AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071884

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071884.t1 MTR_2g435780 83.099 71 8 1 1 67 1 71 2.55e-35 114
MS.gene071884.t1 MTR_2g435740 83.562 73 7 3 1 69 1 72 7.30e-34 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAAGGAAGATTGGCTTAGA+AGG 0.290742 2.2:+53065267 MS.gene071884:CDS
TGCATGCTGCTCCTTCTTGT+TGG 0.293203 2.2:-53065318 None:intergenic
AGCATGCAAGACCTTGCTTC+TGG 0.370001 2.2:+53065333 MS.gene071884:CDS
AGGATGGAACTGTTCTTGTT+GGG 0.402264 2.2:+53065364 MS.gene071884:CDS
AAGGATGGAACTGTTCTTGT+TGG 0.408271 2.2:+53065363 MS.gene071884:CDS
TCATCAGACCTAAGGAAGAT+TGG 0.412607 2.2:+53065258 MS.gene071884:CDS
GCTTTAATAGACAAGTTCTA+TGG 0.431998 2.2:+53065294 MS.gene071884:CDS
GCATGCAAGACCTTGCTTCT+GGG 0.437774 2.2:+53065334 MS.gene071884:CDS
ATCAAAGTCTTCTGTAGCTA+AGG 0.443745 2.2:+53065542 MS.gene071884:CDS
CTTCTAAGCCAATCTTCCTT+AGG 0.445559 2.2:-53065266 None:intergenic
TCAAAGTCTTCTGTAGCTAA+GGG 0.531279 2.2:+53065543 MS.gene071884:CDS
TAAGGAAGATTGGCTTAGAA+GGG 0.540665 2.2:+53065268 MS.gene071884:CDS
GCTTCTGGGATTAGCAAGGA+TGG 0.553628 2.2:+53065348 MS.gene071884:CDS
CACCTCCTTCATCAGACCTA+AGG 0.563117 2.2:+53065250 MS.gene071884:CDS
AGTTCTATGGTCCAACAAGA+AGG 0.572566 2.2:+53065307 MS.gene071884:CDS
GGATGGAACTGTTCTTGTTG+GGG 0.579567 2.2:+53065365 MS.gene071884:CDS
ATCTTCCTTAGGTCTGATGA+AGG 0.601958 2.2:-53065255 None:intergenic
CCTTGCTTCTGGGATTAGCA+AGG 0.605996 2.2:+53065344 MS.gene071884:CDS
CCTTGCTAATCCCAGAAGCA+AGG 0.646637 2.2:-53065344 None:intergenic
TTCCTTAGGTCTGATGAAGG+AGG 0.672818 2.2:-53065252 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAGTGCTTAAAATTTAAA+AGG - chr2.2:53065435-53065454 None:intergenic 15.0%
!! AATTTGCCTTAAATTTAAAG+TGG + chr2.2:53065452-53065471 MS.gene071884:intron 20.0%
!!! ATTTGCCTTAAATTTAAAGT+GGG + chr2.2:53065453-53065472 MS.gene071884:intron 20.0%
AAAATTACCCCAAAATCGTT+GGG + chr2.2:53065404-53065423 MS.gene071884:intron 30.0%
ATATGTAGAAAAAAGCTCGA+AGG + chr2.2:53065502-53065521 MS.gene071884:intron 30.0%
GCTTTAATAGACAAGTTCTA+TGG + chr2.2:53065294-53065313 MS.gene071884:CDS 30.0%
TGAGACCCACTTTAAATTTA+AGG - chr2.2:53065461-53065480 None:intergenic 30.0%
AAATTACCCCAAAATCGTTG+GGG + chr2.2:53065405-53065424 MS.gene071884:intron 35.0%
ATCAAAGTCTTCTGTAGCTA+AGG + chr2.2:53065542-53065561 MS.gene071884:CDS 35.0%
GAAAATTACCCCAAAATCGT+TGG + chr2.2:53065403-53065422 MS.gene071884:intron 35.0%
TCAAAGTCTTCTGTAGCTAA+GGG + chr2.2:53065543-53065562 MS.gene071884:CDS 35.0%
!! TAAGGAAGATTGGCTTAGAA+GGG + chr2.2:53065268-53065287 MS.gene071884:CDS 35.0%
!! TTTGGGGTAATTTTCCCTTA+GGG - chr2.2:53065398-53065417 None:intergenic 35.0%
!!! TTTTGGGGTAATTTTCCCTT+AGG - chr2.2:53065399-53065418 None:intergenic 35.0%
AAGGATGGAACTGTTCTTGT+TGG + chr2.2:53065363-53065382 MS.gene071884:CDS 40.0%
AGGATGGAACTGTTCTTGTT+GGG + chr2.2:53065364-53065383 MS.gene071884:CDS 40.0%
AGTTCTATGGTCCAACAAGA+AGG + chr2.2:53065307-53065326 MS.gene071884:CDS 40.0%
ATCTTCCTTAGGTCTGATGA+AGG - chr2.2:53065258-53065277 None:intergenic 40.0%
CTTCTAAGCCAATCTTCCTT+AGG - chr2.2:53065269-53065288 None:intergenic 40.0%
TCATCAGACCTAAGGAAGAT+TGG + chr2.2:53065258-53065277 MS.gene071884:CDS 40.0%
TGGGTCTCAGTTTCATGTTA+TGG + chr2.2:53065472-53065491 MS.gene071884:intron 40.0%
!! CTAAGGAAGATTGGCTTAGA+AGG + chr2.2:53065267-53065286 MS.gene071884:CDS 40.0%
GGATGGAACTGTTCTTGTTG+GGG + chr2.2:53065365-53065384 MS.gene071884:CDS 45.0%
GTTGGGGTAAGTTACCCTAA+GGG + chr2.2:53065381-53065400 MS.gene071884:intron 45.0%
TGTTGGGGTAAGTTACCCTA+AGG + chr2.2:53065380-53065399 MS.gene071884:intron 45.0%
TTCCTTAGGTCTGATGAAGG+AGG - chr2.2:53065255-53065274 None:intergenic 45.0%
! AAGGTCTACCCCAACGATTT+TGG - chr2.2:53065416-53065435 None:intergenic 45.0%
! AGGTCTACCCCAACGATTTT+GGG - chr2.2:53065415-53065434 None:intergenic 45.0%
AGCATGCAAGACCTTGCTTC+TGG + chr2.2:53065333-53065352 MS.gene071884:CDS 50.0%
CACCTCCTTCATCAGACCTA+AGG + chr2.2:53065250-53065269 MS.gene071884:CDS 50.0%
CCTTGCTAATCCCAGAAGCA+AGG - chr2.2:53065347-53065366 None:intergenic 50.0%
GCATGCAAGACCTTGCTTCT+GGG + chr2.2:53065334-53065353 MS.gene071884:CDS 50.0%
TGCATGCTGCTCCTTCTTGT+TGG - chr2.2:53065321-53065340 None:intergenic 50.0%
! GGTCTACCCCAACGATTTTG+GGG - chr2.2:53065414-53065433 None:intergenic 50.0%
!! CCTTGCTTCTGGGATTAGCA+AGG + chr2.2:53065344-53065363 MS.gene071884:CDS 50.0%
!! GCTTCTGGGATTAGCAAGGA+TGG + chr2.2:53065348-53065367 MS.gene071884:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53065246 53065578 53065246 ID=MS.gene071884
chr2.2 mRNA 53065246 53065578 53065246 ID=MS.gene071884.t1;Parent=MS.gene071884
chr2.2 exon 53065246 53065386 53065246 ID=MS.gene071884.t1.exon1;Parent=MS.gene071884.t1
chr2.2 CDS 53065246 53065386 53065246 ID=cds.MS.gene071884.t1;Parent=MS.gene071884.t1
chr2.2 exon 53065510 53065578 53065510 ID=MS.gene071884.t1.exon2;Parent=MS.gene071884.t1
chr2.2 CDS 53065510 53065578 53065510 ID=cds.MS.gene071884.t1;Parent=MS.gene071884.t1
Gene Sequence

>MS.gene071884

ATGGCACCTCCTTCATCAGACCTAAGGAAGATTGGCTTAGAAGGGTTTGCTTTAATAGACAAGTTCTATGGTCCAACAAGAAGGAGCAGCATGCAAGACCTTGCTTCTGGGATTAGCAAGGATGGAACTGTTCTTGTTGGGGTAAGTTACCCTAAGGGAAAATTACCCCAAAATCGTTGGGGTAGACCTTTTAAATTTTAAGCACTAATTTGCCTTAAATTTAAAGTGGGTCTCAGTTTCATGTTATGGTATATATATATGTAGAAAAAAGCTCGAAGGCATGTGATCATATTTAAATCAAAGTCTTCTGTAGCTAAGGGAGAGTATATGTAG
Protein sequence

>MS.gene071884.t1

MAPPSSDLRKIGLEGFALIDKFYGPTRRSSMQDLASGISKDGTVLVGKKARRHVIIFKSKSSVAKGEYM