AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060873

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 55 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACCGGACTTGGTTTCTTA+TGG 0.276601 2.1:+2234933 MS.gene060873:CDS
GTTTATGCCACCTTGGTAGA+TGG 0.290569 2.1:+2235158 MS.gene060873:CDS
ATTGATGCAAAATACAAGTA+TGG 0.293296 2.1:+2234648 MS.gene060873:CDS
TTGCCGACGTTAGAAACTTA+TGG 0.335709 2.1:+2234513 MS.gene060873:CDS
GGTGTATAACTAAATTTATT+CGG 0.355932 2.1:-2234831 None:intergenic
CATTTCTGAAAGTAGTAGTT+TGG 0.387144 2.1:-2235105 None:intergenic
ATATTGTAAGTCGTAATATC+TGG 0.409159 2.1:-2234726 None:intergenic
ATTGATGGGTTAAGTAAGGT+TGG 0.422336 2.1:+2234543 MS.gene060873:CDS
ACTTATGGTGCTTTGATTGA+TGG 0.432257 2.1:+2234528 MS.gene060873:CDS
TTTATCCATGGAAGTGTAGC+TGG 0.441465 2.1:+2234960 MS.gene060873:CDS
AGGGTGTATTTCCTGATGCT+TGG 0.443116 2.1:+2235030 MS.gene060873:CDS
TAAACAAGGGGATTATGTTA+TGG 0.451868 2.1:+2234872 MS.gene060873:CDS
TTTGATTGATGGGTTAAGTA+AGG 0.454899 2.1:+2234539 MS.gene060873:CDS
TGCTGAAACAGGAGATAAAC+CGG 0.455612 2.1:+2234917 MS.gene060873:CDS
TCATAGAGAGGGCGGAAGAA+AGG 0.472797 2.1:+2234799 MS.gene060873:CDS
TTTATGCCACCTTGGTAGAT+GGG 0.482996 2.1:+2235159 MS.gene060873:CDS
CTTATGGTGCTTTGATTGAT+GGG 0.486525 2.1:+2234529 MS.gene060873:CDS
ATGAGTGGTCTCTGCAAGAA+AGG 0.487223 2.1:+2235068 MS.gene060873:CDS
ACATTGTAAATCCAAGCATC+AGG 0.500423 2.1:-2235041 None:intergenic
GAAAGTAGTAGTTTGGCAGC+AGG 0.505552 2.1:-2235098 None:intergenic
GTGGCATAAACATATGCATC+AGG 0.508594 2.1:-2235146 None:intergenic
TGCAAAATACAAGTATGGTT+TGG 0.514908 2.1:+2234653 MS.gene060873:CDS
TTGAATGAAATGAATGTGAT+GGG 0.523841 2.1:+2234591 MS.gene060873:CDS
CCATGGAAGTGTAGCTGGTG+GGG 0.526547 2.1:+2234965 MS.gene060873:CDS
CCCCACCAGCTACACTTCCA+TGG 0.535623 2.1:-2234965 None:intergenic
TTTGAATGAAATGAATGTGA+TGG 0.547924 2.1:+2234590 MS.gene060873:CDS
ATGCATGCTTACTGTAAACA+AGG 0.551583 2.1:+2234858 MS.gene060873:CDS
AACAGGAGATAAACCGGACT+TGG 0.552984 2.1:+2234923 MS.gene060873:CDS
GGAAATCGATGTTGCACTGA+TGG 0.553650 2.1:+2234986 MS.gene060873:CDS
CCGAGAGAAAATGATGGAGA+AGG 0.556874 2.1:+2235010 MS.gene060873:CDS
AAGCTGCCGAGATGATGAAA+AGG 0.570305 2.1:+2234682 MS.gene060873:CDS
ATTTACAATGTTCTGATGAG+TGG 0.577117 2.1:+2235053 MS.gene060873:CDS
TCCATGGAAGTGTAGCTGGT+GGG 0.577837 2.1:+2234964 MS.gene060873:CDS
GCTCCATAAGAAACCAAGTC+CGG 0.581941 2.1:-2234936 None:intergenic
AGGGGATTATGTTATGGCAT+CGG 0.583182 2.1:+2234878 MS.gene060873:CDS
GATGGTCCGAGAGAAAATGA+TGG 0.586916 2.1:+2235004 MS.gene060873:CDS
AGCTGAAGAATTCATAGAGA+GGG 0.587830 2.1:+2234788 MS.gene060873:CDS
GATGAAAAGGATGTCTGAGA+TGG 0.589043 2.1:+2234695 MS.gene060873:CDS
CGAGAGAAAATGATGGAGAA+GGG 0.591583 2.1:+2235011 MS.gene060873:CDS
TGCATATGTTTATGCCACCT+TGG 0.594141 2.1:+2235151 MS.gene060873:CDS
GTTTACAGTAAGCATGCATG+AGG 0.594418 2.1:-2234854 None:intergenic
ATCCATGGAAGTGTAGCTGG+TGG 0.596016 2.1:+2234963 MS.gene060873:CDS
TTTACAGTAAGCATGCATGA+GGG 0.602682 2.1:-2234853 None:intergenic
AAAATACAAGTATGGTTTGG+TGG 0.609459 2.1:+2234656 MS.gene060873:CDS
TTCTAATAACCCATCTACCA+AGG 0.632664 2.1:-2235168 None:intergenic
ATGAAAAGGATGTCTGAGAT+GGG 0.632768 2.1:+2234696 MS.gene060873:CDS
CAATGAACTTGACAAGGCAG+CGG 0.636132 2.1:+2235192 MS.gene060873:CDS
TGAAGAATTCATAGAGAGGG+CGG 0.637639 2.1:+2234791 MS.gene060873:CDS
TAGAAACAATGAACTTGACA+AGG 0.643103 2.1:+2235186 MS.gene060873:CDS
TTACAGTAAGCATGCATGAG+GGG 0.649206 2.1:-2234852 None:intergenic
TGCATGCTTACTGTAAACAA+GGG 0.655313 2.1:+2234859 MS.gene060873:CDS
AAGCTGAAGAATTCATAGAG+AGG 0.663794 2.1:+2234787 MS.gene060873:CDS
GCACCATAAGTTTCTAACGT+CGG 0.670334 2.1:-2234516 None:intergenic
GCATGCTTACTGTAAACAAG+GGG 0.685140 2.1:+2234860 MS.gene060873:CDS
TAATAACCCATCTACCAAGG+TGG 0.714675 2.1:-2235165 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GGTGTATAACTAAATTTATT+CGG - chr2.1:2234834-2234853 None:intergenic 20.0%
! ATATTGTAAGTCGTAATATC+TGG - chr2.1:2234729-2234748 None:intergenic 25.0%
! ATTGATGCAAAATACAAGTA+TGG + chr2.1:2234648-2234667 MS.gene060873:CDS 25.0%
! TTGAATGAAATGAATGTGAT+GGG + chr2.1:2234591-2234610 MS.gene060873:CDS 25.0%
! TTTGAATGAAATGAATGTGA+TGG + chr2.1:2234590-2234609 MS.gene060873:CDS 25.0%
!! TTGATTAACTTTTCATGTAG+AGG + chr2.1:2234750-2234769 MS.gene060873:CDS 25.0%
ATTTACAATGTTCTGATGAG+TGG + chr2.1:2235053-2235072 MS.gene060873:CDS 30.0%
TAAACAAGGGGATTATGTTA+TGG + chr2.1:2234872-2234891 MS.gene060873:CDS 30.0%
TAGAAACAATGAACTTGACA+AGG + chr2.1:2235186-2235205 MS.gene060873:CDS 30.0%
TGCAAAATACAAGTATGGTT+TGG + chr2.1:2234653-2234672 MS.gene060873:CDS 30.0%
! AAAATACAAGTATGGTTTGG+TGG + chr2.1:2234656-2234675 MS.gene060873:CDS 30.0%
! ATTAACTTTTCATGTAGAGG+TGG + chr2.1:2234753-2234772 MS.gene060873:CDS 30.0%
! CATTTCTGAAAGTAGTAGTT+TGG - chr2.1:2235108-2235127 None:intergenic 30.0%
!! TTTGATTGATGGGTTAAGTA+AGG + chr2.1:2234539-2234558 MS.gene060873:CDS 30.0%
!!! CTTTTTAAGATTGCTGAAAC+AGG + chr2.1:2234906-2234925 MS.gene060873:CDS 30.0%
AAGCTGAAGAATTCATAGAG+AGG + chr2.1:2234787-2234806 MS.gene060873:CDS 35.0%
ACATTGTAAATCCAAGCATC+AGG - chr2.1:2235044-2235063 None:intergenic 35.0%
ACTTATGGTGCTTTGATTGA+TGG + chr2.1:2234528-2234547 MS.gene060873:CDS 35.0%
AGCTGAAGAATTCATAGAGA+GGG + chr2.1:2234788-2234807 MS.gene060873:CDS 35.0%
ATGCATGCTTACTGTAAACA+AGG + chr2.1:2234858-2234877 MS.gene060873:CDS 35.0%
CTTATGGTGCTTTGATTGAT+GGG + chr2.1:2234529-2234548 MS.gene060873:CDS 35.0%
TGCATGCTTACTGTAAACAA+GGG + chr2.1:2234859-2234878 MS.gene060873:CDS 35.0%
TTCTAATAACCCATCTACCA+AGG - chr2.1:2235171-2235190 None:intergenic 35.0%
TTTACAGTAAGCATGCATGA+GGG - chr2.1:2234856-2234875 None:intergenic 35.0%
! AGACATCCTTTTCATCATCT+CGG - chr2.1:2234691-2234710 None:intergenic 35.0%
! ATGAAAAGGATGTCTGAGAT+GGG + chr2.1:2234696-2234715 MS.gene060873:CDS 35.0%
! TCTTATGGAGCTTTTATCCA+TGG + chr2.1:2234948-2234967 MS.gene060873:CDS 35.0%
!! ATTGATGGGTTAAGTAAGGT+TGG + chr2.1:2234543-2234562 MS.gene060873:CDS 35.0%
AGGGGATTATGTTATGGCAT+CGG + chr2.1:2234878-2234897 MS.gene060873:CDS 40.0%
GATGAAAAGGATGTCTGAGA+TGG + chr2.1:2234695-2234714 MS.gene060873:CDS 40.0%
GCACCATAAGTTTCTAACGT+CGG - chr2.1:2234519-2234538 None:intergenic 40.0%
GCATGCTTACTGTAAACAAG+GGG + chr2.1:2234860-2234879 MS.gene060873:CDS 40.0%
GTGGCATAAACATATGCATC+AGG - chr2.1:2235149-2235168 None:intergenic 40.0%
GTTTACAGTAAGCATGCATG+AGG - chr2.1:2234857-2234876 None:intergenic 40.0%
TAATAACCCATCTACCAAGG+TGG - chr2.1:2235168-2235187 None:intergenic 40.0%
TGAAGAATTCATAGAGAGGG+CGG + chr2.1:2234791-2234810 MS.gene060873:CDS 40.0%
TGCATATGTTTATGCCACCT+TGG + chr2.1:2235151-2235170 MS.gene060873:CDS 40.0%
TGCTGAAACAGGAGATAAAC+CGG + chr2.1:2234917-2234936 MS.gene060873:CDS 40.0%
TTACAGTAAGCATGCATGAG+GGG - chr2.1:2234855-2234874 None:intergenic 40.0%
TTGCCGACGTTAGAAACTTA+TGG + chr2.1:2234513-2234532 MS.gene060873:CDS 40.0%
TTTATGCCACCTTGGTAGAT+GGG + chr2.1:2235159-2235178 MS.gene060873:CDS 40.0%
! AAACCGGACTTGGTTTCTTA+TGG + chr2.1:2234933-2234952 MS.gene060873:CDS 40.0%
! ACTTTTCATGTAGAGGTGGA+AGG + chr2.1:2234757-2234776 MS.gene060873:CDS 40.0%
! CCTTCTCCATCATTTTCTCT+CGG - chr2.1:2235013-2235032 None:intergenic 40.0%
! CGAGAGAAAATGATGGAGAA+GGG + chr2.1:2235011-2235030 MS.gene060873:CDS 40.0%
! TTTATCCATGGAAGTGTAGC+TGG + chr2.1:2234960-2234979 MS.gene060873:CDS 40.0%
AACAGGAGATAAACCGGACT+TGG + chr2.1:2234923-2234942 MS.gene060873:CDS 45.0%
AAGCTGCCGAGATGATGAAA+AGG + chr2.1:2234682-2234701 MS.gene060873:CDS 45.0%
AGGGTGTATTTCCTGATGCT+TGG + chr2.1:2235030-2235049 MS.gene060873:CDS 45.0%
ATGAGTGGTCTCTGCAAGAA+AGG + chr2.1:2235068-2235087 MS.gene060873:CDS 45.0%
CAATGAACTTGACAAGGCAG+CGG + chr2.1:2235192-2235211 MS.gene060873:CDS 45.0%
GAAAGTAGTAGTTTGGCAGC+AGG - chr2.1:2235101-2235120 None:intergenic 45.0%
GATGGTCCGAGAGAAAATGA+TGG + chr2.1:2235004-2235023 MS.gene060873:CDS 45.0%
GCTCCATAAGAAACCAAGTC+CGG - chr2.1:2234939-2234958 None:intergenic 45.0%
GGAAATCGATGTTGCACTGA+TGG + chr2.1:2234986-2235005 MS.gene060873:CDS 45.0%
GTTTATGCCACCTTGGTAGA+TGG + chr2.1:2235158-2235177 MS.gene060873:CDS 45.0%
! CCGAGAGAAAATGATGGAGA+AGG + chr2.1:2235010-2235029 MS.gene060873:CDS 45.0%
TCATAGAGAGGGCGGAAGAA+AGG + chr2.1:2234799-2234818 MS.gene060873:CDS 50.0%
! ATCCATGGAAGTGTAGCTGG+TGG + chr2.1:2234963-2234982 MS.gene060873:CDS 50.0%
! TCCATGGAAGTGTAGCTGGT+GGG + chr2.1:2234964-2234983 MS.gene060873:CDS 50.0%
!!! GCAGCGGAGCTTTTTGAAGT+CGG + chr2.1:2235208-2235227 MS.gene060873:CDS 50.0%
! CCATGGAAGTGTAGCTGGTG+GGG + chr2.1:2234965-2234984 MS.gene060873:CDS 55.0%
CCCCACCAGCTACACTTCCA+TGG - chr2.1:2234968-2234987 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 2234506 2235228 2234506 ID=MS.gene060873
chr2.1 mRNA 2234506 2235228 2234506 ID=MS.gene060873.t1;Parent=MS.gene060873
chr2.1 exon 2234506 2235228 2234506 ID=MS.gene060873.t1.exon1;Parent=MS.gene060873.t1
chr2.1 CDS 2234506 2235228 2234506 ID=cds.MS.gene060873.t1;Parent=MS.gene060873.t1
Gene Sequence

>MS.gene060873

GGTTTTTTTGCCGACGTTAGAAACTTATGGTGCTTTGATTGATGGGTTAAGTAAGGTTGGAAAGTTTCAAGTAGTTGATCAGCTTTTGAATGAAATGAATGTGATGGGATTGAATATGAATGTAAAAGTGTTTAATAGTATTATTGATGCAAAATACAAGTATGGTTTGGTGGATGAAGCTGCCGAGATGATGAAAAGGATGTCTGAGATGGGCTGTGAGCCAGATATTACGACTTACAATATTTTGATTAACTTTTCATGTAGAGGTGGAAGGATTAAAGAAGCTGAAGAATTCATAGAGAGGGCGGAAGAAAGGAGATTGTTGCCGAATAAATTTAGTTATACACCCCTCATGCATGCTTACTGTAAACAAGGGGATTATGTTATGGCATCGGATATGCTTTTTAAGATTGCTGAAACAGGAGATAAACCGGACTTGGTTTCTTATGGAGCTTTTATCCATGGAAGTGTAGCTGGTGGGGAAATCGATGTTGCACTGATGGTCCGAGAGAAAATGATGGAGAAGGGTGTATTTCCTGATGCTTGGATTTACAATGTTCTGATGAGTGGTCTCTGCAAGAAAGGAAGATTTCCTGCTGCCAAACTACTACTTTCAGAAATGCTTGATCGAAACTTACAACCTGATGCATATGTTTATGCCACCTTGGTAGATGGGTTATTAGAAACAATGAACTTGACAAGGCAGCGGAGCTTTTTGAAGTC
Protein sequence

>MS.gene060873.t1

GFFADVRNLWCFDUWVKUGWKVSSSUSAFEUNECDGIEYECKSVUUYYUCKIQVWFGGUSCRDDEKDVUDGLUARYYDLQYFDULFMURWKDURSURIHREGGRKEIVAEUIULYTPHACLLUTRGLCYGIGYAFUDCUNRRUTGLGFLWSFYPWKCSWWGNRCCTDGPRENDGEGCISUCLDLQCSDEWSLQERKISCCQTTTFRNAUSKLTTUCICLCHLGRWVIRNNELDKAAELFEV