AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086950


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 7_2:+87628923 Msa1086950:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 7_2:-87628810 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 7_2:+87628725 Msa1086950:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 7_2:-87628862 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 7_2:+87629067 Msa1086950:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 7_2:+87629035 Msa1086950:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 7_2:+87628762 Msa1086950:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 7_2:+87629068 Msa1086950:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 7_2:-87628735 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 7_2:+87629108 Msa1086950:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 7_2:-87628744 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 7_2:+87628678 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 7_2:-87629107 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 7_2:-87629024 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 7_2:+87629113 Msa1086950:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 7_2:+87629036 Msa1086950:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 7_2:+87628924 Msa1086950:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 7_2:-87628686 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 7_2:-87629119 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 7_2:-87628918 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 7_2:-87629101 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 7_2:-87629179 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 7_2:+87628872 Msa1086950:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 7_2:-87628919 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 7_2:-87628809 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 7_2:-87629125 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 7_2:-87629048 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 7_2:-87629153 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 7_2:-87628734 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 7_2:-87629173 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 7_2:+87629145 Msa1086950:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 7_2:-87629154 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 7_2:-87629124 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 7_2:+87629109 Msa1086950:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 7_2:-87628887 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 7_2:-87628986 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 7_2:-87628772 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 7_2:-87629121 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 7_2:-87629068 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 7_2:-87628960 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 7_2:-87629120 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 7_2:-87628855 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 7_2:-87629047 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 7_2:-87628685 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 7_2:-87628854 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 7_2:+87629039 Msa1086950:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 7_2:+87629069 Msa1086950:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 7_2:+87628986 Msa1086950:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 7_2:+87628888 Msa1086950:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 7_2:-87628714 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 7_2:+87628962 Msa1086950:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 7_2:-87629052 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 7_2:-87629180 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 7_2:-87629210 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 7_2:-87628959 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 7_2:-87629077 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 7_2:-87628796 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 7_2:-87629161 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 7_2:-87629049 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 7_2:-87629158 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 7_2:-87628817 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 7_2:-87628947 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 7_2:-87628717 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 7_2:-87628869 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 7_2:-87629019 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 7_2:-87628761 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 7_2:-87629207 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 7_2:+87628839 Msa1086950:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 7_2:-87629065 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 7_2:+87628946 Msa1086950:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 7_2:-87628808 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 7_2:-87628977 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 7_2:-87628872 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 7_2:-87629003 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 7_2:-87629000 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 7_2:+87628755 Msa1086950:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 7_2:-87628917 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr7_2:87628812-87628831 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr7_2:87628737-87628756 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr7_2:87628811-87628830 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr7_2:87628813-87628832 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr7_2:87628820-87628839 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr7_2:87628839-87628858 Msa1086950:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr7_2:87629182-87629201 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr7_2:87629183-87629202 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr7_2:87628738-87628757 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr7_2:87628799-87628818 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr7_2:87628816-87628835 Msa1086950:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr7_2:87628837-87628856 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr7_2:87628904-87628923 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr7_2:87629003-87629022 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr7_2:87629006-87629025 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr7_2:87629022-87629041 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr7_2:87628720-87628739 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr7_2:87628725-87628744 Msa1086950:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr7_2:87628747-87628766 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr7_2:87628755-87628774 Msa1086950:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr7_2:87628905-87628924 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr7_2:87628962-87628981 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr7_2:87628962-87628981 Msa1086950:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr7_2:87629027-87629046 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr7_2:87629067-87629086 Msa1086950:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr7_2:87629080-87629099 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr7_2:87629104-87629123 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr7_2:87628857-87628876 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr7_2:87628858-87628877 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr7_2:87628857-87628876 Msa1086950:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr7_2:87628865-87628884 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr7_2:87628935-87628954 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr7_2:87628963-87628982 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr7_2:87628980-87628999 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr7_2:87629068-87629087 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr7_2:87629068-87629087 Msa1086950:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr7_2:87629069-87629088 Msa1086950:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr7_2:87629109-87629128 Msa1086950:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr7_2:87629122-87629141 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr7_2:87629123-87629142 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr7_2:87629127-87629146 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr7_2:87629128-87629147 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr7_2:87629161-87629180 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr7_2:87629164-87629183 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr7_2:87629176-87629195 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr7_2:87628717-87628736 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr7_2:87628775-87628794 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr7_2:87628890-87628909 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr7_2:87628888-87628907 Msa1086950:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr7_2:87628934-87628953 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr7_2:87628946-87628965 Msa1086950:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr7_2:87628950-87628969 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr7_2:87628989-87629008 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr7_2:87628986-87629005 Msa1086950:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr7_2:87629051-87629070 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr7_2:87629052-87629071 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr7_2:87629055-87629074 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr7_2:87629071-87629090 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr7_2:87629110-87629129 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr7_2:87629108-87629127 Msa1086950:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr7_2:87629124-87629143 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr7_2:87629156-87629175 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr7_2:87629157-87629176 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr7_2:87628764-87628783 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr7_2:87628762-87628781 Msa1086950:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr7_2:87628920-87628939 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr7_2:87628921-87628940 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr7_2:87628922-87628941 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr7_2:87628923-87628942 Msa1086950:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr7_2:87628924-87628943 Msa1086950:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr7_2:87628931-87628950 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr7_2:87629035-87629054 Msa1086950:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr7_2:87629036-87629055 Msa1086950:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr7_2:87629050-87629069 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr7_2:87629113-87629132 Msa1086950:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr7_2:87629145-87629164 Msa1086950:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr7_2:87628872-87628891 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr7_2:87628875-87628894 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr7_2:87628872-87628891 Msa1086950:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr7_2:87628916-87628935 Msa1086950:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr7_2:87629039-87629058 Msa1086950:CDS 75.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87628687 87629222 87628687 ID=Msa1086950;Name=Msa1086950
chr7_2 mRNA 87628687 87629222 87628687 ID=Msa1086950-mRNA-1;Parent=Msa1086950;Name=Msa1086950-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr7_2 exon 87628687 87628824 87628687 ID=Msa1086950-mRNA-1:exon:23946;Parent=Msa1086950-mRNA-1
chr7_2 exon 87628838 87628933 87628838 ID=Msa1086950-mRNA-1:exon:23947;Parent=Msa1086950-mRNA-1
chr7_2 exon 87628938 87629222 87628938 ID=Msa1086950-mRNA-1:exon:23948;Parent=Msa1086950-mRNA-1
chr7_2 CDS 87628687 87628824 87628687 ID=Msa1086950-mRNA-1:cds;Parent=Msa1086950-mRNA-1
chr7_2 CDS 87628838 87628933 87628838 ID=Msa1086950-mRNA-1:cds;Parent=Msa1086950-mRNA-1
chr7_2 CDS 87628938 87629222 87628938 ID=Msa1086950-mRNA-1:cds;Parent=Msa1086950-mRNA-1
Gene Sequence

>Msa1086950

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1086950

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS