AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0399410

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 10 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGTTATATTATAATAAAA+TGG 0.310492 3_2:-22832901 None:intergenic
CTCTTTCAAATTTATCTGCT+TGG 0.338296 3_2:-22832721 None:intergenic
GCAGATAAATTTGAAAGAGT+TGG 0.439260 3_2:+22832725 Msa0399410:three_prime_UTR
GTCGCCCTCTTGAAATTCAT+CGG 0.542086 3_2:-22832674 None:intergenic
ATAAATTTGAAAGAGTTGGA+TGG 0.586941 3_2:+22832729 Msa0399410:three_prime_UTR
CGTGACCGATGAATTTCAAG+AGG 0.644369 3_2:+22832669 Msa0399410:CDS
GAGTTGCCTCCGAAAAGTCA+AGG 0.650095 3_2:+22832075 Msa0399410:CDS
CGAAGGTGTTGAAAAGCTCG+AGG 0.669368 3_2:+22832621 Msa0399410:CDS
ATCCAACAAGGTATCAACGA+AGG 0.674660 3_2:+22832604 Msa0399410:intron
GTGACCGATGAATTTCAAGA+GGG 0.696691 3_2:+22832670 Msa0399410:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATGATGTTAATTACTTTT+TGG + chr3_2:22832104-22832123 Msa0399410:CDS 15.0%
!!! TAATGATGTTAATTACTTTT+TGG + chr3_2:22832104-22832123 Msa0399410:CDS 15.0%
!!! AATTACTTTTTGGATATTGT+TGG + chr3_2:22832114-22832133 Msa0399410:CDS 20.0%
!!! ATTACTTTTTGGATATTGTT+GGG + chr3_2:22832115-22832134 Msa0399410:CDS 20.0%
!! AAGTTGTAGACATTTAAAAA+GGG + chr3_2:22832405-22832424 Msa0399410:intron 20.0%
!!! TAAAACAATTTTCCTATTTG+CGG + chr3_2:22832459-22832478 Msa0399410:intron 20.0%
!! ACATTAACCATATATATTGT+TGG - chr3_2:22832566-22832585 None:intergenic 20.0%
!!! TTTTATTTTCTTATCCAACA+AGG + chr3_2:22832592-22832611 Msa0399410:intron 20.0%
!!! AATTACTTTTTGGATATTGT+TGG + chr3_2:22832114-22832133 Msa0399410:CDS 20.0%
!!! ATTACTTTTTGGATATTGTT+GGG + chr3_2:22832115-22832134 Msa0399410:CDS 20.0%
!! AAGTTGTAGACATTTAAAAA+GGG + chr3_2:22832405-22832424 Msa0399410:intron 20.0%
!!! TAAAACAATTTTCCTATTTG+CGG + chr3_2:22832459-22832478 Msa0399410:intron 20.0%
!! ACATTAACCATATATATTGT+TGG - chr3_2:22832566-22832585 None:intergenic 20.0%
!!! TTTTATTTTCTTATCCAACA+AGG + chr3_2:22832592-22832611 Msa0399410:intron 20.0%
!! TTATTGTAACCTTGACTTTT+CGG - chr3_2:22832087-22832106 None:intergenic 25.0%
!! AAATTGTTTAAGATGTGTGT+GGG + chr3_2:22832188-22832207 Msa0399410:intron 25.0%
! CAAGTTGTAGACATTTAAAA+AGG + chr3_2:22832404-22832423 Msa0399410:intron 25.0%
! AGTTGTAGACATTTAAAAAG+GGG + chr3_2:22832406-22832425 Msa0399410:intron 25.0%
!!! TGGTATTGATAAAATAGTGA+AGG + chr3_2:22832430-22832449 Msa0399410:intron 25.0%
!!! GGTATTGATAAAATAGTGAA+GGG + chr3_2:22832431-22832450 Msa0399410:intron 25.0%
! TATACCTCACACAAATAAAA+AGG - chr3_2:22832512-22832531 None:intergenic 25.0%
! ATAAATTTGAAAGAGTTGGA+TGG + chr3_2:22832729-22832748 Msa0399410:three_prime_UTR 25.0%
!! ACTTGAGTGAAATATGTTTT+TGG + chr3_2:22832785-22832804 Msa0399410:three_prime_UTR 25.0%
!! TTATTGTAACCTTGACTTTT+CGG - chr3_2:22832087-22832106 None:intergenic 25.0%
!! AAATTGTTTAAGATGTGTGT+GGG + chr3_2:22832188-22832207 Msa0399410:intron 25.0%
! CAAGTTGTAGACATTTAAAA+AGG + chr3_2:22832404-22832423 Msa0399410:intron 25.0%
! AGTTGTAGACATTTAAAAAG+GGG + chr3_2:22832406-22832425 Msa0399410:intron 25.0%
!!! TGGTATTGATAAAATAGTGA+AGG + chr3_2:22832430-22832449 Msa0399410:intron 25.0%
!!! GGTATTGATAAAATAGTGAA+GGG + chr3_2:22832431-22832450 Msa0399410:intron 25.0%
! TATACCTCACACAAATAAAA+AGG - chr3_2:22832512-22832531 None:intergenic 25.0%
! ATAAATTTGAAAGAGTTGGA+TGG + chr3_2:22832729-22832748 Msa0399410:three_prime_UTR 25.0%
!! ACTTGAGTGAAATATGTTTT+TGG + chr3_2:22832785-22832804 Msa0399410:three_prime_UTR 25.0%
! GAAATTGTTTAAGATGTGTG+TGG + chr3_2:22832187-22832206 Msa0399410:intron 30.0%
!! CTTTCCTTTTTATTTGTGTG+AGG + chr3_2:22832505-22832524 Msa0399410:intron 30.0%
!! CCATATATATTGTTGGTTCA+AGG - chr3_2:22832559-22832578 None:intergenic 30.0%
CCTTGAACCAACAATATATA+TGG + chr3_2:22832556-22832575 Msa0399410:intron 30.0%
CTCTTTCAAATTTATCTGCT+TGG - chr3_2:22832724-22832743 None:intergenic 30.0%
GCAGATAAATTTGAAAGAGT+TGG + chr3_2:22832725-22832744 Msa0399410:three_prime_UTR 30.0%
!!! AGTTGGATGGTGTTTTATTT+GGG + chr3_2:22832742-22832761 Msa0399410:three_prime_UTR 30.0%
! GAAATTGTTTAAGATGTGTG+TGG + chr3_2:22832187-22832206 Msa0399410:intron 30.0%
!! CTTTCCTTTTTATTTGTGTG+AGG + chr3_2:22832505-22832524 Msa0399410:intron 30.0%
!! CCATATATATTGTTGGTTCA+AGG - chr3_2:22832559-22832578 None:intergenic 30.0%
CCTTGAACCAACAATATATA+TGG + chr3_2:22832556-22832575 Msa0399410:intron 30.0%
CTCTTTCAAATTTATCTGCT+TGG - chr3_2:22832724-22832743 None:intergenic 30.0%
GCAGATAAATTTGAAAGAGT+TGG + chr3_2:22832725-22832744 Msa0399410:three_prime_UTR 30.0%
!!! AGTTGGATGGTGTTTTATTT+GGG + chr3_2:22832742-22832761 Msa0399410:three_prime_UTR 30.0%
! TTTTTGGATATTGTTGGGTC+AGG + chr3_2:22832120-22832139 Msa0399410:CDS 35.0%
TTCAGACAAACAACACAATC+AGG - chr3_2:22832236-22832255 None:intergenic 35.0%
GTTACAATCAAAATCAGACC+CGG - chr3_2:22832278-22832297 None:intergenic 35.0%
! CGTTTGTGTTTTGCATATCT+AGG + chr3_2:22832379-22832398 Msa0399410:intron 35.0%
GTAGACATTTAAAAAGGGGT+TGG + chr3_2:22832410-22832429 Msa0399410:intron 35.0%
!! GAGTTGGATGGTGTTTTATT+TGG + chr3_2:22832741-22832760 Msa0399410:three_prime_UTR 35.0%
! TTTTTGGATATTGTTGGGTC+AGG + chr3_2:22832120-22832139 Msa0399410:CDS 35.0%
TTCAGACAAACAACACAATC+AGG - chr3_2:22832236-22832255 None:intergenic 35.0%
GTTACAATCAAAATCAGACC+CGG - chr3_2:22832278-22832297 None:intergenic 35.0%
! CGTTTGTGTTTTGCATATCT+AGG + chr3_2:22832379-22832398 Msa0399410:intron 35.0%
GTAGACATTTAAAAAGGGGT+TGG + chr3_2:22832410-22832429 Msa0399410:intron 35.0%
!! GAGTTGGATGGTGTTTTATT+TGG + chr3_2:22832741-22832760 Msa0399410:three_prime_UTR 35.0%
! TTGTAACCTTGACTTTTCGG+AGG - chr3_2:22832084-22832103 None:intergenic 40.0%
! ATAGTTTAAGATGCGTGTGC+CGG + chr3_2:22832256-22832275 Msa0399410:intron 40.0%
CTCAAAACAGAACCGCAAAT+AGG - chr3_2:22832474-22832493 None:intergenic 40.0%
! ATCCAACAAGGTATCAACGA+AGG + chr3_2:22832604-22832623 Msa0399410:intron 40.0%
GTGACCGATGAATTTCAAGA+GGG + chr3_2:22832670-22832689 Msa0399410:CDS 40.0%
! TTGTAACCTTGACTTTTCGG+AGG - chr3_2:22832084-22832103 None:intergenic 40.0%
! ATAGTTTAAGATGCGTGTGC+CGG + chr3_2:22832256-22832275 Msa0399410:intron 40.0%
CTCAAAACAGAACCGCAAAT+AGG - chr3_2:22832474-22832493 None:intergenic 40.0%
! ATCCAACAAGGTATCAACGA+AGG + chr3_2:22832604-22832623 Msa0399410:intron 40.0%
GTGACCGATGAATTTCAAGA+GGG + chr3_2:22832670-22832689 Msa0399410:CDS 40.0%
TTGGATATTGTTGGGTCAGG+TGG + chr3_2:22832123-22832142 Msa0399410:intron 45.0%
!!! TTGGGTCAGGTGGCTTTTTT+GGG + chr3_2:22832133-22832152 Msa0399410:intron 45.0%
! GATGTGTGTGGGTCTGATTT+TGG + chr3_2:22832199-22832218 Msa0399410:intron 45.0%
! TAGTTTAAGATGCGTGTGCC+GGG + chr3_2:22832257-22832276 Msa0399410:intron 45.0%
CACCTTCGTTGATACCTTGT+TGG - chr3_2:22832609-22832628 None:intergenic 45.0%
CGTGACCGATGAATTTCAAG+AGG + chr3_2:22832669-22832688 Msa0399410:CDS 45.0%
GTCGCCCTCTTGAAATTCAT+CGG - chr3_2:22832677-22832696 None:intergenic 45.0%
TTGGATATTGTTGGGTCAGG+TGG + chr3_2:22832123-22832142 Msa0399410:intron 45.0%
!!! TTGGGTCAGGTGGCTTTTTT+GGG + chr3_2:22832133-22832152 Msa0399410:intron 45.0%
! GATGTGTGTGGGTCTGATTT+TGG + chr3_2:22832199-22832218 Msa0399410:intron 45.0%
! TAGTTTAAGATGCGTGTGCC+GGG + chr3_2:22832257-22832276 Msa0399410:intron 45.0%
CACCTTCGTTGATACCTTGT+TGG - chr3_2:22832609-22832628 None:intergenic 45.0%
CGTGACCGATGAATTTCAAG+AGG + chr3_2:22832669-22832688 Msa0399410:CDS 45.0%
GTCGCCCTCTTGAAATTCAT+CGG - chr3_2:22832677-22832696 None:intergenic 45.0%
!! AAAGTTATATTATAATAAAA+TGG - chr3_2:22832904-22832923 None:intergenic 5.0%
!! AAAGTTATATTATAATAAAA+TGG - chr3_2:22832904-22832923 None:intergenic 5.0%
GAGTTGCCTCCGAAAAGTCA+AGG + chr3_2:22832075-22832094 Msa0399410:CDS 50.0%
!!! GTTGGGTCAGGTGGCTTTTT+TGG + chr3_2:22832132-22832151 Msa0399410:intron 50.0%
!! CGAAGGTGTTGAAAAGCTCG+AGG + chr3_2:22832621-22832640 Msa0399410:CDS 50.0%
GAGTTGCCTCCGAAAAGTCA+AGG + chr3_2:22832075-22832094 Msa0399410:CDS 50.0%
!!! GTTGGGTCAGGTGGCTTTTT+TGG + chr3_2:22832132-22832151 Msa0399410:intron 50.0%
!! CGAAGGTGTTGAAAAGCTCG+AGG + chr3_2:22832621-22832640 Msa0399410:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 22832069 22832927 22832069 ID=Msa0399410;Name=Msa0399410
chr3_2 mRNA 22832069 22832927 22832069 ID=Msa0399410-mRNA-1;Parent=Msa0399410;Name=Msa0399410-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0.5|0.5|1|1|2|213|57
chr3_2 exon 22832069 22832141 22832069 ID=Msa0399410-mRNA-1:exon:4822;Parent=Msa0399410-mRNA-1
chr3_2 exon 22832614 22832927 22832614 ID=Msa0399410-mRNA-1:exon:4823;Parent=Msa0399410-mRNA-1
chr3_2 CDS 22832069 22832141 22832069 ID=Msa0399410-mRNA-1:cds;Parent=Msa0399410-mRNA-1
chr3_2 CDS 22832614 22832714 22832614 ID=Msa0399410-mRNA-1:cds;Parent=Msa0399410-mRNA-1
chr3_2 three_prime_UTR 22832715 22832927 22832715 ID=Msa0399410-mRNA-1:three_prime_utr;Parent=Msa0399410-mRNA-1
Gene Sequence

>Msa0399410

ATGGTGGAGTTGCCTCCGAAAAGTCAAGGTTACAATAATGATGTTAATTACTTTTTGGATATTGTTGGGTCAGGTATCAACGAAGGTGTTGAAAAGCTCGAGGTAGAGAATCAATTTCAAGAAGACGTCGTGACCGATGAATTTCAAGAGGGCGACATAAGTGATGATGAATGA
Protein sequence

>Msa0399410

MVELPPKSQGYNNDVNYFLDIVGSGINEGVEKLEVENQFQEDVVTDEFQEGDISDDE*