AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908620


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 6_2:-9757465 Msa0908620:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_2:+9757578 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:-9757663 Msa0908620:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:+9757526 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_2:-9757321 Msa0908620:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_2:-9757353 Msa0908620:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:-9757626 Msa0908620:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_2:-9757320 Msa0908620:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:+9757653 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_2:-9757280 Msa0908620:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:+9757644 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:-9757710 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_2:+9757281 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_2:+9757364 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_2:-9757275 Msa0908620:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_2:-9757352 Msa0908620:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_2:-9757464 Msa0908620:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:+9757702 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_2:+9757269 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_2:+9757470 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_2:+9757287 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_2:+9757209 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:-9757516 Msa0908620:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_2:+9757469 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_2:+9757579 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_2:+9757263 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_2:+9757340 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_2:+9757235 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:+9757654 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_2:+9757215 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_2:-9757243 Msa0908620:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_2:+9757234 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_2:+9757264 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_2:-9757279 Msa0908620:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:+9757501 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_2:+9757402 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:+9757616 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_2:+9757267 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_2:+9757320 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_2:+9757428 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_2:+9757268 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:+9757533 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_2:+9757341 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:+9757703 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:+9757534 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_2:-9757349 Msa0908620:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_2:-9757319 Msa0908620:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_2:-9757402 Msa0908620:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_2:-9757500 Msa0908620:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:+9757674 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_2:-9757426 Msa0908620:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_2:+9757336 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_2:+9757208 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_2:+9757178 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_2:+9757429 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_2:+9757311 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_2:+9757592 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_2:+9757227 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_2:+9757339 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_2:+9757230 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:+9757571 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_2:+9757441 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:+9757671 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:+9757519 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_2:+9757369 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:+9757627 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_2:+9757181 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:-9757549 Msa0908620:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_2:+9757323 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_2:-9757442 Msa0908620:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_2:+9757580 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_2:+9757411 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:+9757516 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_2:+9757385 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_2:+9757388 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:-9757633 Msa0908620:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_2:+9757471 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr6_2:9757313-9757332 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr6_2:9757238-9757257 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr6_2:9757312-9757331 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr6_2:9757314-9757333 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr6_2:9757321-9757340 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr6_2:9757340-9757359 Msa0908620:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr6_2:9757683-9757702 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr6_2:9757684-9757703 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr6_2:9757239-9757258 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr6_2:9757300-9757319 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr6_2:9757317-9757336 Msa0908620:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr6_2:9757338-9757357 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr6_2:9757405-9757424 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr6_2:9757504-9757523 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr6_2:9757507-9757526 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr6_2:9757523-9757542 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr6_2:9757221-9757240 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr6_2:9757226-9757245 Msa0908620:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr6_2:9757248-9757267 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr6_2:9757256-9757275 Msa0908620:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr6_2:9757406-9757425 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr6_2:9757463-9757482 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr6_2:9757463-9757482 Msa0908620:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr6_2:9757528-9757547 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr6_2:9757568-9757587 Msa0908620:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr6_2:9757581-9757600 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr6_2:9757605-9757624 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr6_2:9757358-9757377 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr6_2:9757359-9757378 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr6_2:9757358-9757377 Msa0908620:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr6_2:9757366-9757385 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr6_2:9757436-9757455 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr6_2:9757464-9757483 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr6_2:9757481-9757500 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr6_2:9757569-9757588 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr6_2:9757569-9757588 Msa0908620:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr6_2:9757570-9757589 Msa0908620:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr6_2:9757610-9757629 Msa0908620:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr6_2:9757623-9757642 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr6_2:9757624-9757643 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr6_2:9757628-9757647 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr6_2:9757629-9757648 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr6_2:9757662-9757681 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr6_2:9757665-9757684 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr6_2:9757677-9757696 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr6_2:9757218-9757237 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr6_2:9757276-9757295 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr6_2:9757391-9757410 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr6_2:9757389-9757408 Msa0908620:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr6_2:9757435-9757454 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr6_2:9757447-9757466 Msa0908620:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr6_2:9757451-9757470 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr6_2:9757490-9757509 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr6_2:9757487-9757506 Msa0908620:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr6_2:9757552-9757571 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr6_2:9757553-9757572 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr6_2:9757556-9757575 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr6_2:9757572-9757591 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr6_2:9757611-9757630 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr6_2:9757609-9757628 Msa0908620:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr6_2:9757625-9757644 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr6_2:9757657-9757676 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr6_2:9757658-9757677 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr6_2:9757265-9757284 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr6_2:9757263-9757282 Msa0908620:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr6_2:9757421-9757440 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr6_2:9757422-9757441 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr6_2:9757423-9757442 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr6_2:9757424-9757443 Msa0908620:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr6_2:9757425-9757444 Msa0908620:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr6_2:9757432-9757451 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr6_2:9757536-9757555 Msa0908620:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr6_2:9757537-9757556 Msa0908620:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr6_2:9757551-9757570 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr6_2:9757614-9757633 Msa0908620:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr6_2:9757646-9757665 Msa0908620:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr6_2:9757373-9757392 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr6_2:9757376-9757395 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr6_2:9757373-9757392 Msa0908620:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr6_2:9757417-9757436 Msa0908620:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr6_2:9757540-9757559 Msa0908620:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9757188 9757723 9757188 ID=Msa0908620;Name=Msa0908620
chr6_2 mRNA 9757188 9757723 9757188 ID=Msa0908620-mRNA-1;Parent=Msa0908620;Name=Msa0908620-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0.5|0|3|0|173
chr6_2 exon 9757586 9757723 9757586 ID=Msa0908620-mRNA-1:exon:2380;Parent=Msa0908620-mRNA-1
chr6_2 exon 9757477 9757572 9757477 ID=Msa0908620-mRNA-1:exon:2379;Parent=Msa0908620-mRNA-1
chr6_2 exon 9757188 9757472 9757188 ID=Msa0908620-mRNA-1:exon:2378;Parent=Msa0908620-mRNA-1
chr6_2 CDS 9757586 9757723 9757586 ID=Msa0908620-mRNA-1:cds;Parent=Msa0908620-mRNA-1
chr6_2 CDS 9757477 9757572 9757477 ID=Msa0908620-mRNA-1:cds;Parent=Msa0908620-mRNA-1
chr6_2 CDS 9757188 9757472 9757188 ID=Msa0908620-mRNA-1:cds;Parent=Msa0908620-mRNA-1
Gene Sequence

>Msa0908620

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0908620

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS