AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1087100


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 7_2:+87731610 Msa1087100:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 7_2:-87731497 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 7_2:+87731412 Msa1087100:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 7_2:-87731549 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 7_2:+87731754 Msa1087100:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 7_2:+87731722 Msa1087100:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 7_2:+87731449 Msa1087100:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 7_2:+87731755 Msa1087100:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 7_2:-87731422 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 7_2:+87731795 Msa1087100:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 7_2:-87731431 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 7_2:+87731365 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 7_2:-87731794 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 7_2:-87731711 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 7_2:+87731800 Msa1087100:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 7_2:+87731723 Msa1087100:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 7_2:+87731611 Msa1087100:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 7_2:-87731373 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 7_2:-87731806 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 7_2:-87731605 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 7_2:-87731788 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 7_2:-87731866 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 7_2:+87731559 Msa1087100:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 7_2:-87731606 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 7_2:-87731496 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 7_2:-87731812 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 7_2:-87731735 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 7_2:-87731840 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 7_2:-87731421 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 7_2:-87731860 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 7_2:+87731832 Msa1087100:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 7_2:-87731841 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 7_2:-87731811 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 7_2:+87731796 Msa1087100:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 7_2:-87731574 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 7_2:-87731673 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 7_2:-87731459 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 7_2:-87731808 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 7_2:-87731755 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 7_2:-87731647 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 7_2:-87731807 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 7_2:-87731542 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 7_2:-87731734 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 7_2:-87731372 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 7_2:-87731541 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 7_2:+87731726 Msa1087100:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 7_2:+87731756 Msa1087100:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 7_2:+87731673 Msa1087100:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 7_2:+87731575 Msa1087100:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 7_2:-87731401 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 7_2:+87731649 Msa1087100:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 7_2:-87731739 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 7_2:-87731867 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 7_2:-87731897 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 7_2:-87731646 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 7_2:-87731764 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 7_2:-87731483 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 7_2:-87731848 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 7_2:-87731736 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 7_2:-87731845 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 7_2:-87731504 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 7_2:-87731634 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 7_2:-87731404 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 7_2:-87731556 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 7_2:-87731706 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 7_2:-87731448 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 7_2:-87731894 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 7_2:+87731526 Msa1087100:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 7_2:-87731752 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 7_2:+87731633 Msa1087100:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 7_2:-87731495 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 7_2:-87731664 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 7_2:-87731559 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 7_2:-87731690 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 7_2:-87731687 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 7_2:+87731442 Msa1087100:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 7_2:-87731604 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr7_2:87731499-87731518 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr7_2:87731424-87731443 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr7_2:87731498-87731517 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr7_2:87731500-87731519 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr7_2:87731507-87731526 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr7_2:87731526-87731545 Msa1087100:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr7_2:87731869-87731888 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr7_2:87731870-87731889 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr7_2:87731425-87731444 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr7_2:87731486-87731505 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr7_2:87731503-87731522 Msa1087100:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr7_2:87731524-87731543 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr7_2:87731591-87731610 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr7_2:87731690-87731709 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr7_2:87731693-87731712 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr7_2:87731709-87731728 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr7_2:87731407-87731426 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr7_2:87731412-87731431 Msa1087100:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr7_2:87731434-87731453 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr7_2:87731442-87731461 Msa1087100:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr7_2:87731592-87731611 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr7_2:87731649-87731668 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr7_2:87731649-87731668 Msa1087100:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr7_2:87731714-87731733 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr7_2:87731754-87731773 Msa1087100:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr7_2:87731767-87731786 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr7_2:87731791-87731810 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr7_2:87731544-87731563 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr7_2:87731545-87731564 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr7_2:87731544-87731563 Msa1087100:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr7_2:87731552-87731571 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr7_2:87731622-87731641 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr7_2:87731650-87731669 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr7_2:87731667-87731686 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr7_2:87731755-87731774 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr7_2:87731755-87731774 Msa1087100:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr7_2:87731756-87731775 Msa1087100:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr7_2:87731796-87731815 Msa1087100:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr7_2:87731809-87731828 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr7_2:87731810-87731829 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr7_2:87731814-87731833 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr7_2:87731815-87731834 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr7_2:87731848-87731867 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr7_2:87731851-87731870 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr7_2:87731863-87731882 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr7_2:87731404-87731423 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr7_2:87731462-87731481 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr7_2:87731577-87731596 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr7_2:87731575-87731594 Msa1087100:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr7_2:87731621-87731640 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr7_2:87731633-87731652 Msa1087100:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr7_2:87731637-87731656 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr7_2:87731676-87731695 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr7_2:87731673-87731692 Msa1087100:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr7_2:87731738-87731757 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr7_2:87731739-87731758 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr7_2:87731742-87731761 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr7_2:87731758-87731777 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr7_2:87731797-87731816 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr7_2:87731795-87731814 Msa1087100:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr7_2:87731811-87731830 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr7_2:87731843-87731862 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr7_2:87731844-87731863 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr7_2:87731451-87731470 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr7_2:87731449-87731468 Msa1087100:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr7_2:87731607-87731626 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr7_2:87731608-87731627 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr7_2:87731609-87731628 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr7_2:87731610-87731629 Msa1087100:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr7_2:87731611-87731630 Msa1087100:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr7_2:87731618-87731637 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr7_2:87731722-87731741 Msa1087100:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr7_2:87731723-87731742 Msa1087100:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr7_2:87731737-87731756 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr7_2:87731800-87731819 Msa1087100:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr7_2:87731832-87731851 Msa1087100:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr7_2:87731559-87731578 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr7_2:87731562-87731581 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr7_2:87731559-87731578 Msa1087100:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr7_2:87731603-87731622 Msa1087100:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr7_2:87731726-87731745 Msa1087100:CDS 75.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87731374 87731909 87731374 ID=Msa1087100;Name=Msa1087100
chr7_2 mRNA 87731374 87731909 87731374 ID=Msa1087100-mRNA-1;Parent=Msa1087100;Name=Msa1087100-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr7_2 exon 87731374 87731511 87731374 ID=Msa1087100-mRNA-1:exon:23997;Parent=Msa1087100-mRNA-1
chr7_2 exon 87731525 87731620 87731525 ID=Msa1087100-mRNA-1:exon:23998;Parent=Msa1087100-mRNA-1
chr7_2 exon 87731625 87731909 87731625 ID=Msa1087100-mRNA-1:exon:23999;Parent=Msa1087100-mRNA-1
chr7_2 CDS 87731374 87731511 87731374 ID=Msa1087100-mRNA-1:cds;Parent=Msa1087100-mRNA-1
chr7_2 CDS 87731525 87731620 87731525 ID=Msa1087100-mRNA-1:cds;Parent=Msa1087100-mRNA-1
chr7_2 CDS 87731625 87731909 87731625 ID=Msa1087100-mRNA-1:cds;Parent=Msa1087100-mRNA-1
Gene Sequence

>Msa1087100

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1087100

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS