AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0272000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0272000 MtrunA17_Chr2g0279941 100.000 69 0 0 1 69 1 69 3.98e-43 133
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 129 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTTTCTGCCATATATATT+TGG 0.170915 2_3:-3500089 None:intergenic
ATATTCCACAACTTTAATAA+TGG 0.294529 2_3:-3500152 None:intergenic
TATACTCATACACATGCTTT+AGG 0.317198 2_3:-3499231 None:intergenic
AAAATATAACCAAATATATA+TGG 0.338136 2_3:+3500080 Msa0272000:three_prime_UTR
AAAGAAAAGGAAGATAATAA+AGG 0.362142 2_3:-3500055 None:intergenic
TACTCACTCATACAATTAAT+AGG 0.364891 2_3:-3499969 None:intergenic
AAGAAAAGGAAGATAATAAA+GGG 0.377219 2_3:-3500054 None:intergenic
ACCGGAGGTGGTCCTTGATA+AGG 0.377579 2_3:-3499572 None:intergenic
GCTAATGCATTTCACCAAAC+TGG 0.387821 2_3:+3499867 Msa0272000:exon
TATCATATAATATCAAATAT+TGG 0.395323 2_3:-3499997 None:intergenic
GAGATGAGTGAGATCAAATA+TGG 0.409886 2_3:+3499343 Msa0272000:exon
TATGTACCTTGAGCAGGATA+TGG 0.426594 2_3:-3499370 None:intergenic
TTTGTGTTGCTGTTGCCTCT+TGG 0.433493 2_3:+3499808 Msa0272000:CDS
GGTGGTGCCGCCACCGGAGG+TGG 0.452814 2_3:-3499584 None:intergenic
CCGGAGGTGGTCCTTGATAA+GGG 0.453222 2_3:-3499571 None:intergenic
AGTACATTTATTATCTGAAA+GGG 0.466301 2_3:+3500026 Msa0272000:three_prime_UTR
CCCTTATCAAGGACCACCTC+CGG 0.501946 2_3:+3499571 Msa0272000:CDS
TTCATACTAGGCCCTTATCA+AGG 0.506361 2_3:+3499560 Msa0272000:intron
TCAAGGACCACCTCCGGTGG+CGG 0.518251 2_3:+3499577 Msa0272000:CDS
ATGGTGTATGTACCTTGAGC+AGG 0.537878 2_3:-3499376 None:intergenic
TGCGGTGGTGCCGCCACCGG+AGG 0.538797 2_3:-3499587 None:intergenic
TATTGCGGTGGTGCCGCCAC+CGG 0.539716 2_3:-3499590 None:intergenic
TAGTACATTTATTATCTGAA+AGG 0.542095 2_3:+3500025 Msa0272000:three_prime_UTR
GGCTATCCATATCCTGCTCA+AGG 0.571306 2_3:+3499364 Msa0272000:CDS
TACCATCCCTCAAGAAAACC+CGG 0.577880 2_3:-3499647 None:intergenic
AACAGCAACACAAAGCTGCT+AGG 0.601258 2_3:-3499799 None:intergenic
AGAAAAGGAAGATAATAAAG+GGG 0.613618 2_3:-3500053 None:intergenic
TTATCAAGGACCACCTCCGG+TGG 0.637488 2_3:+3499574 Msa0272000:CDS
CACAGCAGCACTCATCCAAG+AGG 0.685776 2_3:-3499823 None:intergenic
GGAGCAGCATAGTATTGCGG+TGG 0.697423 2_3:-3499602 None:intergenic
GGTGGAGCAGCATAGTATTG+CGG 0.699649 2_3:-3499605 None:intergenic
GGAATATAGATACAATAACG+TGG 0.751387 2_3:+3500168 Msa0272000:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTCAAGAATAATTTT+AGG + chr2_3:3499299-3499318 Msa0272000:five_prime_UTR 10.0%
!! TATCATATAATATCAAATAT+TGG - chr2_3:3500000-3500019 None:intergenic 10.0%
!! AAAATATAACCAAATATATA+TGG + chr2_3:3500080-3500099 Msa0272000:three_prime_UTR 10.0%
!!! TTTATTTCAAGAATAATTTT+AGG + chr2_3:3499299-3499318 Msa0272000:five_prime_UTR 10.0%
!! TATCATATAATATCAAATAT+TGG - chr2_3:3500000-3500019 None:intergenic 10.0%
!! AAAATATAACCAAATATATA+TGG + chr2_3:3500080-3500099 Msa0272000:three_prime_UTR 10.0%
!!! AAGTTTTAGTATATAATTTG+AGG - chr2_3:3499420-3499439 None:intergenic 15.0%
!! GTTTCAATATTGTAATAAAA+AGG - chr2_3:3499460-3499479 None:intergenic 15.0%
!! AAAAAAAATACATTGTTTAG+TGG + chr2_3:3499940-3499959 Msa0272000:three_prime_UTR 15.0%
!!! GGTTATATTTTTAAAAGAAA+AGG - chr2_3:3500071-3500090 None:intergenic 15.0%
!!! AACTTTAATAATGGAAAAAA+TGG - chr2_3:3500146-3500165 None:intergenic 15.0%
!!! AAGTTTTAGTATATAATTTG+AGG - chr2_3:3499420-3499439 None:intergenic 15.0%
!! GTTTCAATATTGTAATAAAA+AGG - chr2_3:3499460-3499479 None:intergenic 15.0%
!! AAAAAAAATACATTGTTTAG+TGG + chr2_3:3499940-3499959 Msa0272000:three_prime_UTR 15.0%
!!! GGTTATATTTTTAAAAGAAA+AGG - chr2_3:3500071-3500090 None:intergenic 15.0%
!!! AACTTTAATAATGGAAAAAA+TGG - chr2_3:3500146-3500165 None:intergenic 15.0%
!!! AAGAACTTGTAATTTTATGT+TGG - chr2_3:3499280-3499299 None:intergenic 20.0%
!! GAATGAGAAATATGTATATA+TGG - chr2_3:3499398-3499417 None:intergenic 20.0%
!!! TTGTTGTTATATTTCATACT+AGG + chr2_3:3499548-3499567 Msa0272000:intron 20.0%
!! TAAGCAATTATACACTATAT+AGG + chr2_3:3499668-3499687 Msa0272000:intron 20.0%
!! AAGCAATTATACACTATATA+GGG + chr2_3:3499669-3499688 Msa0272000:intron 20.0%
!! TAGTACATTTATTATCTGAA+AGG + chr2_3:3500025-3500044 Msa0272000:three_prime_UTR 20.0%
!! AGTACATTTATTATCTGAAA+GGG + chr2_3:3500026-3500045 Msa0272000:three_prime_UTR 20.0%
!! AAGAAAAGGAAGATAATAAA+GGG - chr2_3:3500057-3500076 None:intergenic 20.0%
!! AAAGAAAAGGAAGATAATAA+AGG - chr2_3:3500058-3500077 None:intergenic 20.0%
!!! TTTTTCCATTATTAAAGTTG+TGG + chr2_3:3500147-3500166 Msa0272000:three_prime_UTR 20.0%
!! ATATTCCACAACTTTAATAA+TGG - chr2_3:3500155-3500174 None:intergenic 20.0%
!!! AAGAACTTGTAATTTTATGT+TGG - chr2_3:3499280-3499299 None:intergenic 20.0%
!! GAATGAGAAATATGTATATA+TGG - chr2_3:3499398-3499417 None:intergenic 20.0%
!!! TTGTTGTTATATTTCATACT+AGG + chr2_3:3499548-3499567 Msa0272000:intron 20.0%
!! TAAGCAATTATACACTATAT+AGG + chr2_3:3499668-3499687 Msa0272000:intron 20.0%
!! AAGCAATTATACACTATATA+GGG + chr2_3:3499669-3499688 Msa0272000:intron 20.0%
!! TAGTACATTTATTATCTGAA+AGG + chr2_3:3500025-3500044 Msa0272000:three_prime_UTR 20.0%
!! AGTACATTTATTATCTGAAA+GGG + chr2_3:3500026-3500045 Msa0272000:three_prime_UTR 20.0%
!! AAGAAAAGGAAGATAATAAA+GGG - chr2_3:3500057-3500076 None:intergenic 20.0%
!! AAAGAAAAGGAAGATAATAA+AGG - chr2_3:3500058-3500077 None:intergenic 20.0%
!!! TTTTTCCATTATTAAAGTTG+TGG + chr2_3:3500147-3500166 Msa0272000:three_prime_UTR 20.0%
!! ATATTCCACAACTTTAATAA+TGG - chr2_3:3500155-3500174 None:intergenic 20.0%
!! TAATTTTATGTTGGAATGCA+GGG - chr2_3:3499271-3499290 None:intergenic 25.0%
! TACTCACTCATACAATTAAT+AGG - chr2_3:3499972-3499991 None:intergenic 25.0%
! AGAAAAGGAAGATAATAAAG+GGG - chr2_3:3500056-3500075 None:intergenic 25.0%
!! AATAATGGAAAAAATGGAGA+GGG - chr2_3:3500140-3500159 None:intergenic 25.0%
!! TAATAATGGAAAAAATGGAG+AGG - chr2_3:3500141-3500160 None:intergenic 25.0%
!! TAATTTTATGTTGGAATGCA+GGG - chr2_3:3499271-3499290 None:intergenic 25.0%
! TACTCACTCATACAATTAAT+AGG - chr2_3:3499972-3499991 None:intergenic 25.0%
! AGAAAAGGAAGATAATAAAG+GGG - chr2_3:3500056-3500075 None:intergenic 25.0%
!! AATAATGGAAAAAATGGAGA+GGG - chr2_3:3500140-3500159 None:intergenic 25.0%
!! TAATAATGGAAAAAATGGAG+AGG - chr2_3:3500141-3500160 None:intergenic 25.0%
TATACTCATACACATGCTTT+AGG - chr2_3:3499234-3499253 None:intergenic 30.0%
! GTAATTTTATGTTGGAATGC+AGG - chr2_3:3499272-3499291 None:intergenic 30.0%
CAATTATACACTATATAGGG+TGG + chr2_3:3499672-3499691 Msa0272000:intron 30.0%
AGCTCGCAAAAATAATAGTT+GGG - chr2_3:3499850-3499869 None:intergenic 30.0%
TAGCTCGCAAAAATAATAGT+TGG - chr2_3:3499851-3499870 None:intergenic 30.0%
AGCTTTCTGCCATATATATT+TGG - chr2_3:3500092-3500111 None:intergenic 30.0%
AAAATGGAGAGGGTAAAAAA+TGG - chr2_3:3500130-3500149 None:intergenic 30.0%
GGAATATAGATACAATAACG+TGG + chr2_3:3500168-3500187 Msa0272000:three_prime_UTR 30.0%
TATACTCATACACATGCTTT+AGG - chr2_3:3499234-3499253 None:intergenic 30.0%
! GTAATTTTATGTTGGAATGC+AGG - chr2_3:3499272-3499291 None:intergenic 30.0%
CAATTATACACTATATAGGG+TGG + chr2_3:3499672-3499691 Msa0272000:intron 30.0%
AGCTCGCAAAAATAATAGTT+GGG - chr2_3:3499850-3499869 None:intergenic 30.0%
TAGCTCGCAAAAATAATAGT+TGG - chr2_3:3499851-3499870 None:intergenic 30.0%
AGCTTTCTGCCATATATATT+TGG - chr2_3:3500092-3500111 None:intergenic 30.0%
AAAATGGAGAGGGTAAAAAA+TGG - chr2_3:3500130-3500149 None:intergenic 30.0%
GAGATGAGTGAGATCAAATA+TGG + chr2_3:3499343-3499362 Msa0272000:exon 35.0%
! CAATAGCTTCTTTTCCAGTT+TGG - chr2_3:3499884-3499903 None:intergenic 35.0%
GAGATGAGTGAGATCAAATA+TGG + chr2_3:3499343-3499362 Msa0272000:exon 35.0%
! CAATAGCTTCTTTTCCAGTT+TGG - chr2_3:3499884-3499903 None:intergenic 35.0%
TATGTACCTTGAGCAGGATA+TGG - chr2_3:3499373-3499392 None:intergenic 40.0%
TTCATACTAGGCCCTTATCA+AGG + chr2_3:3499560-3499579 Msa0272000:intron 40.0%
CTGCTAGGCTGCATATAATT+GGG - chr2_3:3499787-3499806 None:intergenic 40.0%
GCTAATGCATTTCACCAAAC+TGG + chr2_3:3499867-3499886 Msa0272000:exon 40.0%
TATGTACCTTGAGCAGGATA+TGG - chr2_3:3499373-3499392 None:intergenic 40.0%
TTCATACTAGGCCCTTATCA+AGG + chr2_3:3499560-3499579 Msa0272000:intron 40.0%
CTGCTAGGCTGCATATAATT+GGG - chr2_3:3499787-3499806 None:intergenic 40.0%
GCTAATGCATTTCACCAAAC+TGG + chr2_3:3499867-3499886 Msa0272000:exon 40.0%
ATGGTGTATGTACCTTGAGC+AGG - chr2_3:3499379-3499398 None:intergenic 45.0%
! AGAAAACCCGGCTCTCTTTT+TGG - chr2_3:3499638-3499657 None:intergenic 45.0%
TACCATCCCTCAAGAAAACC+CGG - chr2_3:3499650-3499669 None:intergenic 45.0%
GCTGCTAGGCTGCATATAAT+TGG - chr2_3:3499788-3499807 None:intergenic 45.0%
AACAGCAACACAAAGCTGCT+AGG - chr2_3:3499802-3499821 None:intergenic 45.0%
! TTTGTGTTGCTGTTGCCTCT+TGG + chr2_3:3499808-3499827 Msa0272000:CDS 45.0%
ATGGTGTATGTACCTTGAGC+AGG - chr2_3:3499379-3499398 None:intergenic 45.0%
! AGAAAACCCGGCTCTCTTTT+TGG - chr2_3:3499638-3499657 None:intergenic 45.0%
TACCATCCCTCAAGAAAACC+CGG - chr2_3:3499650-3499669 None:intergenic 45.0%
GCTGCTAGGCTGCATATAAT+TGG - chr2_3:3499788-3499807 None:intergenic 45.0%
AACAGCAACACAAAGCTGCT+AGG - chr2_3:3499802-3499821 None:intergenic 45.0%
! TTTGTGTTGCTGTTGCCTCT+TGG + chr2_3:3499808-3499827 Msa0272000:CDS 45.0%
GGCTATCCATATCCTGCTCA+AGG + chr2_3:3499364-3499383 Msa0272000:CDS 50.0%
GGTGGAGCAGCATAGTATTG+CGG - chr2_3:3499608-3499627 None:intergenic 50.0%
!!! TCTCTTTTTGGTGGTGGTGG+TGG - chr2_3:3499626-3499645 None:intergenic 50.0%
ACCACCACCAAAAAGAGAGC+CGG + chr2_3:3499628-3499647 Msa0272000:CDS 50.0%
! AAACCCGGCTCTCTTTTTGG+TGG - chr2_3:3499635-3499654 None:intergenic 50.0%
! AAGAGAGCCGGGTTTTCTTG+AGG + chr2_3:3499640-3499659 Msa0272000:CDS 50.0%
! AGAGAGCCGGGTTTTCTTGA+GGG + chr2_3:3499641-3499660 Msa0272000:CDS 50.0%
GGCTATCCATATCCTGCTCA+AGG + chr2_3:3499364-3499383 Msa0272000:CDS 50.0%
GGTGGAGCAGCATAGTATTG+CGG - chr2_3:3499608-3499627 None:intergenic 50.0%
!!! TCTCTTTTTGGTGGTGGTGG+TGG - chr2_3:3499626-3499645 None:intergenic 50.0%
ACCACCACCAAAAAGAGAGC+CGG + chr2_3:3499628-3499647 Msa0272000:CDS 50.0%
! AAACCCGGCTCTCTTTTTGG+TGG - chr2_3:3499635-3499654 None:intergenic 50.0%
! AAGAGAGCCGGGTTTTCTTG+AGG + chr2_3:3499640-3499659 Msa0272000:CDS 50.0%
! AGAGAGCCGGGTTTTCTTGA+GGG + chr2_3:3499641-3499660 Msa0272000:CDS 50.0%
CCGGAGGTGGTCCTTGATAA+GGG - chr2_3:3499574-3499593 None:intergenic 55.0%
CCCTTATCAAGGACCACCTC+CGG + chr2_3:3499571-3499590 Msa0272000:CDS 55.0%
ACCGGAGGTGGTCCTTGATA+AGG - chr2_3:3499575-3499594 None:intergenic 55.0%
TTATCAAGGACCACCTCCGG+TGG + chr2_3:3499574-3499593 Msa0272000:CDS 55.0%
GGAGCAGCATAGTATTGCGG+TGG - chr2_3:3499605-3499624 None:intergenic 55.0%
!!! GGCTCTCTTTTTGGTGGTGG+TGG - chr2_3:3499629-3499648 None:intergenic 55.0%
CCACCACCAAAAAGAGAGCC+GGG + chr2_3:3499629-3499648 Msa0272000:CDS 55.0%
! AGCCGGGTTTTCTTGAGGGA+TGG + chr2_3:3499645-3499664 Msa0272000:CDS 55.0%
CACAGCAGCACTCATCCAAG+AGG - chr2_3:3499826-3499845 None:intergenic 55.0%
CCGGAGGTGGTCCTTGATAA+GGG - chr2_3:3499574-3499593 None:intergenic 55.0%
CCCTTATCAAGGACCACCTC+CGG + chr2_3:3499571-3499590 Msa0272000:CDS 55.0%
ACCGGAGGTGGTCCTTGATA+AGG - chr2_3:3499575-3499594 None:intergenic 55.0%
TTATCAAGGACCACCTCCGG+TGG + chr2_3:3499574-3499593 Msa0272000:CDS 55.0%
GGAGCAGCATAGTATTGCGG+TGG - chr2_3:3499605-3499624 None:intergenic 55.0%
!!! GGCTCTCTTTTTGGTGGTGG+TGG - chr2_3:3499629-3499648 None:intergenic 55.0%
CCACCACCAAAAAGAGAGCC+GGG + chr2_3:3499629-3499648 Msa0272000:CDS 55.0%
! AGCCGGGTTTTCTTGAGGGA+TGG + chr2_3:3499645-3499664 Msa0272000:CDS 55.0%
CACAGCAGCACTCATCCAAG+AGG - chr2_3:3499826-3499845 None:intergenic 55.0%
!! CCCGGCTCTCTTTTTGGTGG+TGG - chr2_3:3499632-3499651 None:intergenic 60.0%
!! CCCGGCTCTCTTTTTGGTGG+TGG - chr2_3:3499632-3499651 None:intergenic 60.0%
TCAAGGACCACCTCCGGTGG+CGG + chr2_3:3499577-3499596 Msa0272000:CDS 65.0%
!! TATTGCGGTGGTGCCGCCAC+CGG - chr2_3:3499593-3499612 None:intergenic 65.0%
TCAAGGACCACCTCCGGTGG+CGG + chr2_3:3499577-3499596 Msa0272000:CDS 65.0%
!! TATTGCGGTGGTGCCGCCAC+CGG - chr2_3:3499593-3499612 None:intergenic 65.0%
!!! GGTGGTGCCGCCACCGGAGG+TGG - chr2_3:3499587-3499606 None:intergenic 80.0%
!!! TGCGGTGGTGCCGCCACCGG+AGG - chr2_3:3499590-3499609 None:intergenic 80.0%
!!! GGTGGTGCCGCCACCGGAGG+TGG - chr2_3:3499587-3499606 None:intergenic 80.0%
!!! TGCGGTGGTGCCGCCACCGG+AGG - chr2_3:3499590-3499609 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 3499231 3500190 3499231 ID=Msa0272000;Name=Msa0272000
chr2_3 mRNA 3499231 3500190 3499231 ID=Msa0272000-mRNA-1;Parent=Msa0272000;Name=Msa0272000-mRNA-1;_AED=0.00;_eAED=0.00;_QI=115|1|1|1|1|1|3|319|69
chr2_3 exon 3499231 3499385 3499231 ID=Msa0272000-mRNA-1:exon:1762;Parent=Msa0272000-mRNA-1
chr2_3 exon 3499570 3499666 3499570 ID=Msa0272000-mRNA-1:exon:1763;Parent=Msa0272000-mRNA-1
chr2_3 exon 3499799 3500190 3499799 ID=Msa0272000-mRNA-1:exon:1764;Parent=Msa0272000-mRNA-1
chr2_3 five_prime_UTR 3499231 3499345 3499231 ID=Msa0272000-mRNA-1:five_prime_utr;Parent=Msa0272000-mRNA-1
chr2_3 CDS 3499346 3499385 3499346 ID=Msa0272000-mRNA-1:cds;Parent=Msa0272000-mRNA-1
chr2_3 CDS 3499570 3499666 3499570 ID=Msa0272000-mRNA-1:cds;Parent=Msa0272000-mRNA-1
chr2_3 CDS 3499799 3499871 3499799 ID=Msa0272000-mRNA-1:cds;Parent=Msa0272000-mRNA-1
chr2_3 three_prime_UTR 3499872 3500190 3499872 ID=Msa0272000-mRNA-1:three_prime_utr;Parent=Msa0272000-mRNA-1
Gene Sequence

>Msa0272000

ATGAGTGAGATCAAATATGGCTATCCATATCCTGCTCAAGGCCCTTATCAAGGACCACCTCCGGTGGCGGCACCACCGCAATACTATGCTGCTCCACCACCACCACCAAAAAGAGAGCCGGGTTTTCTTGAGGGATGCCTAGCAGCTTTGTGTTGCTGTTGCCTCTTGGATGAGTGCTGCTGTGACCCAACTATTATTTTTGCGAGCTAA
Protein sequence

>Msa0272000

MSEIKYGYPYPAQGPYQGPPPVAAPPQYYAAPPPPPKREPGFLEGCLAALCCCCLLDECCCDPTIIFAS*