AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908710


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:+9799734 Msa0908710:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_2:-9799621 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:+9799536 Msa0908710:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:-9799673 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_2:+9799878 Msa0908710:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_2:+9799846 Msa0908710:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:+9799573 Msa0908710:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_2:+9799879 Msa0908710:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:-9799546 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_2:+9799919 Msa0908710:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:-9799555 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:+9799489 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_2:-9799918 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_2:-9799835 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_2:+9799924 Msa0908710:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_2:+9799847 Msa0908710:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_2:+9799735 Msa0908710:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:-9799497 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_2:-9799930 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_2:-9799729 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_2:-9799912 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_2:-9799990 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:+9799683 Msa0908710:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_2:-9799730 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_2:-9799620 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_2:-9799936 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_2:-9799859 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_2:-9799964 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:-9799545 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_2:-9799984 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_2:+9799956 Msa0908710:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_2:-9799965 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_2:-9799935 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_2:+9799920 Msa0908710:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:-9799698 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_2:-9799797 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:-9799583 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_2:-9799932 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_2:-9799879 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_2:-9799771 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_2:-9799931 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:-9799666 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_2:-9799858 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:-9799496 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:-9799665 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_2:+9799850 Msa0908710:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_2:+9799880 Msa0908710:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_2:+9799797 Msa0908710:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_2:+9799699 Msa0908710:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:-9799525 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_2:+9799773 Msa0908710:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_2:-9799863 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_2:-9799991 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_2:-9800021 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_2:-9799770 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_2:-9799888 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_2:-9799607 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_2:-9799972 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_2:-9799860 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_2:-9799969 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:-9799628 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_2:-9799758 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:-9799528 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:-9799680 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_2:-9799830 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:-9799572 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_2:-9800018 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:+9799650 Msa0908710:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_2:-9799876 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_2:+9799757 Msa0908710:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_2:-9799619 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_2:-9799788 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:-9799683 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_2:-9799814 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_2:-9799811 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:+9799566 Msa0908710:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_2:-9799728 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr6_2:9799623-9799642 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr6_2:9799548-9799567 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr6_2:9799622-9799641 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr6_2:9799624-9799643 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr6_2:9799631-9799650 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr6_2:9799650-9799669 Msa0908710:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr6_2:9799993-9800012 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr6_2:9799994-9800013 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr6_2:9799549-9799568 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr6_2:9799610-9799629 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr6_2:9799627-9799646 Msa0908710:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr6_2:9799648-9799667 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr6_2:9799715-9799734 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr6_2:9799814-9799833 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr6_2:9799817-9799836 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr6_2:9799833-9799852 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr6_2:9799531-9799550 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr6_2:9799536-9799555 Msa0908710:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr6_2:9799558-9799577 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr6_2:9799566-9799585 Msa0908710:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr6_2:9799716-9799735 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr6_2:9799773-9799792 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr6_2:9799773-9799792 Msa0908710:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr6_2:9799838-9799857 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr6_2:9799878-9799897 Msa0908710:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr6_2:9799891-9799910 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr6_2:9799915-9799934 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr6_2:9799668-9799687 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr6_2:9799669-9799688 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr6_2:9799668-9799687 Msa0908710:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr6_2:9799676-9799695 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr6_2:9799746-9799765 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr6_2:9799774-9799793 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr6_2:9799791-9799810 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr6_2:9799879-9799898 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr6_2:9799879-9799898 Msa0908710:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr6_2:9799880-9799899 Msa0908710:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr6_2:9799920-9799939 Msa0908710:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr6_2:9799933-9799952 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr6_2:9799934-9799953 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr6_2:9799938-9799957 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr6_2:9799939-9799958 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr6_2:9799972-9799991 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr6_2:9799975-9799994 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr6_2:9799987-9800006 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr6_2:9799528-9799547 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr6_2:9799586-9799605 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr6_2:9799701-9799720 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr6_2:9799699-9799718 Msa0908710:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr6_2:9799745-9799764 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr6_2:9799757-9799776 Msa0908710:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr6_2:9799761-9799780 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr6_2:9799800-9799819 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr6_2:9799797-9799816 Msa0908710:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr6_2:9799862-9799881 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr6_2:9799863-9799882 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr6_2:9799866-9799885 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr6_2:9799882-9799901 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr6_2:9799921-9799940 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr6_2:9799919-9799938 Msa0908710:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr6_2:9799935-9799954 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr6_2:9799967-9799986 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr6_2:9799968-9799987 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr6_2:9799575-9799594 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr6_2:9799573-9799592 Msa0908710:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr6_2:9799731-9799750 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr6_2:9799732-9799751 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr6_2:9799733-9799752 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr6_2:9799734-9799753 Msa0908710:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr6_2:9799735-9799754 Msa0908710:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr6_2:9799742-9799761 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr6_2:9799846-9799865 Msa0908710:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr6_2:9799847-9799866 Msa0908710:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr6_2:9799861-9799880 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr6_2:9799924-9799943 Msa0908710:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr6_2:9799956-9799975 Msa0908710:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr6_2:9799683-9799702 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr6_2:9799686-9799705 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr6_2:9799683-9799702 Msa0908710:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr6_2:9799727-9799746 Msa0908710:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr6_2:9799850-9799869 Msa0908710:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9799498 9800033 9799498 ID=Msa0908710;Name=Msa0908710
chr6_2 mRNA 9799498 9800033 9799498 ID=Msa0908710-mRNA-1;Parent=Msa0908710;Name=Msa0908710-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr6_2 exon 9799498 9799635 9799498 ID=Msa0908710-mRNA-1:exon:2457;Parent=Msa0908710-mRNA-1
chr6_2 exon 9799649 9799744 9799649 ID=Msa0908710-mRNA-1:exon:2458;Parent=Msa0908710-mRNA-1
chr6_2 exon 9799749 9800033 9799749 ID=Msa0908710-mRNA-1:exon:2459;Parent=Msa0908710-mRNA-1
chr6_2 CDS 9799498 9799635 9799498 ID=Msa0908710-mRNA-1:cds;Parent=Msa0908710-mRNA-1
chr6_2 CDS 9799649 9799744 9799649 ID=Msa0908710-mRNA-1:cds;Parent=Msa0908710-mRNA-1
chr6_2 CDS 9799749 9800033 9799749 ID=Msa0908710-mRNA-1:cds;Parent=Msa0908710-mRNA-1
Gene Sequence

>Msa0908710

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0908710

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS