AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908520


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 28 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:+9716505 None:intergenic
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:-9716642 Msa0908520:CDS
ACCTGTCCAGGGTTGAGCCC+TGG 0.327938 6_2:+9716448 None:intergenic
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:+9716542 None:intergenic
CCTGTCCAGGGTTGAGCCCT+GGG 0.363036 6_2:+9716449 None:intergenic
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:-9716515 Msa0908520:CDS
ACCGTCATTGTTTCTTCTCC+AGG 0.384151 6_2:+9716596 None:intergenic
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:-9716524 Msa0908520:CDS
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:+9716458 None:intergenic
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:-9716466 Msa0908520:CDS
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:+9716652 None:intergenic
CCCAGGGCTCAACCCTGGAC+AGG 0.508220 6_2:-9716449 Msa0908520:CDS
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:-9716514 Msa0908520:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:-9716667 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:-9716552 Msa0908520:CDS
CAAATCCCAGGGCTCAACCC+TGG 0.557720 6_2:-9716454 Msa0908520:CDS
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:-9716635 Msa0908520:CDS
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:-9716465 Msa0908520:CDS
AGGGCTCAACCCTGGACAGG+TGG 0.567008 6_2:-9716446 Msa0908520:CDS
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:-9716634 Msa0908520:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:-9716494 Msa0908520:CDS
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:-9716597 Msa0908520:intron
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:-9716497 Msa0908520:CDS
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:-9716649 Msa0908520:CDS
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:-9716541 Msa0908520:CDS
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:+9716619 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:-9716652 Msa0908520:CDS
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:+9716535 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr6_2:9716507-9716526 Msa0908520:CDS 35.0%
AAAAGAAGTTCATGACCCGT+AGG + chr6_2:9716480-9716499 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr6_2:9716499-9716518 Msa0908520:CDS 40.0%
GAAGAAACAATGACGGTATC+TGG - chr6_2:9716506-9716525 Msa0908520:CDS 40.0%
AGAAACAATGACGGTATCTG+GGG - chr6_2:9716508-9716527 Msa0908520:CDS 40.0%
AAGCGTTATCCGGAATGATT+GGG - chr6_2:9716582-9716601 Msa0908520:intron 40.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr6_2:9716482-9716501 Msa0908520:CDS 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr6_2:9716503-9716522 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr6_2:9716520-9716539 Msa0908520:CDS 45.0%
CAAGCGTTATCCGGAATGAT+TGG - chr6_2:9716581-9716600 Msa0908520:intron 45.0%
! TAGTTTTCACCACCTGTCCA+GGG + chr6_2:9716662-9716681 None:intergenic 45.0%
TTGCATCCTCTGTCTTACCG+CGG + chr6_2:9716564-9716583 None:intergenic 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr6_2:9716572-9716591 Msa0908520:intron 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr6_2:9716594-9716613 None:intergenic 50.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr6_2:9716599-9716618 Msa0908520:CDS 50.0%
TAAGTTCGCCGTCAAATCCC+AGG - chr6_2:9716630-9716649 Msa0908520:CDS 50.0%
AAGTTCGCCGTCAAATCCCA+GGG - chr6_2:9716631-9716650 Msa0908520:CDS 50.0%
! GTAGTTTTCACCACCTGTCC+AGG + chr6_2:9716663-9716682 None:intergenic 50.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr6_2:9716454-9716473 Msa0908520:CDS 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr6_2:9716462-9716481 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr6_2:9716461-9716480 Msa0908520:CDS 55.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr6_2:9716462-9716481 Msa0908520:CDS 55.0%
GGTTGAGCCCTGGGATTTGA+CGG + chr6_2:9716641-9716660 None:intergenic 55.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr6_2:9716544-9716563 Msa0908520:CDS 60.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr6_2:9716602-9716621 Msa0908520:CDS 60.0%
CAAATCCCAGGGCTCAACCC+TGG - chr6_2:9716642-9716661 Msa0908520:CDS 60.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr6_2:9716557-9716576 None:intergenic 65.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr6_2:9716555-9716574 Msa0908520:CDS 65.0%
CCTGTCCAGGGTTGAGCCCT+GGG + chr6_2:9716650-9716669 None:intergenic 65.0%
ACCTGTCCAGGGTTGAGCCC+TGG + chr6_2:9716651-9716670 None:intergenic 65.0%
AGGGCTCAACCCTGGACAGG+TGG - chr6_2:9716650-9716669 Msa0908520:CDS 65.0%
CCACGCGGCATTGCTCCGTC+AGG + chr6_2:9716447-9716466 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr6_2:9716444-9716463 Msa0908520:CDS 70.0%
GACGGAGCAATGCCGCGTGG+AGG - chr6_2:9716447-9716466 Msa0908520:CDS 70.0%
CCCAGGGCTCAACCCTGGAC+AGG - chr6_2:9716647-9716666 Msa0908520:CDS 70.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9716433 9716685 9716433 ID=Msa0908520;Name=Msa0908520
chr6_2 mRNA 9716433 9716685 9716433 ID=Msa0908520-mRNA-1;Parent=Msa0908520;Name=Msa0908520-mRNA-1;_AED=0.42;_eAED=0.47;_QI=0|0|0|1|1|1|2|0|78
chr6_2 exon 9716598 9716685 9716598 ID=Msa0908520-mRNA-1:exon:2382;Parent=Msa0908520-mRNA-1
chr6_2 exon 9716433 9716581 9716433 ID=Msa0908520-mRNA-1:exon:2381;Parent=Msa0908520-mRNA-1
chr6_2 CDS 9716598 9716685 9716598 ID=Msa0908520-mRNA-1:cds;Parent=Msa0908520-mRNA-1
chr6_2 CDS 9716433 9716581 9716433 ID=Msa0908520-mRNA-1:cds;Parent=Msa0908520-mRNA-1
Gene Sequence

>Msa0908520

ATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGGTAAAAGGCCTACGGGTCATGAACTTCTTTTCCTGGAGAAGAAACAATGACGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTTCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGTGGTGAAAACTACTAA

Protein sequence

>Msa0908520

MGESLTEQCRVEVKGLRVMNFFSWRRNNDASANSVPAAAVRQRMQALSGMIGRKASVGGFLSSPSNPRAQPWTGGENY*