AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268280


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:-70162514 Msa0268280:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 2_2:+70162627 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 2_2:-70162712 Msa0268280:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 2_2:+70162575 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 2_2:-70162370 Msa0268280:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 2_2:-70162402 Msa0268280:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 2_2:-70162675 Msa0268280:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 2_2:-70162369 Msa0268280:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 2_2:+70162702 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 2_2:-70162329 Msa0268280:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 2_2:+70162693 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 2_2:-70162759 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 2_2:+70162330 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 2_2:+70162413 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 2_2:-70162324 Msa0268280:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 2_2:-70162401 Msa0268280:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 2_2:-70162513 Msa0268280:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 2_2:+70162751 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 2_2:+70162318 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 2_2:+70162519 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 2_2:+70162336 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 2_2:+70162258 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 2_2:-70162565 Msa0268280:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 2_2:+70162518 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 2_2:+70162628 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 2_2:+70162312 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 2_2:+70162389 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 2_2:+70162284 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 2_2:+70162703 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 2_2:+70162264 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 2_2:-70162292 Msa0268280:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 2_2:+70162283 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 2_2:+70162313 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 2_2:-70162328 Msa0268280:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 2_2:+70162550 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 2_2:+70162451 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 2_2:+70162665 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 2_2:+70162316 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 2_2:+70162369 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 2_2:+70162477 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 2_2:+70162317 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 2_2:+70162582 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 2_2:+70162390 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 2_2:+70162752 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 2_2:+70162583 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 2_2:-70162398 Msa0268280:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 2_2:-70162368 Msa0268280:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 2_2:-70162451 Msa0268280:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 2_2:-70162549 Msa0268280:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 2_2:+70162723 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 2_2:-70162475 Msa0268280:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 2_2:+70162385 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 2_2:+70162257 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 2_2:+70162227 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 2_2:+70162478 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 2_2:+70162360 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 2_2:+70162641 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 2_2:+70162276 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 2_2:+70162388 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 2_2:+70162279 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 2_2:+70162620 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 2_2:+70162490 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 2_2:+70162720 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 2_2:+70162568 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 2_2:+70162418 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 2_2:+70162676 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 2_2:+70162230 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 2_2:-70162598 Msa0268280:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 2_2:+70162372 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 2_2:-70162491 Msa0268280:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 2_2:+70162629 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 2_2:+70162460 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 2_2:+70162565 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 2_2:+70162434 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 2_2:+70162437 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 2_2:-70162682 Msa0268280:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 2_2:+70162520 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr2_2:70162362-70162381 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr2_2:70162287-70162306 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr2_2:70162361-70162380 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr2_2:70162363-70162382 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr2_2:70162370-70162389 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr2_2:70162389-70162408 Msa0268280:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr2_2:70162732-70162751 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr2_2:70162733-70162752 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr2_2:70162288-70162307 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr2_2:70162349-70162368 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr2_2:70162366-70162385 Msa0268280:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr2_2:70162387-70162406 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr2_2:70162454-70162473 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr2_2:70162553-70162572 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr2_2:70162556-70162575 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr2_2:70162572-70162591 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr2_2:70162270-70162289 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr2_2:70162275-70162294 Msa0268280:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr2_2:70162297-70162316 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr2_2:70162305-70162324 Msa0268280:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr2_2:70162455-70162474 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr2_2:70162512-70162531 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr2_2:70162512-70162531 Msa0268280:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr2_2:70162577-70162596 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr2_2:70162617-70162636 Msa0268280:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr2_2:70162630-70162649 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr2_2:70162654-70162673 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr2_2:70162407-70162426 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr2_2:70162408-70162427 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr2_2:70162407-70162426 Msa0268280:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr2_2:70162415-70162434 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr2_2:70162485-70162504 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr2_2:70162513-70162532 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr2_2:70162530-70162549 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr2_2:70162618-70162637 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr2_2:70162618-70162637 Msa0268280:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr2_2:70162619-70162638 Msa0268280:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr2_2:70162659-70162678 Msa0268280:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr2_2:70162672-70162691 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr2_2:70162673-70162692 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr2_2:70162677-70162696 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr2_2:70162678-70162697 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr2_2:70162711-70162730 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr2_2:70162714-70162733 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr2_2:70162726-70162745 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr2_2:70162267-70162286 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr2_2:70162325-70162344 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr2_2:70162440-70162459 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr2_2:70162438-70162457 Msa0268280:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr2_2:70162484-70162503 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr2_2:70162496-70162515 Msa0268280:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr2_2:70162500-70162519 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr2_2:70162539-70162558 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr2_2:70162536-70162555 Msa0268280:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr2_2:70162601-70162620 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr2_2:70162602-70162621 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr2_2:70162605-70162624 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr2_2:70162621-70162640 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr2_2:70162660-70162679 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr2_2:70162658-70162677 Msa0268280:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr2_2:70162674-70162693 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr2_2:70162706-70162725 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr2_2:70162707-70162726 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr2_2:70162314-70162333 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr2_2:70162312-70162331 Msa0268280:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr2_2:70162470-70162489 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr2_2:70162471-70162490 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr2_2:70162472-70162491 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr2_2:70162473-70162492 Msa0268280:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr2_2:70162474-70162493 Msa0268280:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr2_2:70162481-70162500 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr2_2:70162585-70162604 Msa0268280:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr2_2:70162586-70162605 Msa0268280:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr2_2:70162600-70162619 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr2_2:70162663-70162682 Msa0268280:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr2_2:70162695-70162714 Msa0268280:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr2_2:70162422-70162441 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr2_2:70162425-70162444 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr2_2:70162422-70162441 Msa0268280:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr2_2:70162466-70162485 Msa0268280:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr2_2:70162589-70162608 Msa0268280:CDS 75.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70162237 70162772 70162237 ID=Msa0268280;Name=Msa0268280
chr2_2 mRNA 70162237 70162772 70162237 ID=Msa0268280-mRNA-1;Parent=Msa0268280;Name=Msa0268280-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr2_2 exon 70162635 70162772 70162635 ID=Msa0268280-mRNA-1:exon:22504;Parent=Msa0268280-mRNA-1
chr2_2 exon 70162526 70162621 70162526 ID=Msa0268280-mRNA-1:exon:22503;Parent=Msa0268280-mRNA-1
chr2_2 exon 70162237 70162521 70162237 ID=Msa0268280-mRNA-1:exon:22502;Parent=Msa0268280-mRNA-1
chr2_2 CDS 70162635 70162772 70162635 ID=Msa0268280-mRNA-1:cds;Parent=Msa0268280-mRNA-1
chr2_2 CDS 70162526 70162621 70162526 ID=Msa0268280-mRNA-1:cds;Parent=Msa0268280-mRNA-1
chr2_2 CDS 70162237 70162521 70162237 ID=Msa0268280-mRNA-1:cds;Parent=Msa0268280-mRNA-1
Gene Sequence

>Msa0268280

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0268280

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS