AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0216210


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0216210 MtrunA17_Chr2g0317741 90.411 73 7 0 1 73 1 73 2.01e-38 122
Msa0216210 MtrunA17_Chr2g0317751 66.216 74 22 2 1 73 1 72 1.72e-30 102
Msa0216210 MtrunA17_Chr8g0385311 36.000 75 45 2 1 73 1 74 8.37e-12 54.7
Msa0216210 MtrunA17_Chr8g0337781 36.986 73 42 2 1 70 1 72 3.69e-11 53.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTATATTCATCACTAAGTA+TGG 0.332590 2_1:+61937389 Msa0216210:exon
ATATGATAAAAGTGCATAAC+TGG 0.354165 2_1:-61938772 None:intergenic
AGCAAGGACTTGTGAGCATT+TGG 0.402994 2_1:+61938428 Msa0216210:CDS
AACAAAGCACACTTAATTAG+TGG 0.431618 2_1:+61938507 Msa0216210:CDS
GAACGAGGAAGAGGAAGCAC+AGG 0.435069 2_1:-61937431 None:intergenic
TGCAGAAACATTGAAAGTTA+TGG 0.454489 2_1:-61938536 None:intergenic
CTTGCAAGTTGCATGCATCT+TGG 0.455133 2_1:-61938604 None:intergenic
CGACAAAGAGAACGAGGAAG+AGG 0.484363 2_1:-61937440 None:intergenic
TTAAGTGTTTGTGTCTAATG+TGG 0.522872 2_1:-61937338 None:intergenic
CATTTGGCTGATACATATAG+AGG 0.536909 2_1:+61938444 Msa0216210:CDS
AGTTGCATGCATCTTGGTGT+TGG 0.540849 2_1:-61938598 None:intergenic
ATGGAGAAGAGATCAGTAGC+TGG 0.575142 2_1:+61937408 Msa0216210:CDS
ACGATATTGATGAGTACCTA+TGG 0.577282 2_1:-61938739 None:intergenic
CATCTATGAATTATGTCCAT+AGG 0.585201 2_1:+61938723 Msa0216210:three_prime_UTR
GCACTCAAAACTGTTAAGTG+TGG 0.610534 2_1:+61938556 Msa0216210:exon
AGACACATATATAGCCCCAA+TGG 0.623961 2_1:-61937294 None:intergenic
CAGCTAGCATCTGTGAAGCA+TGG 0.627719 2_1:-61938468 None:intergenic
CATGGATGCAGAAGAAATTG+TGG 0.636627 2_1:+61938398 Msa0216210:intron
AAATTGTGGTGATTGAAGCA+AGG 0.641556 2_1:+61938412 Msa0216210:CDS
AAACTGTTAAGTGTGGAATG+TGG 0.677412 2_1:+61938563 Msa0216210:exon
TACGTGCGACAAAGAGAACG+AGG 0.732491 2_1:-61937446 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATTCTAATATTGTTTAA+TGG + chr2_1:61938373-61938392 Msa0216210:intron 10.0%
!! TATATTCTAATATTGTTTAA+TGG + chr2_1:61938373-61938392 Msa0216210:intron 10.0%
!!! TCTTTCTCTAATTTAATTTT+TGG + chr2_1:61937675-61937694 Msa0216210:intron 15.0%
!! CTTAATTAACAATATACTAA+AGG - chr2_1:61937792-61937811 None:intergenic 15.0%
!!! AATTAAGTTTTTTTTATAGC+AGG + chr2_1:61937805-61937824 Msa0216210:intron 15.0%
!! TATATAAATATTACTTTGTC+AGG - chr2_1:61938027-61938046 None:intergenic 15.0%
!!! TCTTTCTCTAATTTAATTTT+TGG + chr2_1:61937675-61937694 Msa0216210:intron 15.0%
!! CTTAATTAACAATATACTAA+AGG - chr2_1:61937792-61937811 None:intergenic 15.0%
!!! AATTAAGTTTTTTTTATAGC+AGG + chr2_1:61937805-61937824 Msa0216210:intron 15.0%
!! TATATAAATATTACTTTGTC+AGG - chr2_1:61938027-61938046 None:intergenic 15.0%
!! ATTATATTCATCACTAAGTA+TGG + chr2_1:61937389-61937408 Msa0216210:exon 20.0%
!! AAAGTATATCTTAAATTTCG+TGG + chr2_1:61937578-61937597 Msa0216210:intron 20.0%
!! AGCAACAATAATAATTAGAT+GGG - chr2_1:61937728-61937747 None:intergenic 20.0%
!! ATTAACAATATACTAAAGGA+AGG - chr2_1:61937788-61937807 None:intergenic 20.0%
!! AAATAAAAAATCGACACATT+TGG - chr2_1:61937991-61938010 None:intergenic 20.0%
!!! TGTCGATTTTTTATTTGTAA+AGG + chr2_1:61937995-61938014 Msa0216210:intron 20.0%
!!! ATTTTTTATTTGTAAAGGTC+AGG + chr2_1:61938000-61938019 Msa0216210:intron 20.0%
!!! ACTAAGCAATTAAGTTTTAA+TGG - chr2_1:61938244-61938263 None:intergenic 20.0%
!! TAATATTGTTTAATGGTACA+TGG + chr2_1:61938380-61938399 Msa0216210:intron 20.0%
!! ATTATATTCATCACTAAGTA+TGG + chr2_1:61937389-61937408 Msa0216210:exon 20.0%
!! AAAGTATATCTTAAATTTCG+TGG + chr2_1:61937578-61937597 Msa0216210:intron 20.0%
!! AGCAACAATAATAATTAGAT+GGG - chr2_1:61937728-61937747 None:intergenic 20.0%
!! ATTAACAATATACTAAAGGA+AGG - chr2_1:61937788-61937807 None:intergenic 20.0%
!! AAATAAAAAATCGACACATT+TGG - chr2_1:61937991-61938010 None:intergenic 20.0%
!!! TGTCGATTTTTTATTTGTAA+AGG + chr2_1:61937995-61938014 Msa0216210:intron 20.0%
!!! ATTTTTTATTTGTAAAGGTC+AGG + chr2_1:61938000-61938019 Msa0216210:intron 20.0%
!!! ACTAAGCAATTAAGTTTTAA+TGG - chr2_1:61938244-61938263 None:intergenic 20.0%
!! TAATATTGTTTAATGGTACA+TGG + chr2_1:61938380-61938399 Msa0216210:intron 20.0%
! CAGCAACAATAATAATTAGA+TGG - chr2_1:61937729-61937748 None:intergenic 25.0%
!!! TAAGTTTTTTTTATAGCAGG+AGG + chr2_1:61937808-61937827 Msa0216210:intron 25.0%
! GAAAAATTCGATTTACTAAG+TGG - chr2_1:61938188-61938207 None:intergenic 25.0%
!! ATATGATAAAAGTGCATAAC+TGG - chr2_1:61938775-61938794 None:intergenic 25.0%
! CAGCAACAATAATAATTAGA+TGG - chr2_1:61937729-61937748 None:intergenic 25.0%
!!! TAAGTTTTTTTTATAGCAGG+AGG + chr2_1:61937808-61937827 Msa0216210:intron 25.0%
! GAAAAATTCGATTTACTAAG+TGG - chr2_1:61938188-61938207 None:intergenic 25.0%
!! ATATGATAAAAGTGCATAAC+TGG - chr2_1:61938775-61938794 None:intergenic 25.0%
TTAAGTGTTTGTGTCTAATG+TGG - chr2_1:61937341-61937360 None:intergenic 30.0%
AGACATCATGTCTAAAAGAA+AGG + chr2_1:61937613-61937632 Msa0216210:intron 30.0%
AAAAGACAAATTGAACCGTT+TGG + chr2_1:61937884-61937903 Msa0216210:intron 30.0%
! CACATCTATTTCTTAGTGTA+TGG + chr2_1:61938109-61938128 Msa0216210:intron 30.0%
AACAAAGCACACTTAATTAG+TGG + chr2_1:61938507-61938526 Msa0216210:CDS 30.0%
TGCAGAAACATTGAAAGTTA+TGG - chr2_1:61938539-61938558 None:intergenic 30.0%
CATCTATGAATTATGTCCAT+AGG + chr2_1:61938723-61938742 Msa0216210:three_prime_UTR 30.0%
TTAAGTGTTTGTGTCTAATG+TGG - chr2_1:61937341-61937360 None:intergenic 30.0%
AGACATCATGTCTAAAAGAA+AGG + chr2_1:61937613-61937632 Msa0216210:intron 30.0%
AAAAGACAAATTGAACCGTT+TGG + chr2_1:61937884-61937903 Msa0216210:intron 30.0%
! CACATCTATTTCTTAGTGTA+TGG + chr2_1:61938109-61938128 Msa0216210:intron 30.0%
AACAAAGCACACTTAATTAG+TGG + chr2_1:61938507-61938526 Msa0216210:CDS 30.0%
TGCAGAAACATTGAAAGTTA+TGG - chr2_1:61938539-61938558 None:intergenic 30.0%
CATCTATGAATTATGTCCAT+AGG + chr2_1:61938723-61938742 Msa0216210:three_prime_UTR 30.0%
CATCAATACGTAGAAATGTG+TGG + chr2_1:61937958-61937977 Msa0216210:intron 35.0%
AAATTGTGGTGATTGAAGCA+AGG + chr2_1:61938412-61938431 Msa0216210:CDS 35.0%
CATTTGGCTGATACATATAG+AGG + chr2_1:61938444-61938463 Msa0216210:CDS 35.0%
AAACTGTTAAGTGTGGAATG+TGG + chr2_1:61938563-61938582 Msa0216210:exon 35.0%
ACGATATTGATGAGTACCTA+TGG - chr2_1:61938742-61938761 None:intergenic 35.0%
CATCAATACGTAGAAATGTG+TGG + chr2_1:61937958-61937977 Msa0216210:intron 35.0%
AAATTGTGGTGATTGAAGCA+AGG + chr2_1:61938412-61938431 Msa0216210:CDS 35.0%
CATTTGGCTGATACATATAG+AGG + chr2_1:61938444-61938463 Msa0216210:CDS 35.0%
AAACTGTTAAGTGTGGAATG+TGG + chr2_1:61938563-61938582 Msa0216210:exon 35.0%
ACGATATTGATGAGTACCTA+TGG - chr2_1:61938742-61938761 None:intergenic 35.0%
GACAAATTGAACCGTTTGGA+CGG + chr2_1:61937888-61937907 Msa0216210:intron 40.0%
! TTGTCTGAAATCCGTCCAAA+CGG - chr2_1:61937902-61937921 None:intergenic 40.0%
CATGGATGCAGAAGAAATTG+TGG + chr2_1:61938398-61938417 Msa0216210:intron 40.0%
GCACTCAAAACTGTTAAGTG+TGG + chr2_1:61938556-61938575 Msa0216210:exon 40.0%
GACAAATTGAACCGTTTGGA+CGG + chr2_1:61937888-61937907 Msa0216210:intron 40.0%
! TTGTCTGAAATCCGTCCAAA+CGG - chr2_1:61937902-61937921 None:intergenic 40.0%
CATGGATGCAGAAGAAATTG+TGG + chr2_1:61938398-61938417 Msa0216210:intron 40.0%
GCACTCAAAACTGTTAAGTG+TGG + chr2_1:61938556-61938575 Msa0216210:exon 40.0%
ATGGAGAAGAGATCAGTAGC+TGG + chr2_1:61937408-61937427 Msa0216210:CDS 45.0%
AGCAAGGACTTGTGAGCATT+TGG + chr2_1:61938428-61938447 Msa0216210:CDS 45.0%
! AGTTGCATGCATCTTGGTGT+TGG - chr2_1:61938601-61938620 None:intergenic 45.0%
CTTGCAAGTTGCATGCATCT+TGG - chr2_1:61938607-61938626 None:intergenic 45.0%
ATGGAGAAGAGATCAGTAGC+TGG + chr2_1:61937408-61937427 Msa0216210:CDS 45.0%
AGCAAGGACTTGTGAGCATT+TGG + chr2_1:61938428-61938447 Msa0216210:CDS 45.0%
! AGTTGCATGCATCTTGGTGT+TGG - chr2_1:61938601-61938620 None:intergenic 45.0%
CTTGCAAGTTGCATGCATCT+TGG - chr2_1:61938607-61938626 None:intergenic 45.0%
!! GTTAATTTATAAAAAAAAAA+AGG - chr2_1:61937541-61937560 None:intergenic 5.0%
!!! GAATATATTTTTTTTAAATA+GGG - chr2_1:61938360-61938379 None:intergenic 5.0%
!!! AGAATATATTTTTTTTAAAT+AGG - chr2_1:61938361-61938380 None:intergenic 5.0%
!! GTTAATTTATAAAAAAAAAA+AGG - chr2_1:61937541-61937560 None:intergenic 5.0%
!!! GAATATATTTTTTTTAAATA+GGG - chr2_1:61938360-61938379 None:intergenic 5.0%
!!! AGAATATATTTTTTTTAAAT+AGG - chr2_1:61938361-61938380 None:intergenic 5.0%
CGACAAAGAGAACGAGGAAG+AGG - chr2_1:61937443-61937462 None:intergenic 50.0%
TACGTGCGACAAAGAGAACG+AGG - chr2_1:61937449-61937468 None:intergenic 50.0%
CAGCTAGCATCTGTGAAGCA+TGG - chr2_1:61938471-61938490 None:intergenic 50.0%
CGACAAAGAGAACGAGGAAG+AGG - chr2_1:61937443-61937462 None:intergenic 50.0%
TACGTGCGACAAAGAGAACG+AGG - chr2_1:61937449-61937468 None:intergenic 50.0%
CAGCTAGCATCTGTGAAGCA+TGG - chr2_1:61938471-61938490 None:intergenic 50.0%
! GAACGAGGAAGAGGAAGCAC+AGG - chr2_1:61937434-61937453 None:intergenic 55.0%
! GAACGAGGAAGAGGAAGCAC+AGG - chr2_1:61937434-61937453 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 61937297 61938833 61937297 ID=Msa0216210;Name=Msa0216210
chr2_1 mRNA 61937297 61938833 61937297 ID=Msa0216210-mRNA-1;Parent=Msa0216210;Name=Msa0216210-mRNA-1;_AED=0.37;_eAED=0.37;_QI=111|1|1|1|0|0|2|261|73
chr2_1 exon 61937297 61937465 61937297 ID=Msa0216210-mRNA-1:exon:17108;Parent=Msa0216210-mRNA-1
chr2_1 exon 61938409 61938833 61938409 ID=Msa0216210-mRNA-1:exon:17109;Parent=Msa0216210-mRNA-1
chr2_1 five_prime_UTR 61937297 61937407 61937297 ID=Msa0216210-mRNA-1:five_prime_utr;Parent=Msa0216210-mRNA-1
chr2_1 CDS 61937408 61937465 61937408 ID=Msa0216210-mRNA-1:cds;Parent=Msa0216210-mRNA-1
chr2_1 CDS 61938409 61938572 61938409 ID=Msa0216210-mRNA-1:cds;Parent=Msa0216210-mRNA-1
chr2_1 three_prime_UTR 61938573 61938833 61938573 ID=Msa0216210-mRNA-1:three_prime_utr;Parent=Msa0216210-mRNA-1
Gene Sequence

>Msa0216210

ATGGAGAAGAGATCAGTAGCTGGCCTGTGCTTCCTCTTCCTCGTTCTCTTTGTCGCACAAGAAATTGTGGTGATTGAAGCAAGGACTTGTGAGCATTTGGCTGATACATATAGAGGACCATGCTTCACAGATGCTAGCTGTGACGATCACTGCAAGAACAAAGCACACTTAATTAGTGGCACTTGCCATAACTTTCAATGTTTCTGCACTCAAAACTGTTAA

Protein sequence

>Msa0216210

MEKRSVAGLCFLFLVLFVAQEIVVIEARTCEHLADTYRGPCFTDASCDDHCKNKAHLISGTCHNFQCFCTQNC*