGTGGTGG+TGG 0.442865 1.1:+1442456 MS.gene27276:CDS
GGTTCTTCCGGTGGTGGCAG+CGG 0.446891 1.1:+1443462 MS.gene27276:CDS
TTCGCCACCGCTGCCACCAC+CGG 0.449406 1.1:-1443469 None:intergenic
CCAAATGCTGCTGCTGGTGG+TGG 0.457278 1.1:+1443435 MS.gene27276:CDS
AAACTCATGTGAAAAGTACT+TGG 0.464467 1.1:+1442571 MS.gene27276:CDS
TGCTGCTGCTGGTGGTGGCG+AGG 0.465038 1.1:+1443440 MS.gene27276:CDS
TTGTATGATCAAGGACTTGA+AGG 0.474373 1.1:+1443399 MS.gene27276:CDS
GAAAATCAAAATGATCCCTC+TGG 0.474468 1.1:+1442696 MS.gene27276:CDS
TGTCTTTAGGATCTTGGAGG+TGG 0.488834 1.1:-1443606 None:intergenic
GCTGCTGCTGGTGGTGGCGA+GGG 0.489260 1.1:+1443441 MS.gene27276:CDS
TCATGTCTTTAGGATCTTGG+AGG 0.489282 1.1:-1443609 None:intergenic
TATAGTGAAGAATACTCAAA+TGG 0.492700 1.1:-1443540 None:intergenic
TCAAGTGGTGGTTTAGGTGG+TGG 0.495997 1.1:+1442453 MS.gene27276:CDS
ATGAAAGCATTAAGAGGAGC+TGG 0.499046 1.1:-1443564 None:intergenic
CCTGTGGTAGTAATAGGTAC+TGG 0.504192 1.1:-1442744 None:intergenic
ATTGTTAACATTTGTTGTGG+TGG 0.506186 1.1:-1443517 None:intergenic
TCTTCCGGTGGTGGCAGCGG+TGG 0.515802 1.1:+1443465 MS.gene27276:CDS
TCTTCAAGTGGTGGTTTAGG+TGG 0.516785 1.1:+1442450 MS.gene27276:CDS
AGTAATAGGTACTGGAGTAC+AGG 0.518362 1.1:-1442736 None:intergenic
CCAGCCATGAAAGCATTAAG+AGG 0.523927 1.1:-1443570 None:intergenic
TTTGAAATTAGGGTTGGAGT+TGG 0.534737 1.1:+1443245 MS.gene27276:intron
GGTGGTGGCAGCGGTGGCGA+AGG 0.539736 1.1:+1443471 MS.gene27276:CDS
TTTACACACCTGAACACCGC+CGG 0.552531 1.1:-1443294 None:intergenic
TCCACCGGAGCTGAATTCAC+CGG 0.555263 1.1:+1443275 MS.gene27276:CDS
GAACTTGTTGCAAGAGTCGA+GGG 0.557726 1.1:+1442538 MS.gene27276:CDS
CAGCTGCTAAACGCCGCGAA+CGG 0.557914 1.1:+1442598 MS.gene27276:CDS
GTCTTTAGGATCTTGGAGGT+GGG 0.561171 1.1:-1443605 None:intergenic
CCAGTACCTATTACTACCAC+AGG 0.564967 1.1:+1442744 MS.gene27276:CDS
CAAACTGCTGTGAACATAGG+AGG 0.565014 1.1:+1443357 MS.gene27276:CDS
ACTAGTCCAAATGCTGCTGC+TGG 0.565581 1.1:+1443429 MS.gene27276:CDS
GCCGGTGAATTCAGCTCCGG+TGG 0.569608 1.1:-1443276 None:intergenic
TATCAAACTGCTGTGAACAT+AGG 0.572121 1.1:+1443354 MS.gene27276:CDS
GGTGGCGAGGGTTCTTCCGG+TGG 0.572206 1.1:+1443453 MS.gene27276:CDS
ACCGCCGGTGAATTCAGCTC+CGG 0.574562 1.1:-1443279 None:intergenic
TAGAGAACCAGAAGCTCCAG+AGG 0.578477 1.1:-1442712 None:intergenic
AGTCCAAATGCTGCTGCTGG+TGG 0.584415 1.1:+1443432 MS.gene27276:CDS
AACTCATGTGAAAAGTACTT+GGG 0.591492 1.1:+1442572 MS.gene27276:CDS
TGGATTGTTAACATTTGTTG+TGG 0.600855 1.1:-1443520 None:intergenic
AGAACTTGTTGCAAGAGTCG+AGG 0.603647 1.1:+1442537 MS.gene27276:CDS
GTGATGAGGTCTTCAAGTGG+TGG 0.621009 1.1:+1442441 None:intergenic
CAAGTTCTACATCTAAGATG+TGG 0.632750 1.1:-1442522 None:intergenic
GGAATGAACTGTCAAGATTG+TGG 0.658447 1.1:+1442477 MS.gene27276:CDS
ACCGGAGCTGAATTCACCGG+CGG 0.668533 1.1:+1443278 MS.gene27276:CDS
AGAGAACCAGAAGCTCCAGA+GGG 0.671479 1.1:-1442711 None:intergenic
GTGTGTAAAAGTGAGTGCAA+TGG 0.678715 1.1:+1443308 MS.gene27276:CDS
ACAGTGATGAGGTCTTCAAG+TGG 0.705760 1.1:+1442438 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTTGATTTGAAATTA+GGG + chr1.1:1443235-1443254 MS.gene27276:intron 10.0%
!!! TTTTTATTTGATTTGAAATT+AGG + chr1.1:1443234-1443253 MS.gene27276:intron 10.0%
!! ATAGAATATATAGACTAATT+AGG - chr1.1:1443020-1443039 None:intergenic 15.0%
!!! TAATTTTTTGATATATAGCT+AGG + chr1.1:1442906-1442925 MS.gene27276:intron 15.0%
!!! TCTTTTTGAATTTTTTGATT+TGG + chr1.1:1443200-1443219 MS.gene27276:intron 15.0%
!! AAAATGAAAAGATATTACGA+GGG + chr1.1:1442867-1442886 MS.gene27276:intron 20.0%
!! TAAAATGAAAAGATATTACG+AGG + chr1.1:1442866-1442885 MS.gene27276:intron 20.0%
!! TCTATGAATCTATGATAAAT+AGG + chr1.1:1442991-1443010 MS.gene27276:intron 20.0%
! TAGCTATATAGAAACAATTG+AGG + chr1.1:1443173-1443192 MS.gene27276:intron 25.0%
! TATAGTGAAGAATACTCAAA+TGG - chr1.1:1443543-1443562 None:intergenic 25.0%
! TGAAAAAATTGTTAGGTAAG+TGG + chr1.1:1443121-1443140 MS.gene27276:intron 25.0%
! TGAAGGATGAAAAAATTGTT+AGG + chr1.1:1443114-1443133 MS.gene27276:intron 25.0%
! TTTCTACATATATATACCTG+TGG - chr1.1:1442763-1442782 None:intergenic 25.0%
!!! ATTTGATTTGAAATTAGGGT+TGG + chr1.1:1443239-1443258 MS.gene27276:intron 25.0%
TATATACCTGTGGTAGTAAT+AGG - chr1.1:1442753-1442772 None:intergenic 30.0%
TTGATAGAGTATGAAAGGAA+TGG - chr1.1:1443047-1443066 None:intergenic 30.0%
! AAGGGAATTTTGTATGATCA+AGG + chr1.1:1443390-1443409 MS.gene27276:CDS 30.0%
! TGGATTGTTAACATTTGTTG+TGG - chr1.1:1443523-1443542 None:intergenic 30.0%
! TTCTCTTTCTTTTCTTCTGA+AGG + chr1.1:1443097-1443116 MS.gene27276:intron 30.0%
!! AAACTCATGTGAAAAGTACT+TGG + chr1.1:1442571-1442590 MS.gene27276:CDS 30.0%
!! AACTCATGTGAAAAGTACTT+GGG + chr1.1:1442572-1442591 MS.gene27276:CDS 30.0%
!! ATTGTTAACATTTGTTGTGG+TGG - chr1.1:1443520-1443539 None:intergenic 30.0%
!! CTAAGTTGATAGAGTATGAA+AGG - chr1.1:1443052-1443071 None:intergenic 30.0%
GAAAATCAAAATGATCCCTC+TGG + chr1.1:1442696-1442715 MS.gene27276:CDS 35.0%
TATCAAACTGCTGTGAACAT+AGG + chr1.1:1443354-1443373 MS.gene27276:CDS 35.0%
TTGAAATTAGGGTTGGAGTT+GGG + chr1.1:1443246-1443265 MS.gene27276:intron 35.0%
TTGTATGATCAAGGACTTGA+AGG + chr1.1:1443399-1443418 MS.gene27276:CDS 35.0%
! ATAGGAGGAAGAGTTTTCAA+GGG + chr1.1:1443372-1443391 MS.gene27276:CDS 35.0%
! CAAGTTCTACATCTAAGATG+TGG - chr1.1:1442525-1442544 None:intergenic 35.0%
! TTTGAAATTAGGGTTGGAGT+TGG + chr1.1:1443245-1443264 MS.gene27276:intron 35.0%
AGCTCCTCTTAATGCTTTCA+TGG + chr1.1:1443566-1443585 MS.gene27276:CDS 40.0%
GGAATGAACTGTCAAGATTG+TGG + chr1.1:1442477-1442496 MS.gene27276:CDS 40.0%
GTGGACAATCTTTCTTAGCT+TGG - chr1.1:1442506-1442525 None:intergenic 40.0%
GTGTGTAAAAGTGAGTGCAA+TGG + chr1.1:1443308-1443327 MS.gene27276:CDS 40.0%
! CATAGGAGGAAGAGTTTTCA+AGG + chr1.1:1443371-1443390 MS.gene27276:CDS 40.0%
!! AGTAATAGGTACTGGAGTAC+AGG - chr1.1:1442739-1442758 None:intergenic 40.0%
!! ATGAAAGCATTAAGAGGAGC+TGG - chr1.1:1443567-1443586 None:intergenic 40.0%
AGGTCTTCAAGTGGTGGTTT+AGG + chr1.1:1442447-1442466 MS.gene27276:CDS 45.0%
CAAACTGCTGTGAACATAGG+AGG + chr1.1:1443357-1443376 MS.gene27276:CDS 45.0%
CCAGTACCTATTACTACCAC+AGG + chr1.1:1442744-1442763 MS.gene27276:CDS 45.0%
CCTCTTAATGCTTTCATGGC+TGG + chr1.1:1443570-1443589 MS.gene27276:CDS 45.0%
CCTGTGGTAGTAATAGGTAC+TGG - chr1.1:1442747-1442766 None:intergenic 45.0%
GCTTAGTGATAGAGATCTCG+AGG + chr1.1:1442955-1442974 MS.gene27276:intron 45.0%
TCTTCAAGTGGTGGTTTAGG+TGG + chr1.1:1442450-1442469 MS.gene27276:CDS 45.0%
! GGAGTTGGGAAATTTTCCAC+CGG + chr1.1:1443260-1443279 MS.gene27276:CDS 45.0%
!! AGAACTTGTTGCAAGAGTCG+AGG + chr1.1:1442537-1442556 MS.gene27276:CDS 45.0%
!! CCAGCCATGAAAGCATTAAG+AGG - chr1.1:1443573-1443592 None:intergenic 45.0%
!! GAACTTGTTGCAAGAGTCGA+GGG + chr1.1:1442538-1442557 MS.gene27276:CDS 45.0%
ACTAGTCCAAATGCTGCTGC+TGG + chr1.1:1443429-1443448 MS.gene27276:CDS 50.0%
AGAGAACCAGAAGCTCCAGA+GGG - chr1.1:1442714-1442733 None:intergenic 50.0%
TAGAGAACCAGAAGCTCCAG+AGG - chr1.1:1442715-1442734 None:intergenic 50.0%
TCAAGTGGTGGTTTAGGTGG+TGG + chr1.1:1442453-1442472 MS.gene27276:CDS 50.0%
TTTACACACCTGAACACCGC+CGG - chr1.1:1443297-1443316 None:intergenic 50.0%
!! AATGATCCCTCTGGAGCTTC+TGG + chr1.1:1442705-1442724 MS.gene27276:CDS 50.0%
AGTCCAAATGCTGCTGCTGG+TGG + chr1.1:1443432-1443451 MS.gene27276:CDS 55.0%
TCCACCGGAGCTGAATTCAC+CGG + chr1.1:1443275-1443294 MS.gene27276:CDS 55.0%
TGAATTCACCGGCGGTGTTC+AGG + chr1.1:1443286-1443305 MS.gene27276:CDS 55.0%
TGAGTTGTTGCTGCCGTTCG+CGG - chr1.1:1442614-1442633 None:intergenic 55.0%
! AGTGGTGGTTTAGGTGGTGG+TGG + chr1.1:1442456-1442475 MS.gene27276:CDS 55.0%
ACCGCCGGTGAATTCAGCTC+CGG - chr1.1:1443282-1443301 None:intergenic 60.0%
ACCGGAGCTGAATTCACCGG+CGG + chr1.1:1443278-1443297 MS.gene27276:CDS 60.0%
CAGCTGCTAAACGCCGCGAA+CGG + chr1.1:1442598-1442617 MS.gene27276:CDS 60.0%
CCAAATGCTGCTGCTGGTGG+TGG + chr1.1:1443435-1443454 MS.gene27276:CDS 60.0%
CCACCACCAGCAGCAGCATT+TGG - chr1.1:1443438-1443457 None:intergenic 60.0%
CGTTCGCGGCGTTTAGCAGC+TGG - chr1.1:1442600-1442619 None:intergenic 65.0%
GCCGGTGAATTCAGCTCCGG+TGG - chr1.1:1443279-1443298 None:intergenic 65.0%
! GGTGGTGGCGAGGGTTCTTC+CGG + chr1.1:1443450-1443469 MS.gene27276:CDS 65.0%
! GGTTCTTCCGGTGGTGGCAG+CGG + chr1.1:1443462-1443481 MS.gene27276:CDS 65.0%
GGCGAGGGTTCTTCCGGTGG+TGG + chr1.1:1443456-1443475 MS.gene27276:CDS 70.0%
GGTGGCGAGGGTTCTTCCGG+TGG + chr1.1:1443453-1443472 MS.gene27276:CDS 70.0%
TTCGCCACCGCTGCCACCAC+CGG - chr1.1:1443472-1443491 None:intergenic 70.0%
! TCTTCCGGTGGTGGCAGCGG+TGG + chr1.1:1443465-1443484 MS.gene27276:CDS 70.0%
!! GCTGCTGCTGGTGGTGGCGA+GGG + chr1.1:1443441-1443460 MS.gene27276:CDS 70.0%
!! TGCTGCTGCTGGTGGTGGCG+AGG + chr1.1:1443440-1443459 MS.gene27276:CDS 70.0%
! GGTGGTGGCAGCGGTGGCGA+AGG + chr1.1:1443471-1443490 MS.gene27276:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 1442444 1443623 1442444 ID=MS.gene27276
chr1.1 mRNA 1442444 1443623 1442444 ID=MS.gene27276.t1;Parent=MS.gene27276
chr1.1 exon 1442444 1442765 1442444 ID=MS.gene27276.t1.exon1;Parent=MS.gene27276.t1
chr1.1 CDS 1442444 1442765 1442444 ID=cds.MS.gene27276.t1;Parent=MS.gene27276.t1
chr1.1 exon 1443256 1443623 1443256 ID=MS.gene27276.t1.exon2;Parent=MS.gene27276.t1
chr1.1 CDS 1443256 1443623 1443256 ID=cds.MS.gene27276.t1;Parent=MS.gene27276.t1
Gene Sequence

>MS.gene27276

ATGAGGTCTTCAAGTGGTGGTTTAGGTGGTGGTGGAATGAACTGTCAAGATTGTGGTAACCAAGCTAAGAAAGATTGTCCACATCTTAGATGTAGAACTTGTTGCAAGAGTCGAGGGTTTCAGTGTCAAACTCATGTGAAAAGTACTTGGGTTCCAGCTGCTAAACGCCGCGAACGGCAGCAACAACTCACGTCGTTGCAGCAACAAAATCAGCAGCAGCAACAACAGTTTCACTCATCAAGAAGACACAGAGAAAATCAAAATGATCCCTCTGGAGCTTCTGGTTCTCTAACCTGTACTCCAGTACCTATTACTACCACAGGTATATATATGTAGAAATATAAACTTTTGATCGATATACATCAACTTTCTTTGACTCACTTGTATTTCTTTGCAGAAGAGTCGTTGAAAGAGAGAGTATATAAAATGAAAAGATATTACGAGGGTTTGAATTATAGTGTTTAATTTTTTGATATATAGCTAGGTCAGTGACGAATTTTCAAACTATATAGCTTAGTGATAGAGATCTCGAGGAGAAACTATAGTTTCTATGAATCTATGATAAATAGGATACCTAATTAGTCTATATATTCTATATATCCATTCCTTTCATACTCTATCAACTTAGTTTTTTTCTTTTCTCTCTCTCTTTTTTCTCTTTCTTTTCTTCTGAAGGATGAAAAAATTGTTAGGTAAGTGGTTCTTTCTTTCTTTTAAATTTGAAAATGATAGCTATATAGAAACAATTGAGGTTTCTCTTTTTGAATTTTTTGATTTGGATTTAATTTTTTTTTTATTTGATTTGAAATTAGGGTTGGAGTTGGGAAATTTTCCACCGGAGCTGAATTCACCGGCGGTGTTCAGGTGTGTAAAAGTGAGTGCAATGGATGCACAAGATGAACGTTATGCTTATCAAACTGCTGTGAACATAGGAGGAAGAGTTTTCAAGGGAATTTTGTATGATCAAGGACTTGAAGGTAGCTACACTAGTCCAAATGCTGCTGCTGGTGGTGGCGAGGGTTCTTCCGGTGGTGGCAGCGGTGGCGAAGGAAATCAACAAAATCTCATAACAACCACCACAACAAATGTTAACAATCCATTTGAGTATTCTTCACTATATCCAGCTCCTCTTAATGCTTTCATGGCTGGTACGCAATTCTTCCCACCTCCAAGATCCTAA
Protein sequence

>MS.gene27276.t1

MRSSSGGLGGGGMNCQDCGNQAKKDCPHLRCRTCCKSRGFQCQTHVKSTWVPAAKRRERQQQLTSLQQQNQQQQQQFHSSRRHRENQNDPSGASGSLTCTPVPITTTGLELGNFPPELNSPAVFRCVKVSAMDAQDERYAYQTAVNIGGRVFKGILYDQGLEGSYTSPNAAAGGGEGSSGGGSGGEGNQQNLITTTTTNVNNPFEYSSLYPAPLNAFMAGTQFFPPPRS