AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0997120


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0997120 MtrunA17_Chr6g0482371 54.701 117 34 1 1 98 8 124 7.38e-34 113
Msa0997120 MtrunA17_Chr6g0482501 38.889 144 41 1 1 97 388 531 5.71e-20 83.2
Msa0997120 MtrunA17_Chr1g0172551 58.929 56 23 0 2 57 91 146 7.42e-15 65.9
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 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTTACACTCGTCTTCTT+TGG 0.265768 6_4:+76200197 None:intergenic
TTTCCTCAAAGGATTGATTA+AGG 0.300302 6_4:+76200737 None:intergenic
AGAATATCCTTTGCCAGGTT+TGG 0.313974 6_4:+76200981 None:intergenic
CATCAAGAATGCGTCAGATT+TGG 0.343857 6_4:-76200253 Msa0997120:CDS
GTCCGAATTATCACTGCATT+TGG 0.381704 6_4:+76201020 None:intergenic
CACCAAATGCAGTGATAATT+CGG 0.387621 6_4:-76201022 Msa0997120:five_prime_UTR
TGATTCCATTTCCCTGCCTC+AGG 0.390409 6_4:-76200941 Msa0997120:CDS
GGATAACAATCTTTCATCAT+TGG 0.397150 6_4:-76200683 Msa0997120:intron
CAATGTAGATCAAACTGGTT+TGG 0.399242 6_4:-76200713 Msa0997120:CDS
TACCTCCTGAGGCAGGGAAA+TGG 0.417978 6_4:+76200936 None:intergenic
AAGCCTTAATCAATCCTTTG+AGG 0.420274 6_4:-76200740 Msa0997120:CDS
CCCTCAGAATATCCTTTGCC+AGG 0.426000 6_4:+76200976 None:intergenic
ACCTTCTTGCAAGGTCAGTC+TGG 0.427797 6_4:+76200515 None:intergenic
GAAACCAATGTAGATCAAAC+TGG 0.445612 6_4:-76200718 Msa0997120:CDS
TCAAACTGGTTTGGATGAAT+CGG 0.469296 6_4:-76200704 Msa0997120:CDS
GAAGGTATACCTCCTGAGGC+AGG 0.477144 6_4:+76200929 None:intergenic
CAAACCAGTTTGATCTACAT+TGG 0.479317 6_4:+76200714 None:intergenic
CTCTCAGGTGTTGACTGTGC+AGG 0.482350 6_4:+76201140 None:intergenic
ATCTACATTGGTTTCCTCAA+AGG 0.486879 6_4:+76200726 None:intergenic
GAACCGAGCAACAATCTCTC+AGG 0.525201 6_4:+76201125 None:intergenic
ACTCGTCTTCTTTGGTCACA+TGG 0.531127 6_4:+76200205 None:intergenic
TTCCATTTCCCTGCCTCAGG+AGG 0.537186 6_4:-76200938 Msa0997120:intron
AGTGTAGACATGTCCAAACC+TGG 0.561902 6_4:-76200994 Msa0997120:exon
GACATGTCCAAACCTGGCAA+AGG 0.587270 6_4:-76200988 Msa0997120:CDS
GAAGATACCACCTTCTTGCA+AGG 0.602323 6_4:+76200506 None:intergenic
ACCTGGCAAAGGATATTCTG+AGG 0.611952 6_4:-76200977 Msa0997120:CDS
AAGGTATACCTCCTGAGGCA+GGG 0.624468 6_4:+76200930 None:intergenic
AGACTGACCTTGCAAGAAGG+TGG 0.638902 6_4:-76200513 Msa0997120:intron
CCTGGCAAAGGATATTCTGA+GGG 0.645926 6_4:-76200976 Msa0997120:CDS
ACACCTGAGAGATTGTTGCT+CGG 0.646918 6_4:-76201128 Msa0997120:five_prime_UTR
GATGGAAGGTATACCTCCTG+AGG 0.662058 6_4:+76200925 None:intergenic
GCCAGACTGACCTTGCAAGA+AGG 0.667163 6_4:-76200516 Msa0997120:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATGTTTGTTATCTATTA+TGG - chr6_4:76200993-76201012 Msa0997120:exon 15.0%
!!! TTATGTTTGTTATCTATTAT+GGG - chr6_4:76200994-76201013 Msa0997120:exon 15.0%
!!! TTTATGTTTGTTATCTATTA+TGG - chr6_4:76200993-76201012 Msa0997120:exon 15.0%
!!! TTATGTTTGTTATCTATTAT+GGG - chr6_4:76200994-76201013 Msa0997120:exon 15.0%
!! AAATTAAAACCAAAACAAGA+TGG + chr6_4:76200461-76200480 None:intergenic 20.0%
!!! TCTTGTTTTGGTTTTAATTT+TGG - chr6_4:76200461-76200480 Msa0997120:intron 20.0%
!!! ACAATAAAATTGCTTTTGAA+AGG + chr6_4:76200537-76200556 None:intergenic 20.0%
!! AGAAGAATAAGAACTAAATA+AGG + chr6_4:76201065-76201084 None:intergenic 20.0%
!! AAATTAAAACCAAAACAAGA+TGG + chr6_4:76200461-76200480 None:intergenic 20.0%
!!! TCTTGTTTTGGTTTTAATTT+TGG - chr6_4:76200461-76200480 Msa0997120:intron 20.0%
!!! ACAATAAAATTGCTTTTGAA+AGG + chr6_4:76200537-76200556 None:intergenic 20.0%
!! AGAAGAATAAGAACTAAATA+AGG + chr6_4:76201065-76201084 None:intergenic 20.0%
!! GTAATTGCTTTCTTGATAAT+TGG - chr6_4:76200581-76200600 Msa0997120:intron 25.0%
! ATAAACACAGAATTCTAACT+CGG + chr6_4:76200978-76200997 None:intergenic 25.0%
!! GTAATTGCTTTCTTGATAAT+TGG - chr6_4:76200581-76200600 Msa0997120:intron 25.0%
! ATAAACACAGAATTCTAACT+CGG + chr6_4:76200978-76200997 None:intergenic 25.0%
TAAAACCAAAACAAGATGGA+AGG + chr6_4:76200457-76200476 None:intergenic 30.0%
TTTCCTCAAAGGATTGATTA+AGG + chr6_4:76200631-76200650 None:intergenic 30.0%
GGATAACAATCTTTCATCAT+TGG - chr6_4:76200682-76200701 Msa0997120:intron 30.0%
ACTAATCTTATCCTCTCAAT+AGG - chr6_4:76200787-76200806 Msa0997120:intron 30.0%
!! TTGGAGTATCAGTCTATTTT+AGG - chr6_4:76200941-76200960 Msa0997120:CDS 30.0%
!! TGGAGTATCAGTCTATTTTA+GGG - chr6_4:76200942-76200961 Msa0997120:CDS 30.0%
! TACAACATCAGAACTTTTGA+TGG - chr6_4:76201039-76201058 Msa0997120:five_prime_UTR 30.0%
GCTGCAAATATAACATGTTA+TGG + chr6_4:76201093-76201112 None:intergenic 30.0%
TAAAACCAAAACAAGATGGA+AGG + chr6_4:76200457-76200476 None:intergenic 30.0%
TTTCCTCAAAGGATTGATTA+AGG + chr6_4:76200631-76200650 None:intergenic 30.0%
GGATAACAATCTTTCATCAT+TGG - chr6_4:76200682-76200701 Msa0997120:intron 30.0%
ACTAATCTTATCCTCTCAAT+AGG - chr6_4:76200787-76200806 Msa0997120:intron 30.0%
!! TTGGAGTATCAGTCTATTTT+AGG - chr6_4:76200941-76200960 Msa0997120:CDS 30.0%
!! TGGAGTATCAGTCTATTTTA+GGG - chr6_4:76200942-76200961 Msa0997120:CDS 30.0%
! TACAACATCAGAACTTTTGA+TGG - chr6_4:76201039-76201058 Msa0997120:five_prime_UTR 30.0%
GCTGCAAATATAACATGTTA+TGG + chr6_4:76201093-76201112 None:intergenic 30.0%
! CTTTTGACAGTCAAATTCTG+AGG + chr6_4:76200276-76200295 None:intergenic 35.0%
CACCAAATGCAGTGATAATT+CGG - chr6_4:76200343-76200362 Msa0997120:intron 35.0%
!! GTATACCTTCCATCTTGTTT+TGG - chr6_4:76200449-76200468 Msa0997120:intron 35.0%
! GATAATTGGTTTCTCAATGC+AGG - chr6_4:76200595-76200614 Msa0997120:intron 35.0%
AAGCCTTAATCAATCCTTTG+AGG - chr6_4:76200625-76200644 Msa0997120:intron 35.0%
!! ATCTACATTGGTTTCCTCAA+AGG + chr6_4:76200642-76200661 None:intergenic 35.0%
GAAACCAATGTAGATCAAAC+TGG - chr6_4:76200647-76200666 Msa0997120:intron 35.0%
CAAACCAGTTTGATCTACAT+TGG + chr6_4:76200654-76200673 None:intergenic 35.0%
CAATGTAGATCAAACTGGTT+TGG - chr6_4:76200652-76200671 Msa0997120:intron 35.0%
!! TCAAACTGGTTTGGATGAAT+CGG - chr6_4:76200661-76200680 Msa0997120:intron 35.0%
! GGTGTGATTGACTCTATATT+TGG - chr6_4:76200703-76200722 Msa0997120:CDS 35.0%
! CTGATCAACTGTTGTTCTTT+TGG - chr6_4:76200922-76200941 Msa0997120:intron 35.0%
CAATTTACACTCGTCTTCTT+TGG + chr6_4:76201171-76201190 None:intergenic 35.0%
! CTTTTGACAGTCAAATTCTG+AGG + chr6_4:76200276-76200295 None:intergenic 35.0%
CACCAAATGCAGTGATAATT+CGG - chr6_4:76200343-76200362 Msa0997120:intron 35.0%
!! GTATACCTTCCATCTTGTTT+TGG - chr6_4:76200449-76200468 Msa0997120:intron 35.0%
! GATAATTGGTTTCTCAATGC+AGG - chr6_4:76200595-76200614 Msa0997120:intron 35.0%
AAGCCTTAATCAATCCTTTG+AGG - chr6_4:76200625-76200644 Msa0997120:intron 35.0%
!! ATCTACATTGGTTTCCTCAA+AGG + chr6_4:76200642-76200661 None:intergenic 35.0%
GAAACCAATGTAGATCAAAC+TGG - chr6_4:76200647-76200666 Msa0997120:intron 35.0%
CAAACCAGTTTGATCTACAT+TGG + chr6_4:76200654-76200673 None:intergenic 35.0%
CAATGTAGATCAAACTGGTT+TGG - chr6_4:76200652-76200671 Msa0997120:intron 35.0%
!! TCAAACTGGTTTGGATGAAT+CGG - chr6_4:76200661-76200680 Msa0997120:intron 35.0%
! GGTGTGATTGACTCTATATT+TGG - chr6_4:76200703-76200722 Msa0997120:CDS 35.0%
! CTGATCAACTGTTGTTCTTT+TGG - chr6_4:76200922-76200941 Msa0997120:intron 35.0%
CAATTTACACTCGTCTTCTT+TGG + chr6_4:76201171-76201190 None:intergenic 35.0%
! AAGTCGAGCAATCTTTTTGC+AGG + chr6_4:76200317-76200336 None:intergenic 40.0%
GTCCGAATTATCACTGCATT+TGG + chr6_4:76200348-76200367 None:intergenic 40.0%
AGAATATCCTTTGCCAGGTT+TGG + chr6_4:76200387-76200406 None:intergenic 40.0%
TTTCAGCTTCTCCTATTGAG+AGG + chr6_4:76200801-76200820 None:intergenic 40.0%
TGATGTTGTACCAAACTGCT+AGG + chr6_4:76201029-76201048 None:intergenic 40.0%
CATCAAGAATGCGTCAGATT+TGG - chr6_4:76201112-76201131 Msa0997120:five_prime_UTR 40.0%
! AAGTCGAGCAATCTTTTTGC+AGG + chr6_4:76200317-76200336 None:intergenic 40.0%
GTCCGAATTATCACTGCATT+TGG + chr6_4:76200348-76200367 None:intergenic 40.0%
AGAATATCCTTTGCCAGGTT+TGG + chr6_4:76200387-76200406 None:intergenic 40.0%
TTTCAGCTTCTCCTATTGAG+AGG + chr6_4:76200801-76200820 None:intergenic 40.0%
TGATGTTGTACCAAACTGCT+AGG + chr6_4:76201029-76201048 None:intergenic 40.0%
CATCAAGAATGCGTCAGATT+TGG - chr6_4:76201112-76201131 Msa0997120:five_prime_UTR 40.0%
ACACCTGAGAGATTGTTGCT+CGG - chr6_4:76200237-76200256 Msa0997120:CDS 45.0%
AGTGTAGACATGTCCAAACC+TGG - chr6_4:76200371-76200390 Msa0997120:intron 45.0%
ACCTGGCAAAGGATATTCTG+AGG - chr6_4:76200388-76200407 Msa0997120:intron 45.0%
CCTGGCAAAGGATATTCTGA+GGG - chr6_4:76200389-76200408 Msa0997120:intron 45.0%
GAAGATACCACCTTCTTGCA+AGG + chr6_4:76200862-76200881 None:intergenic 45.0%
TGCAAGAAGGTGGTATCTTC+TGG - chr6_4:76200862-76200881 Msa0997120:intron 45.0%
GATAGCAGAACCTAGCAGTT+TGG - chr6_4:76201016-76201035 Msa0997120:five_prime_UTR 45.0%
ACTCGTCTTCTTTGGTCACA+TGG + chr6_4:76201163-76201182 None:intergenic 45.0%
ACACCTGAGAGATTGTTGCT+CGG - chr6_4:76200237-76200256 Msa0997120:CDS 45.0%
AGTGTAGACATGTCCAAACC+TGG - chr6_4:76200371-76200390 Msa0997120:intron 45.0%
ACCTGGCAAAGGATATTCTG+AGG - chr6_4:76200388-76200407 Msa0997120:intron 45.0%
CCTGGCAAAGGATATTCTGA+GGG - chr6_4:76200389-76200408 Msa0997120:intron 45.0%
GAAGATACCACCTTCTTGCA+AGG + chr6_4:76200862-76200881 None:intergenic 45.0%
TGCAAGAAGGTGGTATCTTC+TGG - chr6_4:76200862-76200881 Msa0997120:intron 45.0%
GATAGCAGAACCTAGCAGTT+TGG - chr6_4:76201016-76201035 Msa0997120:five_prime_UTR 45.0%
ACTCGTCTTCTTTGGTCACA+TGG + chr6_4:76201163-76201182 None:intergenic 45.0%
GAACCGAGCAACAATCTCTC+AGG + chr6_4:76200243-76200262 None:intergenic 50.0%
GACATGTCCAAACCTGGCAA+AGG - chr6_4:76200377-76200396 Msa0997120:intron 50.0%
CCCTCAGAATATCCTTTGCC+AGG + chr6_4:76200392-76200411 None:intergenic 50.0%
TGATTCCATTTCCCTGCCTC+AGG - chr6_4:76200424-76200443 Msa0997120:intron 50.0%
AAGGTATACCTCCTGAGGCA+GGG + chr6_4:76200438-76200457 None:intergenic 50.0%
! GATGGAAGGTATACCTCCTG+AGG + chr6_4:76200443-76200462 None:intergenic 50.0%
ACCTTCTTGCAAGGTCAGTC+TGG + chr6_4:76200853-76200872 None:intergenic 50.0%
AGACTGACCTTGCAAGAAGG+TGG - chr6_4:76200852-76200871 Msa0997120:intron 50.0%
! CTTCTGGAGACACTGTGTAC+TGG - chr6_4:76200878-76200897 Msa0997120:intron 50.0%
! TGGAGACACTGTGTACTGGT+GGG - chr6_4:76200882-76200901 Msa0997120:intron 50.0%
GAACCGAGCAACAATCTCTC+AGG + chr6_4:76200243-76200262 None:intergenic 50.0%
GACATGTCCAAACCTGGCAA+AGG - chr6_4:76200377-76200396 Msa0997120:intron 50.0%
CCCTCAGAATATCCTTTGCC+AGG + chr6_4:76200392-76200411 None:intergenic 50.0%
TGATTCCATTTCCCTGCCTC+AGG - chr6_4:76200424-76200443 Msa0997120:intron 50.0%
AAGGTATACCTCCTGAGGCA+GGG + chr6_4:76200438-76200457 None:intergenic 50.0%
! GATGGAAGGTATACCTCCTG+AGG + chr6_4:76200443-76200462 None:intergenic 50.0%
ACCTTCTTGCAAGGTCAGTC+TGG + chr6_4:76200853-76200872 None:intergenic 50.0%
AGACTGACCTTGCAAGAAGG+TGG - chr6_4:76200852-76200871 Msa0997120:intron 50.0%
! CTTCTGGAGACACTGTGTAC+TGG - chr6_4:76200878-76200897 Msa0997120:intron 50.0%
! TGGAGACACTGTGTACTGGT+GGG - chr6_4:76200882-76200901 Msa0997120:intron 50.0%
!! CTCTCAGGTGTTGACTGTGC+AGG + chr6_4:76200228-76200247 None:intergenic 55.0%
TTCCATTTCCCTGCCTCAGG+AGG - chr6_4:76200427-76200446 Msa0997120:intron 55.0%
TACCTCCTGAGGCAGGGAAA+TGG + chr6_4:76200432-76200451 None:intergenic 55.0%
! GAAGGTATACCTCCTGAGGC+AGG + chr6_4:76200439-76200458 None:intergenic 55.0%
GCCAGACTGACCTTGCAAGA+AGG - chr6_4:76200849-76200868 Msa0997120:intron 55.0%
CTGGAGACACTGTGTACTGG+TGG - chr6_4:76200881-76200900 Msa0997120:intron 55.0%
!! CTCTCAGGTGTTGACTGTGC+AGG + chr6_4:76200228-76200247 None:intergenic 55.0%
TTCCATTTCCCTGCCTCAGG+AGG - chr6_4:76200427-76200446 Msa0997120:intron 55.0%
TACCTCCTGAGGCAGGGAAA+TGG + chr6_4:76200432-76200451 None:intergenic 55.0%
! GAAGGTATACCTCCTGAGGC+AGG + chr6_4:76200439-76200458 None:intergenic 55.0%
GCCAGACTGACCTTGCAAGA+AGG - chr6_4:76200849-76200868 Msa0997120:intron 55.0%
CTGGAGACACTGTGTACTGG+TGG - chr6_4:76200881-76200900 Msa0997120:intron 55.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 76200182 76201205 76200182 ID=Msa0997120;Name=Msa0997120
chr6_4 mRNA 76200182 76201205 76200182 ID=Msa0997120-mRNA-1;Parent=Msa0997120;Name=Msa0997120-mRNA-1;_AED=0.35;_eAED=0.44;_QI=198|0.33|0.25|1|0.66|0.75|4|0|104
chr6_4 exon 76200182 76200275 76200182 ID=Msa0997120-mRNA-1:exon:14339;Parent=Msa0997120-mRNA-1
chr6_4 exon 76200514 76200578 76200514 ID=Msa0997120-mRNA-1:exon:14338;Parent=Msa0997120-mRNA-1
chr6_4 exon 76200684 76200770 76200684 ID=Msa0997120-mRNA-1:exon:14337;Parent=Msa0997120-mRNA-1
chr6_4 exon 76200939 76201205 76200939 ID=Msa0997120-mRNA-1:exon:14336;Parent=Msa0997120-mRNA-1
chr6_4 five_prime_UTR 76201008 76201205 76201008 ID=Msa0997120-mRNA-1:five_prime_utr;Parent=Msa0997120-mRNA-1
chr6_4 CDS 76200939 76201007 76200939 ID=Msa0997120-mRNA-1:cds;Parent=Msa0997120-mRNA-1
chr6_4 CDS 76200684 76200770 76200684 ID=Msa0997120-mRNA-1:cds;Parent=Msa0997120-mRNA-1
chr6_4 CDS 76200514 76200578 76200514 ID=Msa0997120-mRNA-1:cds;Parent=Msa0997120-mRNA-1
chr6_4 CDS 76200182 76200275 76200182 ID=Msa0997120-mRNA-1:cds;Parent=Msa0997120-mRNA-1
Gene Sequence

>Msa0997120

ATGTCCAAACCTGGCAAAGGATATTCTGAGGGTCTCAAATCTTTTGATTCCATTTCCCTGCCTCAGGAGGTAGAAGAAAGCCTTAATCAATCCTTTGAGGAAACCAATGTAGATCAAACTGGTTTGGATGAATCGGATAACAATCTTTCATCATTGGAGAAGCTGAAAAACAGATTGAGATTTTGCAAAAGATTGTGCCAGACTGACCTTGCAAGAAGGTGCATCAAGAATGCGTCAGATTTGGACTCAGTTCGATCAAGACTTCTCAGCCATGTGACCAAAGAAGACGAGTGTAAATTGCATTGTTGCAAATGA

Protein sequence

>Msa0997120

MSKPGKGYSEGLKSFDSISLPQEVEESLNQSFEETNVDQTGLDESDNNLSSLEKLKNRLRFCKRLCQTDLARRCIKNASDLDSVRSRLLSHVTKEDECKLHCCK*