AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354670


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 63 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0014543:-449324 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0014543:+449239 Msa1354670:CDS
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0014543:+449581 Msa1354670:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0014543:+449549 Msa1354670:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0014543:+449276 Msa1354670:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0014543:+449582 Msa1354670:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0014543:-449249 None:intergenic
ACCGTCATTGTTTCTTCTCC+AGG 0.384151 tig0014543:+449330 Msa1354670:CDS
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0014543:+449622 Msa1354670:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0014543:-449258 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0014543:+449192 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0014543:-449621 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0014543:-449538 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0014543:+449627 Msa1354670:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0014543:+449550 Msa1354670:CDS
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0014543:-449200 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0014543:-449633 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0014543:-449615 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0014543:-449693 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0014543:-449323 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0014543:-449639 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0014543:-449562 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0014543:-449667 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0014543:-449248 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0014543:-449687 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0014543:+449659 Msa1354670:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0014543:-449668 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0014543:-449638 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0014543:+449623 Msa1354670:CDS
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0014543:-449500 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0014543:-449286 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0014543:-449635 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0014543:-449582 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0014543:-449474 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0014543:-449634 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0014543:-449561 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0014543:-449199 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0014543:+449553 Msa1354670:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0014543:+449583 Msa1354670:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0014543:+449500 Msa1354670:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0014543:-449228 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0014543:+449476 Msa1354670:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0014543:-449566 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0014543:-449694 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0014543:-449724 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0014543:-449473 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0014543:-449591 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0014543:-449310 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0014543:-449675 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0014543:-449563 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0014543:-449672 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0014543:-449331 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0014543:-449231 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0014543:-449533 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0014543:-449275 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0014543:-449721 None:intergenic
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0014543:-449579 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0014543:+449460 Msa1354670:intron
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0014543:-449322 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0014543:-449491 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0014543:-449517 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0014543:-449514 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0014543:+449269 Msa1354670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - tig0014543:449326-449345 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - tig0014543:449251-449270 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - tig0014543:449325-449344 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - tig0014543:449327-449346 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - tig0014543:449334-449353 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + tig0014543:449353-449372 Msa1354670:intron 40.0%
TTTACACATGCAAGTCGAAC+GGG - tig0014543:449696-449715 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - tig0014543:449697-449716 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - tig0014543:449252-449271 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - tig0014543:449313-449332 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + tig0014543:449330-449349 Msa1354670:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - tig0014543:449351-449370 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - tig0014543:449418-449437 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - tig0014543:449517-449536 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - tig0014543:449520-449539 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - tig0014543:449536-449555 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - tig0014543:449234-449253 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + tig0014543:449239-449258 Msa1354670:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - tig0014543:449261-449280 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + tig0014543:449269-449288 Msa1354670:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - tig0014543:449419-449438 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - tig0014543:449476-449495 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + tig0014543:449476-449495 Msa1354670:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - tig0014543:449541-449560 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + tig0014543:449581-449600 Msa1354670:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - tig0014543:449594-449613 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - tig0014543:449618-449637 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - tig0014543:449371-449390 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - tig0014543:449372-449391 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + tig0014543:449371-449390 Msa1354670:intron 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - tig0014543:449379-449398 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - tig0014543:449449-449468 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - tig0014543:449477-449496 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - tig0014543:449494-449513 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - tig0014543:449582-449601 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + tig0014543:449582-449601 Msa1354670:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + tig0014543:449583-449602 Msa1354670:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + tig0014543:449623-449642 Msa1354670:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - tig0014543:449636-449655 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - tig0014543:449637-449656 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - tig0014543:449641-449660 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - tig0014543:449642-449661 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - tig0014543:449675-449694 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - tig0014543:449678-449697 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - tig0014543:449690-449709 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - tig0014543:449231-449250 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - tig0014543:449289-449308 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - tig0014543:449404-449423 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + tig0014543:449402-449421 Msa1354670:intron 60.0%
GACAAGGCCCAGACTCCTAC+GGG - tig0014543:449448-449467 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + tig0014543:449460-449479 Msa1354670:intron 60.0%
GCCACACTGGGACTGAGACA+AGG - tig0014543:449464-449483 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - tig0014543:449503-449522 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + tig0014543:449500-449519 Msa1354670:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - tig0014543:449565-449584 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - tig0014543:449566-449585 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - tig0014543:449569-449588 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - tig0014543:449585-449604 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - tig0014543:449624-449643 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + tig0014543:449622-449641 Msa1354670:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - tig0014543:449638-449657 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - tig0014543:449670-449689 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - tig0014543:449671-449690 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - tig0014543:449278-449297 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + tig0014543:449276-449295 Msa1354670:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - tig0014543:449434-449453 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - tig0014543:449435-449454 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - tig0014543:449436-449455 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + tig0014543:449437-449456 Msa1354670:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + tig0014543:449438-449457 Msa1354670:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - tig0014543:449445-449464 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + tig0014543:449549-449568 Msa1354670:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + tig0014543:449550-449569 Msa1354670:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - tig0014543:449564-449583 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + tig0014543:449627-449646 Msa1354670:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + tig0014543:449659-449678 Msa1354670:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - tig0014543:449386-449405 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - tig0014543:449389-449408 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + tig0014543:449386-449405 Msa1354670:intron 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + tig0014543:449430-449449 Msa1354670:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + tig0014543:449553-449572 Msa1354670:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 449201 449739 449201 ID=Msa1354670;Name=Msa1354670
tig0014543 mRNA 449201 449739 449201 ID=Msa1354670-mRNA-1;Parent=Msa1354670;Name=Msa1354670-mRNA-1;_AED=0.25;_eAED=0.34;_QI=0|0|0|1|1|1|2|0|145
tig0014543 exon 449201 449370 449201 ID=Msa1354670-mRNA-1:exon:9174;Parent=Msa1354670-mRNA-1
tig0014543 exon 449472 449739 449472 ID=Msa1354670-mRNA-1:exon:9175;Parent=Msa1354670-mRNA-1
tig0014543 CDS 449201 449370 449201 ID=Msa1354670-mRNA-1:cds;Parent=Msa1354670-mRNA-1
tig0014543 CDS 449472 449739 449472 ID=Msa1354670-mRNA-1:cds;Parent=Msa1354670-mRNA-1
Gene Sequence

>Msa1354670

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGTTTCTTCTCCAGGAAAAGAAGTTCATGACCCTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCCTGA

Protein sequence

>Msa1354670

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIVSSPGKEVHDPPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS*