AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086780


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:+87559431 Msa1086780:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 7_2:-87559318 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 7_2:+87559233 Msa1086780:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 7_2:-87559370 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 7_2:+87559575 Msa1086780:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 7_2:+87559543 Msa1086780:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 7_2:+87559270 Msa1086780:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 7_2:+87559576 Msa1086780:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 7_2:-87559243 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 7_2:+87559616 Msa1086780:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 7_2:-87559252 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 7_2:+87559186 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 7_2:-87559615 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 7_2:-87559532 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 7_2:+87559621 Msa1086780:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 7_2:+87559544 Msa1086780:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 7_2:+87559432 Msa1086780:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 7_2:-87559194 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 7_2:-87559627 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 7_2:-87559426 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 7_2:-87559609 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 7_2:-87559687 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 7_2:+87559380 Msa1086780:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 7_2:-87559427 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 7_2:-87559317 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 7_2:-87559633 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 7_2:-87559556 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 7_2:-87559661 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 7_2:-87559242 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 7_2:-87559681 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 7_2:+87559653 Msa1086780:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 7_2:-87559662 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 7_2:-87559632 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 7_2:+87559617 Msa1086780:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 7_2:-87559395 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 7_2:-87559494 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 7_2:-87559280 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 7_2:-87559629 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 7_2:-87559576 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 7_2:-87559468 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 7_2:-87559628 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 7_2:-87559363 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 7_2:-87559555 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 7_2:-87559193 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 7_2:-87559362 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 7_2:+87559547 Msa1086780:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 7_2:+87559577 Msa1086780:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 7_2:+87559494 Msa1086780:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 7_2:+87559396 Msa1086780:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 7_2:-87559222 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 7_2:+87559470 Msa1086780:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 7_2:-87559560 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 7_2:-87559688 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 7_2:-87559718 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 7_2:-87559467 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 7_2:-87559585 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 7_2:-87559304 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 7_2:-87559669 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 7_2:-87559557 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 7_2:-87559666 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 7_2:-87559325 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 7_2:-87559455 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 7_2:-87559225 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 7_2:-87559377 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 7_2:-87559527 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 7_2:-87559269 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 7_2:-87559715 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 7_2:+87559347 Msa1086780:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 7_2:-87559573 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 7_2:+87559454 Msa1086780:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 7_2:-87559316 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 7_2:-87559485 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 7_2:-87559380 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 7_2:-87559511 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 7_2:-87559508 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 7_2:+87559263 Msa1086780:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 7_2:-87559425 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr7_2:87559320-87559339 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr7_2:87559245-87559264 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr7_2:87559319-87559338 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr7_2:87559321-87559340 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr7_2:87559328-87559347 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr7_2:87559347-87559366 Msa1086780:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr7_2:87559690-87559709 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr7_2:87559691-87559710 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr7_2:87559246-87559265 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr7_2:87559307-87559326 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr7_2:87559324-87559343 Msa1086780:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr7_2:87559345-87559364 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr7_2:87559412-87559431 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr7_2:87559511-87559530 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr7_2:87559514-87559533 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr7_2:87559530-87559549 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr7_2:87559228-87559247 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr7_2:87559233-87559252 Msa1086780:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr7_2:87559255-87559274 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr7_2:87559263-87559282 Msa1086780:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr7_2:87559413-87559432 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr7_2:87559470-87559489 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr7_2:87559470-87559489 Msa1086780:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr7_2:87559535-87559554 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr7_2:87559575-87559594 Msa1086780:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr7_2:87559588-87559607 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr7_2:87559612-87559631 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr7_2:87559365-87559384 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr7_2:87559366-87559385 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr7_2:87559365-87559384 Msa1086780:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr7_2:87559373-87559392 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr7_2:87559443-87559462 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr7_2:87559471-87559490 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr7_2:87559488-87559507 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr7_2:87559576-87559595 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr7_2:87559576-87559595 Msa1086780:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr7_2:87559577-87559596 Msa1086780:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr7_2:87559617-87559636 Msa1086780:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr7_2:87559630-87559649 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr7_2:87559631-87559650 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr7_2:87559635-87559654 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr7_2:87559636-87559655 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr7_2:87559669-87559688 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr7_2:87559672-87559691 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr7_2:87559684-87559703 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr7_2:87559225-87559244 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr7_2:87559283-87559302 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr7_2:87559398-87559417 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr7_2:87559396-87559415 Msa1086780:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr7_2:87559442-87559461 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr7_2:87559454-87559473 Msa1086780:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr7_2:87559458-87559477 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr7_2:87559497-87559516 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr7_2:87559494-87559513 Msa1086780:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr7_2:87559559-87559578 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr7_2:87559560-87559579 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr7_2:87559563-87559582 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr7_2:87559579-87559598 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr7_2:87559618-87559637 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr7_2:87559616-87559635 Msa1086780:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr7_2:87559632-87559651 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr7_2:87559664-87559683 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr7_2:87559665-87559684 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr7_2:87559272-87559291 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr7_2:87559270-87559289 Msa1086780:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr7_2:87559428-87559447 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr7_2:87559429-87559448 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr7_2:87559430-87559449 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr7_2:87559431-87559450 Msa1086780:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr7_2:87559432-87559451 Msa1086780:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr7_2:87559439-87559458 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr7_2:87559543-87559562 Msa1086780:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr7_2:87559544-87559563 Msa1086780:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr7_2:87559558-87559577 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr7_2:87559621-87559640 Msa1086780:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr7_2:87559653-87559672 Msa1086780:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr7_2:87559380-87559399 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr7_2:87559383-87559402 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr7_2:87559380-87559399 Msa1086780:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr7_2:87559424-87559443 Msa1086780:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr7_2:87559547-87559566 Msa1086780:CDS 75.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87559195 87559730 87559195 ID=Msa1086780;Name=Msa1086780
chr7_2 mRNA 87559195 87559730 87559195 ID=Msa1086780-mRNA-1;Parent=Msa1086780;Name=Msa1086780-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr7_2 exon 87559195 87559332 87559195 ID=Msa1086780-mRNA-1:exon:23892;Parent=Msa1086780-mRNA-1
chr7_2 exon 87559346 87559441 87559346 ID=Msa1086780-mRNA-1:exon:23893;Parent=Msa1086780-mRNA-1
chr7_2 exon 87559446 87559730 87559446 ID=Msa1086780-mRNA-1:exon:23894;Parent=Msa1086780-mRNA-1
chr7_2 CDS 87559195 87559332 87559195 ID=Msa1086780-mRNA-1:cds;Parent=Msa1086780-mRNA-1
chr7_2 CDS 87559346 87559441 87559346 ID=Msa1086780-mRNA-1:cds;Parent=Msa1086780-mRNA-1
chr7_2 CDS 87559446 87559730 87559446 ID=Msa1086780-mRNA-1:cds;Parent=Msa1086780-mRNA-1
Gene Sequence

>Msa1086780

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1086780

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS