AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354510


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 tig0014543:-304410 Msa1354510:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0014543:+304523 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0014543:-304608 Msa1354510:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0014543:+304471 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0014543:-304266 Msa1354510:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0014543:-304298 Msa1354510:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0014543:-304571 Msa1354510:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0014543:-304265 Msa1354510:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0014543:+304598 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0014543:-304225 Msa1354510:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0014543:+304589 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0014543:-304655 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0014543:+304226 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0014543:+304309 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0014543:-304220 Msa1354510:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0014543:-304297 Msa1354510:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0014543:-304409 Msa1354510:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0014543:+304647 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0014543:+304214 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0014543:+304415 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0014543:+304232 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0014543:+304154 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0014543:-304461 Msa1354510:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0014543:+304414 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0014543:+304524 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0014543:+304208 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0014543:+304285 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0014543:+304180 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0014543:+304599 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0014543:+304160 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0014543:-304188 Msa1354510:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0014543:+304179 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0014543:+304209 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0014543:-304224 Msa1354510:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0014543:+304446 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0014543:+304347 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0014543:+304561 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0014543:+304212 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0014543:+304265 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0014543:+304373 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0014543:+304213 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0014543:+304478 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0014543:+304286 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0014543:+304648 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0014543:+304479 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0014543:-304294 Msa1354510:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0014543:-304264 Msa1354510:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0014543:-304347 Msa1354510:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0014543:-304445 Msa1354510:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0014543:+304619 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0014543:-304371 Msa1354510:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0014543:+304281 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0014543:+304153 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0014543:+304123 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0014543:+304374 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0014543:+304256 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0014543:+304537 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0014543:+304172 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0014543:+304284 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0014543:+304175 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0014543:+304516 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0014543:+304386 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0014543:+304616 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0014543:+304464 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0014543:+304314 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0014543:+304572 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0014543:+304126 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0014543:-304494 Msa1354510:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0014543:+304268 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0014543:-304387 Msa1354510:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0014543:+304525 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0014543:+304356 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0014543:+304461 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0014543:+304330 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0014543:+304333 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0014543:-304578 Msa1354510:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0014543:+304416 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + tig0014543:304258-304277 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + tig0014543:304183-304202 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + tig0014543:304257-304276 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + tig0014543:304259-304278 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + tig0014543:304266-304285 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - tig0014543:304285-304304 Msa1354510:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + tig0014543:304628-304647 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + tig0014543:304629-304648 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + tig0014543:304184-304203 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + tig0014543:304245-304264 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - tig0014543:304262-304281 Msa1354510:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + tig0014543:304283-304302 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + tig0014543:304350-304369 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + tig0014543:304449-304468 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + tig0014543:304452-304471 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + tig0014543:304468-304487 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + tig0014543:304166-304185 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - tig0014543:304171-304190 Msa1354510:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + tig0014543:304193-304212 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - tig0014543:304201-304220 Msa1354510:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + tig0014543:304351-304370 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + tig0014543:304408-304427 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - tig0014543:304408-304427 Msa1354510:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + tig0014543:304473-304492 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - tig0014543:304513-304532 Msa1354510:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + tig0014543:304526-304545 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + tig0014543:304550-304569 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + tig0014543:304303-304322 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + tig0014543:304304-304323 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - tig0014543:304303-304322 Msa1354510:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + tig0014543:304311-304330 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + tig0014543:304381-304400 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + tig0014543:304409-304428 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + tig0014543:304426-304445 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + tig0014543:304514-304533 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - tig0014543:304514-304533 Msa1354510:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - tig0014543:304515-304534 Msa1354510:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - tig0014543:304555-304574 Msa1354510:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + tig0014543:304568-304587 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + tig0014543:304569-304588 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + tig0014543:304573-304592 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + tig0014543:304574-304593 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + tig0014543:304607-304626 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + tig0014543:304610-304629 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + tig0014543:304622-304641 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + tig0014543:304163-304182 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + tig0014543:304221-304240 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + tig0014543:304336-304355 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - tig0014543:304334-304353 Msa1354510:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + tig0014543:304380-304399 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - tig0014543:304392-304411 Msa1354510:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + tig0014543:304396-304415 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + tig0014543:304435-304454 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - tig0014543:304432-304451 Msa1354510:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + tig0014543:304497-304516 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + tig0014543:304498-304517 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + tig0014543:304501-304520 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + tig0014543:304517-304536 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + tig0014543:304556-304575 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - tig0014543:304554-304573 Msa1354510:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + tig0014543:304570-304589 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + tig0014543:304602-304621 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + tig0014543:304603-304622 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + tig0014543:304210-304229 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - tig0014543:304208-304227 Msa1354510:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + tig0014543:304366-304385 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + tig0014543:304367-304386 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + tig0014543:304368-304387 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - tig0014543:304369-304388 Msa1354510:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - tig0014543:304370-304389 Msa1354510:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + tig0014543:304377-304396 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - tig0014543:304481-304500 Msa1354510:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - tig0014543:304482-304501 Msa1354510:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + tig0014543:304496-304515 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - tig0014543:304559-304578 Msa1354510:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - tig0014543:304591-304610 Msa1354510:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + tig0014543:304318-304337 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + tig0014543:304321-304340 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - tig0014543:304318-304337 Msa1354510:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - tig0014543:304362-304381 Msa1354510:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - tig0014543:304485-304504 Msa1354510:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 304133 304668 304133 ID=Msa1354510;Name=Msa1354510
tig0014543 mRNA 304133 304668 304133 ID=Msa1354510-mRNA-1;Parent=Msa1354510;Name=Msa1354510-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0014543 exon 304531 304668 304531 ID=Msa1354510-mRNA-1:exon:9163;Parent=Msa1354510-mRNA-1
tig0014543 exon 304422 304517 304422 ID=Msa1354510-mRNA-1:exon:9162;Parent=Msa1354510-mRNA-1
tig0014543 exon 304133 304417 304133 ID=Msa1354510-mRNA-1:exon:9161;Parent=Msa1354510-mRNA-1
tig0014543 CDS 304531 304668 304531 ID=Msa1354510-mRNA-1:cds;Parent=Msa1354510-mRNA-1
tig0014543 CDS 304422 304517 304422 ID=Msa1354510-mRNA-1:cds;Parent=Msa1354510-mRNA-1
tig0014543 CDS 304133 304417 304133 ID=Msa1354510-mRNA-1:cds;Parent=Msa1354510-mRNA-1
Gene Sequence

>Msa1354510

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1354510

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS