AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1234000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1234000 MtrunA17_Chr8g0353741 99.038 104 1 0 1 104 246 349 1.02e-71 219
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTGGTTACATGGTCTAAC+TGG 0.224137 8_2:-11187969 Msa1234000:five_prime_UTR
TGACAAATGGCTCGAGAAAA+AGG 0.250141 8_2:-11188013 Msa1234000:five_prime_UTR
CTGTTAGCTGGATCAACTTA+AGG 0.272045 8_2:-11187795 Msa1234000:intron
CTTGTAAGCACTTGGTTGTT+CGG 0.324737 8_2:+11187552 None:intergenic
GTTCCTTTCAGTGAGGTATT+TGG 0.330408 8_2:-11187772 Msa1234000:CDS
TTGTAAGCACTTGGTTGTTC+GGG 0.331399 8_2:+11187553 None:intergenic
AGCATTTACCGGTTGAAATA+AGG 0.337859 8_2:+11187892 None:intergenic
GATAGCAGGCTTGGCATGGC+AGG 0.353519 8_2:-11187716 Msa1234000:CDS
TGTTAGCTGGATCAACTTAA+GGG 0.364997 8_2:-11187794 Msa1234000:intron
CTGCTGATCGATCACTGATA+TGG 0.379826 8_2:-11187585 Msa1234000:CDS
ATCAGCAGTCTGCCACATAA+TGG 0.411049 8_2:+11187600 None:intergenic
GCTGGCACTGCTCATGCATA+GGG 0.413949 8_2:-11187647 Msa1234000:CDS
CCAACTTTGCTGTGGTTACA+TGG 0.432008 8_2:-11187978 Msa1234000:five_prime_UTR
TGCTGGCACTGCTCATGCAT+AGG 0.451328 8_2:-11187648 Msa1234000:CDS
CCACATAATGGAGTTGGTAA+TGG 0.454379 8_2:+11187612 None:intergenic
GGCTGTTGAGATAGCAGGCT+TGG 0.474217 8_2:-11187725 Msa1234000:CDS
CCATGTAACCACAGCAAAGT+TGG 0.477162 8_2:+11187978 None:intergenic
CATTGAGTGAAGCTCTACTT+AGG 0.486355 8_2:-11188038 Msa1234000:five_prime_UTR
GAAAGCCACCTTATTTCAAC+CGG 0.492823 8_2:-11187900 Msa1234000:intron
TTCTGTGAGGTGCAATCTAA+AGG 0.503920 8_2:-11187749 Msa1234000:CDS
TATCTTAACTTGTAAGCACT+TGG 0.518187 8_2:+11187544 None:intergenic
CTCTACTTAGGCATGACAAA+TGG 0.520429 8_2:-11188026 Msa1234000:five_prime_UTR
CCATTACCAACTCCATTATG+TGG 0.523018 8_2:-11187612 Msa1234000:CDS
AAGGAGGCTGTTGAGATAGC+AGG 0.526134 8_2:-11187730 Msa1234000:CDS
TTGAGATAGCAGGCTTGGCA+TGG 0.531721 8_2:-11187720 Msa1234000:CDS
TGTGGTTACATGGTCTAACT+GGG 0.550055 8_2:-11187968 Msa1234000:five_prime_UTR
TAAATAAAGAACCTTCACTT+AGG 0.560908 8_2:-11188292 None:intergenic
ATAGCAGGCTTGGCATGGCA+GGG 0.561447 8_2:-11187715 Msa1234000:CDS
ATTTACCGGTTGAAATAAGG+TGG 0.581719 8_2:+11187895 None:intergenic
AGTCTGCCACATAATGGAGT+TGG 0.588727 8_2:+11187606 None:intergenic
GAACCAAATACCTCACTGAA+AGG 0.590238 8_2:+11187769 None:intergenic
AAAGAATGCCAACTTTGCTG+TGG 0.610380 8_2:-11187986 Msa1234000:five_prime_UTR
TGGCAGGGCCGTGCTCATTG+TGG 0.610622 8_2:-11187700 Msa1234000:CDS
CATCAAGACCACAATGAGCA+CGG 0.626290 8_2:+11187692 None:intergenic
CTGGCACTGCTCATGCATAG+GGG 0.636374 8_2:-11187646 Msa1234000:CDS
CTGAGCCCATACCTAAGTGA+AGG 0.651802 8_2:+11188281 None:intergenic
CTTAAGGGTTCCTTTCAGTG+AGG 0.652944 8_2:-11187779 Msa1234000:CDS
GTGAGGTATTTGGTTCTGTG+AGG 0.653734 8_2:-11187762 Msa1234000:CDS
TGTGAGGTGCAATCTAAAGG+AGG 0.669292 8_2:-11187746 Msa1234000:CDS
TATATGGTTCAGGTGGACAG+AGG 0.693553 8_2:-11188066 Msa1234000:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCGTATTTCTTATTGTATA+TGG - chr8_2:11187740-11187759 Msa1234000:CDS 20.0%
!! ATCGTATTTCTTATTGTATA+TGG - chr8_2:11187740-11187759 Msa1234000:CDS 20.0%
!! CAAAGTATTTCTGTCATTAA+AGG + chr8_2:11187633-11187652 None:intergenic 25.0%
! TAGTATTTGACAAGCAAAAT+AGG + chr8_2:11187680-11187699 None:intergenic 25.0%
! TTTCTTATTGTATATGGTTC+AGG - chr8_2:11187746-11187765 Msa1234000:CDS 25.0%
! AATGATAACCTATGTTTATC+AGG - chr8_2:11187963-11187982 Msa1234000:five_prime_UTR 25.0%
! AATGAAATCCTGATAAACAT+AGG + chr8_2:11187974-11187993 None:intergenic 25.0%
!! CAAAGTATTTCTGTCATTAA+AGG + chr8_2:11187633-11187652 None:intergenic 25.0%
! TAGTATTTGACAAGCAAAAT+AGG + chr8_2:11187680-11187699 None:intergenic 25.0%
! TTTCTTATTGTATATGGTTC+AGG - chr8_2:11187746-11187765 Msa1234000:CDS 25.0%
! AATGATAACCTATGTTTATC+AGG - chr8_2:11187963-11187982 Msa1234000:five_prime_UTR 25.0%
! AATGAAATCCTGATAAACAT+AGG + chr8_2:11187974-11187993 None:intergenic 25.0%
TCAAAAGAGATTGTCTGTAA+GGG + chr8_2:11187580-11187599 None:intergenic 30.0%
TTCAAAAGAGATTGTCTGTA+AGG + chr8_2:11187581-11187600 None:intergenic 30.0%
TTGCTTGTCAAATACTACTT+TGG - chr8_2:11187683-11187702 Msa1234000:CDS 30.0%
! GCTTTCGAATTTTCTTGAAA+CGG + chr8_2:11187908-11187927 None:intergenic 30.0%
!! TATCTTAACTTGTAAGCACT+TGG + chr8_2:11188281-11188300 None:intergenic 30.0%
TCAAAAGAGATTGTCTGTAA+GGG + chr8_2:11187580-11187599 None:intergenic 30.0%
TTCAAAAGAGATTGTCTGTA+AGG + chr8_2:11187581-11187600 None:intergenic 30.0%
TTGCTTGTCAAATACTACTT+TGG - chr8_2:11187683-11187702 Msa1234000:CDS 30.0%
! GCTTTCGAATTTTCTTGAAA+CGG + chr8_2:11187908-11187927 None:intergenic 30.0%
!! TATCTTAACTTGTAAGCACT+TGG + chr8_2:11188281-11188300 None:intergenic 30.0%
CTGTCATTAAAGGTCAGTTT+GGG + chr8_2:11187623-11187642 None:intergenic 35.0%
TCTGTCATTAAAGGTCAGTT+TGG + chr8_2:11187624-11187643 None:intergenic 35.0%
GATTAACAATCTTCACCCAA+AGG + chr8_2:11187723-11187742 None:intergenic 35.0%
CTTATTGTATATGGTTCAGG+TGG - chr8_2:11187749-11187768 Msa1234000:CDS 35.0%
! ATTTACCGGTTGAAATAAGG+TGG + chr8_2:11187930-11187949 None:intergenic 35.0%
! AGCATTTACCGGTTGAAATA+AGG + chr8_2:11187933-11187952 None:intergenic 35.0%
TTATACTGTGCAGCATTTAC+CGG + chr8_2:11187944-11187963 None:intergenic 35.0%
TGTTAGCTGGATCAACTTAA+GGG - chr8_2:11188028-11188047 Msa1234000:five_prime_UTR 35.0%
CTGTCATTAAAGGTCAGTTT+GGG + chr8_2:11187623-11187642 None:intergenic 35.0%
TCTGTCATTAAAGGTCAGTT+TGG + chr8_2:11187624-11187643 None:intergenic 35.0%
GATTAACAATCTTCACCCAA+AGG + chr8_2:11187723-11187742 None:intergenic 35.0%
CTTATTGTATATGGTTCAGG+TGG - chr8_2:11187749-11187768 Msa1234000:CDS 35.0%
! ATTTACCGGTTGAAATAAGG+TGG + chr8_2:11187930-11187949 None:intergenic 35.0%
! AGCATTTACCGGTTGAAATA+AGG + chr8_2:11187933-11187952 None:intergenic 35.0%
TTATACTGTGCAGCATTTAC+CGG + chr8_2:11187944-11187963 None:intergenic 35.0%
TGTTAGCTGGATCAACTTAA+GGG - chr8_2:11188028-11188047 Msa1234000:five_prime_UTR 35.0%
GCTTGTTCATTCTTGCCTTT+GGG - chr8_2:11187705-11187724 Msa1234000:CDS 40.0%
CATTGAGTGAAGCTCTACTT+AGG - chr8_2:11187784-11187803 Msa1234000:CDS 40.0%
CTCTACTTAGGCATGACAAA+TGG - chr8_2:11187796-11187815 Msa1234000:intron 40.0%
TGACAAATGGCTCGAGAAAA+AGG - chr8_2:11187809-11187828 Msa1234000:intron 40.0%
GACAAATGGCTCGAGAAAAA+GGG - chr8_2:11187810-11187829 Msa1234000:intron 40.0%
AAAGAATGCCAACTTTGCTG+TGG - chr8_2:11187836-11187855 Msa1234000:intron 40.0%
TGTGGTTACATGGTCTAACT+GGG - chr8_2:11187854-11187873 Msa1234000:intron 40.0%
! GAAAGCCACCTTATTTCAAC+CGG - chr8_2:11187922-11187941 Msa1234000:CDS 40.0%
! GCTTTTGAACTTCTGTTAGC+TGG - chr8_2:11188015-11188034 Msa1234000:five_prime_UTR 40.0%
CTGTTAGCTGGATCAACTTA+AGG - chr8_2:11188027-11188046 Msa1234000:five_prime_UTR 40.0%
! GTTCCTTTCAGTGAGGTATT+TGG - chr8_2:11188050-11188069 Msa1234000:five_prime_UTR 40.0%
GAACCAAATACCTCACTGAA+AGG + chr8_2:11188056-11188075 None:intergenic 40.0%
TTCTGTGAGGTGCAATCTAA+AGG - chr8_2:11188073-11188092 Msa1234000:intron 40.0%
!! CCACATAATGGAGTTGGTAA+TGG + chr8_2:11188213-11188232 None:intergenic 40.0%
CCATTACCAACTCCATTATG+TGG - chr8_2:11188210-11188229 Msa1234000:intron 40.0%
TTGTAAGCACTTGGTTGTTC+GGG + chr8_2:11188272-11188291 None:intergenic 40.0%
CTTGTAAGCACTTGGTTGTT+CGG + chr8_2:11188273-11188292 None:intergenic 40.0%
GCTTGTTCATTCTTGCCTTT+GGG - chr8_2:11187705-11187724 Msa1234000:CDS 40.0%
CATTGAGTGAAGCTCTACTT+AGG - chr8_2:11187784-11187803 Msa1234000:CDS 40.0%
CTCTACTTAGGCATGACAAA+TGG - chr8_2:11187796-11187815 Msa1234000:intron 40.0%
TGACAAATGGCTCGAGAAAA+AGG - chr8_2:11187809-11187828 Msa1234000:intron 40.0%
GACAAATGGCTCGAGAAAAA+GGG - chr8_2:11187810-11187829 Msa1234000:intron 40.0%
AAAGAATGCCAACTTTGCTG+TGG - chr8_2:11187836-11187855 Msa1234000:intron 40.0%
TGTGGTTACATGGTCTAACT+GGG - chr8_2:11187854-11187873 Msa1234000:intron 40.0%
! GAAAGCCACCTTATTTCAAC+CGG - chr8_2:11187922-11187941 Msa1234000:CDS 40.0%
! GCTTTTGAACTTCTGTTAGC+TGG - chr8_2:11188015-11188034 Msa1234000:five_prime_UTR 40.0%
CTGTTAGCTGGATCAACTTA+AGG - chr8_2:11188027-11188046 Msa1234000:five_prime_UTR 40.0%
! GTTCCTTTCAGTGAGGTATT+TGG - chr8_2:11188050-11188069 Msa1234000:five_prime_UTR 40.0%
GAACCAAATACCTCACTGAA+AGG + chr8_2:11188056-11188075 None:intergenic 40.0%
TTCTGTGAGGTGCAATCTAA+AGG - chr8_2:11188073-11188092 Msa1234000:intron 40.0%
!! CCACATAATGGAGTTGGTAA+TGG + chr8_2:11188213-11188232 None:intergenic 40.0%
CCATTACCAACTCCATTATG+TGG - chr8_2:11188210-11188229 Msa1234000:intron 40.0%
TTGTAAGCACTTGGTTGTTC+GGG + chr8_2:11188272-11188291 None:intergenic 40.0%
CTTGTAAGCACTTGGTTGTT+CGG + chr8_2:11188273-11188292 None:intergenic 40.0%
! GGCTTGTTCATTCTTGCCTT+TGG - chr8_2:11187704-11187723 Msa1234000:CDS 45.0%
TATATGGTTCAGGTGGACAG+AGG - chr8_2:11187756-11187775 Msa1234000:CDS 45.0%
CCATGTAACCACAGCAAAGT+TGG + chr8_2:11187847-11187866 None:intergenic 45.0%
! CCAACTTTGCTGTGGTTACA+TGG - chr8_2:11187844-11187863 Msa1234000:intron 45.0%
CTGTGGTTACATGGTCTAAC+TGG - chr8_2:11187853-11187872 Msa1234000:intron 45.0%
CTTAAGGGTTCCTTTCAGTG+AGG - chr8_2:11188043-11188062 Msa1234000:five_prime_UTR 45.0%
!! GTGAGGTATTTGGTTCTGTG+AGG - chr8_2:11188060-11188079 Msa1234000:intron 45.0%
TGTGAGGTGCAATCTAAAGG+AGG - chr8_2:11188076-11188095 Msa1234000:intron 45.0%
CATCAAGACCACAATGAGCA+CGG + chr8_2:11188133-11188152 None:intergenic 45.0%
! CAGCAGACGAGCAGTATTTT+TGG + chr8_2:11188159-11188178 None:intergenic 45.0%
CAAAAATACTGCTCGTCTGC+TGG - chr8_2:11188157-11188176 Msa1234000:intron 45.0%
! AGTCTGCCACATAATGGAGT+TGG + chr8_2:11188219-11188238 None:intergenic 45.0%
ATCAGCAGTCTGCCACATAA+TGG + chr8_2:11188225-11188244 None:intergenic 45.0%
CTGCTGATCGATCACTGATA+TGG - chr8_2:11188237-11188256 Msa1234000:intron 45.0%
! GGCTTGTTCATTCTTGCCTT+TGG - chr8_2:11187704-11187723 Msa1234000:CDS 45.0%
TATATGGTTCAGGTGGACAG+AGG - chr8_2:11187756-11187775 Msa1234000:CDS 45.0%
CCATGTAACCACAGCAAAGT+TGG + chr8_2:11187847-11187866 None:intergenic 45.0%
! CCAACTTTGCTGTGGTTACA+TGG - chr8_2:11187844-11187863 Msa1234000:intron 45.0%
CTGTGGTTACATGGTCTAAC+TGG - chr8_2:11187853-11187872 Msa1234000:intron 45.0%
CTTAAGGGTTCCTTTCAGTG+AGG - chr8_2:11188043-11188062 Msa1234000:five_prime_UTR 45.0%
!! GTGAGGTATTTGGTTCTGTG+AGG - chr8_2:11188060-11188079 Msa1234000:intron 45.0%
TGTGAGGTGCAATCTAAAGG+AGG - chr8_2:11188076-11188095 Msa1234000:intron 45.0%
CATCAAGACCACAATGAGCA+CGG + chr8_2:11188133-11188152 None:intergenic 45.0%
! CAGCAGACGAGCAGTATTTT+TGG + chr8_2:11188159-11188178 None:intergenic 45.0%
CAAAAATACTGCTCGTCTGC+TGG - chr8_2:11188157-11188176 Msa1234000:intron 45.0%
! AGTCTGCCACATAATGGAGT+TGG + chr8_2:11188219-11188238 None:intergenic 45.0%
ATCAGCAGTCTGCCACATAA+TGG + chr8_2:11188225-11188244 None:intergenic 45.0%
CTGCTGATCGATCACTGATA+TGG - chr8_2:11188237-11188256 Msa1234000:intron 45.0%
CTGAGCCCATACCTAAGTGA+AGG + chr8_2:11187544-11187563 None:intergenic 50.0%
AAGGAGGCTGTTGAGATAGC+AGG - chr8_2:11188092-11188111 Msa1234000:intron 50.0%
TTGAGATAGCAGGCTTGGCA+TGG - chr8_2:11188102-11188121 Msa1234000:intron 50.0%
CTGAGCCCATACCTAAGTGA+AGG + chr8_2:11187544-11187563 None:intergenic 50.0%
AAGGAGGCTGTTGAGATAGC+AGG - chr8_2:11188092-11188111 Msa1234000:intron 50.0%
TTGAGATAGCAGGCTTGGCA+TGG - chr8_2:11188102-11188121 Msa1234000:intron 50.0%
GGCTGTTGAGATAGCAGGCT+TGG - chr8_2:11188097-11188116 Msa1234000:intron 55.0%
ATAGCAGGCTTGGCATGGCA+GGG - chr8_2:11188107-11188126 Msa1234000:intron 55.0%
TGCTGGCACTGCTCATGCAT+AGG - chr8_2:11188174-11188193 Msa1234000:intron 55.0%
GCTGGCACTGCTCATGCATA+GGG - chr8_2:11188175-11188194 Msa1234000:intron 55.0%
CTGGCACTGCTCATGCATAG+GGG - chr8_2:11188176-11188195 Msa1234000:intron 55.0%
GGCTGTTGAGATAGCAGGCT+TGG - chr8_2:11188097-11188116 Msa1234000:intron 55.0%
ATAGCAGGCTTGGCATGGCA+GGG - chr8_2:11188107-11188126 Msa1234000:intron 55.0%
TGCTGGCACTGCTCATGCAT+AGG - chr8_2:11188174-11188193 Msa1234000:intron 55.0%
GCTGGCACTGCTCATGCATA+GGG - chr8_2:11188175-11188194 Msa1234000:intron 55.0%
CTGGCACTGCTCATGCATAG+GGG - chr8_2:11188176-11188195 Msa1234000:intron 55.0%
GATAGCAGGCTTGGCATGGC+AGG - chr8_2:11188106-11188125 Msa1234000:intron 60.0%
GATAGCAGGCTTGGCATGGC+AGG - chr8_2:11188106-11188125 Msa1234000:intron 60.0%
TGGCAGGGCCGTGCTCATTG+TGG - chr8_2:11188122-11188141 Msa1234000:intron 65.0%
TGGCAGGGCCGTGCTCATTG+TGG - chr8_2:11188122-11188141 Msa1234000:intron 65.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 11187537 11188307 11187537 ID=Msa1234000;Name=Msa1234000
chr8_2 mRNA 11187537 11188307 11187537 ID=Msa1234000-mRNA-1;Parent=Msa1234000;Name=Msa1234000-mRNA-1;_AED=0.02;_eAED=0.02;_QI=135|1|0.66|1|0.5|0.33|3|0|109
chr8_2 exon 11187537 11187810 11187537 ID=Msa1234000-mRNA-1:exon:4334;Parent=Msa1234000-mRNA-1
chr8_2 exon 11187901 11188076 11187901 ID=Msa1234000-mRNA-1:exon:4333;Parent=Msa1234000-mRNA-1
chr8_2 exon 11188293 11188307 11188293 ID=Msa1234000-mRNA-1:exon:4332;Parent=Msa1234000-mRNA-1
chr8_2 five_prime_UTR 11188293 11188307 11188293 ID=Msa1234000-mRNA-1:five_prime_utr;Parent=Msa1234000-mRNA-1
chr8_2 five_prime_UTR 11187957 11188076 11187957 ID=Msa1234000-mRNA-1:five_prime_utr;Parent=Msa1234000-mRNA-1
chr8_2 CDS 11187901 11187956 11187901 ID=Msa1234000-mRNA-1:cds;Parent=Msa1234000-mRNA-1
chr8_2 CDS 11187537 11187810 11187537 ID=Msa1234000-mRNA-1:cds;Parent=Msa1234000-mRNA-1
Gene Sequence

>Msa1234000

ATGCTTGAATCTGAGTGCCGTTTCAAGAAAATTCGAAAGCCACCTTATTTCAACCGCTGGATCAACTTAAGGGTTCCTTTCAGTGAGGTATTTGGTTCTGTGAGGTGCAATCTAAAGGAGGCTGTTGAGATAGCAGGCTTGGCATGGCAGGGCCGTGCTCATTGTGGTCTTGATGATGCCAAAAATACTGCTCGTCTGCTGGCACTGCTCATGCATAGGGGTTTTAAGTTTTCCATTACCAACTCCATTATGTGGCAGACTGCTGATCGATCACTGATATGGAAGCAGTCTCCCGAACAACCAAGTGCTTACAAGTTAAGATATTTTTAG
Protein sequence

>Msa1234000

MLESECRFKKIRKPPYFNRWINLRVPFSEVFGSVRCNLKEAVEIAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSIMWQTADRSLIWKQSPEQPSAYKLRYF*