AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354540


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:+376369 Msa1354540:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0014543:-376256 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0014543:+376171 Msa1354540:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0014543:-376308 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0014543:+376513 Msa1354540:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0014543:+376481 Msa1354540:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0014543:+376208 Msa1354540:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0014543:+376514 Msa1354540:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0014543:-376181 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0014543:+376554 Msa1354540:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0014543:-376190 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0014543:+376124 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0014543:-376553 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0014543:-376470 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0014543:+376559 Msa1354540:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0014543:+376482 Msa1354540:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0014543:+376370 Msa1354540:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0014543:-376132 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0014543:-376565 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0014543:-376364 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0014543:-376547 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0014543:-376625 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0014543:+376318 Msa1354540:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0014543:-376365 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0014543:-376255 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0014543:-376571 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0014543:-376494 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0014543:-376599 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0014543:-376180 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0014543:-376619 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0014543:+376591 Msa1354540:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0014543:-376600 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0014543:-376570 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0014543:+376555 Msa1354540:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0014543:-376333 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0014543:-376432 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0014543:-376218 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0014543:-376567 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0014543:-376514 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0014543:-376406 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0014543:-376566 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0014543:-376301 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0014543:-376493 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0014543:-376131 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0014543:-376300 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0014543:+376485 Msa1354540:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0014543:+376515 Msa1354540:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0014543:+376432 Msa1354540:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0014543:+376334 Msa1354540:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0014543:-376160 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0014543:+376408 Msa1354540:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0014543:-376498 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0014543:-376626 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0014543:-376656 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0014543:-376405 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0014543:-376523 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0014543:-376242 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0014543:-376607 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0014543:-376495 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0014543:-376604 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0014543:-376263 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0014543:-376393 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0014543:-376163 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0014543:-376315 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0014543:-376465 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0014543:-376207 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0014543:-376653 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0014543:+376285 Msa1354540:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0014543:-376511 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0014543:+376392 Msa1354540:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0014543:-376254 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0014543:-376423 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0014543:-376318 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0014543:-376449 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0014543:-376446 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0014543:+376201 Msa1354540:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0014543:-376363 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - tig0014543:376258-376277 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - tig0014543:376183-376202 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - tig0014543:376257-376276 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - tig0014543:376259-376278 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - tig0014543:376266-376285 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + tig0014543:376285-376304 Msa1354540:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - tig0014543:376628-376647 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - tig0014543:376629-376648 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - tig0014543:376184-376203 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - tig0014543:376245-376264 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + tig0014543:376262-376281 Msa1354540:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - tig0014543:376283-376302 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - tig0014543:376350-376369 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - tig0014543:376449-376468 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - tig0014543:376452-376471 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - tig0014543:376468-376487 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - tig0014543:376166-376185 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + tig0014543:376171-376190 Msa1354540:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - tig0014543:376193-376212 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + tig0014543:376201-376220 Msa1354540:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - tig0014543:376351-376370 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - tig0014543:376408-376427 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + tig0014543:376408-376427 Msa1354540:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - tig0014543:376473-376492 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + tig0014543:376513-376532 Msa1354540:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - tig0014543:376526-376545 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - tig0014543:376550-376569 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - tig0014543:376303-376322 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - tig0014543:376304-376323 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + tig0014543:376303-376322 Msa1354540:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - tig0014543:376311-376330 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - tig0014543:376381-376400 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - tig0014543:376409-376428 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - tig0014543:376426-376445 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - tig0014543:376514-376533 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + tig0014543:376514-376533 Msa1354540:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + tig0014543:376515-376534 Msa1354540:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + tig0014543:376555-376574 Msa1354540:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - tig0014543:376568-376587 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - tig0014543:376569-376588 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - tig0014543:376573-376592 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - tig0014543:376574-376593 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - tig0014543:376607-376626 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - tig0014543:376610-376629 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - tig0014543:376622-376641 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - tig0014543:376163-376182 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - tig0014543:376221-376240 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - tig0014543:376336-376355 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + tig0014543:376334-376353 Msa1354540:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - tig0014543:376380-376399 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + tig0014543:376392-376411 Msa1354540:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - tig0014543:376396-376415 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - tig0014543:376435-376454 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + tig0014543:376432-376451 Msa1354540:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - tig0014543:376497-376516 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - tig0014543:376498-376517 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - tig0014543:376501-376520 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - tig0014543:376517-376536 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - tig0014543:376556-376575 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + tig0014543:376554-376573 Msa1354540:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - tig0014543:376570-376589 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - tig0014543:376602-376621 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - tig0014543:376603-376622 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - tig0014543:376210-376229 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + tig0014543:376208-376227 Msa1354540:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - tig0014543:376366-376385 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - tig0014543:376367-376386 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - tig0014543:376368-376387 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + tig0014543:376369-376388 Msa1354540:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + tig0014543:376370-376389 Msa1354540:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - tig0014543:376377-376396 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + tig0014543:376481-376500 Msa1354540:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + tig0014543:376482-376501 Msa1354540:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - tig0014543:376496-376515 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + tig0014543:376559-376578 Msa1354540:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + tig0014543:376591-376610 Msa1354540:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - tig0014543:376318-376337 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - tig0014543:376321-376340 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + tig0014543:376318-376337 Msa1354540:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + tig0014543:376362-376381 Msa1354540:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + tig0014543:376485-376504 Msa1354540:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 376133 376668 376133 ID=Msa1354540;Name=Msa1354540
tig0014543 mRNA 376133 376668 376133 ID=Msa1354540-mRNA-1;Parent=Msa1354540;Name=Msa1354540-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0014543 exon 376133 376270 376133 ID=Msa1354540-mRNA-1:exon:9158;Parent=Msa1354540-mRNA-1
tig0014543 exon 376284 376379 376284 ID=Msa1354540-mRNA-1:exon:9159;Parent=Msa1354540-mRNA-1
tig0014543 exon 376384 376668 376384 ID=Msa1354540-mRNA-1:exon:9160;Parent=Msa1354540-mRNA-1
tig0014543 CDS 376133 376270 376133 ID=Msa1354540-mRNA-1:cds;Parent=Msa1354540-mRNA-1
tig0014543 CDS 376284 376379 376284 ID=Msa1354540-mRNA-1:cds;Parent=Msa1354540-mRNA-1
tig0014543 CDS 376384 376668 376384 ID=Msa1354540-mRNA-1:cds;Parent=Msa1354540-mRNA-1
Gene Sequence

>Msa1354540

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1354540

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS