AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene010901

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010901.t1 MTR_7g050560 84.239 184 28 1 2 185 121 303 7.96e-116 332
MS.gene010901.t1 MTR_7g050590 72.043 186 48 4 6 189 114 297 6.59e-94 275
MS.gene010901.t1 MTR_3g098790 65.946 185 55 3 6 189 139 316 3.22e-80 241
MS.gene010901.t1 MTR_7g050710 64.362 188 63 3 5 189 138 324 1.41e-77 235
MS.gene010901.t1 MTR_7g050580 65.934 182 45 3 5 185 138 303 3.00e-76 231
MS.gene010901.t1 MTR_7g050720 53.073 179 74 6 6 174 139 317 9.86e-55 176
MS.gene010901.t1 MTR_1g035460 40.541 111 54 4 63 172 188 287 5.37e-18 80.9
MS.gene010901.t1 MTR_1g108780 31.944 144 83 4 29 172 162 290 9.39e-17 77.8
MS.gene010901.t1 MTR_8g103940 31.977 172 96 5 12 172 170 331 8.88e-14 68.9
MS.gene010901.t1 MTR_4g068320 30.000 130 84 3 49 177 270 393 2.11e-12 65.1
MS.gene010901.t1 MTR_5g044670 32.500 120 76 2 60 179 196 310 3.77e-12 63.9
MS.gene010901.t1 MTR_1g034240 28.244 131 87 3 49 178 274 398 1.99e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGTTAAATGAAGGAATT+TGG 0.170862 7.2:+52975238 MS.gene010901:CDS
TTCCATCAACCATGTGAAAT+TGG 0.262872 7.2:+52974540 MS.gene010901:CDS
CTAATCAGGATGACCCTTAC+AGG 0.321649 7.2:+52975273 MS.gene010901:CDS
ATCCTGATTAGGTACTTTGC+AGG 0.384916 7.2:-52975261 None:intergenic
TGGTAATAGACACTTTGATT+TGG 0.391800 7.2:+52975191 MS.gene010901:CDS
TTCCAATTTCACATGGTTGA+TGG 0.398771 7.2:-52974542 None:intergenic
CAGAATATACCACGTATGTT+TGG 0.412403 7.2:+52975171 MS.gene010901:intron
GTTTATTTGTTGTTAAATGA+AGG 0.421453 7.2:+52975231 MS.gene010901:CDS
GGCCTGCAAAGTACCTAATC+AGG 0.423211 7.2:+52975259 MS.gene010901:CDS
CTGTAAGGGTCATCCTGATT+AGG 0.427523 7.2:-52975272 None:intergenic
GATCAATTTGTGGTCCTGTA+AGG 0.446598 7.2:-52975287 None:intergenic
GCAGCTAAAATGGTCTCTAA+TGG 0.456051 7.2:+52974486 None:intergenic
ACTTTGAGATGCTGAACAAT+TGG 0.487702 7.2:-52975442 None:intergenic
TGAAGTTGAGAAATTGCAAA+AGG 0.487851 7.2:+52974578 MS.gene010901:CDS
AATGAAGGTAAGTATAGTGC+TGG 0.512079 7.2:-52975385 None:intergenic
TCTAAAGATGTGCACAATGA+AGG 0.513673 7.2:-52975400 None:intergenic
GAGGACAATAACTTGAAAGT+TGG 0.514989 7.2:+52975336 MS.gene010901:CDS
CCAACTGTGAGATCAATTTG+TGG 0.524959 7.2:-52975297 None:intergenic
TGCAACTTACCAGACGAAAA+CGG 0.547167 7.2:-52974903 None:intergenic
ATTGTTCAGCATCTCAAAGT+AGG 0.547839 7.2:+52975445 MS.gene010901:CDS
ATCAATTTGTGGTCCTGTAA+GGG 0.548089 7.2:-52975286 None:intergenic
CGCATGGCAACAACAAAGGA+TGG 0.550805 7.2:-52974862 None:intergenic
CCACAAATTGATCTCACAGT+TGG 0.558906 7.2:+52975297 MS.gene010901:CDS
CTATTGCTTCCAATTTCACA+TGG 0.560323 7.2:-52974549 None:intergenic
TTTGATTTGGATAAGAAGAG+AGG 0.576081 7.2:+52975204 MS.gene010901:CDS
AAATTGATCTCACAGTTGGA+TGG 0.578678 7.2:+52975301 MS.gene010901:CDS
TGGTTGATGGAATTTAAAAG+AGG 0.579281 7.2:-52974529 None:intergenic
GTAGCAACTTTATATCATGC+TGG 0.590309 7.2:+52974600 MS.gene010901:CDS
TTCAACGTATGATGCACGCA+TGG 0.638803 7.2:-52974878 None:intergenic
TGCACGCATGGCAACAACAA+AGG 0.639444 7.2:-52974866 None:intergenic
TGGATGGAAGACATTTGCAG+AGG 0.667798 7.2:+52975317 MS.gene010901:CDS
TGTCTATTACCAAACATACG+TGG 0.737084 7.2:-52975180 None:intergenic
CATGCTGGCAGAGAGTCCAG+AGG 0.751318 7.2:+52974615 MS.gene010901:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATTAGAAAGTTCTTGT+TGG - chr7.2:52975119-52975138 None:intergenic 20.0%
!!! GTTTATTTGTTGTTAAATGA+AGG + chr7.2:52975231-52975250 MS.gene010901:CDS 20.0%
! TGCAAAATTTGAACACAATA+AGG - chr7.2:52974770-52974789 None:intergenic 25.0%
! TGTTAACATAAATCTTTAGC+AGG + chr7.2:52974702-52974721 MS.gene010901:intron 25.0%
! TGTTGTTAAATGAAGGAATT+TGG + chr7.2:52975238-52975257 MS.gene010901:CDS 25.0%
!! CATTTGTCTTTTCTTTTGAT+TGG + chr7.2:52975148-52975167 MS.gene010901:intron 25.0%
!! TTATTGTGTTCAAATTTTGC+AGG + chr7.2:52974769-52974788 MS.gene010901:intron 25.0%
AAGGGGTGAGAAATATATAT+TGG + chr7.2:52975006-52975025 MS.gene010901:intron 30.0%
GTAAAGACAAGAGAAAGAAT+TGG - chr7.2:52974980-52974999 None:intergenic 30.0%
GTAAGTTGCAAAGAAACATT+TGG + chr7.2:52974916-52974935 MS.gene010901:intron 30.0%
TCTTGTCTTTACCAGATTAA+GGG + chr7.2:52974988-52975007 MS.gene010901:intron 30.0%
TGAAGTTGAGAAATTGCAAA+AGG + chr7.2:52974578-52974597 MS.gene010901:CDS 30.0%
TGGTAATAGACACTTTGATT+TGG + chr7.2:52975191-52975210 MS.gene010901:CDS 30.0%
!! TGGTTGATGGAATTTAAAAG+AGG - chr7.2:52974532-52974551 None:intergenic 30.0%
!! TTTGATTTGGATAAGAAGAG+AGG + chr7.2:52975204-52975223 MS.gene010901:CDS 30.0%
AAATTGATCTCACAGTTGGA+TGG + chr7.2:52975301-52975320 MS.gene010901:CDS 35.0%
AATGAAGGTAAGTATAGTGC+TGG - chr7.2:52975388-52975407 None:intergenic 35.0%
ATATTTCTCACCCCTTAATC+TGG - chr7.2:52975002-52975021 None:intergenic 35.0%
ATCAATTTGTGGTCCTGTAA+GGG - chr7.2:52975289-52975308 None:intergenic 35.0%
ATTGTTCAGCATCTCAAAGT+AGG + chr7.2:52975445-52975464 MS.gene010901:CDS 35.0%
CAGAATATACCACGTATGTT+TGG + chr7.2:52975171-52975190 MS.gene010901:intron 35.0%
CTATTGCTTCCAATTTCACA+TGG - chr7.2:52974552-52974571 None:intergenic 35.0%
CTCTTGTCTTTACCAGATTA+AGG + chr7.2:52974987-52975006 MS.gene010901:intron 35.0%
CTTGTCTTTACCAGATTAAG+GGG + chr7.2:52974989-52975008 MS.gene010901:intron 35.0%
GACACAAAATTGTATACCTC+TGG - chr7.2:52974634-52974653 None:intergenic 35.0%
GAGGACAATAACTTGAAAGT+TGG + chr7.2:52975336-52975355 MS.gene010901:CDS 35.0%
GTAGCAACTTTATATCATGC+TGG + chr7.2:52974600-52974619 MS.gene010901:CDS 35.0%
TCTAAAGATGTGCACAATGA+AGG - chr7.2:52975403-52975422 None:intergenic 35.0%
TGTCTATTACCAAACATACG+TGG - chr7.2:52975183-52975202 None:intergenic 35.0%
TTCCAATTTCACATGGTTGA+TGG - chr7.2:52974545-52974564 None:intergenic 35.0%
TTCCATCAACCATGTGAAAT+TGG + chr7.2:52974540-52974559 MS.gene010901:CDS 35.0%
! GTTGTAATTTTCTCAGCAGT+AGG - chr7.2:52974808-52974827 None:intergenic 35.0%
!! ACTTTGAGATGCTGAACAAT+TGG - chr7.2:52975445-52975464 None:intergenic 35.0%
ATCCTGATTAGGTACTTTGC+AGG - chr7.2:52975264-52975283 None:intergenic 40.0%
CCAACTGTGAGATCAATTTG+TGG - chr7.2:52975300-52975319 None:intergenic 40.0%
CCACAAATTGATCTCACAGT+TGG + chr7.2:52975297-52975316 MS.gene010901:CDS 40.0%
GATCAATTTGTGGTCCTGTA+AGG - chr7.2:52975290-52975309 None:intergenic 40.0%
TGCAACTTACCAGACGAAAA+CGG - chr7.2:52974906-52974925 None:intergenic 40.0%
CTAATCAGGATGACCCTTAC+AGG + chr7.2:52975273-52975292 MS.gene010901:CDS 45.0%
CTGTAAGGGTCATCCTGATT+AGG - chr7.2:52975275-52975294 None:intergenic 45.0%
TGGATGGAAGACATTTGCAG+AGG + chr7.2:52975317-52975336 MS.gene010901:CDS 45.0%
TTCAACGTATGATGCACGCA+TGG - chr7.2:52974881-52974900 None:intergenic 45.0%
CGCATGGCAACAACAAAGGA+TGG - chr7.2:52974865-52974884 None:intergenic 50.0%
TGCACGCATGGCAACAACAA+AGG - chr7.2:52974869-52974888 None:intergenic 50.0%
! CGTTGAACACCGTTTTCGTC+TGG + chr7.2:52974894-52974913 MS.gene010901:CDS 50.0%
! GGCCTGCAAAGTACCTAATC+AGG + chr7.2:52975259-52975278 MS.gene010901:CDS 50.0%
CATGCTGGCAGAGAGTCCAG+AGG + chr7.2:52974615-52974634 MS.gene010901:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 52974495 52975476 52974495 ID=MS.gene010901
chr7.2 mRNA 52974495 52975476 52974495 ID=MS.gene010901.t1;Parent=MS.gene010901
chr7.2 exon 52974495 52974636 52974495 ID=MS.gene010901.t1.exon1;Parent=MS.gene010901.t1
chr7.2 CDS 52974495 52974636 52974495 ID=cds.MS.gene010901.t1;Parent=MS.gene010901.t1
chr7.2 exon 52974791 52974915 52974791 ID=MS.gene010901.t1.exon2;Parent=MS.gene010901.t1
chr7.2 CDS 52974791 52974915 52974791 ID=cds.MS.gene010901.t1;Parent=MS.gene010901.t1
chr7.2 exon 52975174 52975476 52975174 ID=MS.gene010901.t1.exon3;Parent=MS.gene010901.t1
chr7.2 CDS 52975174 52975476 52975174 ID=cds.MS.gene010901.t1;Parent=MS.gene010901.t1
Gene Sequence

>MS.gene010901

ATGGTCTCTAATGGTCAAAAGAGAAAAGCTAACTCCTCTTTTAAATTCCATCAACCATGTGAAATTGGAAGCAATAGTTGTGTTGAAGTTGAGAAATTGCAAAAGGTAGCAACTTTATATCATGCTGGCAGAGAGTCCAGAGGTATACAATTTTGTGTCTTCATTGTCTCATAAAAGTTTCTCAAGTTAATATAAATTATTAGCTTTTGTTAACATAAATCTTTAGCAGGTTTCAATATATAGAAACATGAAAGATGATCATGAAATATCAGCCTTATTGTGTTCAAATTTTGCAGGAAAACAAGTGATTCCTACTGCTGAGAAAATTACAACTGTTGAAAGAGCACAATCTTTCAAAACAAGTAATCCATCCTTTGTTGTTGCCATGCGTGCATCATACGTTGAACACCGTTTTCGTCTGGTAAGTTGCAAAGAAACATTTGGCTTTTAGAACATAAGTTGTTAATCAACAACATCAATAACCAATTCTTTCTCTTGTCTTTACCAGATTAAGGGGTGAGAAATATATATTGGAATATTAGTAGATATATTATAATATAACAAAGTGATATTATGATTAGATTAGATAACTATGTAAGAAAATACACAATGTTAAGAACTCCAACAAGAACTTTCTAATTTTTATTCATTAACATTTGTCTTTTCTTTTGATTGGCAGAATATACCACGTATGTTTGGTAATAGACACTTTGATTTGGATAAGAAGAGAGGAGATGTTTATTTGTTGTTAAATGAAGGAATTTGGCCTGCAAAGTACCTAATCAGGATGACCCTTACAGGACCACAAATTGATCTCACAGTTGGATGGAAGACATTTGCAGAGGACAATAACTTGAAAGTTGGCGATATTTGCAAATTTGAGCTCATCTCCAGCACTATACTTACCTTCATTGTGCACATCTTTAGAGAGACTGACAATGACAACACCAATTGTTCAGCATCTCAAAGTAGGATGAATTGA
Protein sequence

>MS.gene010901.t1

MVSNGQKRKANSSFKFHQPCEIGSNSCVEVEKLQKVATLYHAGRESRGKQVIPTAEKITTVERAQSFKTSNPSFVVAMRASYVEHRFRLNIPRMFGNRHFDLDKKRGDVYLLLNEGIWPAKYLIRMTLTGPQIDLTVGWKTFAEDNNLKVGDICKFELISSTILTFIVHIFRETDNDNTNCSASQSRMN