AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908680


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:-9780884 Msa0908680:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_2:+9780997 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:-9781082 Msa0908680:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:+9780945 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_2:-9780740 Msa0908680:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_2:-9780772 Msa0908680:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:-9781045 Msa0908680:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_2:-9780739 Msa0908680:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:+9781072 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_2:-9780699 Msa0908680:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:+9781063 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:-9781129 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_2:+9780700 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_2:+9780783 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_2:-9780694 Msa0908680:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_2:-9780771 Msa0908680:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_2:-9780883 Msa0908680:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:+9781121 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_2:+9780688 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_2:+9780889 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_2:+9780706 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_2:+9780628 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:-9780935 Msa0908680:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_2:+9780888 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_2:+9780998 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_2:+9780682 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_2:+9780759 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_2:+9780654 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:+9781073 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_2:+9780634 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_2:-9780662 Msa0908680:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_2:+9780653 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_2:+9780683 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_2:-9780698 Msa0908680:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:+9780920 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_2:+9780821 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:+9781035 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_2:+9780686 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_2:+9780739 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_2:+9780847 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_2:+9780687 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:+9780952 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_2:+9780760 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:+9781122 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:+9780953 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_2:-9780768 Msa0908680:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_2:-9780738 Msa0908680:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_2:-9780821 Msa0908680:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_2:-9780919 Msa0908680:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:+9781093 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_2:-9780845 Msa0908680:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_2:+9780755 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_2:+9780627 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_2:+9780597 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_2:+9780848 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_2:+9780730 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_2:+9781011 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_2:+9780646 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_2:+9780758 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_2:+9780649 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:+9780990 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_2:+9780860 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:+9781090 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:+9780938 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_2:+9780788 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:+9781046 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_2:+9780600 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:-9780968 Msa0908680:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_2:+9780742 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_2:-9780861 Msa0908680:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_2:+9780999 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_2:+9780830 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:+9780935 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_2:+9780804 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_2:+9780807 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:-9781052 Msa0908680:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_2:+9780890 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr6_2:9780732-9780751 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr6_2:9780657-9780676 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr6_2:9780731-9780750 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr6_2:9780733-9780752 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr6_2:9780740-9780759 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr6_2:9780759-9780778 Msa0908680:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr6_2:9781102-9781121 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr6_2:9781103-9781122 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr6_2:9780658-9780677 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr6_2:9780719-9780738 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr6_2:9780736-9780755 Msa0908680:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr6_2:9780757-9780776 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr6_2:9780824-9780843 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr6_2:9780923-9780942 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr6_2:9780926-9780945 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr6_2:9780942-9780961 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr6_2:9780640-9780659 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr6_2:9780645-9780664 Msa0908680:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr6_2:9780667-9780686 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr6_2:9780675-9780694 Msa0908680:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr6_2:9780825-9780844 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr6_2:9780882-9780901 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr6_2:9780882-9780901 Msa0908680:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr6_2:9780947-9780966 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr6_2:9780987-9781006 Msa0908680:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr6_2:9781000-9781019 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr6_2:9781024-9781043 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr6_2:9780777-9780796 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr6_2:9780778-9780797 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr6_2:9780777-9780796 Msa0908680:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr6_2:9780785-9780804 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr6_2:9780855-9780874 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr6_2:9780883-9780902 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr6_2:9780900-9780919 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr6_2:9780988-9781007 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr6_2:9780988-9781007 Msa0908680:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr6_2:9780989-9781008 Msa0908680:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr6_2:9781029-9781048 Msa0908680:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr6_2:9781042-9781061 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr6_2:9781043-9781062 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr6_2:9781047-9781066 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr6_2:9781048-9781067 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr6_2:9781081-9781100 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr6_2:9781084-9781103 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr6_2:9781096-9781115 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr6_2:9780637-9780656 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr6_2:9780695-9780714 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr6_2:9780810-9780829 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr6_2:9780808-9780827 Msa0908680:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr6_2:9780854-9780873 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr6_2:9780866-9780885 Msa0908680:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr6_2:9780870-9780889 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr6_2:9780909-9780928 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr6_2:9780906-9780925 Msa0908680:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr6_2:9780971-9780990 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr6_2:9780972-9780991 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr6_2:9780975-9780994 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr6_2:9780991-9781010 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr6_2:9781030-9781049 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr6_2:9781028-9781047 Msa0908680:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr6_2:9781044-9781063 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr6_2:9781076-9781095 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr6_2:9781077-9781096 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr6_2:9780684-9780703 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr6_2:9780682-9780701 Msa0908680:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr6_2:9780840-9780859 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr6_2:9780841-9780860 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr6_2:9780842-9780861 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr6_2:9780843-9780862 Msa0908680:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr6_2:9780844-9780863 Msa0908680:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr6_2:9780851-9780870 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr6_2:9780955-9780974 Msa0908680:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr6_2:9780956-9780975 Msa0908680:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr6_2:9780970-9780989 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr6_2:9781033-9781052 Msa0908680:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr6_2:9781065-9781084 Msa0908680:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr6_2:9780792-9780811 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr6_2:9780795-9780814 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr6_2:9780792-9780811 Msa0908680:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr6_2:9780836-9780855 Msa0908680:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr6_2:9780959-9780978 Msa0908680:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9780607 9781142 9780607 ID=Msa0908680;Name=Msa0908680
chr6_2 mRNA 9780607 9781142 9780607 ID=Msa0908680-mRNA-1;Parent=Msa0908680;Name=Msa0908680-mRNA-1;_AED=0.42;_eAED=0.45;_QI=0|0|0|1|0|0|3|0|173
chr6_2 exon 9781005 9781142 9781005 ID=Msa0908680-mRNA-1:exon:2415;Parent=Msa0908680-mRNA-1
chr6_2 exon 9780896 9780991 9780896 ID=Msa0908680-mRNA-1:exon:2414;Parent=Msa0908680-mRNA-1
chr6_2 exon 9780607 9780891 9780607 ID=Msa0908680-mRNA-1:exon:2413;Parent=Msa0908680-mRNA-1
chr6_2 CDS 9781005 9781142 9781005 ID=Msa0908680-mRNA-1:cds;Parent=Msa0908680-mRNA-1
chr6_2 CDS 9780896 9780991 9780896 ID=Msa0908680-mRNA-1:cds;Parent=Msa0908680-mRNA-1
chr6_2 CDS 9780607 9780891 9780607 ID=Msa0908680-mRNA-1:cds;Parent=Msa0908680-mRNA-1
Gene Sequence

>Msa0908680

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0908680

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS