AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0924910


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 77 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 6_2:+67483735 Msa0924910:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_2:-67483622 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:+67483537 Msa0924910:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:-67483674 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_2:+67483879 Msa0924910:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_2:+67483847 Msa0924910:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:+67483574 Msa0924910:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_2:+67483880 Msa0924910:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:-67483547 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_2:+67483920 Msa0924910:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:-67483556 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:+67483490 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_2:-67483919 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_2:-67483836 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_2:+67483925 Msa0924910:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_2:+67483848 Msa0924910:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_2:+67483736 Msa0924910:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:-67483498 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_2:-67483931 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_2:-67483730 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_2:-67483913 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_2:-67483991 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:+67483684 Msa0924910:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_2:-67483731 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_2:-67483621 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_2:-67483937 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_2:-67483860 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_2:-67483965 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:-67483546 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_2:-67483985 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_2:+67483957 Msa0924910:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_2:-67483966 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_2:-67483936 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_2:+67483921 Msa0924910:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:-67483699 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_2:-67483798 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:-67483584 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_2:-67483933 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_2:-67483880 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_2:-67483772 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_2:-67483932 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:-67483667 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_2:-67483859 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:-67483497 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:-67483666 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_2:+67483851 Msa0924910:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_2:+67483881 Msa0924910:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_2:+67483798 Msa0924910:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_2:+67483700 Msa0924910:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:-67483526 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_2:+67483774 Msa0924910:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_2:-67483864 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_2:-67483992 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_2:-67484022 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_2:-67483771 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_2:-67483889 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_2:-67483608 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_2:-67483973 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_2:-67483861 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_2:-67483970 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:-67483629 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_2:-67483759 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:-67483529 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:-67483681 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_2:-67483831 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:-67483573 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_2:-67484019 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:+67483651 Msa0924910:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_2:-67483877 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_2:+67483758 Msa0924910:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_2:-67483620 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_2:-67483789 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:-67483684 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_2:-67483815 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_2:-67483812 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:+67483567 Msa0924910:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_2:-67483729 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr6_2:67483624-67483643 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr6_2:67483549-67483568 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr6_2:67483623-67483642 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr6_2:67483625-67483644 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr6_2:67483632-67483651 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr6_2:67483651-67483670 Msa0924910:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr6_2:67483994-67484013 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr6_2:67483995-67484014 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr6_2:67483550-67483569 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr6_2:67483611-67483630 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr6_2:67483628-67483647 Msa0924910:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr6_2:67483649-67483668 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr6_2:67483716-67483735 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr6_2:67483815-67483834 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr6_2:67483818-67483837 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr6_2:67483834-67483853 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr6_2:67483532-67483551 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr6_2:67483537-67483556 Msa0924910:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr6_2:67483559-67483578 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr6_2:67483567-67483586 Msa0924910:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr6_2:67483717-67483736 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr6_2:67483774-67483793 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr6_2:67483774-67483793 Msa0924910:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr6_2:67483839-67483858 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr6_2:67483879-67483898 Msa0924910:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr6_2:67483892-67483911 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr6_2:67483916-67483935 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr6_2:67483669-67483688 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr6_2:67483670-67483689 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr6_2:67483669-67483688 Msa0924910:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr6_2:67483677-67483696 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr6_2:67483747-67483766 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr6_2:67483775-67483794 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr6_2:67483792-67483811 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr6_2:67483880-67483899 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr6_2:67483880-67483899 Msa0924910:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr6_2:67483881-67483900 Msa0924910:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr6_2:67483921-67483940 Msa0924910:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr6_2:67483934-67483953 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr6_2:67483935-67483954 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr6_2:67483939-67483958 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr6_2:67483940-67483959 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr6_2:67483973-67483992 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr6_2:67483976-67483995 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr6_2:67483988-67484007 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr6_2:67483529-67483548 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr6_2:67483587-67483606 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr6_2:67483702-67483721 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr6_2:67483700-67483719 Msa0924910:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr6_2:67483746-67483765 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr6_2:67483758-67483777 Msa0924910:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr6_2:67483762-67483781 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr6_2:67483801-67483820 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr6_2:67483798-67483817 Msa0924910:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr6_2:67483863-67483882 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr6_2:67483864-67483883 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr6_2:67483867-67483886 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr6_2:67483883-67483902 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr6_2:67483922-67483941 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr6_2:67483920-67483939 Msa0924910:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr6_2:67483936-67483955 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr6_2:67483968-67483987 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr6_2:67483969-67483988 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr6_2:67483576-67483595 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr6_2:67483574-67483593 Msa0924910:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr6_2:67483732-67483751 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr6_2:67483733-67483752 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr6_2:67483734-67483753 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr6_2:67483735-67483754 Msa0924910:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr6_2:67483736-67483755 Msa0924910:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr6_2:67483743-67483762 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr6_2:67483847-67483866 Msa0924910:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr6_2:67483848-67483867 Msa0924910:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr6_2:67483862-67483881 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr6_2:67483925-67483944 Msa0924910:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr6_2:67483957-67483976 Msa0924910:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr6_2:67483684-67483703 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr6_2:67483687-67483706 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr6_2:67483684-67483703 Msa0924910:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr6_2:67483728-67483747 Msa0924910:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr6_2:67483851-67483870 Msa0924910:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 67483499 67484034 67483499 ID=Msa0924910;Name=Msa0924910
chr6_2 mRNA 67483499 67484034 67483499 ID=Msa0924910-mRNA-1;Parent=Msa0924910;Name=Msa0924910-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr6_2 exon 67483499 67483636 67483499 ID=Msa0924910-mRNA-1:exon:10671;Parent=Msa0924910-mRNA-1
chr6_2 exon 67483650 67483745 67483650 ID=Msa0924910-mRNA-1:exon:10672;Parent=Msa0924910-mRNA-1
chr6_2 exon 67483750 67484034 67483750 ID=Msa0924910-mRNA-1:exon:10673;Parent=Msa0924910-mRNA-1
chr6_2 CDS 67483499 67483636 67483499 ID=Msa0924910-mRNA-1:cds;Parent=Msa0924910-mRNA-1
chr6_2 CDS 67483650 67483745 67483650 ID=Msa0924910-mRNA-1:cds;Parent=Msa0924910-mRNA-1
chr6_2 CDS 67483750 67484034 67483750 ID=Msa0924910-mRNA-1:cds;Parent=Msa0924910-mRNA-1
Gene Sequence

>Msa0924910

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0924910

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS