AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480019865.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480019865.01.T01 MTR_4g123470 85.714 84 12 0 2 85 130 213 5.88e-49 154
MsG0480019865.01.T01 MTR_7g113060 85.185 27 4 0 59 85 3 29 3.40e-11 57.0
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 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGAACTACCTTATACTTT+TGG 0.309505 4:+28690524 MsG0480019865.01.T01:intron
AATTGTGATGCTTCACTCTA+AGG 0.318115 4:-28690553 None:intergenic
AGGAATTTGCCAAAAGTATA+AGG 0.322050 4:-28690533 None:intergenic
GTTCTTCACAGTGCTGGATA+TGG 0.361284 4:+28690383 MsG0480019865.01.T01:CDS
ATGTTCGTTCTTCACAGTGC+TGG 0.402371 4:+28690377 MsG0480019865.01.T01:CDS
CCCATGCCAAATGTGATGTT+CGG 0.420417 4:+28690638 MsG0480019865.01.T01:CDS
TTGTGCTGCCAATGGTATTG+AGG 0.438364 4:+28690679 MsG0480019865.01.T01:CDS
CCGAACATCACATTTGGCAT+GGG 0.451739 4:-28690638 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.463687 4:+28690680 MsG0480019865.01.T01:CDS
CACAATTACGTTGTGTTGTG+CGG 0.483742 4:+28690569 MsG0480019865.01.T01:CDS
GTTGTGTTGTGCGGACCTTA+TGG 0.490236 4:+28690578 MsG0480019865.01.T01:CDS
TCCGAACATCACATTTGGCA+TGG 0.494351 4:-28690639 None:intergenic
TCTGTATATTTGAGTCTCAC+TGG 0.509877 4:-28690611 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.530190 4:+28690644 MsG0480019865.01.T01:CDS
ACTGGAATGATATTGCCATA+AGG 0.559370 4:-28690593 None:intergenic
GTCTCCACCCTCAATACCAT+TGG 0.566256 4:-28690687 None:intergenic
CGAACATCACATTTGGCATG+GGG 0.577258 4:-28690637 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 4:+28690648 MsG0480019865.01.T01:CDS
GCTGCCAATGGTATTGAGGG+TGG 0.691580 4:+28690683 MsG0480019865.01.T01:CDS
TGGATCGACGAAATCACCGA+AGG 0.700849 4:+28690403 MsG0480019865.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTTATATATGCTATAATAA+AGG + Chr4:28690461-28690480 MsG0480019865.01.T01:intron 15.0%
!!! TTTTTTTTCCTTTTCTTTTT+AGG + Chr4:28690505-28690524 MsG0480019865.01.T01:intron 15.0%
!! AAAAAACAATAAACAACCTT+CGG - Chr4:28690422-28690441 None:intergenic 20.0%
!! TTTTGATGCTATTCATTTAG+AGG + Chr4:28690439-28690458 MsG0480019865.01.T01:intron 25.0%
AGGTAGTTCCTAAAAAGAAA+AGG - Chr4:28690516-28690535 None:intergenic 30.0%
! AGGAATTTGCCAAAAGTATA+AGG - Chr4:28690536-28690555 None:intergenic 30.0%
! TAGGAACTACCTTATACTTT+TGG + Chr4:28690524-28690543 MsG0480019865.01.T01:intron 30.0%
AATTGTGATGCTTCACTCTA+AGG - Chr4:28690556-28690575 None:intergenic 35.0%
ACTGGAATGATATTGCCATA+AGG - Chr4:28690596-28690615 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+TGG - Chr4:28690614-28690633 None:intergenic 35.0%
!!! ATTTTCAAGTGCAAGTGTCA+TGG + Chr4:28690716-28690735 MsG0480019865.01.T01:CDS 35.0%
ATGTGATGTTCGGAAAAGGT+TGG + Chr4:28690648-28690667 MsG0480019865.01.T01:CDS 40.0%
CACAATTACGTTGTGTTGTG+CGG + Chr4:28690569-28690588 MsG0480019865.01.T01:CDS 40.0%
CCAAATGTGATGTTCGGAAA+AGG + Chr4:28690644-28690663 MsG0480019865.01.T01:CDS 40.0%
! CCTTTTCCGAACATCACATT+TGG - Chr4:28690647-28690666 None:intergenic 40.0%
ATGTTCGTTCTTCACAGTGC+TGG + Chr4:28690377-28690396 MsG0480019865.01.T01:CDS 45.0%
CCCATGCCAAATGTGATGTT+CGG + Chr4:28690638-28690657 MsG0480019865.01.T01:CDS 45.0%
CCGAACATCACATTTGGCAT+GGG - Chr4:28690641-28690660 None:intergenic 45.0%
CGAACATCACATTTGGCATG+GGG - Chr4:28690640-28690659 None:intergenic 45.0%
TCCGAACATCACATTTGGCA+TGG - Chr4:28690642-28690661 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG + Chr4:28690679-28690698 MsG0480019865.01.T01:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + Chr4:28690671-28690690 MsG0480019865.01.T01:CDS 45.0%
! GTTCTTCACAGTGCTGGATA+TGG + Chr4:28690383-28690402 MsG0480019865.01.T01:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + Chr4:28690680-28690699 MsG0480019865.01.T01:CDS 45.0%
GTCTCCACCCTCAATACCAT+TGG - Chr4:28690690-28690709 None:intergenic 50.0%
GTTGTGTTGTGCGGACCTTA+TGG + Chr4:28690578-28690597 MsG0480019865.01.T01:CDS 50.0%
TGGATCGACGAAATCACCGA+AGG + Chr4:28690403-28690422 MsG0480019865.01.T01:CDS 50.0%
! GCTGCCAATGGTATTGAGGG+TGG + Chr4:28690683-28690702 MsG0480019865.01.T01:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr4 gene 28690377 28690754 28690377 ID=MsG0480019865.01;Name=MsG0480019865.01
Chr4 mRNA 28690377 28690754 28690377 ID=MsG0480019865.01.T01;Parent=MsG0480019865.01;Name=MsG0480019865.01.T01;_AED=0.44;_eAED=0.44;_QI=0|0|0|1|0|0.5|2|0|91
Chr4 exon 28690377 28690424 28690377 ID=MsG0480019865.01.T01:exon:9442;Parent=MsG0480019865.01.T01
Chr4 exon 28690527 28690754 28690527 ID=MsG0480019865.01.T01:exon:9443;Parent=MsG0480019865.01.T01
Chr4 CDS 28690377 28690424 28690377 ID=MsG0480019865.01.T01:cds;Parent=MsG0480019865.01.T01
Chr4 CDS 28690527 28690754 28690527 ID=MsG0480019865.01.T01:cds;Parent=MsG0480019865.01.T01
Gene Sequence

>MsG0480019865.01.T01

ATGTTCGTTCTTCACAGTGCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTTATACTTTTGGCAAATTCCTTAGAGTGAAGCATCACAATTACGTTGTGTTGTGCGGACCTTATGGCAATATCATTCCAGTGAGACTCAAATATACAGACGACCCCATGCCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGTGGAGACGTGTTGATTTTCAAGTGCAAGTGTCATGGACAAAAAATATGTTAA
Protein sequence

>MsG0480019865.01.T01

MFVLHSAGYGSTKSPKELPYTFGKFLRVKHHNYVVLCGPYGNIIPVRLKYTDDPMPNVMFGKGWTSFCAANGIEGGDVLIFKCKCHGQKIC*