AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0405470


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 43 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCACGCCTCCGTTACCTTT+TGG 0.196515 3_2:-40194940 Msa0405470:CDS
CTGTTCCCTGGGATTGGCTT+TGG 0.228349 3_2:+40194755 None:intergenic
TGTTCCCTGGGATTGGCTTT+GGG 0.270024 3_2:+40194756 None:intergenic
TCTCAGGTAGACAGTTTCTA+TGG 0.287253 3_2:+40194905 None:intergenic
GGCAAAGAAGGCCTCCTTCC+GGG 0.289862 3_2:+40194804 None:intergenic
TCCTCGGGCCAGACGGAGAT+TGG 0.349112 3_2:+40194969 None:intergenic
GCTTCACTGTTCCCTGGGAT+TGG 0.355814 3_2:+40194749 None:intergenic
AGGCAAAGAAGGCCTCCTTC+CGG 0.382980 3_2:+40194803 None:intergenic
CCCTTCTGCCTTTGCACTCG+AGG 0.411231 3_2:-40194993 Msa0405470:CDS
GACTGTCCCTTGGTCTGTAT+TGG 0.425548 3_2:-40194884 Msa0405470:CDS
CCTTCTGCCTTTGCACTCGA+GGG 0.461384 3_2:-40194992 Msa0405470:CDS
AAAAGCCCAAAGCCAATCCC+AGG 0.461472 3_2:-40194761 Msa0405470:CDS
ATGAAGCTTCACTGTTCCCT+GGG 0.472889 3_2:+40194744 None:intergenic
ACAGACCAAGGGACAGTCTC+AGG 0.474421 3_2:+40194889 None:intergenic
TATGAAGCTTCACTGTTCCC+TGG 0.477188 3_2:+40194743 None:intergenic
CTCGAGGGCCAATCTCCGTC+TGG 0.480699 3_2:-40194977 Msa0405470:CDS
GCCTTCCACCTAAGCTGCGC+AGG 0.489457 3_2:-40194784 Msa0405470:CDS
TCCTGCGCAGCTTAGGTGGA+AGG 0.508478 3_2:+40194783 None:intergenic
CTCAGGTAGACAGTTTCTAT+GGG 0.510655 3_2:+40194906 None:intergenic
CCCTCGAGTGCAAAGGCAGA+AGG 0.511073 3_2:+40194992 None:intergenic
CCTTGGTCTGTATTGGCACA+AGG 0.514139 3_2:-40194877 Msa0405470:intron
GCAAAGAAGGCCTCCTTCCG+GGG 0.515468 3_2:+40194805 None:intergenic
GAGGCGTGCAAAGGTTTCCT+CGG 0.526013 3_2:+40194953 None:intergenic
AGGCGTGCAAAGGTTTCCTC+GGG 0.527025 3_2:+40194954 None:intergenic
CCAGAGTGGTATCTCACTGA+TGG 0.527423 3_2:-40194837 Msa0405470:intron
CAAAGAAGGCCTCCTTCCGG+GGG 0.550054 3_2:+40194806 None:intergenic
GCTTAGGTGGAAGGCAAAGA+AGG 0.550243 3_2:+40194792 None:intergenic
GCCAATCTCCGTCTGGCCCG+AGG 0.562208 3_2:-40194970 Msa0405470:CDS
GTCTACCTGAGACTGTCCCT+TGG 0.586612 3_2:-40194894 Msa0405470:CDS
AAGGTAACGGAGGCGTGCAA+AGG 0.595805 3_2:+40194944 None:intergenic
CCTCGAGTGCAAAGGCAGAA+GGG 0.595841 3_2:+40194993 None:intergenic
AAAGGTTTCCTCGGGCCAGA+CGG 0.597813 3_2:+40194962 None:intergenic
AAGAAGGCCTCCTTCCGGGG+GGG 0.600255 3_2:+40194808 None:intergenic
TGGGGCGTAGGCCTCCCAAA+AGG 0.606913 3_2:+40194925 None:intergenic
CCTTGTGCCAATACAGACCA+AGG 0.618599 3_2:+40194877 None:intergenic
AAAGCCCAAAGCCAATCCCA+GGG 0.619579 3_2:-40194760 Msa0405470:CDS
AGACAGTTTCTATGGGGCGT+AGG 0.622986 3_2:+40194913 None:intergenic
AAAGAAGGCCTCCTTCCGGG+GGG 0.627949 3_2:+40194807 None:intergenic
GTAGGCCTCCCAAAAGGTAA+CGG 0.632223 3_2:+40194931 None:intergenic
AGATTGGCCCTCGAGTGCAA+AGG 0.670375 3_2:+40194985 None:intergenic
GGCCTCCCAAAAGGTAACGG+AGG 0.683463 3_2:+40194934 None:intergenic
CTTGTGCCAATACAGACCAA+GGG 0.693537 3_2:+40194878 None:intergenic
TCAGGTAGACAGTTTCTATG+GGG 0.720720 3_2:+40194907 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCAGGTAGACAGTTTCTATG+GGG + chr3_2:40194840-40194859 None:intergenic 40.0%
CTCAGGTAGACAGTTTCTAT+GGG + chr3_2:40194841-40194860 None:intergenic 40.0%
TCTCAGGTAGACAGTTTCTA+TGG + chr3_2:40194842-40194861 None:intergenic 40.0%
CTTGTGCCAATACAGACCAA+GGG + chr3_2:40194869-40194888 None:intergenic 45.0%
!! GAATTCTAGCTCTTCCAGAG+TGG - chr3_2:40194893-40194912 Msa0405470:CDS 45.0%
GTAGGCCTCCCAAAAGGTAA+CGG + chr3_2:40194816-40194835 None:intergenic 50.0%
AGACAGTTTCTATGGGGCGT+AGG + chr3_2:40194834-40194853 None:intergenic 50.0%
GACTGTCCCTTGGTCTGTAT+TGG - chr3_2:40194860-40194879 Msa0405470:intron 50.0%
CCTTGTGCCAATACAGACCA+AGG + chr3_2:40194870-40194889 None:intergenic 50.0%
! CCTTGGTCTGTATTGGCACA+AGG - chr3_2:40194867-40194886 Msa0405470:intron 50.0%
CCATCAGTGAGATACCACTC+TGG + chr3_2:40194910-40194929 None:intergenic 50.0%
CCAGAGTGGTATCTCACTGA+TGG - chr3_2:40194907-40194926 Msa0405470:CDS 50.0%
GCTTAGGTGGAAGGCAAAGA+AGG + chr3_2:40194955-40194974 None:intergenic 50.0%
AAAAGCCCAAAGCCAATCCC+AGG - chr3_2:40194983-40195002 Msa0405470:CDS 50.0%
AAAGCCCAAAGCCAATCCCA+GGG - chr3_2:40194984-40195003 Msa0405470:CDS 50.0%
!! TGTTCCCTGGGATTGGCTTT+GGG + chr3_2:40194991-40195010 None:intergenic 50.0%
CCTCGAGTGCAAAGGCAGAA+GGG + chr3_2:40194754-40194773 None:intergenic 55.0%
CCTTCTGCCTTTGCACTCGA+GGG - chr3_2:40194752-40194771 Msa0405470:CDS 55.0%
! AGATTGGCCCTCGAGTGCAA+AGG + chr3_2:40194762-40194781 None:intergenic 55.0%
AAAGGTTTCCTCGGGCCAGA+CGG + chr3_2:40194785-40194804 None:intergenic 55.0%
AGGCGTGCAAAGGTTTCCTC+GGG + chr3_2:40194793-40194812 None:intergenic 55.0%
GAGGCGTGCAAAGGTTTCCT+CGG + chr3_2:40194794-40194813 None:intergenic 55.0%
!! AAGGTAACGGAGGCGTGCAA+AGG + chr3_2:40194803-40194822 None:intergenic 55.0%
! TGCACGCCTCCGTTACCTTT+TGG - chr3_2:40194804-40194823 Msa0405470:CDS 55.0%
! GCACGCCTCCGTTACCTTTT+GGG - chr3_2:40194805-40194824 Msa0405470:CDS 55.0%
GTCTACCTGAGACTGTCCCT+TGG - chr3_2:40194850-40194869 Msa0405470:intron 55.0%
ACAGACCAAGGGACAGTCTC+AGG + chr3_2:40194858-40194877 None:intergenic 55.0%
AGGCAAAGAAGGCCTCCTTC+CGG + chr3_2:40194944-40194963 None:intergenic 55.0%
! CTTTTCCTGCGCAGCTTAGG+TGG + chr3_2:40194968-40194987 None:intergenic 55.0%
!! CTGTTCCCTGGGATTGGCTT+TGG + chr3_2:40194992-40195011 None:intergenic 55.0%
GCTTCACTGTTCCCTGGGAT+TGG + chr3_2:40194998-40195017 None:intergenic 55.0%
CCCTTCTGCCTTTGCACTCG+AGG - chr3_2:40194751-40194770 Msa0405470:CDS 60.0%
CCCTCGAGTGCAAAGGCAGA+AGG + chr3_2:40194755-40194774 None:intergenic 60.0%
! CGCCTCCGTTACCTTTTGGG+AGG - chr3_2:40194808-40194827 Msa0405470:CDS 60.0%
! GGCCTCCCAAAAGGTAACGG+AGG + chr3_2:40194813-40194832 None:intergenic 60.0%
AAAGAAGGCCTCCTTCCGGG+GGG + chr3_2:40194940-40194959 None:intergenic 60.0%
CAAAGAAGGCCTCCTTCCGG+GGG + chr3_2:40194941-40194960 None:intergenic 60.0%
GCAAAGAAGGCCTCCTTCCG+GGG + chr3_2:40194942-40194961 None:intergenic 60.0%
GGCAAAGAAGGCCTCCTTCC+GGG + chr3_2:40194943-40194962 None:intergenic 60.0%
TCCTGCGCAGCTTAGGTGGA+AGG + chr3_2:40194964-40194983 None:intergenic 60.0%
! GGGCTTTTCCTGCGCAGCTT+AGG + chr3_2:40194971-40194990 None:intergenic 60.0%
CTCGAGGGCCAATCTCCGTC+TGG - chr3_2:40194767-40194786 Msa0405470:CDS 65.0%
TCCTCGGGCCAGACGGAGAT+TGG + chr3_2:40194778-40194797 None:intergenic 65.0%
TGGGGCGTAGGCCTCCCAAA+AGG + chr3_2:40194822-40194841 None:intergenic 65.0%
AAGAAGGCCTCCTTCCGGGG+GGG + chr3_2:40194939-40194958 None:intergenic 65.0%
GCCTTCCACCTAAGCTGCGC+AGG - chr3_2:40194960-40194979 Msa0405470:CDS 65.0%
GCCAATCTCCGTCTGGCCCG+AGG - chr3_2:40194774-40194793 Msa0405470:CDS 70.0%
ACTGATGGCTCGAGCCCCCC+CGG - chr3_2:40194922-40194941 Msa0405470:CDS 70.0%
ATGGCTCGAGCCCCCCCGGA+AGG - chr3_2:40194926-40194945 Msa0405470:CDS 75.0%
! GCTCGAGCCCCCCCGGAAGG+AGG - chr3_2:40194929-40194948 Msa0405470:CDS 80.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 40194745 40195021 40194745 ID=Msa0405470;Name=Msa0405470
chr3_2 mRNA 40194745 40195021 40194745 ID=Msa0405470-mRNA-1;Parent=Msa0405470;Name=Msa0405470-mRNA-1;_AED=0.38;_eAED=0.65;_QI=0|0|0|1|0|0|2|0|85
chr3_2 exon 40194878 40195021 40194878 ID=Msa0405470-mRNA-1:exon:7820;Parent=Msa0405470-mRNA-1
chr3_2 exon 40194745 40194855 40194745 ID=Msa0405470-mRNA-1:exon:7819;Parent=Msa0405470-mRNA-1
chr3_2 CDS 40194878 40195021 40194878 ID=Msa0405470-mRNA-1:cds;Parent=Msa0405470-mRNA-1
chr3_2 CDS 40194745 40194855 40194745 ID=Msa0405470-mRNA-1:cds;Parent=Msa0405470-mRNA-1
Gene Sequence

>Msa0405470

CAAGCTCCCTTCTGCCTTTGCACTCGAGGGCCAATCTCCGTCTGGCCCGAGGAAACCTTTGCACGCCTCCGTTACCTTTTGGGAGGCCTACGCCCCATAGAAACTGTCTACCTGAGACTGTCCCTTGGTCTGTATTGGCACAAGAGTGGTATCTCACTGATGGCTCGAGCCCCCCCGGAAGGAGGCCTTCTTTGCCTTCCACCTAAGCTGCGCAGGAAAAGCCCAAAGCCAATCCCAGGGAACAGTGAAGCTTCA

Protein sequence

>Msa0405470

QAPFCLCTRGPISVWPEETFARLRYLLGGLRPIETVYLRLSLGLYWHKSGISLMARAPPEGGLLCLPPKLRRKSPKPIPGNSEAS