AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0589410

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 23 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGAATCATTGAAGATAAA+AGG 0.193549 4_2:+12268759 Msa0589410:CDS
CACTTTCTTCTTATTGTTGC+AGG 0.218575 4_2:+12268425 Msa0589410:five_prime_UTR
TCACCCACGTCTTATTATTA+AGG 0.222696 4_2:+12267998 None:intergenic
ACTTCTCTCCTTCAAACTTT+TGG 0.253847 4_2:+12268249 Msa0589410:five_prime_UTR
GGGGAAAGCAATAAAGAAAA+TGG 0.306822 4_2:+12268780 Msa0589410:CDS
ATAATCTATTTATTACAGTT+TGG 0.362570 4_2:-12268578 None:intergenic
TTTCAGATCTATAATAAAGT+TGG 0.393377 4_2:+12268600 Msa0589410:CDS
CACCCACGTCTTATTATTAA+GGG 0.395731 4_2:+12267999 None:intergenic
AAGAATCATTGAAGATAAAA+GGG 0.399502 4_2:+12268760 Msa0589410:CDS
CCTTCATTGGTCTTCTTCAT+CGG 0.404313 4_2:-12268466 None:intergenic
TTTGAGAGCCAAAAGTTTGA+AGG 0.407150 4_2:-12268257 None:intergenic
ACAACAAGATACATAATGTC+AGG 0.448762 4_2:+12268202 Msa0589410:five_prime_UTR
AAAGGAAAACAACAAACTAA+TGG 0.459607 4_2:-12268100 None:intergenic
CTATGATGTTATCTAAGTAC+TGG 0.488189 4_2:+12268073 Msa0589410:five_prime_UTR
GTTTGGATGTGAATGCCATT+TGG 0.501084 4_2:-12268561 None:intergenic
AAAGAGTGAGAGAAAGAAGA+AGG 0.512793 4_2:-12268362 None:intergenic
TATCACACATACATATAAGT+TGG 0.521733 4_2:-12268813 None:intergenic
ACAAATTCATCAGTACCAAA+TGG 0.523287 4_2:+12268546 Msa0589410:CDS
CCGATGAAGAAGACCAATGA+AGG 0.555749 4_2:+12268466 Msa0589410:five_prime_UTR
TACCCTTAATAATAAGACGT+GGG 0.618201 4_2:-12268001 None:intergenic
CAACAAGATACATAATGTCA+GGG 0.628783 4_2:+12268203 Msa0589410:five_prime_UTR
AGAATCATTGAAGATAAAAG+GGG 0.634800 4_2:+12268761 Msa0589410:CDS
TTACCCTTAATAATAAGACG+TGG 0.663798 4_2:-12268002 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATCTATTTATTACAGTT+TGG - chr4_2:12268581-12268600 None:intergenic 15.0%
!! ATAATCTATTTATTACAGTT+TGG - chr4_2:12268581-12268600 None:intergenic 15.0%
!!! TGACAATGTAAATTTTTGAA+AGG - chr4_2:12268121-12268140 None:intergenic 20.0%
!! TTTCAGATCTATAATAAAGT+TGG + chr4_2:12268600-12268619 Msa0589410:CDS 20.0%
!! AAGAATCATTGAAGATAAAA+GGG + chr4_2:12268760-12268779 Msa0589410:CDS 20.0%
!!! TGACAATGTAAATTTTTGAA+AGG - chr4_2:12268121-12268140 None:intergenic 20.0%
!! TTTCAGATCTATAATAAAGT+TGG + chr4_2:12268600-12268619 Msa0589410:CDS 20.0%
!! AAGAATCATTGAAGATAAAA+GGG + chr4_2:12268760-12268779 Msa0589410:CDS 20.0%
! AAAGGAAAACAACAAACTAA+TGG - chr4_2:12268103-12268122 None:intergenic 25.0%
! GAAAGTGAAGATTAGAAAAA+TGG - chr4_2:12268412-12268431 None:intergenic 25.0%
!! TCTTTTTATCTTTGTACTCA+TGG - chr4_2:12268709-12268728 None:intergenic 25.0%
! GAAGAATCATTGAAGATAAA+AGG + chr4_2:12268759-12268778 Msa0589410:CDS 25.0%
! AGAATCATTGAAGATAAAAG+GGG + chr4_2:12268761-12268780 Msa0589410:CDS 25.0%
! AAAGGAAAACAACAAACTAA+TGG - chr4_2:12268103-12268122 None:intergenic 25.0%
! GAAAGTGAAGATTAGAAAAA+TGG - chr4_2:12268412-12268431 None:intergenic 25.0%
!! TCTTTTTATCTTTGTACTCA+TGG - chr4_2:12268709-12268728 None:intergenic 25.0%
! GAAGAATCATTGAAGATAAA+AGG + chr4_2:12268759-12268778 Msa0589410:CDS 25.0%
! AGAATCATTGAAGATAAAAG+GGG + chr4_2:12268761-12268780 Msa0589410:CDS 25.0%
TACCCTTAATAATAAGACGT+GGG - chr4_2:12268004-12268023 None:intergenic 30.0%
TTACCCTTAATAATAAGACG+TGG - chr4_2:12268005-12268024 None:intergenic 30.0%
CTATGATGTTATCTAAGTAC+TGG + chr4_2:12268073-12268092 Msa0589410:five_prime_UTR 30.0%
AACTACAGAAAAACACCTAT+CGG + chr4_2:12268150-12268169 Msa0589410:five_prime_UTR 30.0%
ACAACAAGATACATAATGTC+AGG + chr4_2:12268202-12268221 Msa0589410:five_prime_UTR 30.0%
CAACAAGATACATAATGTCA+GGG + chr4_2:12268203-12268222 Msa0589410:five_prime_UTR 30.0%
ACAAATTCATCAGTACCAAA+TGG + chr4_2:12268546-12268565 Msa0589410:CDS 30.0%
!!! ACAGTTTATCCTCTGTTTTT+TGG + chr4_2:12268654-12268673 Msa0589410:CDS 30.0%
! TTTTTCTGTCCAAAAAACAG+AGG - chr4_2:12268666-12268685 None:intergenic 30.0%
TACCCTTAATAATAAGACGT+GGG - chr4_2:12268004-12268023 None:intergenic 30.0%
TTACCCTTAATAATAAGACG+TGG - chr4_2:12268005-12268024 None:intergenic 30.0%
CTATGATGTTATCTAAGTAC+TGG + chr4_2:12268073-12268092 Msa0589410:five_prime_UTR 30.0%
AACTACAGAAAAACACCTAT+CGG + chr4_2:12268150-12268169 Msa0589410:five_prime_UTR 30.0%
ACAACAAGATACATAATGTC+AGG + chr4_2:12268202-12268221 Msa0589410:five_prime_UTR 30.0%
CAACAAGATACATAATGTCA+GGG + chr4_2:12268203-12268222 Msa0589410:five_prime_UTR 30.0%
ACAAATTCATCAGTACCAAA+TGG + chr4_2:12268546-12268565 Msa0589410:CDS 30.0%
!!! ACAGTTTATCCTCTGTTTTT+TGG + chr4_2:12268654-12268673 Msa0589410:CDS 30.0%
! TTTTTCTGTCCAAAAAACAG+AGG - chr4_2:12268666-12268685 None:intergenic 30.0%
! GATAGGTGTTTTTCTGTAGT+TGG - chr4_2:12268151-12268170 None:intergenic 35.0%
!!! ATCACTTTTTGTCAACCGAT+AGG - chr4_2:12268168-12268187 None:intergenic 35.0%
! ACTTCTCTCCTTCAAACTTT+TGG + chr4_2:12268249-12268268 Msa0589410:five_prime_UTR 35.0%
TTTGAGAGCCAAAAGTTTGA+AGG - chr4_2:12268260-12268279 None:intergenic 35.0%
AAAGAGTGAGAGAAAGAAGA+AGG - chr4_2:12268365-12268384 None:intergenic 35.0%
CACTTTCTTCTTATTGTTGC+AGG + chr4_2:12268425-12268444 Msa0589410:five_prime_UTR 35.0%
AGACCAATGAAGGAAAAACA+TGG + chr4_2:12268476-12268495 Msa0589410:exon 35.0%
GACCAATGAAGGAAAAACAT+GGG + chr4_2:12268477-12268496 Msa0589410:exon 35.0%
! TACCCATGTTTTTCCTTCAT+TGG - chr4_2:12268482-12268501 None:intergenic 35.0%
ATGAAGGAAAAACATGGGTA+AGG + chr4_2:12268482-12268501 Msa0589410:exon 35.0%
GGGGAAAGCAATAAAGAAAA+TGG + chr4_2:12268780-12268799 Msa0589410:CDS 35.0%
! GATAGGTGTTTTTCTGTAGT+TGG - chr4_2:12268151-12268170 None:intergenic 35.0%
!!! ATCACTTTTTGTCAACCGAT+AGG - chr4_2:12268168-12268187 None:intergenic 35.0%
! ACTTCTCTCCTTCAAACTTT+TGG + chr4_2:12268249-12268268 Msa0589410:five_prime_UTR 35.0%
TTTGAGAGCCAAAAGTTTGA+AGG - chr4_2:12268260-12268279 None:intergenic 35.0%
AAAGAGTGAGAGAAAGAAGA+AGG - chr4_2:12268365-12268384 None:intergenic 35.0%
CACTTTCTTCTTATTGTTGC+AGG + chr4_2:12268425-12268444 Msa0589410:five_prime_UTR 35.0%
AGACCAATGAAGGAAAAACA+TGG + chr4_2:12268476-12268495 Msa0589410:exon 35.0%
GACCAATGAAGGAAAAACAT+GGG + chr4_2:12268477-12268496 Msa0589410:exon 35.0%
! TACCCATGTTTTTCCTTCAT+TGG - chr4_2:12268482-12268501 None:intergenic 35.0%
ATGAAGGAAAAACATGGGTA+AGG + chr4_2:12268482-12268501 Msa0589410:exon 35.0%
GGGGAAAGCAATAAAGAAAA+TGG + chr4_2:12268780-12268799 Msa0589410:CDS 35.0%
!! CCTTCATTGGTCTTCTTCAT+CGG - chr4_2:12268469-12268488 None:intergenic 40.0%
GTTTGGATGTGAATGCCATT+TGG - chr4_2:12268564-12268583 None:intergenic 40.0%
!! CCTTCATTGGTCTTCTTCAT+CGG - chr4_2:12268469-12268488 None:intergenic 40.0%
GTTTGGATGTGAATGCCATT+TGG - chr4_2:12268564-12268583 None:intergenic 40.0%
CCGATGAAGAAGACCAATGA+AGG + chr4_2:12268466-12268485 Msa0589410:five_prime_UTR 45.0%
CCGATGAAGAAGACCAATGA+AGG + chr4_2:12268466-12268485 Msa0589410:five_prime_UTR 45.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 12268001 12268833 12268001 ID=Msa0589410;Name=Msa0589410
chr4_2 mRNA 12268001 12268833 12268001 ID=Msa0589410-mRNA-1;Parent=Msa0589410;Name=Msa0589410-mRNA-1;_AED=0.20;_eAED=0.39;_QI=494|0|0.5|1|1|1|2|0|102
chr4_2 exon 12268001 12268503 12268001 ID=Msa0589410-mRNA-1:exon:3564;Parent=Msa0589410-mRNA-1
chr4_2 exon 12268534 12268833 12268534 ID=Msa0589410-mRNA-1:exon:3565;Parent=Msa0589410-mRNA-1
chr4_2 five_prime_UTR 12268001 12268494 12268001 ID=Msa0589410-mRNA-1:five_prime_utr;Parent=Msa0589410-mRNA-1
chr4_2 CDS 12268495 12268503 12268495 ID=Msa0589410-mRNA-1:cds;Parent=Msa0589410-mRNA-1
chr4_2 CDS 12268534 12268833 12268534 ID=Msa0589410-mRNA-1:cds;Parent=Msa0589410-mRNA-1
Gene Sequence

>Msa0589410

ATGGGTAAGCTGCATAACATGACAAATTCATCAGTACCAAATGGCATTCACATCCAAACTGTAATAAATAGATTATTTCAGATCTATAATAAAGTTGGACACTATACTCAATCTTCTTCAAATACTTTTACAGTTTATCCTCTGTTTTTTGGACAGAAAAATAGACAAGAAATGAAGATCACCATGAGTACAAAGATAAAAAGAAGTAGCAATCATGTCTGTTGTGATTTAACAGAAGAATCATTGAAGATAAAAGGGGAAAGCAATAAAGAAAATGGAGCAGAAGAACCAACTTATATGTATGTGTGA
Protein sequence

>Msa0589410

MGKLHNMTNSSVPNGIHIQTVINRLFQIYNKVGHYTQSSSNTFTVYPLFFGQKNRQEMKITMSTKIKRSSNHVCCDLTEESLKIKGESNKENGAEEPTYMYV*