AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0650900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0650900 MtrunA17_Chr4g0043191 96.629 89 3 0 1 89 1 89 9.42e-58 172
Msa0650900 MtrunA17_Chr4g0043181 80.899 89 13 1 1 89 1 85 5.05e-40 127
Msa0650900 MtrunA17_Chr8g0376661 79.545 88 18 0 1 88 1 88 1.65e-36 118
Msa0650900 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
Msa0650900 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_3:-58177465 Msa0650900:CDS
AACAATCACTGAAGAGGATA+TGG 0.331678 4_3:-58177572 Msa0650900:CDS
GTGTTCTATGAACTTCCTTC+AGG 0.381163 4_3:+58177437 None:intergenic
GCGTAGAACATCAAAGATGA+TGG 0.510830 4_3:-58177596 Msa0650900:CDS
CCTAGAATTAACAACTGCAT+TGG 0.551602 4_3:+58177465 None:intergenic
AACAACTGCATTGGTAGAAG+AGG 0.557920 4_3:+58177474 None:intergenic
TGGCGAATTCTCGCATTGCA+AGG 0.566271 4_3:-58177663 Msa0650900:CDS
CACAGTATGTTAGCGTGATG+AGG 0.569645 4_3:-58177618 Msa0650900:CDS
TAATTCTAGGTACTTCCTGA+AGG 0.589595 4_3:-58177452 Msa0650900:CDS
GATGGAAACAATCACTGAAG+AGG 0.591147 4_3:-58177578 Msa0650900:CDS
CTCATCACGCTAACATACTG+TGG 0.654266 4_3:+58177619 None:intergenic
ATCACGCTAACATACTGTGG+TGG 0.690677 4_3:+58177622 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATGAAGTTGATGAACTTTT+AGG + chr4_3:58177567-58177586 None:intergenic 30.0%
AACAATCACTGAAGAGGATA+TGG - chr4_3:58177509-58177528 Msa0650900:CDS 35.0%
!!! GAAGTTGATGAACTTTTAGG+TGG + chr4_3:58177564-58177583 None:intergenic 35.0%
CCTAGAATTAACAACTGCAT+TGG + chr4_3:58177619-58177638 None:intergenic 35.0%
CCAATGCAGTTGTTAATTCT+AGG - chr4_3:58177616-58177635 Msa0650900:CDS 35.0%
TAATTCTAGGTACTTCCTGA+AGG - chr4_3:58177629-58177648 Msa0650900:CDS 35.0%
! TCGCATTGCAAGGTTTTTCA+TGG - chr4_3:58177428-58177447 Msa0650900:CDS 40.0%
! CATTGCAAGGTTTTTCATGG+AGG - chr4_3:58177431-58177450 Msa0650900:CDS 40.0%
GCGTAGAACATCAAAGATGA+TGG - chr4_3:58177485-58177504 Msa0650900:CDS 40.0%
GATGGAAACAATCACTGAAG+AGG - chr4_3:58177503-58177522 Msa0650900:CDS 40.0%
!! GTTGATGAACTTTTAGGTGG+TGG + chr4_3:58177561-58177580 None:intergenic 40.0%
! AACAACTGCATTGGTAGAAG+AGG + chr4_3:58177610-58177629 None:intergenic 40.0%
GTGTTCTATGAACTTCCTTC+AGG + chr4_3:58177647-58177666 None:intergenic 40.0%
! TGCAAGGTTTTTCATGGAGG+TGG - chr4_3:58177434-58177453 Msa0650900:CDS 45.0%
ATCACGCTAACATACTGTGG+TGG + chr4_3:58177462-58177481 None:intergenic 45.0%
CTCATCACGCTAACATACTG+TGG + chr4_3:58177465-58177484 None:intergenic 45.0%
CACAGTATGTTAGCGTGATG+AGG - chr4_3:58177463-58177482 Msa0650900:CDS 45.0%
TGGCGAATTCTCGCATTGCA+AGG - chr4_3:58177418-58177437 Msa0650900:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 58177417 58177686 58177417 ID=Msa0650900;Name=Msa0650900
chr4_3 mRNA 58177417 58177686 58177417 ID=Msa0650900-mRNA-1;Parent=Msa0650900;Name=Msa0650900-mRNA-1;_AED=0.27;_eAED=0.27;_QI=0|-1|0|1|-1|1|1|0|89
chr4_3 exon 58177417 58177686 58177417 ID=Msa0650900-mRNA-1:exon:15342;Parent=Msa0650900-mRNA-1
chr4_3 CDS 58177417 58177686 58177417 ID=Msa0650900-mRNA-1:cds;Parent=Msa0650900-mRNA-1
Gene Sequence

>Msa0650900

ATGGCGAATTCTCGCATTGCAAGGTTTTTCATGGAGGTGGCACCACCACAGTATGTTAGCGTGATGAGGCGTAGAACATCAAAGATGATGGAAACAATCACTGAAGAGGATATGGAAATGAGTTCAAATGATAGTGTAATTCCACCACCTAAAAGTTCATCAACTTCATCACTTGCTGCTTCTGCATGTGCCTCTTCTACCAATGCAGTTGTTAATTCTAGGTACTTCCTGAAGGAAGTTCATAGAACACTCTCAAGTTTGAATCACTGA
Protein sequence

>Msa0650900

MANSRIARFFMEVAPPQYVSVMRRRTSKMMETITEEDMEMSSNDSVIPPPKSSSTSSLAASACASSTNAVVNSRYFLKEVHRTLSSLNH*