AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908300


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 65 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 6_2:+9523671 Msa0908300:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_2:-9523558 Msa0908290:intron
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:-9523610 Msa0908290:CDS
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_2:+9523815 Msa0908300:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_2:+9523783 Msa0908300:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_2:+9523816 Msa0908300:CDS
ACCGTCATTGTTTCTTCTCC+AGG 0.384151 6_2:+9523564 Msa0908300:CDS
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_2:+9523856 Msa0908300:CDS
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_2:-9523855 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_2:-9523772 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_2:+9523861 Msa0908300:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_2:+9523784 Msa0908300:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_2:+9523672 Msa0908300:intron
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_2:-9523867 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_2:-9523666 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_2:-9523849 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_2:-9523927 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:+9523620 Msa0908300:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_2:-9523667 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_2:-9523557 Msa0908290:intron
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_2:-9523873 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_2:-9523796 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_2:-9523901 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_2:-9523921 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_2:+9523893 Msa0908300:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_2:-9523902 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_2:-9523872 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_2:+9523857 Msa0908300:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:-9523635 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_2:-9523734 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_2:-9523869 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_2:-9523816 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_2:-9523708 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_2:-9523868 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:-9523603 Msa0908290:CDS
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_2:-9523795 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:-9523602 Msa0908290:CDS
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_2:+9523787 Msa0908300:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_2:+9523817 Msa0908300:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_2:+9523734 Msa0908300:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_2:+9523636 Msa0908300:CDS
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_2:+9523710 Msa0908300:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_2:-9523800 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_2:-9523928 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_2:-9523958 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_2:-9523707 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_2:-9523825 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_2:-9523544 Msa0908290:intron
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_2:-9523909 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_2:-9523797 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_2:-9523906 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:-9523565 Msa0908290:intron
GCCACACTGGGACTGAGACA+AGG 0.629204 6_2:-9523695 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:-9523617 Msa0908290:CDS
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_2:-9523767 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_2:-9523955 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:+9523587 Msa0908300:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_2:-9523813 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_2:+9523694 Msa0908300:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_2:-9523556 Msa0908290:intron
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_2:-9523725 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:-9523620 Msa0908290:CDS
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_2:-9523751 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_2:-9523748 None:intergenic
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_2:-9523665 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr6_2:9523560-9523579 Msa0908290:intron 35.0%
AGAAACAATGACGGTATCTG+GGG - chr6_2:9523559-9523578 Msa0908290:intron 40.0%
GAAGAAACAATGACGGTATC+TGG - chr6_2:9523561-9523580 Msa0908290:intron 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr6_2:9523568-9523587 Msa0908290:CDS 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr6_2:9523587-9523606 Msa0908300:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr6_2:9523930-9523949 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr6_2:9523931-9523950 None:intergenic 40.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr6_2:9523564-9523583 Msa0908300:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr6_2:9523585-9523604 Msa0908290:CDS 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr6_2:9523652-9523671 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr6_2:9523751-9523770 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr6_2:9523754-9523773 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr6_2:9523770-9523789 None:intergenic 45.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr6_2:9523653-9523672 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr6_2:9523710-9523729 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr6_2:9523710-9523729 Msa0908300:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr6_2:9523775-9523794 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr6_2:9523815-9523834 Msa0908300:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr6_2:9523828-9523847 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr6_2:9523852-9523871 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr6_2:9523605-9523624 Msa0908290:CDS 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr6_2:9523606-9523625 Msa0908290:CDS 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr6_2:9523605-9523624 Msa0908300:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr6_2:9523613-9523632 Msa0908290:CDS 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr6_2:9523683-9523702 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr6_2:9523711-9523730 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr6_2:9523728-9523747 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr6_2:9523816-9523835 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr6_2:9523816-9523835 Msa0908300:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr6_2:9523817-9523836 Msa0908300:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr6_2:9523857-9523876 Msa0908300:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr6_2:9523870-9523889 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr6_2:9523871-9523890 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr6_2:9523875-9523894 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr6_2:9523876-9523895 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr6_2:9523909-9523928 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr6_2:9523912-9523931 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr6_2:9523924-9523943 None:intergenic 55.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr6_2:9523638-9523657 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr6_2:9523636-9523655 Msa0908300:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr6_2:9523682-9523701 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr6_2:9523694-9523713 Msa0908300:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr6_2:9523698-9523717 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr6_2:9523737-9523756 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr6_2:9523734-9523753 Msa0908300:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr6_2:9523799-9523818 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr6_2:9523800-9523819 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr6_2:9523803-9523822 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr6_2:9523819-9523838 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr6_2:9523858-9523877 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr6_2:9523856-9523875 Msa0908300:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr6_2:9523872-9523891 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr6_2:9523904-9523923 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr6_2:9523905-9523924 None:intergenic 60.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr6_2:9523668-9523687 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr6_2:9523669-9523688 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr6_2:9523670-9523689 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr6_2:9523671-9523690 Msa0908300:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr6_2:9523672-9523691 Msa0908300:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr6_2:9523679-9523698 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr6_2:9523783-9523802 Msa0908300:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr6_2:9523784-9523803 Msa0908300:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr6_2:9523798-9523817 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr6_2:9523861-9523880 Msa0908300:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr6_2:9523893-9523912 Msa0908300:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr6_2:9523620-9523639 Msa0908290:CDS 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr6_2:9523623-9523642 Msa0908290:CDS 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr6_2:9523620-9523639 Msa0908300:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr6_2:9523664-9523683 Msa0908300:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr6_2:9523787-9523806 Msa0908300:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9523547 9523973 9523547 ID=Msa0908300;Name=Msa0908300
chr6_2 mRNA 9523547 9523973 9523547 ID=Msa0908300-mRNA-1;Parent=Msa0908300;Name=Msa0908300-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|0|0|1|0|0.5|2|0|140
chr6_2 exon 9523547 9523681 9523547 ID=Msa0908300-mRNA-1:exon:2275;Parent=Msa0908300-mRNA-1
chr6_2 exon 9523686 9523973 9523686 ID=Msa0908300-mRNA-1:exon:2276;Parent=Msa0908300-mRNA-1
chr6_2 CDS 9523547 9523681 9523547 ID=Msa0908300-mRNA-1:cds;Parent=Msa0908300-mRNA-1
chr6_2 CDS 9523686 9523973 9523686 ID=Msa0908300-mRNA-1:cds;Parent=Msa0908300-mRNA-1
Gene Sequence

>Msa0908300

ATGCTTATTCCCCAGATACCGTCATTGTTTCTTCTCCAGGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCCTGA

Protein sequence

>Msa0908300

MLIPQIPSLFLLQEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS*