AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0957090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0957090 MtrunA17_Chr5g0393501 27.879 165 116 1 3 164 77 241 7.86e-21 85.5
Msa0957090 MtrunA17_Chr4g0044671 28.667 150 99 3 5 150 62 207 2.28e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 42 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATACACTGTTTGACTTCT+AGG 0.096747 6_3:-66896989 Msa0957090:five_prime_UTR
GAAATTCCTATCGCTGGATA+TGG 0.237538 6_3:-66896659 Msa0957090:CDS
CCCATACCAATTGTGATGTT+TGG 0.340839 6_3:-66896404 Msa0957090:CDS
AGGAATTTGCCAAAAGTATC+AGG 0.344083 6_3:+66896509 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 6_3:-66896518 Msa0957090:CDS
AGTCGTGATGTTTCACTCTA+AGG 0.360647 6_3:+66896489 None:intergenic
ATTGCTTTCCAGTACCTTGA+TGG 0.369871 6_3:-66896782 Msa0957090:CDS
CGATTATTCAACGAATTTAG+TGG 0.380966 6_3:-66896815 Msa0957090:CDS
TCCAAACATCACAATTGGTA+TGG 0.411232 6_3:+66896403 None:intergenic
ATCTACTTCCATCAAGGTAC+TGG 0.438577 6_3:+66896774 None:intergenic
CCAAACATCACAATTGGTAT+GGG 0.452680 6_3:+66896404 None:intergenic
GAGCAATGGCACTTGCTAGA+TGG 0.455163 6_3:-66896913 Msa0957090:five_prime_UTR
CTGTTTGACTTCTAGGATGT+TGG 0.457667 6_3:-66896982 Msa0957090:five_prime_UTR
TTGTGCTGCCAATGGTATTG+AGG 0.463000 6_3:-66896363 Msa0957090:CDS
GGCCGTTGTTGACAGATGGT+TGG 0.487397 6_3:-66896847 Msa0957090:CDS
ACACGATGCTACCGCACTCA+TGG 0.499582 6_3:+66896694 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 6_3:-66896362 Msa0957090:CDS
ACAGGAATGACATAGTCATA+TGG 0.506205 6_3:+66896449 None:intergenic
CCAATTGTGATGTTTGGAAA+AGG 0.511741 6_3:-66896398 Msa0957090:CDS
AAATATTGAGCAACGAAGAA+TGG 0.513098 6_3:+66896949 None:intergenic
TTTGAAATCTACTTCCATCA+AGG 0.513455 6_3:+66896768 None:intergenic
TCAATATTTCTACAAGCTAC+CGG 0.523846 6_3:-66896935 Msa0957090:five_prime_UTR
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 6_3:-66896851 Msa0957090:CDS
TCTAGCAAGTGCCATTGCTC+CGG 0.534587 6_3:+66896916 None:intergenic
AAGGGAAAACAACTGCAAGC+TGG 0.535824 6_3:+66897015 None:intergenic
TTGTGATGTTTGGAAAAGGC+TGG 0.536068 6_3:-66896394 Msa0957090:CDS
TGGTAAGGTGGATAATCAGC+TGG 0.541144 6_3:+66896719 None:intergenic
TTTCAAGTGCAAGTGTGTCA+TGG 0.544420 6_3:-66896324 Msa0957090:CDS
ATGCTACCGCACTCATGGAA+TGG 0.547467 6_3:+66896699 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 6_3:+66896431 None:intergenic
GTCTCCGCCCTCAATACCAT+TGG 0.581950 6_3:+66896355 None:intergenic
ACCGCACTCATGGAATGGTA+AGG 0.593653 6_3:+66896704 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.603582 6_3:-66896907 Msa0957090:five_prime_UTR
TCTACAAGCTACCGGAGCAA+TGG 0.612965 6_3:-66896927 Msa0957090:five_prime_UTR
TGTTAAACAAATCAGTTAGT+CGG 0.616534 6_3:-66896868 Msa0957090:CDS
GTCGATCCATATCCAGCGAT+AGG 0.621657 6_3:+66896653 None:intergenic
CAAACATCACAATTGGTATG+GGG 0.630299 6_3:+66896405 None:intergenic
GCACTCATGGAATGGTAAGG+TGG 0.647237 6_3:+66896707 None:intergenic
ACCTTACCATTCCATGAGTG+CGG 0.651296 6_3:-66896705 Msa0957090:CDS
CTCCAACCATCTGTCAACAA+CGG 0.679074 6_3:+66896845 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 6_3:-66896639 Msa0957090:intron
GCTGCCAATGGTATTGAGGG+CGG 0.739556 6_3:-66896359 Msa0957090:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATATATGCTATTTTAATA+CGG - chr6_3:66896758-66896777 Msa0957090:CDS 10.0%
!!! CTAAATTTTTTGTTTTTTTT+AGG - chr6_3:66896800-66896819 Msa0957090:CDS 10.0%
!!! TTATATATGCTATTTTAATA+CGG - chr6_3:66896758-66896777 Msa0957090:CDS 10.0%
!!! CTAAATTTTTTGTTTTTTTT+AGG - chr6_3:66896800-66896819 Msa0957090:CDS 10.0%
!! TCAAACAGTGTATAAAAAAA+GGG + chr6_3:66896343-66896362 None:intergenic 20.0%
!! TCAAACAGTGTATAAAAAAA+GGG + chr6_3:66896343-66896362 None:intergenic 20.0%
! GTCAAACAGTGTATAAAAAA+AGG + chr6_3:66896344-66896363 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG - chr6_3:66896469-66896488 Msa0957090:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG + chr6_3:66896717-66896736 None:intergenic 25.0%
!! TTTTCATGCTATTCAATTAG+AGG - chr6_3:66896734-66896753 Msa0957090:CDS 25.0%
! AAAAATATGTTATCGTATCC+AGG - chr6_3:66897039-66897058 Msa0957090:five_prime_UTR 25.0%
! GTCAAACAGTGTATAAAAAA+AGG + chr6_3:66896344-66896363 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG - chr6_3:66896469-66896488 Msa0957090:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG + chr6_3:66896717-66896736 None:intergenic 25.0%
!! TTTTCATGCTATTCAATTAG+AGG - chr6_3:66896734-66896753 Msa0957090:CDS 25.0%
! AAAAATATGTTATCGTATCC+AGG - chr6_3:66897039-66897058 Msa0957090:five_prime_UTR 25.0%
! TTATACACTGTTTGACTTCT+AGG - chr6_3:66896348-66896367 Msa0957090:CDS 30.0%
AAATATTGAGCAACGAAGAA+TGG + chr6_3:66896391-66896410 None:intergenic 30.0%
! TCAATATTTCTACAAGCTAC+CGG - chr6_3:66896402-66896421 Msa0957090:CDS 30.0%
CGATTATTCAACGAATTTAG+TGG - chr6_3:66896522-66896541 Msa0957090:intron 30.0%
! TTTGAAATCTACTTCCATCA+AGG + chr6_3:66896572-66896591 None:intergenic 30.0%
! TTATACACTGTTTGACTTCT+AGG - chr6_3:66896348-66896367 Msa0957090:CDS 30.0%
AAATATTGAGCAACGAAGAA+TGG + chr6_3:66896391-66896410 None:intergenic 30.0%
! TCAATATTTCTACAAGCTAC+CGG - chr6_3:66896402-66896421 Msa0957090:CDS 30.0%
CGATTATTCAACGAATTTAG+TGG - chr6_3:66896522-66896541 Msa0957090:intron 30.0%
! TTTGAAATCTACTTCCATCA+AGG + chr6_3:66896572-66896591 None:intergenic 30.0%
!!! ACTTTTGAAATTCCTATCGC+TGG - chr6_3:66896672-66896691 Msa0957090:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr6_3:66896819-66896838 Msa0957090:CDS 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr6_3:66896831-66896850 None:intergenic 35.0%
ACAGGAATGACATAGTCATA+TGG + chr6_3:66896891-66896910 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr6_3:66896909-66896928 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG + chr6_3:66896935-66896954 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG + chr6_3:66896936-66896955 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG + chr6_3:66896937-66896956 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG + chr6_3:66896942-66896961 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG - chr6_3:66896939-66896958 Msa0957090:five_prime_UTR 35.0%
!!! ACTTTTGAAATTCCTATCGC+TGG - chr6_3:66896672-66896691 Msa0957090:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr6_3:66896819-66896838 Msa0957090:CDS 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr6_3:66896831-66896850 None:intergenic 35.0%
ACAGGAATGACATAGTCATA+TGG + chr6_3:66896891-66896910 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr6_3:66896909-66896928 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG + chr6_3:66896935-66896954 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG + chr6_3:66896936-66896955 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG + chr6_3:66896937-66896956 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG + chr6_3:66896942-66896961 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG - chr6_3:66896939-66896958 Msa0957090:five_prime_UTR 35.0%
!! CTGTTTGACTTCTAGGATGT+TGG - chr6_3:66896355-66896374 Msa0957090:CDS 40.0%
ATTGCTTTCCAGTACCTTGA+TGG - chr6_3:66896555-66896574 Msa0957090:intron 40.0%
ATCTACTTCCATCAAGGTAC+TGG + chr6_3:66896566-66896585 None:intergenic 40.0%
GAAATTCCTATCGCTGGATA+TGG - chr6_3:66896678-66896697 Msa0957090:CDS 40.0%
AGTCGTGATGTTTCACTCTA+AGG + chr6_3:66896851-66896870 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG - chr6_3:66896933-66896952 Msa0957090:five_prime_UTR 40.0%
TTGTGATGTTTGGAAAAGGC+TGG - chr6_3:66896943-66896962 Msa0957090:five_prime_UTR 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG - chr6_3:66897013-66897032 Msa0957090:five_prime_UTR 40.0%
!! CTGTTTGACTTCTAGGATGT+TGG - chr6_3:66896355-66896374 Msa0957090:CDS 40.0%
ATTGCTTTCCAGTACCTTGA+TGG - chr6_3:66896555-66896574 Msa0957090:intron 40.0%
ATCTACTTCCATCAAGGTAC+TGG + chr6_3:66896566-66896585 None:intergenic 40.0%
GAAATTCCTATCGCTGGATA+TGG - chr6_3:66896678-66896697 Msa0957090:CDS 40.0%
AGTCGTGATGTTTCACTCTA+AGG + chr6_3:66896851-66896870 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG - chr6_3:66896933-66896952 Msa0957090:five_prime_UTR 40.0%
TTGTGATGTTTGGAAAAGGC+TGG - chr6_3:66896943-66896962 Msa0957090:five_prime_UTR 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG - chr6_3:66897013-66897032 Msa0957090:five_prime_UTR 40.0%
AAGGGAAAACAACTGCAAGC+TGG + chr6_3:66896325-66896344 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr6_3:66896495-66896514 None:intergenic 45.0%
TGGTAAGGTGGATAATCAGC+TGG + chr6_3:66896621-66896640 None:intergenic 45.0%
ACCTTACCATTCCATGAGTG+CGG - chr6_3:66896632-66896651 Msa0957090:intron 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr6_3:66896966-66896985 Msa0957090:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr6_3:66896974-66896993 Msa0957090:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr6_3:66896975-66896994 Msa0957090:five_prime_UTR 45.0%
!! TTATCGTATCCAGGCGTTGA+TGG - chr6_3:66897048-66897067 Msa0957090:five_prime_UTR 45.0%
AAGGGAAAACAACTGCAAGC+TGG + chr6_3:66896325-66896344 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr6_3:66896495-66896514 None:intergenic 45.0%
TGGTAAGGTGGATAATCAGC+TGG + chr6_3:66896621-66896640 None:intergenic 45.0%
ACCTTACCATTCCATGAGTG+CGG - chr6_3:66896632-66896651 Msa0957090:intron 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr6_3:66896966-66896985 Msa0957090:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr6_3:66896974-66896993 Msa0957090:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr6_3:66896975-66896994 Msa0957090:five_prime_UTR 45.0%
TCTACAAGCTACCGGAGCAA+TGG - chr6_3:66896410-66896429 Msa0957090:CDS 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG + chr6_3:66896424-66896443 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG - chr6_3:66896424-66896443 Msa0957090:CDS 50.0%
! TGGCACTTGCTAGATGGTGA+TGG - chr6_3:66896430-66896449 Msa0957090:CDS 50.0%
GCACTCATGGAATGGTAAGG+TGG + chr6_3:66896633-66896652 None:intergenic 50.0%
ACCGCACTCATGGAATGGTA+AGG + chr6_3:66896636-66896655 None:intergenic 50.0%
ATGCTACCGCACTCATGGAA+TGG + chr6_3:66896641-66896660 None:intergenic 50.0%
GTCGATCCATATCCAGCGAT+AGG + chr6_3:66896687-66896706 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr6_3:66896698-66896717 Msa0957090:CDS 50.0%
TCTACAAGCTACCGGAGCAA+TGG - chr6_3:66896410-66896429 Msa0957090:CDS 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG + chr6_3:66896424-66896443 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG - chr6_3:66896424-66896443 Msa0957090:CDS 50.0%
! TGGCACTTGCTAGATGGTGA+TGG - chr6_3:66896430-66896449 Msa0957090:CDS 50.0%
GCACTCATGGAATGGTAAGG+TGG + chr6_3:66896633-66896652 None:intergenic 50.0%
ACCGCACTCATGGAATGGTA+AGG + chr6_3:66896636-66896655 None:intergenic 50.0%
ATGCTACCGCACTCATGGAA+TGG + chr6_3:66896641-66896660 None:intergenic 50.0%
GTCGATCCATATCCAGCGAT+AGG + chr6_3:66896687-66896706 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr6_3:66896698-66896717 Msa0957090:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr6_3:66896486-66896505 Msa0957090:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr6_3:66896490-66896509 Msa0957090:CDS 55.0%
ACACGATGCTACCGCACTCA+TGG + chr6_3:66896646-66896665 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr6_3:66896978-66896997 Msa0957090:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr6_3:66896985-66897004 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr6_3:66896486-66896505 Msa0957090:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr6_3:66896490-66896509 Msa0957090:CDS 55.0%
ACACGATGCTACCGCACTCA+TGG + chr6_3:66896646-66896665 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr6_3:66896978-66896997 Msa0957090:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr6_3:66896985-66897004 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 66896292 66897067 66896292 ID=Msa0957090;Name=Msa0957090
chr6_3 mRNA 66896292 66897067 66896292 ID=Msa0957090-mRNA-1;Parent=Msa0957090;Name=Msa0957090-mRNA-1;_AED=0.07;_eAED=0.07;_QI=176|1|0.5|1|1|1|2|0|165
chr6_3 exon 66896292 66896537 66896292 ID=Msa0957090-mRNA-1:exon:12448;Parent=Msa0957090-mRNA-1
chr6_3 exon 66896640 66897067 66896640 ID=Msa0957090-mRNA-1:exon:12447;Parent=Msa0957090-mRNA-1
chr6_3 five_prime_UTR 66896892 66897067 66896892 ID=Msa0957090-mRNA-1:five_prime_utr;Parent=Msa0957090-mRNA-1
chr6_3 CDS 66896640 66896891 66896640 ID=Msa0957090-mRNA-1:cds;Parent=Msa0957090-mRNA-1
chr6_3 CDS 66896292 66896537 66896292 ID=Msa0957090-mRNA-1:cds;Parent=Msa0957090-mRNA-1
Gene Sequence

>Msa0957090

ATGTTAAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTACGATTATTCAACGAATTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGATGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCCAGCTGATTATCCACCTTACCATTCCATGAGTGCGGTAGCATCGTGTTATTGTACTTTTGAAATTCCTATCGCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGACTACGTCATGTTGTGCGCTCCATATGACTATGTCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAATTGTGATGTTTGGAAAAGGCTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTAATTTTCAAGTGCAAGTGTGTCATGGACAAAAAATATGTTATCGTATCCAGGCGTTGA
Protein sequence

>Msa0957090

MLNKSVSRPLLTDGWSALRLFNEFSGSKIIAFQYLDGSRFQIFVFAHNITPADYPPYHSMSAVASCYCTFEIPIAGYGSTKSPKELPDTFGKFLRVKHHDYVMLCAPYDYVIPVRLKYTDDPIPIVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSRR*