AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0660730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0660730 MtrunA17_Chr3g0130361 87.615 218 24 2 1 218 26 240 5.90e-114 326
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTACACACTCGTTCTGTTTC+TGG 0.079801 4_3:-71710514 None:intergenic
TTCATCCAATCAAGAGAAAT+TGG 0.200595 4_3:-71710679 None:intergenic
GAAGCAAAGAATTCAGTTTC+TGG 0.205168 4_3:+71710242 Msa0660730:CDS
AGAAGGAAAGAAAGAACTTA+TGG 0.267453 4_3:+71710405 Msa0660730:CDS
TCTTTCCAATTTCTCTTGAT+TGG 0.268105 4_3:+71710674 Msa0660730:CDS
GAAGATGTTGTGATGGTATT+TGG 0.269025 4_3:-71710271 None:intergenic
ACTCGTTCTGTTTCTGGTTC+TGG 0.321144 4_3:-71710508 None:intergenic
AAAATATCTTTGCTTCTTGA+AGG 0.353302 4_3:-71710382 None:intergenic
AAGACTACTAAAGTACAAAA+TGG 0.354772 4_3:+71710703 Msa0660730:CDS
TCTGTTTCTGGTTCTGGTTG+TGG 0.412004 4_3:-71710502 None:intergenic
TTGGAAAGAACATCTTCAAT+AGG 0.415472 4_3:-71710660 None:intergenic
TTCAGGAGTGTGTGTTGGGA+AGG 0.475544 4_3:-71710206 None:intergenic
GATTGTCATAATATTCAACT+TGG 0.495379 4_3:+71710304 Msa0660730:CDS
GCTGCTCAACAACCATGTCT+TGG 0.495601 4_3:-71710471 None:intergenic
ACTCCTGAAAATACTGATGA+AGG 0.513649 4_3:+71710220 Msa0660730:CDS
AAAGAACATCTTCAATAGGA+AGG 0.518061 4_3:-71710656 None:intergenic
TAAGAAGAAGAAGAATAAGA+AGG 0.519269 4_3:+71710576 Msa0660730:CDS
TGGGAAGGTTGAGTAGCTCA+TGG 0.522255 4_3:-71710191 None:intergenic
AAACTATTGAACATCGATGA+TGG 0.533656 4_3:-71710354 None:intergenic
GCAACAGCAATGATAAAAGC+AGG 0.577812 4_3:+71710818 Msa0660730:CDS
TGAACTCTCTTTCCAAGACA+TGG 0.580676 4_3:+71710459 Msa0660730:CDS
AATGTTAAGAGTTGAAAGCA+TGG 0.584686 4_3:+71710624 Msa0660730:CDS
AGAGAGTTCATAGCTTGACT+CGG 0.600807 4_3:-71710446 None:intergenic
GAGAGTTCATAGCTTGACTC+GGG 0.607485 4_3:-71710445 None:intergenic
TAAAGTACAAAATGGCTCCG+AGG 0.683941 4_3:+71710711 Msa0660730:CDS
GAAAACAAAAGCAATAGACA+TGG 0.703147 4_3:+71710598 Msa0660730:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGAACAAAAAGATAAAGAA+TGG + chr4_3:71710734-71710753 Msa0660730:CDS 20.0%
! GATTGTCATAATATTCAACT+TGG + chr4_3:71710304-71710323 Msa0660730:CDS 25.0%
! AAAATATCTTTGCTTCTTGA+AGG - chr4_3:71710385-71710404 None:intergenic 25.0%
!!! AGAAGCAAAGATATTTTAGA+AGG + chr4_3:71710388-71710407 Msa0660730:CDS 25.0%
! TAAGAAGAAGAAGAATAAGA+AGG + chr4_3:71710576-71710595 Msa0660730:CDS 25.0%
! AAGACTACTAAAGTACAAAA+TGG + chr4_3:71710703-71710722 Msa0660730:CDS 25.0%
!! TTTATCTTTTTGTTCTACCT+CGG - chr4_3:71710731-71710750 None:intergenic 25.0%
!! TTTTTCAGAAGATGTTGTGA+TGG - chr4_3:71710281-71710300 None:intergenic 30.0%
AAACTATTGAACATCGATGA+TGG - chr4_3:71710357-71710376 None:intergenic 30.0%
AGAAGGAAAGAAAGAACTTA+TGG + chr4_3:71710405-71710424 Msa0660730:CDS 30.0%
! TTATTCAGCTTTTTGTGTTG+TGG - chr4_3:71710553-71710572 None:intergenic 30.0%
GAAAACAAAAGCAATAGACA+TGG + chr4_3:71710598-71710617 Msa0660730:CDS 30.0%
AATGTTAAGAGTTGAAAGCA+TGG + chr4_3:71710624-71710643 Msa0660730:CDS 30.0%
AAAGAACATCTTCAATAGGA+AGG - chr4_3:71710659-71710678 None:intergenic 30.0%
TTGGAAAGAACATCTTCAAT+AGG - chr4_3:71710663-71710682 None:intergenic 30.0%
TCTTTCCAATTTCTCTTGAT+TGG + chr4_3:71710674-71710693 Msa0660730:CDS 30.0%
TTCATCCAATCAAGAGAAAT+TGG - chr4_3:71710682-71710701 None:intergenic 30.0%
!! TATTTTCAGGAGTGTGTGTT+GGG - chr4_3:71710213-71710232 None:intergenic 35.0%
ACTCCTGAAAATACTGATGA+AGG + chr4_3:71710220-71710239 Msa0660730:CDS 35.0%
! CTTCCTTCATCAGTATTTTC+AGG - chr4_3:71710226-71710245 None:intergenic 35.0%
GAAGCAAAGAATTCAGTTTC+TGG + chr4_3:71710242-71710261 Msa0660730:CDS 35.0%
GAAGATGTTGTGATGGTATT+TGG - chr4_3:71710274-71710293 None:intergenic 35.0%
!! GTATTTTCAGGAGTGTGTGT+TGG - chr4_3:71710214-71710233 None:intergenic 40.0%
AGAGAGTTCATAGCTTGACT+CGG - chr4_3:71710449-71710468 None:intergenic 40.0%
TGAACTCTCTTTCCAAGACA+TGG + chr4_3:71710459-71710478 Msa0660730:CDS 40.0%
TAAAGTACAAAATGGCTCCG+AGG + chr4_3:71710711-71710730 Msa0660730:CDS 40.0%
GCAACAGCAATGATAAAAGC+AGG + chr4_3:71710818-71710837 Msa0660730:CDS 40.0%
GAGAGTTCATAGCTTGACTC+GGG - chr4_3:71710448-71710467 None:intergenic 45.0%
!! TCTGTTTCTGGTTCTGGTTG+TGG - chr4_3:71710505-71710524 None:intergenic 45.0%
!! ACTCGTTCTGTTTCTGGTTC+TGG - chr4_3:71710511-71710530 None:intergenic 45.0%
CTACACACTCGTTCTGTTTC+TGG - chr4_3:71710517-71710536 None:intergenic 45.0%
! TTCAGGAGTGTGTGTTGGGA+AGG - chr4_3:71710209-71710228 None:intergenic 50.0%
GCTGCTCAACAACCATGTCT+TGG - chr4_3:71710474-71710493 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 71710193 71710849 71710193 ID=Msa0660730;Name=Msa0660730
chr4_3 mRNA 71710193 71710849 71710193 ID=Msa0660730-mRNA-1;Parent=Msa0660730;Name=Msa0660730-mRNA-1;_AED=0.43;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|218
chr4_3 exon 71710193 71710849 71710193 ID=Msa0660730-mRNA-1:exon:21484;Parent=Msa0660730-mRNA-1
chr4_3 CDS 71710193 71710849 71710193 ID=Msa0660730-mRNA-1:cds;Parent=Msa0660730-mRNA-1
Gene Sequence

>Msa0660730

ATGAGCTACTCAACCTTCCCAACACACACTCCTGAAAATACTGATGAAGGAAGCAAAGAATTCAGTTTCTGGACTTCACCAAATACCATCACAACATCTTCTGAAAAATGTGATTGTCATAATATTCAACTTGGAAGCAATGAAACACAAGAGCTCAATAACCATCATCGATGTTCAATAGTTTCAGAACCTTCAAGAAGCAAAGATATTTTAGAAGGAAAGAAAGAACTTATGGAAATGATGCGAGACATGCCCGAGTCAAGCTATGAACTCTCTTTCCAAGACATGGTTGTTGAGCAGCTTCAAGTTCCACAACCAGAACCAGAAACAGAACGAGTGTGTAGTAAAGTTCAACAACCACAACACAAAAAGCTGAATAAGAATAAGAAGAAGAAGAATAAGAAGGAAAACAAAAGCAATAGACATGGTAAAATGTTAAGAGTTGAAAGCATGGACAGTGAAACCTTCCTATTGAAGATGTTCTTTCCAATTTCTCTTGATTGGATGAAGAAGACTACTAAAGTACAAAATGGCTCCGAGGTAGAACAAAAAGATAAAGAATGGAGAATCAAAAGATTTTTCACTGAAGATAGACAAAATACTAGTAGTAGTAGCACTAGCAGCAGCAACAGCAATGATAAAAGCAGGTACATATGA
Protein sequence

>Msa0660730

MSYSTFPTHTPENTDEGSKEFSFWTSPNTITTSSEKCDCHNIQLGSNETQELNNHHRCSIVSEPSRSKDILEGKKELMEMMRDMPESSYELSFQDMVVEQLQVPQPEPETERVCSKVQQPQHKKLNKNKKKKNKKENKSNRHGKMLRVESMDSETFLLKMFFPISLDWMKKTTKVQNGSEVEQKDKEWRIKRFFTEDRQNTSSSSTSSSNSNDKSRYI*