AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0983590


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_4:-26680449 Msa0983590:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_4:+26680562 None:intergenic
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_4:+26680510 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_4:-26680305 Msa0983590:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_4:-26680337 Msa0983590:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_4:-26680304 Msa0983590:CDS
ACCGTCATTGTTTCTTCTCC+AGG 0.384151 6_4:-26680556 Msa0983590:CDS
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_4:-26680264 Msa0983590:CDS
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_4:+26680265 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_4:+26680348 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_4:-26680259 Msa0983590:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_4:-26680336 Msa0983590:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_4:-26680448 Msa0983590:intron
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_4:+26680253 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_4:+26680454 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_4:+26680271 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_4:+26680193 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_4:-26680500 Msa0983590:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_4:+26680453 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_4:+26680563 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_4:+26680247 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_4:+26680324 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_4:+26680219 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_4:+26680199 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_4:-26680227 Msa0983590:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_4:+26680218 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_4:+26680248 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_4:-26680263 Msa0983590:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_4:+26680485 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_4:+26680386 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_4:+26680251 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_4:+26680304 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_4:+26680412 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_4:+26680252 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_4:+26680517 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_4:+26680325 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_4:+26680518 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_4:-26680333 Msa0983590:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_4:-26680303 Msa0983590:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_4:-26680386 Msa0983590:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_4:-26680484 Msa0983590:CDS
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_4:-26680410 Msa0983590:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_4:+26680320 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_4:+26680192 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_4:+26680162 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_4:+26680413 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_4:+26680295 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_4:+26680576 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_4:+26680211 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_4:+26680323 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_4:+26680214 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_4:+26680555 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_4:+26680425 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_4:+26680503 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_4:+26680353 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_4:+26680165 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_4:-26680533 Msa0983590:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_4:+26680307 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_4:-26680426 Msa0983590:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_4:+26680564 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_4:+26680395 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_4:+26680500 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_4:+26680369 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_4:+26680372 None:intergenic
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_4:+26680455 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr6_4:26680182-26680201 None:intergenic 35.0%
AGAAACAATGACGGTATCTG+GGG + chr6_4:26680181-26680200 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr6_4:26680183-26680202 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr6_4:26680190-26680209 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr6_4:26680209-26680228 Msa0983590:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr6_4:26680552-26680571 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr6_4:26680553-26680572 None:intergenic 40.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr6_4:26680186-26680205 Msa0983590:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr6_4:26680207-26680226 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr6_4:26680274-26680293 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr6_4:26680373-26680392 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr6_4:26680376-26680395 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr6_4:26680392-26680411 None:intergenic 45.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr6_4:26680275-26680294 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr6_4:26680332-26680351 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr6_4:26680332-26680351 Msa0983590:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr6_4:26680397-26680416 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr6_4:26680437-26680456 Msa0983590:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr6_4:26680450-26680469 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr6_4:26680474-26680493 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr6_4:26680227-26680246 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr6_4:26680228-26680247 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr6_4:26680227-26680246 Msa0983590:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr6_4:26680235-26680254 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr6_4:26680305-26680324 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr6_4:26680333-26680352 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr6_4:26680350-26680369 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr6_4:26680438-26680457 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr6_4:26680438-26680457 Msa0983590:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr6_4:26680439-26680458 Msa0983590:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr6_4:26680479-26680498 Msa0983590:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr6_4:26680492-26680511 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr6_4:26680493-26680512 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr6_4:26680497-26680516 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr6_4:26680498-26680517 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr6_4:26680531-26680550 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr6_4:26680534-26680553 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr6_4:26680546-26680565 None:intergenic 55.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr6_4:26680260-26680279 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr6_4:26680258-26680277 Msa0983590:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr6_4:26680304-26680323 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr6_4:26680316-26680335 Msa0983590:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr6_4:26680320-26680339 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr6_4:26680359-26680378 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr6_4:26680356-26680375 Msa0983590:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr6_4:26680421-26680440 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr6_4:26680422-26680441 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr6_4:26680425-26680444 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr6_4:26680441-26680460 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr6_4:26680480-26680499 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr6_4:26680478-26680497 Msa0983590:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr6_4:26680494-26680513 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr6_4:26680526-26680545 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr6_4:26680527-26680546 None:intergenic 60.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr6_4:26680290-26680309 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr6_4:26680291-26680310 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr6_4:26680292-26680311 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr6_4:26680293-26680312 Msa0983590:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr6_4:26680294-26680313 Msa0983590:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr6_4:26680301-26680320 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr6_4:26680405-26680424 Msa0983590:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr6_4:26680406-26680425 Msa0983590:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr6_4:26680420-26680439 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr6_4:26680483-26680502 Msa0983590:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr6_4:26680515-26680534 Msa0983590:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr6_4:26680242-26680261 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr6_4:26680245-26680264 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr6_4:26680242-26680261 Msa0983590:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr6_4:26680286-26680305 Msa0983590:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr6_4:26680409-26680428 Msa0983590:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 26680169 26680595 26680169 ID=Msa0983590;Name=Msa0983590
chr6_4 mRNA 26680169 26680595 26680169 ID=Msa0983590-mRNA-1;Parent=Msa0983590;Name=Msa0983590-mRNA-1;_AED=0.26;_eAED=0.27;_QI=0|0|0|1|0|0.5|2|0|140
chr6_4 exon 26680461 26680595 26680461 ID=Msa0983590-mRNA-1:exon:7526;Parent=Msa0983590-mRNA-1
chr6_4 exon 26680169 26680456 26680169 ID=Msa0983590-mRNA-1:exon:7525;Parent=Msa0983590-mRNA-1
chr6_4 CDS 26680461 26680595 26680461 ID=Msa0983590-mRNA-1:cds;Parent=Msa0983590-mRNA-1
chr6_4 CDS 26680169 26680456 26680169 ID=Msa0983590-mRNA-1:cds;Parent=Msa0983590-mRNA-1
Gene Sequence

>Msa0983590

ATGCTTATTCCCCAGATACCGTCATTGTTTCTTCTCCAGGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCCTGA

Protein sequence

>Msa0983590

MLIPQIPSLFLLQEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS*