AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0269160


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:-70538693 Msa0269160:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 2_2:+70538806 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 2_2:-70538891 Msa0269160:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 2_2:+70538754 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 2_2:-70538549 Msa0269160:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 2_2:-70538581 Msa0269160:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 2_2:-70538854 Msa0269160:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 2_2:-70538548 Msa0269160:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 2_2:+70538881 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 2_2:-70538508 Msa0269160:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 2_2:+70538872 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 2_2:-70538938 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 2_2:+70538509 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 2_2:+70538592 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 2_2:-70538503 Msa0269160:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 2_2:-70538580 Msa0269160:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 2_2:-70538692 Msa0269160:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 2_2:+70538930 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 2_2:+70538497 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 2_2:+70538698 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 2_2:+70538515 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 2_2:+70538437 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 2_2:-70538744 Msa0269160:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 2_2:+70538697 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 2_2:+70538807 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 2_2:+70538491 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 2_2:+70538568 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 2_2:+70538463 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 2_2:+70538882 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 2_2:+70538443 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 2_2:-70538471 Msa0269160:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 2_2:+70538462 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 2_2:+70538492 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 2_2:-70538507 Msa0269160:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 2_2:+70538729 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 2_2:+70538630 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 2_2:+70538844 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 2_2:+70538495 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 2_2:+70538548 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 2_2:+70538656 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 2_2:+70538496 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 2_2:+70538761 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 2_2:+70538569 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 2_2:+70538931 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 2_2:+70538762 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 2_2:-70538577 Msa0269160:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 2_2:-70538547 Msa0269160:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 2_2:-70538630 Msa0269160:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 2_2:-70538728 Msa0269160:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 2_2:+70538902 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 2_2:-70538654 Msa0269160:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 2_2:+70538564 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 2_2:+70538436 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 2_2:+70538406 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 2_2:+70538657 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 2_2:+70538539 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 2_2:+70538820 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 2_2:+70538455 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 2_2:+70538567 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 2_2:+70538458 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 2_2:+70538799 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 2_2:+70538669 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 2_2:+70538899 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 2_2:+70538747 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 2_2:+70538597 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 2_2:+70538855 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 2_2:+70538409 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 2_2:-70538777 Msa0269160:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 2_2:+70538551 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 2_2:-70538670 Msa0269160:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 2_2:+70538808 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 2_2:+70538639 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 2_2:+70538744 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 2_2:+70538613 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 2_2:+70538616 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 2_2:-70538861 Msa0269160:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 2_2:+70538699 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr2_2:70538541-70538560 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr2_2:70538466-70538485 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr2_2:70538540-70538559 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr2_2:70538542-70538561 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr2_2:70538549-70538568 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr2_2:70538568-70538587 Msa0269160:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr2_2:70538911-70538930 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr2_2:70538912-70538931 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr2_2:70538467-70538486 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr2_2:70538528-70538547 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr2_2:70538545-70538564 Msa0269160:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr2_2:70538566-70538585 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr2_2:70538633-70538652 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr2_2:70538732-70538751 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr2_2:70538735-70538754 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr2_2:70538751-70538770 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr2_2:70538449-70538468 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr2_2:70538454-70538473 Msa0269160:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr2_2:70538476-70538495 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr2_2:70538484-70538503 Msa0269160:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr2_2:70538634-70538653 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr2_2:70538691-70538710 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr2_2:70538691-70538710 Msa0269160:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr2_2:70538756-70538775 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr2_2:70538796-70538815 Msa0269160:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr2_2:70538809-70538828 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr2_2:70538833-70538852 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr2_2:70538586-70538605 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr2_2:70538587-70538606 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr2_2:70538586-70538605 Msa0269160:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr2_2:70538594-70538613 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr2_2:70538664-70538683 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr2_2:70538692-70538711 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr2_2:70538709-70538728 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr2_2:70538797-70538816 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr2_2:70538797-70538816 Msa0269160:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr2_2:70538798-70538817 Msa0269160:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr2_2:70538838-70538857 Msa0269160:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr2_2:70538851-70538870 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr2_2:70538852-70538871 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr2_2:70538856-70538875 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr2_2:70538857-70538876 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr2_2:70538890-70538909 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr2_2:70538893-70538912 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr2_2:70538905-70538924 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr2_2:70538446-70538465 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr2_2:70538504-70538523 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr2_2:70538619-70538638 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr2_2:70538617-70538636 Msa0269160:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr2_2:70538663-70538682 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr2_2:70538675-70538694 Msa0269160:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr2_2:70538679-70538698 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr2_2:70538718-70538737 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr2_2:70538715-70538734 Msa0269160:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr2_2:70538780-70538799 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr2_2:70538781-70538800 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr2_2:70538784-70538803 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr2_2:70538800-70538819 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr2_2:70538839-70538858 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr2_2:70538837-70538856 Msa0269160:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr2_2:70538853-70538872 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr2_2:70538885-70538904 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr2_2:70538886-70538905 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr2_2:70538493-70538512 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr2_2:70538491-70538510 Msa0269160:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr2_2:70538649-70538668 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr2_2:70538650-70538669 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr2_2:70538651-70538670 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr2_2:70538652-70538671 Msa0269160:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr2_2:70538653-70538672 Msa0269160:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr2_2:70538660-70538679 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr2_2:70538764-70538783 Msa0269160:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr2_2:70538765-70538784 Msa0269160:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr2_2:70538779-70538798 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr2_2:70538842-70538861 Msa0269160:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr2_2:70538874-70538893 Msa0269160:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr2_2:70538601-70538620 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr2_2:70538604-70538623 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr2_2:70538601-70538620 Msa0269160:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr2_2:70538645-70538664 Msa0269160:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr2_2:70538768-70538787 Msa0269160:CDS 75.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70538416 70538951 70538416 ID=Msa0269160;Name=Msa0269160
chr2_2 mRNA 70538416 70538951 70538416 ID=Msa0269160-mRNA-1;Parent=Msa0269160;Name=Msa0269160-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr2_2 exon 70538814 70538951 70538814 ID=Msa0269160-mRNA-1:exon:22759;Parent=Msa0269160-mRNA-1
chr2_2 exon 70538705 70538800 70538705 ID=Msa0269160-mRNA-1:exon:22758;Parent=Msa0269160-mRNA-1
chr2_2 exon 70538416 70538700 70538416 ID=Msa0269160-mRNA-1:exon:22757;Parent=Msa0269160-mRNA-1
chr2_2 CDS 70538814 70538951 70538814 ID=Msa0269160-mRNA-1:cds;Parent=Msa0269160-mRNA-1
chr2_2 CDS 70538705 70538800 70538705 ID=Msa0269160-mRNA-1:cds;Parent=Msa0269160-mRNA-1
chr2_2 CDS 70538416 70538700 70538416 ID=Msa0269160-mRNA-1:cds;Parent=Msa0269160-mRNA-1
Gene Sequence

>Msa0269160

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0269160

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS