AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0013730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0013730 MtrunA17_Chr1g0163201 76.404 89 21 0 2 90 313 401 9.79e-43 143
Msa0013730 MtrunA17_Chr1g0163181 75.904 83 20 0 6 88 354 436 1.87e-38 132
Msa0013730 MtrunA17_Chr1g0163111 73.077 78 21 0 6 83 153 230 1.10e-37 125
Msa0013730 MtrunA17_Chr1g0163151 74.026 77 20 0 6 82 146 222 2.96e-36 122
Msa0013730 MtrunA17_Chr1g0163131 53.165 79 33 2 7 83 232 308 6.21e-19 79.0
Msa0013730 MtrunA17_Chr6g0476171 47.619 63 33 0 19 81 183 245 1.73e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGTTCTATTGTTCTTTA+AGG 0.164818 1_1:-21186148 None:intergenic
AAACTCTCTGGAGTTGAAAA+TGG 0.208119 1_1:-21186356 Msa0013730:CDS
ACGATAGTATTCATGGTTAT+AGG 0.290213 1_1:-21186300 Msa0013730:CDS
AATTATTACGATAGTATTCA+TGG 0.354510 1_1:-21186307 Msa0013730:CDS
GTGTTTGATGTTTCAATTGT+TGG 0.364550 1_1:-21186187 Msa0013730:CDS
AACTCTCTGGAGTTGAAAAT+GGG 0.410653 1_1:-21186355 Msa0013730:CDS
AAAGAATTCAAAGTGGAGAT+TGG 0.425579 1_1:-21186250 Msa0013730:CDS
CCAAAGGAGTTTATGAAAAG+AGG 0.438669 1_1:-21186388 Msa0013730:CDS
AGGAAGTCATGAAAACTCTC+TGG 0.451275 1_1:-21186368 Msa0013730:CDS
GTTATAGGTTCTCTGAAGGT+TGG 0.464034 1_1:-21186285 Msa0013730:CDS
AACAATAGAACAAACAGCTA+AGG 0.501698 1_1:+21186156 None:intergenic
ACAATAGAACAAACAGCTAA+GGG 0.530051 1_1:+21186157 None:intergenic
CATGGTTATAGGTTCTCTGA+AGG 0.540492 1_1:-21186289 Msa0013730:CDS
TGTGTTTCTCCAGATTCAGA+AGG 0.578280 1_1:-21186568 Msa0013730:intron
ATATTTGCAGAATGTTCCAA+AGG 0.598638 1_1:-21186404 Msa0013730:intron
CTCTCTGGAGTTGAAAATGG+GGG 0.599653 1_1:-21186353 Msa0013730:CDS
ATTCATAAAAGAATTCAAAG+TGG 0.616700 1_1:-21186257 Msa0013730:CDS
ACTCTCTGGAGTTGAAAATG+GGG 0.658989 1_1:-21186354 Msa0013730:CDS
CAATAGAACAAACAGCTAAG+GGG 0.667474 1_1:+21186158 None:intergenic
TCTCTGGAGTTGAAAATGGG+GGG 0.680996 1_1:-21186352 Msa0013730:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAATTTTTTAAGTTCTA+AGG - chr1_1:21186197-21186216 Msa0013730:CDS 10.0%
!! CTTAAAAAATTAAAATGATG+TGG + chr1_1:21186192-21186211 None:intergenic 15.0%
!!! TTTTATGTAATTAATCGTTC+CGG + chr1_1:21186365-21186384 None:intergenic 20.0%
!! AATTATTACGATAGTATTCA+TGG - chr1_1:21186548-21186567 Msa0013730:intron 20.0%
!! ATTCATAAAAGAATTCAAAG+TGG - chr1_1:21186598-21186617 Msa0013730:intron 20.0%
!! ACATCAATCTTGAATGTTTT+AGG + chr1_1:21186329-21186348 None:intergenic 25.0%
! TTTATGTAATTAATCGTTCC+GGG + chr1_1:21186364-21186383 None:intergenic 25.0%
TGCAACATTCTTTGACATAA+GGG + chr1_1:21186165-21186184 None:intergenic 30.0%
TGATGTGTATTCAAAATACC+CGG - chr1_1:21186343-21186362 Msa0013730:CDS 30.0%
ATATTTGCAGAATGTTCCAA+AGG - chr1_1:21186451-21186470 Msa0013730:intron 30.0%
ACGATAGTATTCATGGTTAT+AGG - chr1_1:21186555-21186574 Msa0013730:intron 30.0%
AAAGAATTCAAAGTGGAGAT+TGG - chr1_1:21186605-21186624 Msa0013730:intron 30.0%
GTGTTTGATGTTTCAATTGT+TGG - chr1_1:21186668-21186687 Msa0013730:intron 30.0%
ACAATAGAACAAACAGCTAA+GGG + chr1_1:21186701-21186720 None:intergenic 30.0%
AACAATAGAACAAACAGCTA+AGG + chr1_1:21186702-21186721 None:intergenic 30.0%
CTGCAACATTCTTTGACATA+AGG + chr1_1:21186166-21186185 None:intergenic 35.0%
ACATTATCACCTTCTGAATC+TGG + chr1_1:21186299-21186318 None:intergenic 35.0%
! CCTCTTTTCATAAACTCCTT+TGG + chr1_1:21186470-21186489 None:intergenic 35.0%
CCAAAGGAGTTTATGAAAAG+AGG - chr1_1:21186467-21186486 Msa0013730:intron 35.0%
!! AAACTCTCTGGAGTTGAAAA+TGG - chr1_1:21186499-21186518 Msa0013730:intron 35.0%
!! AACTCTCTGGAGTTGAAAAT+GGG - chr1_1:21186500-21186519 Msa0013730:intron 35.0%
CAATAGAACAAACAGCTAAG+GGG + chr1_1:21186700-21186719 None:intergenic 35.0%
TGTGTTTCTCCAGATTCAGA+AGG - chr1_1:21186287-21186306 Msa0013730:CDS 40.0%
AGGAAGTCATGAAAACTCTC+TGG - chr1_1:21186487-21186506 Msa0013730:intron 40.0%
!! ACTCTCTGGAGTTGAAAATG+GGG - chr1_1:21186501-21186520 Msa0013730:intron 40.0%
CATGGTTATAGGTTCTCTGA+AGG - chr1_1:21186566-21186585 Msa0013730:intron 40.0%
! GTTATAGGTTCTCTGAAGGT+TGG - chr1_1:21186570-21186589 Msa0013730:intron 40.0%
!! CTCTCTGGAGTTGAAAATGG+GGG - chr1_1:21186502-21186521 Msa0013730:intron 45.0%
!! TCTCTGGAGTTGAAAATGGG+GGG - chr1_1:21186503-21186522 Msa0013730:intron 45.0%
TGAAAATGGGGGGACGATCA+TGG - chr1_1:21186513-21186532 Msa0013730:intron 50.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 21186150 21186727 21186150 ID=Msa0013730;Name=Msa0013730
chr1_1 mRNA 21186150 21186727 21186150 ID=Msa0013730-mRNA-1;Parent=Msa0013730;Name=Msa0013730-mRNA-1;_AED=0.47;_eAED=0.49;_QI=0|0|0|0.66|0|0.33|3|0|93
chr1_1 exon 21186722 21186727 21186722 ID=Msa0013730-mRNA-1:exon:7597;Parent=Msa0013730-mRNA-1
chr1_1 exon 21186569 21186577 21186569 ID=Msa0013730-mRNA-1:exon:7596;Parent=Msa0013730-mRNA-1
chr1_1 exon 21186150 21186416 21186150 ID=Msa0013730-mRNA-1:exon:7595;Parent=Msa0013730-mRNA-1
chr1_1 CDS 21186722 21186727 21186722 ID=Msa0013730-mRNA-1:cds;Parent=Msa0013730-mRNA-1
chr1_1 CDS 21186569 21186577 21186569 ID=Msa0013730-mRNA-1:cds;Parent=Msa0013730-mRNA-1
chr1_1 CDS 21186150 21186416 21186150 ID=Msa0013730-mRNA-1:cds;Parent=Msa0013730-mRNA-1
Gene Sequence

>Msa0013730

ATGCACATTCAGAAGAATGTTCCAAAGGAGTTTATGAAAAGAGGAAGTCATGAAAACTCTCTGGAGTTGAAAATGGGGGGACGATCATGGTTTGTAAAAGTGAATTATTACGATAGTATTCATGGTTATAGGTTCTCTGAAGGTTGGAGACAATTCATAAAAGAATTCAAAGTGGAGATTGGAGATACTCTTCTCTTCAAGTTGATTGATGAGAGCAAGTTTGTGTTTGATGTTTCAATTGTTGGAAAGAACCCCTTAGCTGTTTGTTCTATTGTTCTTTAA
Protein sequence

>Msa0013730

MHIQKNVPKEFMKRGSHENSLELKMGGRSWFVKVNYYDSIHGYRFSEGWRQFIKEFKVEIGDTLLFKLIDESKFVFDVSIVGKNPLAVCSIVL*