AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0555950

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0555950 MtrunA17_Chr4g0043191 96.629 89 3 0 1 89 1 89 9.42e-58 172
Msa0555950 MtrunA17_Chr4g0043181 80.899 89 13 1 1 89 1 85 5.05e-40 127
Msa0555950 MtrunA17_Chr8g0376661 79.545 88 18 0 1 88 1 88 1.65e-36 118
Msa0555950 MtrunA17_Chr5g0434291 77.528 89 20 0 1 89 1 89 2.91e-36 117
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0555950 AT1G30260.1 60.417 48 18 1 1 48 1 47 3.72e-15 65.1

Find 12 sgRNAs with CRISPR-Local

Find 18 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATGCAGTTGTTAATTCT+AGG 0.257861 4_1:+53961665 Msa0555950:CDS
AACAATCACTGAAGAGGATA+TGG 0.331678 4_1:+53961558 Msa0555950:CDS
GTGTTCTATGAACTTCCTTC+AGG 0.381163 4_1:-53961693 None:intergenic
GCGTAGAACATCAAAGATGA+TGG 0.510830 4_1:+53961534 Msa0555950:CDS
CCTAGAATTAACAACTGCAT+TGG 0.551602 4_1:-53961665 None:intergenic
AACAACTGCATTGGTAGAAG+AGG 0.557920 4_1:-53961656 None:intergenic
TGGCGAATTCTCGCATTGCA+AGG 0.566271 4_1:+53961467 Msa0555950:CDS
CACAGTATGTTAGCGTGATG+AGG 0.569645 4_1:+53961512 Msa0555950:CDS
TAATTCTAGGTACTTCCTGA+AGG 0.589595 4_1:+53961678 Msa0555950:CDS
GATGGAAACAATCACTGAAG+AGG 0.591147 4_1:+53961552 Msa0555950:CDS
CTCATCACGCTAACATACTG+TGG 0.654266 4_1:-53961511 None:intergenic
ATCACGCTAACATACTGTGG+TGG 0.690677 4_1:-53961508 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATGAAGTTGATGAACTTTT+AGG - chr4_1:53961616-53961635 None:intergenic 30.0%
AACAATCACTGAAGAGGATA+TGG + chr4_1:53961558-53961577 Msa0555950:CDS 35.0%
!!! GAAGTTGATGAACTTTTAGG+TGG - chr4_1:53961613-53961632 None:intergenic 35.0%
CCTAGAATTAACAACTGCAT+TGG - chr4_1:53961668-53961687 None:intergenic 35.0%
CCAATGCAGTTGTTAATTCT+AGG + chr4_1:53961665-53961684 Msa0555950:CDS 35.0%
TAATTCTAGGTACTTCCTGA+AGG + chr4_1:53961678-53961697 Msa0555950:CDS 35.0%
! TCGCATTGCAAGGTTTTTCA+TGG + chr4_1:53961477-53961496 Msa0555950:CDS 40.0%
! CATTGCAAGGTTTTTCATGG+AGG + chr4_1:53961480-53961499 Msa0555950:CDS 40.0%
GCGTAGAACATCAAAGATGA+TGG + chr4_1:53961534-53961553 Msa0555950:CDS 40.0%
GATGGAAACAATCACTGAAG+AGG + chr4_1:53961552-53961571 Msa0555950:CDS 40.0%
!! GTTGATGAACTTTTAGGTGG+TGG - chr4_1:53961610-53961629 None:intergenic 40.0%
! AACAACTGCATTGGTAGAAG+AGG - chr4_1:53961659-53961678 None:intergenic 40.0%
GTGTTCTATGAACTTCCTTC+AGG - chr4_1:53961696-53961715 None:intergenic 40.0%
! TGCAAGGTTTTTCATGGAGG+TGG + chr4_1:53961483-53961502 Msa0555950:CDS 45.0%
ATCACGCTAACATACTGTGG+TGG - chr4_1:53961511-53961530 None:intergenic 45.0%
CTCATCACGCTAACATACTG+TGG - chr4_1:53961514-53961533 None:intergenic 45.0%
CACAGTATGTTAGCGTGATG+AGG + chr4_1:53961512-53961531 Msa0555950:CDS 45.0%
TGGCGAATTCTCGCATTGCA+AGG + chr4_1:53961467-53961486 Msa0555950:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 53961466 53961735 53961466 ID=Msa0555950;Name=Msa0555950
chr4_1 mRNA 53961466 53961735 53961466 ID=Msa0555950-mRNA-1;Parent=Msa0555950;Name=Msa0555950-mRNA-1;_AED=0.27;_eAED=0.27;_QI=0|-1|0|1|-1|1|1|0|89
chr4_1 exon 53961466 53961735 53961466 ID=Msa0555950-mRNA-1:exon:15776;Parent=Msa0555950-mRNA-1
chr4_1 CDS 53961466 53961735 53961466 ID=Msa0555950-mRNA-1:cds;Parent=Msa0555950-mRNA-1
Gene Sequence

>Msa0555950

ATGGCGAATTCTCGCATTGCAAGGTTTTTCATGGAGGTGGCACCACCACAGTATGTTAGCGTGATGAGGCGTAGAACATCAAAGATGATGGAAACAATCACTGAAGAGGATATGGAAATGAGTTCAAATGATAGTGTAATTCCACCACCTAAAAGTTCATCAACTTCATCACTTGCTGCTTCTGCATGTGCCTCTTCTACCAATGCAGTTGTTAATTCTAGGTACTTCCTGAAGGAAGTTCATAGAACACTCTCAAGTTTGAATCACTGA
Protein sequence

>Msa0555950

MANSRIARFFMEVAPPQYVSVMRRRTSKMMETITEEDMEMSSNDSVIPPPKSSSTSSLAASACASSTNAVVNSRYFLKEVHRTLSSLNH*