AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044326


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044326.t1 MTR_3g082340 83.929 224 31 3 1 220 1 223 2.81e-135 379
MS.gene044326.t1 MTR_3g082420 76.233 223 47 3 3 220 1 222 6.98e-121 342
MS.gene044326.t1 MTR_3g080680 43.415 205 100 7 24 220 3 199 6.49e-39 133
MS.gene044326.t1 MTR_3g083030 39.834 241 111 9 1 219 1 229 2.93e-36 127
MS.gene044326.t1 MTR_3g083050 41.546 207 99 6 1 203 1 189 4.26e-34 121
MS.gene044326.t1 MTR_3g083080 36.607 224 118 8 1 219 1 205 7.49e-31 112
MS.gene044326.t1 MTR_8g461300 38.889 198 105 7 30 219 9 198 4.10e-23 92.8
MS.gene044326.t1 MTR_4g055800 39.744 156 74 5 52 203 134 273 2.77e-21 89.7
MS.gene044326.t1 MTR_3g083150 36.283 226 122 11 1 219 1 211 4.01e-21 87.8
MS.gene044326.t1 MTR_3g086030 45.783 83 39 2 48 126 15 95 1.26e-12 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 67 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGAATTCGGAACCGGAATT+AGG 0.215538 3.4:+77787948 MS.gene044326:CDS
CCCTGCTTTAACAACTTTCC+AGG 0.234656 3.4:+77788659 MS.gene044326:CDS
CCTAATTCCGGTTCCGAATT+CGG 0.263860 3.4:-77787948 None:intergenic
GAACCCCGCGGTTTCGGTTT+GGG 0.291128 3.4:-77787984 None:intergenic
AACTTTCCAGGCCCAAGTTT+GGG 0.324224 3.4:+77788671 MS.gene044326:CDS
CGAAACCGCGGGGTTCTGTT+TGG 0.344981 3.4:+77787991 MS.gene044326:CDS
CAAACAGAACCCCGCGGTTT+CGG 0.345423 3.4:-77787990 None:intergenic
TGGAGTGTATTAGACTTTAA+TGG 0.348558 3.4:-77788730 None:intergenic
CAACTTTCCAGGCCCAAGTT+TGG 0.351722 3.4:+77788670 MS.gene044326:CDS
TTCGTGTTGCAGAATGTCTA+TGG 0.360071 3.4:+77787857 None:intergenic
GAAACCGCGGGGTTCTGTTT+GGG 0.361275 3.4:+77787992 MS.gene044326:CDS
TCTTGTTCCGATCCTAATTC+CGG 0.362062 3.4:-77787960 None:intergenic
TATCAAAACCGTCCCAAACT+TGG 0.364944 3.4:-77788683 None:intergenic
AGAACCCCGCGGTTTCGGTT+TGG 0.382583 3.4:-77787985 None:intergenic
CCGCCACATAACAGTGTTCC+TGG 0.391171 3.4:-77788323 None:intergenic
AAGAAGGAAGATGCCGAATT+CGG 0.415849 3.4:+77787935 MS.gene044326:CDS
GCGGGGTTCTGTTTGGGAGG+AGG 0.429584 3.4:+77787998 MS.gene044326:CDS
GAAGATGCCGAATTCGGAAC+CGG 0.437745 3.4:+77787941 MS.gene044326:CDS
CAGTGCAAACAATAATAATC+AGG 0.440939 3.4:+77788421 MS.gene044326:CDS
GCCTGGAAAGTTGTTAAAGC+AGG 0.451734 3.4:-77788660 None:intergenic
ATCGGTTATGAAGAGGGGTT+GGG 0.467286 3.4:-77788348 None:intergenic
AACCGTCCCAAACTTGGGCC+TGG 0.470738 3.4:-77788677 None:intergenic
TGAACTCTCCCGGCTTGCAT+TGG 0.475836 3.4:+77788391 MS.gene044326:CDS
TAACAGTGTTCCTGGCGGAC+GGG 0.484854 3.4:-77788315 None:intergenic
TTATCACAAATATATATGTA+AGG 0.491342 3.4:-77788077 None:intergenic
GTGGGAGTTCGTGTGACTGC+GGG 0.493011 3.4:-77787897 None:intergenic
ACTTGATGAAACTCAAATGT+TGG 0.500719 3.4:-77788537 None:intergenic
CATCGGTTATGAAGAGGGGT+TGG 0.502034 3.4:-77788349 None:intergenic
AACAGTGTTCCTGGCGGACG+GGG 0.502549 3.4:-77788314 None:intergenic
GGGAGAGTTCATTGAGAGTA+GGG 0.505718 3.4:-77788379 None:intergenic
ATCAAAACCGTCCCAAACTT+GGG 0.509684 3.4:-77788682 None:intergenic
ATAGATAATTCACTCAACTC+TGG 0.516445 3.4:-77788035 None:intergenic
GTAATAGTCCAATGCAAGCC+GGG 0.518943 3.4:-77788399 None:intergenic
AGCAGCAATACCAACATCAT+AGG 0.521515 3.4:-77788571 None:intergenic
CGGGAGAGTTCATTGAGAGT+AGG 0.523682 3.4:-77788380 None:intergenic
CGGAAAACTGCAGAGAAAGA+AGG 0.523922 3.4:+77787919 MS.gene044326:CDS
ATCTTCATCGGTTATGAAGA+GGG 0.524106 3.4:-77788354 None:intergenic
TATGATGTTGGTATTGCTGC+TGG 0.533144 3.4:+77788573 MS.gene044326:CDS
TGTAATAGTCCAATGCAAGC+CGG 0.540454 3.4:-77788400 None:intergenic
GAGAGTAGGGCGATCTTCAT+CGG 0.549057 3.4:-77788366 None:intergenic
ATAACAGTGTTCCTGGCGGA+CGG 0.549223 3.4:-77788316 None:intergenic
ATGTCTATGGAATTCAATAC+CGG 0.569805 3.4:+77787870 MS.gene044326:CDS
CGCAGTCACACGAACTCCCA+CGG 0.573058 3.4:+77787899 MS.gene044326:CDS
ACCGCGGGGTTCTGTTTGGG+AGG 0.573859 3.4:+77787995 MS.gene044326:CDS
TTCCAGGCCCAAGTTTGGGA+CGG 0.574885 3.4:+77788675 MS.gene044326:CDS
AGAACCCAAACCGAAACCGC+GGG 0.577512 3.4:+77787980 MS.gene044326:CDS
CCTGGAAAGTTGTTAAAGCA+GGG 0.579311 3.4:-77788659 None:intergenic
CTACTCTCAATGAACTCTCC+CGG 0.588355 3.4:+77788381 MS.gene044326:CDS
CGTGGGAGTTCGTGTGACTG+CGG 0.590663 3.4:-77787898 None:intergenic
TCGTGTGACTGCGGGCACGC+CGG 0.604081 3.4:-77787889 None:intergenic
GAGCATTTAGAGCGTTCTCG+CGG 0.611708 3.4:+77788149 MS.gene044326:CDS
CCGCCAGGAACACTGTTATG+TGG 0.616088 3.4:+77788320 MS.gene044326:CDS
TTCGGAACCGGAATTAGGAT+CGG 0.619721 3.4:+77787953 MS.gene044326:CDS
TGGAAAGTTGTTAAAGCAGG+GGG 0.622860 3.4:-77788657 None:intergenic
ACAGTGTTCCTGGCGGACGG+GGG 0.624136 3.4:-77788313 None:intergenic
GATCTTCATCGGTTATGAAG+AGG 0.624382 3.4:-77788355 None:intergenic
GTCAAGTGTACCTATGATGT+TGG 0.629074 3.4:+77788561 MS.gene044326:CDS
CTGGAAAGTTGTTAAAGCAG+GGG 0.630786 3.4:-77788658 None:intergenic
TCTTCATCGGTTATGAAGAG+GGG 0.634517 3.4:-77788353 None:intergenic
AAGAACCCAAACCGAAACCG+CGG 0.646068 3.4:+77787979 MS.gene044326:CDS
TAAACTCAGGAAGAAACTAG+AGG 0.667176 3.4:+77788115 MS.gene044326:CDS
TTGTGTACAAGAATAAACTC+AGG 0.668106 3.4:+77788102 MS.gene044326:CDS
CCAGGAACACTGTTATGTGG+CGG 0.691865 3.4:+77788323 MS.gene044326:CDS
GAACCCAAACCGAAACCGCG+GGG 0.744268 3.4:+77787981 MS.gene044326:CDS
TCCTCCCAAACAGAACCCCG+CGG 0.747056 3.4:-77787996 None:intergenic
GGAAAGTTGTTAAAGCAGGG+GGG 0.752617 3.4:-77788656 None:intergenic
CCACATAACAGTGTTCCTGG+CGG 0.759130 3.4:-77788320 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTCTTCTTAATTAATTATT+AGG + chr3.4:77788512-77788531 MS.gene044326:intron 15.0%
!! TTATCACAAATATATATGTA+AGG - chr3.4:77788080-77788099 None:intergenic 15.0%
!!! TAATTAATTTTGATTCTTTC+TGG + chr3.4:77788252-77788271 MS.gene044326:intron 15.0%
ACTTGATGAAACTCAAATGT+TGG - chr3.4:77788540-77788559 None:intergenic 30.0%
ATAGATAATTCACTCAACTC+TGG - chr3.4:77788038-77788057 None:intergenic 30.0%
ATGTCTATGGAATTCAATAC+CGG + chr3.4:77787870-77787889 MS.gene044326:CDS 30.0%
CAGTGCAAACAATAATAATC+AGG + chr3.4:77788421-77788440 MS.gene044326:CDS 30.0%
TTGTGTACAAGAATAAACTC+AGG + chr3.4:77788102-77788121 MS.gene044326:CDS 30.0%
TAAACTCAGGAAGAAACTAG+AGG + chr3.4:77788115-77788134 MS.gene044326:CDS 35.0%
! ATCTTCATCGGTTATGAAGA+GGG - chr3.4:77788357-77788376 None:intergenic 35.0%
!! GTCTTTTGCATTAGCTTGAA+AGG - chr3.4:77788616-77788635 None:intergenic 35.0%
AACACAACACAACACAACAC+AGG + chr3.4:77788277-77788296 MS.gene044326:intron 40.0%
AAGAAGGAAGATGCCGAATT+CGG + chr3.4:77787935-77787954 MS.gene044326:CDS 40.0%
AGCAGCAATACCAACATCAT+AGG - chr3.4:77788574-77788593 None:intergenic 40.0%
ATAGACGCATACGTACACTT+AGG - chr3.4:77788175-77788194 None:intergenic 40.0%
ATCAAAACCGTCCCAAACTT+GGG - chr3.4:77788685-77788704 None:intergenic 40.0%
CCTGGAAAGTTGTTAAAGCA+GGG - chr3.4:77788662-77788681 None:intergenic 40.0%
CTGGAAAGTTGTTAAAGCAG+GGG - chr3.4:77788661-77788680 None:intergenic 40.0%
GTCAAGTGTACCTATGATGT+TGG + chr3.4:77788561-77788580 MS.gene044326:CDS 40.0%
TATCAAAACCGTCCCAAACT+TGG - chr3.4:77788686-77788705 None:intergenic 40.0%
TATGATGTTGGTATTGCTGC+TGG + chr3.4:77788573-77788592 MS.gene044326:CDS 40.0%
TCTTGTTCCGATCCTAATTC+CGG - chr3.4:77787963-77787982 None:intergenic 40.0%
TGGAAAGTTGTTAAAGCAGG+GGG - chr3.4:77788660-77788679 None:intergenic 40.0%
TGTAATAGTCCAATGCAAGC+CGG - chr3.4:77788403-77788422 None:intergenic 40.0%
! GATCTTCATCGGTTATGAAG+AGG - chr3.4:77788358-77788377 None:intergenic 40.0%
! TCTTCATCGGTTATGAAGAG+GGG - chr3.4:77788356-77788375 None:intergenic 40.0%
AACTTTCCAGGCCCAAGTTT+GGG + chr3.4:77788671-77788690 MS.gene044326:CDS 45.0%
ATCGGTTATGAAGAGGGGTT+GGG - chr3.4:77788351-77788370 None:intergenic 45.0%
CCCTGCTTTAACAACTTTCC+AGG + chr3.4:77788659-77788678 MS.gene044326:CDS 45.0%
CCTAATTCCGGTTCCGAATT+CGG - chr3.4:77787951-77787970 None:intergenic 45.0%
CGGAAAACTGCAGAGAAAGA+AGG + chr3.4:77787919-77787938 MS.gene044326:CDS 45.0%
CTACTCTCAATGAACTCTCC+CGG + chr3.4:77788381-77788400 MS.gene044326:CDS 45.0%
GCCTGGAAAGTTGTTAAAGC+AGG - chr3.4:77788663-77788682 None:intergenic 45.0%
GGAAAGTTGTTAAAGCAGGG+GGG - chr3.4:77788659-77788678 None:intergenic 45.0%
GGGAGAGTTCATTGAGAGTA+GGG - chr3.4:77788382-77788401 None:intergenic 45.0%
GTAATAGTCCAATGCAAGCC+GGG - chr3.4:77788402-77788421 None:intergenic 45.0%
TTCGGAACCGGAATTAGGAT+CGG + chr3.4:77787953-77787972 MS.gene044326:CDS 45.0%
! CTTTCTCTGCAGTTTTCCGT+GGG - chr3.4:77787918-77787937 None:intergenic 45.0%
! TCTTTCTCTGCAGTTTTCCG+TGG - chr3.4:77787919-77787938 None:intergenic 45.0%
AAGAACCCAAACCGAAACCG+CGG + chr3.4:77787979-77787998 MS.gene044326:CDS 50.0%
ATAACAGTGTTCCTGGCGGA+CGG - chr3.4:77788319-77788338 None:intergenic 50.0%
CAACTTTCCAGGCCCAAGTT+TGG + chr3.4:77788670-77788689 MS.gene044326:CDS 50.0%
CCACATAACAGTGTTCCTGG+CGG - chr3.4:77788323-77788342 None:intergenic 50.0%
CCAGGAACACTGTTATGTGG+CGG + chr3.4:77788323-77788342 MS.gene044326:CDS 50.0%
CCGAATTCGGAACCGGAATT+AGG + chr3.4:77787948-77787967 MS.gene044326:CDS 50.0%
CGGGAGAGTTCATTGAGAGT+AGG - chr3.4:77788383-77788402 None:intergenic 50.0%
GAAGATGCCGAATTCGGAAC+CGG + chr3.4:77787941-77787960 MS.gene044326:CDS 50.0%
GAGAGTAGGGCGATCTTCAT+CGG - chr3.4:77788369-77788388 None:intergenic 50.0%
! CATCGGTTATGAAGAGGGGT+TGG - chr3.4:77788352-77788371 None:intergenic 50.0%
! GAGCATTTAGAGCGTTCTCG+CGG + chr3.4:77788149-77788168 MS.gene044326:CDS 50.0%
AGAACCCAAACCGAAACCGC+GGG + chr3.4:77787980-77787999 MS.gene044326:CDS 55.0%
CAAACAGAACCCCGCGGTTT+CGG - chr3.4:77787993-77788012 None:intergenic 55.0%
CCGCCACATAACAGTGTTCC+TGG - chr3.4:77788326-77788345 None:intergenic 55.0%
CCGCCAGGAACACTGTTATG+TGG + chr3.4:77788320-77788339 MS.gene044326:CDS 55.0%
GAAACCGCGGGGTTCTGTTT+GGG + chr3.4:77787992-77788011 MS.gene044326:CDS 55.0%
TGTTAAAGCAGGGGGGCTGT+CGG - chr3.4:77788652-77788671 None:intergenic 55.0%
TTCCAGGCCCAAGTTTGGGA+CGG + chr3.4:77788675-77788694 MS.gene044326:CDS 55.0%
! TAACAGTGTTCCTGGCGGAC+GGG - chr3.4:77788318-77788337 None:intergenic 55.0%
! TGAACTCTCCCGGCTTGCAT+TGG + chr3.4:77788391-77788410 MS.gene044326:CDS 55.0%
AACCGTCCCAAACTTGGGCC+TGG - chr3.4:77788680-77788699 None:intergenic 60.0%
AGAACCCCGCGGTTTCGGTT+TGG - chr3.4:77787988-77788007 None:intergenic 60.0%
CGAAACCGCGGGGTTCTGTT+TGG + chr3.4:77787991-77788010 MS.gene044326:CDS 60.0%
CGCAGTCACACGAACTCCCA+CGG + chr3.4:77787899-77787918 MS.gene044326:CDS 60.0%
CGTGGGAGTTCGTGTGACTG+CGG - chr3.4:77787901-77787920 None:intergenic 60.0%
GAACCCAAACCGAAACCGCG+GGG + chr3.4:77787981-77788000 MS.gene044326:CDS 60.0%
GAACCCCGCGGTTTCGGTTT+GGG - chr3.4:77787987-77788006 None:intergenic 60.0%
GTGGGAGTTCGTGTGACTGC+GGG - chr3.4:77787900-77787919 None:intergenic 60.0%
TCCTCCCAAACAGAACCCCG+CGG - chr3.4:77787999-77788018 None:intergenic 60.0%
! AACAGTGTTCCTGGCGGACG+GGG - chr3.4:77788317-77788336 None:intergenic 60.0%
AAAGCAGGGGGGCTGTCGGA+AGG - chr3.4:77788648-77788667 None:intergenic 65.0%
AAGCAGGGGGGCTGTCGGAA+GGG - chr3.4:77788647-77788666 None:intergenic 65.0%
ACCGCGGGGTTCTGTTTGGG+AGG + chr3.4:77787995-77788014 MS.gene044326:CDS 65.0%
GCGGGGTTCTGTTTGGGAGG+AGG + chr3.4:77787998-77788017 MS.gene044326:CDS 65.0%
! ACAGTGTTCCTGGCGGACGG+GGG - chr3.4:77788316-77788335 None:intergenic 65.0%
GATGTTCTCCCCCGTCCGCC+AGG + chr3.4:77788305-77788324 MS.gene044326:CDS 70.0%
TCGTGTGACTGCGGGCACGC+CGG - chr3.4:77787892-77787911 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 77787870 77788743 77787870 ID=MS.gene044326
chr3.4 mRNA 77787870 77788743 77787870 ID=MS.gene044326.t1;Parent=MS.gene044326
chr3.4 exon 77787870 77788178 77787870 ID=MS.gene044326.t1.exon1;Parent=MS.gene044326.t1
chr3.4 CDS 77787870 77788178 77787870 ID=cds.MS.gene044326.t1;Parent=MS.gene044326.t1
chr3.4 exon 77788299 77788442 77788299 ID=MS.gene044326.t1.exon2;Parent=MS.gene044326.t1
chr3.4 CDS 77788299 77788442 77788299 ID=cds.MS.gene044326.t1;Parent=MS.gene044326.t1
chr3.4 exon 77788534 77788743 77788534 ID=MS.gene044326.t1.exon3;Parent=MS.gene044326.t1
chr3.4 CDS 77788534 77788743 77788534 ID=cds.MS.gene044326.t1;Parent=MS.gene044326.t1
Gene Sequence

>MS.gene044326

ATGTCTATGGAATTCAATACCGGCGTGCCCGCAGTCACACGAACTCCCACGGAAAACTGCAGAGAAAGAAGGAAGATGCCGAATTCGGAACCGGAATTAGGATCGGAACAAGAACCCAAACCGAAACCGCGGGGTTCTGTTTGGGAGGAGGTGTACGATGAAGATCCAGAGTTGAGTGAATTATCTATCTATGATGATGATGACGAGCCTTACATATATATTTGTGATAAATTTGTGTACAAGAATAAACTCAGGAAGAAACTAGAGGAAGCAGATAATGAGCATTTAGAGCGTTCTCGCGGCCTAAGTGTACGTATGCGTCTATCTATCTATTTCATTTTTGTTTTCAATTCACTGTTTTTCTTCAATTCTGTTTCACTCTTAATTAATTTTGATTCTTTCTGGACAACACAACACAACACAACACAGGTGTACGATGTTCTCCCCCGTCCGCCAGGAACACTGTTATGTGGCGGTACCCAACCCCTCTTCATAACCGATGAAGATCGCCCTACTCTCAATGAACTCTCCCGGCTTGCATTGGACTATTACAGTGCAAACAATAATAATCAGGTTCAATACTTAATACTTAACTGAAGAGAATGAATGAATATTGTATGTTGTTTATTCACTAAACTAATTGTTCTTCTTAATTAATTATTAGGCTCCAACATTTGAGTTTCATCAAGTTGTCAAGTGTACCTATGATGTTGGTATTGCTGCTGGCAATATGTTTTACATTACCTTTCAAGCTAATGCAAAAGACAAAGAAGACCCTTCCGACAGCCCCCCTGCTTTAACAACTTTCCAGGCCCAAGTTTGGGACGGTTTTGATAAATCACGCAATGTCATCAAGTGCACCATTAAAGTCTAA

Protein sequence

>MS.gene044326.t1

MSMEFNTGVPAVTRTPTENCRERRKMPNSEPELGSEQEPKPKPRGSVWEEVYDEDPELSELSIYDDDDEPYIYICDKFVYKNKLRKKLEEADNEHLERSRGLSVYDVLPRPPGTLLCGGTQPLFITDEDRPTLNELSRLALDYYSANNNNQAPTFEFHQVVKCTYDVGIAAGNMFYITFQANAKDKEDPSDSPPALTTFQAQVWDGFDKSRNVIKCTIKV