AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354640


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 79 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:+404620 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0014543:-404705 Msa1354640:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0014543:+404568 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0014543:-404365 Msa1354640:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0014543:-404397 Msa1354640:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0014543:-404668 Msa1354640:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0014543:-404364 Msa1354640:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0014543:+404695 None:intergenic
ACCGTCATTGTTTCTTCTCC+AGG 0.384151 tig0014543:-404614 Msa1354640:CDS
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0014543:-404324 Msa1354640:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0014543:+404686 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0014543:-404752 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0014543:+404325 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0014543:+404408 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0014543:-404319 Msa1354640:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0014543:-404396 Msa1354640:CDS
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0014543:+404744 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0014543:+404313 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0014543:+404331 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0014543:+404253 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.480758 tig0014543:+404512 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0014543:-404558 Msa1354640:CDS
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0014543:+404621 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0014543:+404307 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0014543:+404384 None:intergenic
CTGCTGCCTCCCGTAGGAGT+GGG 0.504687 tig0014543:-404508 Msa1354640:CDS
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0014543:+404279 None:intergenic
ACTCCTACGGGAGGCAGCAG+TGG 0.506466 tig0014543:+404511 None:intergenic
TGAGACAAGGCCCACTCCTA+CGG 0.510609 tig0014543:+404498 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0014543:+404696 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0014543:+404259 None:intergenic
ACTGCTGCCTCCCGTAGGAG+TGG 0.512437 tig0014543:-404509 Msa1354640:CDS
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0014543:-404287 Msa1354640:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0014543:+404278 None:intergenic
GAGACAAGGCCCACTCCTAC+GGG 0.528077 tig0014543:+404499 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0014543:+404308 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0014543:-404323 Msa1354640:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0014543:+404543 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0014543:+404446 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0014543:+404658 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0014543:+404311 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0014543:+404364 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0014543:+404472 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0014543:+404312 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0014543:+404385 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0014543:+404745 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0014543:-404393 Msa1354640:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0014543:-404363 Msa1354640:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0014543:-404446 Msa1354640:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0014543:-404542 Msa1354640:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0014543:+404716 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0014543:-404470 Msa1354640:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0014543:+404380 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0014543:+404252 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0014543:+404222 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0014543:+404473 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0014543:+404355 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0014543:+404634 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0014543:+404271 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0014543:+404383 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0014543:+404274 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0014543:+404613 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0014543:+404485 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0014543:+404713 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.636970 tig0014543:-404486 Msa1354640:CDS
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0014543:+404561 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0014543:+404413 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0014543:+404669 None:intergenic
ACAAGGCCCACTCCTACGGG+AGG 0.650306 tig0014543:+404502 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0014543:+404225 None:intergenic
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0014543:+404367 None:intergenic
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0014543:+404622 None:intergenic
TCCCCACTGCTGCCTCCCGT+AGG 0.661092 tig0014543:-404514 Msa1354640:CDS
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0014543:+404455 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0014543:+404558 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0014543:+404429 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0014543:+404432 None:intergenic
TCCTACGGGAGGCAGCAGTG+GGG 0.758530 tig0014543:+404513 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0014543:-404675 Msa1354640:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + tig0014543:404357-404376 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + tig0014543:404282-404301 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + tig0014543:404356-404375 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + tig0014543:404358-404377 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + tig0014543:404365-404384 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - tig0014543:404384-404403 Msa1354640:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + tig0014543:404725-404744 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + tig0014543:404726-404745 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + tig0014543:404283-404302 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + tig0014543:404344-404363 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - tig0014543:404361-404380 Msa1354640:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + tig0014543:404382-404401 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + tig0014543:404449-404468 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + tig0014543:404546-404565 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + tig0014543:404549-404568 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + tig0014543:404565-404584 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + tig0014543:404265-404284 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - tig0014543:404270-404289 Msa1354640:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + tig0014543:404292-404311 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - tig0014543:404300-404319 Msa1354640:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + tig0014543:404450-404469 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + tig0014543:404505-404524 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - tig0014543:404505-404524 Msa1354640:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + tig0014543:404570-404589 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - tig0014543:404610-404629 Msa1354640:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG + tig0014543:404623-404642 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + tig0014543:404647-404666 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + tig0014543:404402-404421 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + tig0014543:404403-404422 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - tig0014543:404402-404421 Msa1354640:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + tig0014543:404410-404429 None:intergenic 55.0%
TGAGACAAGGCCCACTCCTA+CGG + tig0014543:404480-404499 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + tig0014543:404506-404525 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + tig0014543:404523-404542 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + tig0014543:404611-404630 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - tig0014543:404611-404630 Msa1354640:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - tig0014543:404612-404631 Msa1354640:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - tig0014543:404652-404671 Msa1354640:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + tig0014543:404665-404684 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + tig0014543:404666-404685 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + tig0014543:404670-404689 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + tig0014543:404671-404690 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + tig0014543:404704-404723 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + tig0014543:404707-404726 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + tig0014543:404719-404738 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + tig0014543:404262-404281 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + tig0014543:404320-404339 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + tig0014543:404435-404454 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - tig0014543:404433-404452 Msa1354640:CDS 60.0%
GAGACAAGGCCCACTCCTAC+GGG + tig0014543:404479-404498 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - tig0014543:404489-404508 Msa1354640:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + tig0014543:404493-404512 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + tig0014543:404532-404551 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - tig0014543:404529-404548 Msa1354640:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + tig0014543:404594-404613 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + tig0014543:404595-404614 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + tig0014543:404598-404617 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + tig0014543:404614-404633 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + tig0014543:404653-404672 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - tig0014543:404651-404670 Msa1354640:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + tig0014543:404667-404686 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + tig0014543:404699-404718 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + tig0014543:404700-404719 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + tig0014543:404309-404328 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - tig0014543:404307-404326 Msa1354640:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + tig0014543:404465-404484 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + tig0014543:404466-404485 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + tig0014543:404467-404486 None:intergenic 65.0%
ACTGCTGCCTCCCGTAGGAG+TGG - tig0014543:404466-404485 Msa1354640:CDS 65.0%
CTGCTGCCTCCCGTAGGAGT+GGG - tig0014543:404467-404486 Msa1354640:CDS 65.0%
ACAAGGCCCACTCCTACGGG+AGG + tig0014543:404476-404495 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - tig0014543:404578-404597 Msa1354640:intron 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - tig0014543:404579-404598 Msa1354640:intron 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + tig0014543:404593-404612 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - tig0014543:404656-404675 Msa1354640:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - tig0014543:404688-404707 Msa1354640:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + tig0014543:404417-404436 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + tig0014543:404420-404439 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - tig0014543:404417-404436 Msa1354640:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - tig0014543:404461-404480 Msa1354640:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - tig0014543:404582-404601 Msa1354640:intron 75.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 404232 404765 404232 ID=Msa1354640;Name=Msa1354640
tig0014543 mRNA 404232 404765 404232 ID=Msa1354640-mRNA-1;Parent=Msa1354640;Name=Msa1354640-mRNA-1;_AED=0.42;_eAED=0.45;_QI=0|0|0|1|0|0|2|0|173
tig0014543 exon 404607 404765 404607 ID=Msa1354640-mRNA-1:exon:9206;Parent=Msa1354640-mRNA-1
tig0014543 exon 404232 404591 404232 ID=Msa1354640-mRNA-1:exon:9205;Parent=Msa1354640-mRNA-1
tig0014543 CDS 404607 404765 404607 ID=Msa1354640-mRNA-1:cds;Parent=Msa1354640-mRNA-1
tig0014543 CDS 404232 404591 404232 ID=Msa1354640-mRNA-1:cds;Parent=Msa1354640-mRNA-1
Gene Sequence

>Msa1354640

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGTTTCTTCTCCAGGAAAAGAAGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGTAGGAGTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1354640

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIVSSPGKEAFYLHAALLRQAFAHCGKFPTAASRRSGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS