AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268290


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 2_2:+70165795 Msa0268290:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 2_2:-70165682 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 2_2:+70165597 Msa0268290:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 2_2:-70165734 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 2_2:+70165939 Msa0268290:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 2_2:+70165907 Msa0268290:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 2_2:+70165634 Msa0268290:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 2_2:+70165940 Msa0268290:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 2_2:-70165607 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 2_2:+70165980 Msa0268290:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 2_2:-70165616 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 2_2:+70165550 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 2_2:-70165979 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 2_2:-70165896 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 2_2:+70165985 Msa0268290:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 2_2:+70165908 Msa0268290:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 2_2:+70165796 Msa0268290:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 2_2:-70165558 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 2_2:-70165991 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 2_2:-70165790 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 2_2:-70165973 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 2_2:-70166051 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 2_2:+70165744 Msa0268290:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 2_2:-70165791 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 2_2:-70165681 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 2_2:-70165997 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 2_2:-70165920 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 2_2:-70166025 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 2_2:-70165606 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 2_2:-70166045 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 2_2:+70166017 Msa0268290:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 2_2:-70166026 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 2_2:-70165996 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 2_2:+70165981 Msa0268290:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 2_2:-70165759 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 2_2:-70165858 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 2_2:-70165644 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 2_2:-70165993 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 2_2:-70165940 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 2_2:-70165832 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 2_2:-70165992 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 2_2:-70165727 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 2_2:-70165919 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 2_2:-70165557 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 2_2:-70165726 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 2_2:+70165911 Msa0268290:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 2_2:+70165941 Msa0268290:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 2_2:+70165858 Msa0268290:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 2_2:+70165760 Msa0268290:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 2_2:-70165586 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 2_2:+70165834 Msa0268290:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 2_2:-70165924 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 2_2:-70166052 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 2_2:-70166082 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 2_2:-70165831 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 2_2:-70165949 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 2_2:-70165668 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 2_2:-70166033 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 2_2:-70165921 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 2_2:-70166030 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 2_2:-70165689 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 2_2:-70165819 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 2_2:-70165589 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 2_2:-70165741 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 2_2:-70165891 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 2_2:-70165633 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 2_2:-70166079 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 2_2:+70165711 Msa0268290:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 2_2:-70165937 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 2_2:+70165818 Msa0268290:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 2_2:-70165680 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 2_2:-70165849 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 2_2:-70165744 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 2_2:-70165875 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 2_2:-70165872 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 2_2:+70165627 Msa0268290:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 2_2:-70165789 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr2_2:70165684-70165703 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr2_2:70165609-70165628 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr2_2:70165683-70165702 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr2_2:70165685-70165704 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr2_2:70165692-70165711 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr2_2:70165711-70165730 Msa0268290:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr2_2:70166054-70166073 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr2_2:70166055-70166074 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr2_2:70165610-70165629 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr2_2:70165671-70165690 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr2_2:70165688-70165707 Msa0268290:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr2_2:70165709-70165728 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr2_2:70165776-70165795 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr2_2:70165875-70165894 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr2_2:70165878-70165897 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr2_2:70165894-70165913 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr2_2:70165592-70165611 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr2_2:70165597-70165616 Msa0268290:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr2_2:70165619-70165638 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr2_2:70165627-70165646 Msa0268290:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr2_2:70165777-70165796 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr2_2:70165834-70165853 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr2_2:70165834-70165853 Msa0268290:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr2_2:70165899-70165918 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr2_2:70165939-70165958 Msa0268290:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr2_2:70165952-70165971 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr2_2:70165976-70165995 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr2_2:70165729-70165748 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr2_2:70165730-70165749 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr2_2:70165729-70165748 Msa0268290:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr2_2:70165737-70165756 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr2_2:70165807-70165826 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr2_2:70165835-70165854 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr2_2:70165852-70165871 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr2_2:70165940-70165959 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr2_2:70165940-70165959 Msa0268290:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr2_2:70165941-70165960 Msa0268290:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr2_2:70165981-70166000 Msa0268290:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr2_2:70165994-70166013 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr2_2:70165995-70166014 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr2_2:70165999-70166018 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr2_2:70166000-70166019 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr2_2:70166033-70166052 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr2_2:70166036-70166055 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr2_2:70166048-70166067 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr2_2:70165589-70165608 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr2_2:70165647-70165666 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr2_2:70165762-70165781 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr2_2:70165760-70165779 Msa0268290:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr2_2:70165806-70165825 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr2_2:70165818-70165837 Msa0268290:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr2_2:70165822-70165841 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr2_2:70165861-70165880 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr2_2:70165858-70165877 Msa0268290:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr2_2:70165923-70165942 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr2_2:70165924-70165943 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr2_2:70165927-70165946 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr2_2:70165943-70165962 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr2_2:70165982-70166001 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr2_2:70165980-70165999 Msa0268290:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr2_2:70165996-70166015 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr2_2:70166028-70166047 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr2_2:70166029-70166048 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr2_2:70165636-70165655 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr2_2:70165634-70165653 Msa0268290:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr2_2:70165792-70165811 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr2_2:70165793-70165812 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr2_2:70165794-70165813 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr2_2:70165795-70165814 Msa0268290:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr2_2:70165796-70165815 Msa0268290:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr2_2:70165803-70165822 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr2_2:70165907-70165926 Msa0268290:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr2_2:70165908-70165927 Msa0268290:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr2_2:70165922-70165941 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr2_2:70165985-70166004 Msa0268290:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr2_2:70166017-70166036 Msa0268290:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr2_2:70165744-70165763 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr2_2:70165747-70165766 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr2_2:70165744-70165763 Msa0268290:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr2_2:70165788-70165807 Msa0268290:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr2_2:70165911-70165930 Msa0268290:CDS 75.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70165559 70166094 70165559 ID=Msa0268290;Name=Msa0268290
chr2_2 mRNA 70165559 70166094 70165559 ID=Msa0268290-mRNA-1;Parent=Msa0268290;Name=Msa0268290-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr2_2 exon 70165559 70165696 70165559 ID=Msa0268290-mRNA-1:exon:22499;Parent=Msa0268290-mRNA-1
chr2_2 exon 70165710 70165805 70165710 ID=Msa0268290-mRNA-1:exon:22500;Parent=Msa0268290-mRNA-1
chr2_2 exon 70165810 70166094 70165810 ID=Msa0268290-mRNA-1:exon:22501;Parent=Msa0268290-mRNA-1
chr2_2 CDS 70165559 70165696 70165559 ID=Msa0268290-mRNA-1:cds;Parent=Msa0268290-mRNA-1
chr2_2 CDS 70165710 70165805 70165710 ID=Msa0268290-mRNA-1:cds;Parent=Msa0268290-mRNA-1
chr2_2 CDS 70165810 70166094 70165810 ID=Msa0268290-mRNA-1:cds;Parent=Msa0268290-mRNA-1
Gene Sequence

>Msa0268290

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0268290

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS