AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0083710

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 53 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGCGACCGCCCGGGGTCGC+TGG 0.207871 1_2:-62823178 None:intergenic
CAGGTCTTAGGAAACAAATT+TGG 0.216973 1_2:+62824193 Msa0083710:CDS
ACGGAGCCGGGGCGACCGCC+CGG 0.275320 1_2:-62823187 None:intergenic
CGGAGCCGGGGCGACCGCCC+GGG 0.277719 1_2:-62823186 None:intergenic
CCACATTAGGCCCAAGCTTT+TGG 0.287770 1_2:+62823221 Msa0083710:five_prime_UTR
TCATTGGCTACTTCGGCTTC+CGG 0.318480 1_2:-62824156 None:intergenic
TTGTGCGTGATCCAGGTCTT+AGG 0.337344 1_2:+62824181 Msa0083710:CDS
GGCGACCGCCCGGGGTCGCT+GGG 0.341802 1_2:-62823177 None:intergenic
TGGGAGTATGCGGTGATGTT+TGG 0.349332 1_2:+62824213 Msa0083710:CDS
TGGAATTTGATGGAATTTCA+TGG 0.382517 1_2:+62823869 Msa0083710:five_prime_UTR
GCGACCCCGGGCGGTCGCCC+CGG 0.382965 1_2:+62823181 Msa0083710:five_prime_UTR
GGGAGTATGCGGTGATGTTT+GGG 0.392710 1_2:+62824214 Msa0083710:CDS
CACCGCCATTTGCTCTTTGA+CGG 0.398780 1_2:-62824288 None:intergenic
GGAGCCGGGGCGACCGCCCG+GGG 0.399005 1_2:-62823185 None:intergenic
TGCGGTGATGTTTGGGAGCT+TGG 0.404102 1_2:+62824221 Msa0083710:CDS
AGGTCTTAGGAAACAAATTT+GGG 0.408520 1_2:+62824194 Msa0083710:CDS
AATGAGATTGTGCGTGATCC+AGG 0.422235 1_2:+62824174 Msa0083710:CDS
GGTAAAGTACAGACGGAGCC+GGG 0.424499 1_2:-62823199 None:intergenic
ATGAGTTTGATGGAATTTGA+TGG 0.425202 1_2:+62823859 Msa0083710:five_prime_UTR
GAAAGCTGCTGTAGCCTTTG+TGG 0.435734 1_2:-62823319 None:intergenic
CACAATCTCATTGGCTACTT+CGG 0.444118 1_2:-62824163 None:intergenic
CTTAGGTGAGATGAGTTTGA+TGG 0.466099 1_2:+62823849 Msa0083710:five_prime_UTR
CAAATTTGTTTCCTAAGACC+TGG 0.470424 1_2:-62824192 None:intergenic
GTGTAAATGGGCCAAAAGCT+TGG 0.473146 1_2:-62823232 None:intergenic
TGTAAATGGGCCAAAAGCTT+GGG 0.473427 1_2:-62823231 None:intergenic
GAGGAACTGCAGCAGCCAGC+AGG 0.477012 1_2:-62823957 None:intergenic
CTGAAGAGTTTGATGAGCTT+AGG 0.479230 1_2:+62823832 Msa0083710:five_prime_UTR
CATTCACTCTAATTCTCTAA+AGG 0.488492 1_2:+62823444 Msa0083710:five_prime_UTR
TGGATCACGCACAATCTCAT+TGG 0.489029 1_2:-62824172 None:intergenic
GACCGCCCGGGGTCGCTGGG+CGG 0.492985 1_2:-62823174 None:intergenic
CTCTCATCAATCATCTCTCT+CGG 0.496967 1_2:+62823357 Msa0083710:five_prime_UTR
GAATGTAAATGTTGTGAAAC+CGG 0.498538 1_2:+62824137 Msa0083710:CDS
ATTAGTTCTCTCATCTCTCT+CGG 0.503929 1_2:+62823392 Msa0083710:five_prime_UTR
AATGCGAATGGAGTGCCTGC+TGG 0.517339 1_2:+62823942 Msa0083710:exon
CATCAATCATCTCTCTCGGC+AGG 0.519196 1_2:+62823361 Msa0083710:five_prime_UTR
CCAAAAGCTTGGGCCTAATG+TGG 0.520380 1_2:-62823221 None:intergenic
TATATCCGTCAAAGAGCAAA+TGG 0.527675 1_2:+62824283 Msa0083710:CDS
GGGTAAAGTACAGACGGAGC+CGG 0.549020 1_2:-62823200 None:intergenic
AGCAGGCACTCCATTCGCAT+TGG 0.552459 1_2:-62823940 None:intergenic
GTTCCTCCTCAATCGAATCT+CGG 0.569366 1_2:+62823973 Msa0083710:CDS
GTCTGTACTTTACCCACATT+AGG 0.583824 1_2:+62823208 Msa0083710:five_prime_UTR
TTCTCACCGAGATTCGATTG+AGG 0.592211 1_2:-62823979 None:intergenic
CAAAAGCTTGGGCCTAATGT+GGG 0.615109 1_2:-62823220 None:intergenic
GAAACAAATTTGGGAGTATG+CGG 0.620477 1_2:+62824203 Msa0083710:CDS
AGATCATGTTTGAGCAGGGG+CGG 0.621020 1_2:+62823146 None:intergenic
TCACCGAGATTCGATTGAGG+AGG 0.624509 1_2:-62823976 None:intergenic
TACCGCCCAGCGACCCCGGG+CGG 0.630814 1_2:+62823172 Msa0083710:five_prime_UTR
TGAATGAGAGATTAGCAACA+AGG 0.630982 1_2:-62823427 None:intergenic
TAATGTGGGTAAAGTACAGA+CGG 0.638044 1_2:-62823206 None:intergenic
TAAAGATCATGTTTGAGCAG+GGG 0.655462 1_2:+62823143 None:intergenic
GTAAAGTACAGACGGAGCCG+GGG 0.678767 1_2:-62823198 None:intergenic
AGTAATTCACAACACCACAA+AGG 0.700809 1_2:+62823305 Msa0083710:five_prime_UTR
ATCCGTCAAAGAGCAAATGG+CGG 0.716513 1_2:+62824286 Msa0083710:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATATTTATTTGTTTGTTTT+TGG + chr1_2:62823790-62823809 Msa0083710:intron 10.0%
!! ACACTTGAAAAAAAAAAAAT+GGG + chr1_2:62823253-62823272 Msa0083710:five_prime_UTR 15.0%
!!! TTTTAGGAAAATTGTAAAAT+TGG + chr1_2:62823507-62823526 Msa0083710:intron 15.0%
!!! GTTGAAAAGTATTTTTTTTT+TGG + chr1_2:62824024-62824043 Msa0083710:intron 15.0%
!!! TTTTTTTCAAGTGTGTAAAT+GGG - chr1_2:62823247-62823266 None:intergenic 20.0%
!!! TTTTTTTTCAAGTGTGTAAA+TGG - chr1_2:62823248-62823267 None:intergenic 20.0%
!! CACACTTGAAAAAAAAAAAA+TGG + chr1_2:62823252-62823271 Msa0083710:five_prime_UTR 20.0%
!! CACTTGAAAAAAAAAAAATG+GGG + chr1_2:62823254-62823273 Msa0083710:five_prime_UTR 20.0%
!!! GTTAGTTTAATTTGAAGTTT+TGG + chr1_2:62823599-62823618 Msa0083710:intron 20.0%
!! TTTATTTCGATTTACTCAAA+TGG + chr1_2:62823729-62823748 Msa0083710:intron 20.0%
!! TTATTTCGATTTACTCAAAT+GGG + chr1_2:62823730-62823749 Msa0083710:intron 20.0%
!!! TTATTTGTTTGTTTTTGGAT+TGG + chr1_2:62823795-62823814 Msa0083710:intron 20.0%
!!! ACACATTTTCTTGATTAATT+AGG + chr1_2:62824001-62824020 Msa0083710:intron 20.0%
!!! CACATTTTCTTGATTAATTA+GGG + chr1_2:62824002-62824021 Msa0083710:intron 20.0%
!!! GGATGATTTTGTTTTAATTT+AGG + chr1_2:62824045-62824064 Msa0083710:intron 20.0%
! AAAACAAAAAACAACCAGAA+GGG - chr1_2:62823711-62823730 None:intergenic 25.0%
! AAAAACAAAAAACAACCAGA+AGG - chr1_2:62823712-62823731 None:intergenic 25.0%
!! TTTTCTTATGTGGTAAAGAT+TGG + chr1_2:62823756-62823775 Msa0083710:intron 25.0%
!!! TTTTGGATTGGTTGATTTTT+AGG + chr1_2:62823807-62823826 Msa0083710:intron 25.0%
!!! TGTTTTTGTTAGATAGAACA+AGG + chr1_2:62824109-62824128 Msa0083710:intron 25.0%
CATTCACTCTAATTCTCTAA+AGG + chr1_2:62823444-62823463 Msa0083710:five_prime_UTR 30.0%
TAAAACAAGGAAAGAAAGGA+AGG - chr1_2:62823484-62823503 None:intergenic 30.0%
!!! TTCCTTTCTTTCCTTGTTTT+AGG + chr1_2:62823483-62823502 Msa0083710:intron 30.0%
!!! TCCTTTCTTTCCTTGTTTTA+GGG + chr1_2:62823484-62823503 Msa0083710:intron 30.0%
!!! TTTCCTTGTTTTAGGGTTTT+AGG + chr1_2:62823491-62823510 Msa0083710:intron 30.0%
TTTCCTAAAACCCTAAAACA+AGG - chr1_2:62823497-62823516 None:intergenic 30.0%
AAACAAAAAACAACCAGAAG+GGG - chr1_2:62823710-62823729 None:intergenic 30.0%
!! AAATGGGTCATTTTCTTATG+TGG + chr1_2:62823746-62823765 Msa0083710:intron 30.0%
ATGAGTTTGATGGAATTTGA+TGG + chr1_2:62823859-62823878 Msa0083710:five_prime_UTR 30.0%
TGGAATTTGATGGAATTTCA+TGG + chr1_2:62823869-62823888 Msa0083710:five_prime_UTR 30.0%
!! ATGGAGTTTTATGAGTTTGA+TGG + chr1_2:62823888-62823907 Msa0083710:five_prime_UTR 30.0%
!! GTTTTATGAGTTTGATGGAT+TGG + chr1_2:62823893-62823912 Msa0083710:five_prime_UTR 30.0%
GAATGTAAATGTTGTGAAAC+CGG + chr1_2:62824137-62824156 Msa0083710:CDS 30.0%
AGGTCTTAGGAAACAAATTT+GGG + chr1_2:62824194-62824213 Msa0083710:CDS 30.0%
TAATGTGGGTAAAGTACAGA+CGG - chr1_2:62823209-62823228 None:intergenic 35.0%
AGTAATTCACAACACCACAA+AGG + chr1_2:62823305-62823324 Msa0083710:five_prime_UTR 35.0%
! ATTAGTTCTCTCATCTCTCT+CGG + chr1_2:62823392-62823411 Msa0083710:five_prime_UTR 35.0%
TGAATGAGAGATTAGCAACA+AGG - chr1_2:62823430-62823449 None:intergenic 35.0%
ACCCTAAAACAAGGAAAGAA+AGG - chr1_2:62823488-62823507 None:intergenic 35.0%
GCAGACTGCAATTGAAAAAT+TGG + chr1_2:62823537-62823556 Msa0083710:intron 35.0%
GTGAGTGTGTTTACTTGATT+AGG + chr1_2:62824074-62824093 Msa0083710:intron 35.0%
! CAAATTTGTTTCCTAAGACC+TGG - chr1_2:62824195-62824214 None:intergenic 35.0%
CAGGTCTTAGGAAACAAATT+TGG + chr1_2:62824193-62824212 Msa0083710:CDS 35.0%
! GAAACAAATTTGGGAGTATG+CGG + chr1_2:62824203-62824222 Msa0083710:CDS 35.0%
TATATCCGTCAAAGAGCAAA+TGG + chr1_2:62824283-62824302 Msa0083710:CDS 35.0%
GTCTGTACTTTACCCACATT+AGG + chr1_2:62823208-62823227 Msa0083710:five_prime_UTR 40.0%
TGTAAATGGGCCAAAAGCTT+GGG - chr1_2:62823234-62823253 None:intergenic 40.0%
CTCTCATCAATCATCTCTCT+CGG + chr1_2:62823357-62823376 Msa0083710:five_prime_UTR 40.0%
CTGAAGAGTTTGATGAGCTT+AGG + chr1_2:62823832-62823851 Msa0083710:five_prime_UTR 40.0%
CTTAGGTGAGATGAGTTTGA+TGG + chr1_2:62823849-62823868 Msa0083710:five_prime_UTR 40.0%
! TTTTCGTTGACCAATGCGAA+TGG + chr1_2:62823930-62823949 Msa0083710:exon 40.0%
! CACAATCTCATTGGCTACTT+CGG - chr1_2:62824166-62824185 None:intergenic 40.0%
CAAAAGCTTGGGCCTAATGT+GGG - chr1_2:62823223-62823242 None:intergenic 45.0%
GTGTAAATGGGCCAAAAGCT+TGG - chr1_2:62823235-62823254 None:intergenic 45.0%
! GAGATTTTCACAACCCCTTC+TGG + chr1_2:62823694-62823713 Msa0083710:intron 45.0%
GTTCCTCCTCAATCGAATCT+CGG + chr1_2:62823973-62823992 Msa0083710:CDS 45.0%
TTCTCACCGAGATTCGATTG+AGG - chr1_2:62823982-62824001 None:intergenic 45.0%
TGGATCACGCACAATCTCAT+TGG - chr1_2:62824175-62824194 None:intergenic 45.0%
AATGAGATTGTGCGTGATCC+AGG + chr1_2:62824174-62824193 Msa0083710:CDS 45.0%
ATCCGTCAAAGAGCAAATGG+CGG + chr1_2:62824286-62824305 Msa0083710:CDS 45.0%
CCAAAAGCTTGGGCCTAATG+TGG - chr1_2:62823224-62823243 None:intergenic 50.0%
! CCACATTAGGCCCAAGCTTT+TGG + chr1_2:62823221-62823240 Msa0083710:five_prime_UTR 50.0%
GAAAGCTGCTGTAGCCTTTG+TGG - chr1_2:62823322-62823341 None:intergenic 50.0%
CATCAATCATCTCTCTCGGC+AGG + chr1_2:62823361-62823380 Msa0083710:five_prime_UTR 50.0%
TCACCGAGATTCGATTGAGG+AGG - chr1_2:62823979-62823998 None:intergenic 50.0%
! TCATTGGCTACTTCGGCTTC+CGG - chr1_2:62824159-62824178 None:intergenic 50.0%
TTGTGCGTGATCCAGGTCTT+AGG + chr1_2:62824181-62824200 Msa0083710:CDS 50.0%
! TGGGAGTATGCGGTGATGTT+TGG + chr1_2:62824213-62824232 Msa0083710:CDS 50.0%
! GGGAGTATGCGGTGATGTTT+GGG + chr1_2:62824214-62824233 Msa0083710:CDS 50.0%
CACCGCCATTTGCTCTTTGA+CGG - chr1_2:62824291-62824310 None:intergenic 50.0%
GTAAAGTACAGACGGAGCCG+GGG - chr1_2:62823201-62823220 None:intergenic 55.0%
GGTAAAGTACAGACGGAGCC+GGG - chr1_2:62823202-62823221 None:intergenic 55.0%
GGGTAAAGTACAGACGGAGC+CGG - chr1_2:62823203-62823222 None:intergenic 55.0%
AGCAGGCACTCCATTCGCAT+TGG - chr1_2:62823943-62823962 None:intergenic 55.0%
! AATGCGAATGGAGTGCCTGC+TGG + chr1_2:62823942-62823961 Msa0083710:exon 55.0%
TGCGGTGATGTTTGGGAGCT+TGG + chr1_2:62824221-62824240 Msa0083710:CDS 55.0%
! GTTTTACCGCCCAGCGACCC+CGG + chr1_2:62823168-62823187 Msa0083710:five_prime_UTR 65.0%
! TTTTACCGCCCAGCGACCCC+GGG + chr1_2:62823169-62823188 Msa0083710:five_prime_UTR 65.0%
GAGGAACTGCAGCAGCCAGC+AGG - chr1_2:62823960-62823979 None:intergenic 65.0%
! TACCGCCCAGCGACCCCGGG+CGG + chr1_2:62823172-62823191 Msa0083710:five_prime_UTR 80.0%
! GACCGCCCGGGGTCGCTGGG+CGG - chr1_2:62823177-62823196 None:intergenic 85.0%
! GGCGACCGCCCGGGGTCGCT+GGG - chr1_2:62823180-62823199 None:intergenic 85.0%
! ACGGAGCCGGGGCGACCGCC+CGG - chr1_2:62823190-62823209 None:intergenic 85.0%
! GGGCGACCGCCCGGGGTCGC+TGG - chr1_2:62823181-62823200 None:intergenic 90.0%
! GCGACCCCGGGCGGTCGCCC+CGG + chr1_2:62823181-62823200 Msa0083710:five_prime_UTR 90.0%
! GGAGCCGGGGCGACCGCCCG+GGG - chr1_2:62823188-62823207 None:intergenic 90.0%
! CGGAGCCGGGGCGACCGCCC+GGG - chr1_2:62823189-62823208 None:intergenic 90.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 62823158 62824311 62823158 ID=Msa0083710;Name=Msa0083710
chr1_2 mRNA 62823158 62824311 62823158 ID=Msa0083710-mRNA-1;Parent=Msa0083710;Name=Msa0083710-mRNA-1;_AED=0.30;_eAED=0.30;_QI=422|0.33|0.5|1|0.66|0.5|4|0|81
chr1_2 exon 62823158 62823465 62823158 ID=Msa0083710-mRNA-1:exon:20975;Parent=Msa0083710-mRNA-1
chr1_2 exon 62823829 62823994 62823829 ID=Msa0083710-mRNA-1:exon:20976;Parent=Msa0083710-mRNA-1
chr1_2 exon 62824067 62824073 62824067 ID=Msa0083710-mRNA-1:exon:20977;Parent=Msa0083710-mRNA-1
chr1_2 exon 62824125 62824311 62824125 ID=Msa0083710-mRNA-1:exon:20978;Parent=Msa0083710-mRNA-1
chr1_2 five_prime_UTR 62823158 62823465 62823158 ID=Msa0083710-mRNA-1:five_prime_utr;Parent=Msa0083710-mRNA-1
chr1_2 five_prime_UTR 62823829 62823942 62823829 ID=Msa0083710-mRNA-1:five_prime_utr;Parent=Msa0083710-mRNA-1
chr1_2 CDS 62823943 62823994 62823943 ID=Msa0083710-mRNA-1:cds;Parent=Msa0083710-mRNA-1
chr1_2 CDS 62824067 62824073 62824067 ID=Msa0083710-mRNA-1:cds;Parent=Msa0083710-mRNA-1
chr1_2 CDS 62824125 62824311 62824125 ID=Msa0083710-mRNA-1:cds;Parent=Msa0083710-mRNA-1
Gene Sequence

>Msa0083710

ATGCGAATGGAGTGCCTGCTGGCTGCTGCAGTTCCTCCTCAATCGAATCTCGGTTATGTAACAAGGATTGAGAATGTAAATGTTGTGAAACCGGAAGCCGAAGTAGCCAATGAGATTGTGCGTGATCCAGGTCTTAGGAAACAAATTTGGGAGTATGCGGTGATGTTTGGGAGCTTGGTGATAAACAATTCTCTGTGCTTATTGATGAGTCACGTGATATATCCGTCAAAGAGCAAATGGCGGTGA
Protein sequence

>Msa0083710

MRMECLLAAAVPPQSNLGYVTRIENVNVVKPEAEVANEIVRDPGLRKQIWEYAVMFGSLVINNSLCLLMSHVIYPSKSKWR*