AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0897730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0897730 MtrunA17_Chr6g0483561 87.500 144 11 1 1 144 97 233 9.61e-71 212
Msa0897730 MtrunA17_Chr6g0483581 86.806 144 12 1 1 144 97 233 8.90e-57 177
Msa0897730 MtrunA17_Chr6g0483511 50.833 120 27 4 1 119 93 181 9.75e-26 96.3
Msa0897730 MtrunA17_Chr6g0483521 54.110 146 40 8 4 144 100 223 2.93e-24 93.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGATATGGAGCGTAGCATTT+AGG 0.197418 6_1:+90089395 None:intergenic
GTAGGTGTAGGAGGCTTCTT+AGG 0.298324 6_1:+90089491 None:intergenic
TCATAAACAACCTTACAATA+AGG 0.334241 6_1:+90089341 None:intergenic
CCCTTATCCACCTTATTGTA+AGG 0.360745 6_1:-90089351 Msa0897730:CDS
GATATGGAGCGTAGCATTTA+GGG 0.368487 6_1:+90089396 None:intergenic
CAAGGTGGATAAGGTCGATA+TGG 0.371321 6_1:+90089380 None:intergenic
ACCTTACAATAAGGTGGATA+AGG 0.398003 6_1:+90089350 None:intergenic
CACATGATGGAGCAAGTCTC+GGG 0.415773 6_1:+90089311 None:intergenic
AAAGTGTGATGGTAAGTGTA+AGG 0.433385 6_1:-90089570 Msa0897730:CDS
GGAGGCTTCTTAGGAGGTGC+AGG 0.451480 6_1:+90089500 None:intergenic
GGGTTAGAACAAGGTGGATA+AGG 0.458184 6_1:+90089371 None:intergenic
CCTTACAATAAGGTGGATAA+GGG 0.481422 6_1:+90089351 None:intergenic
CATTGTTGGATGGGTGGTGA+AGG 0.488818 6_1:+90089437 None:intergenic
TTCTTCTGAGGAGGTGTAGG+AGG 0.505145 6_1:+90089461 None:intergenic
TGCACCATTGAGGACATTGT+TGG 0.507565 6_1:+90089423 None:intergenic
GGCTTCTCAGTAGGTGTAGG+AGG 0.515844 6_1:+90089482 None:intergenic
TGTCACGACTTGAGTTGTAA+TGG 0.519079 6_1:-90089677 Msa0897730:CDS
GGATTCTTCTGAGGAGGTGT+AGG 0.532987 6_1:+90089458 None:intergenic
TCACATGATGGAGCAAGTCT+CGG 0.533242 6_1:+90089310 None:intergenic
GGTGTAGGAGGCTTCTCAGT+AGG 0.538901 6_1:+90089473 None:intergenic
CCATCCAACAATGTCCTCAA+TGG 0.539149 6_1:-90089427 Msa0897730:CDS
GGAGGCTTCTCAGTAGGTGT+AGG 0.547951 6_1:+90089479 None:intergenic
CATTGAGGACATTGTTGGAT+GGG 0.558013 6_1:+90089428 None:intergenic
CCATTGAGGACATTGTTGGA+TGG 0.560801 6_1:+90089427 None:intergenic
AAGTGTGATGGTAAGTGTAA+GGG 0.566876 6_1:-90089569 Msa0897730:CDS
TTAGGGCATGTGCACCATTG+AGG 0.567668 6_1:+90089413 None:intergenic
GGTGAAGGATTCTTCTGAGG+AGG 0.569735 6_1:+90089452 None:intergenic
GGTGTAGGAGGCTTCTTAGG+AGG 0.582175 6_1:+90089494 None:intergenic
TAAACAACCTTACAATAAGG+TGG 0.594529 6_1:+90089344 None:intergenic
TGAGGACATTGTTGGATGGG+TGG 0.615195 6_1:+90089431 None:intergenic
GGTGGATAAGGGTTAGAACA+AGG 0.617288 6_1:+90089362 None:intergenic
GGATAAGGGTTAGAACAAGG+TGG 0.619498 6_1:+90089365 None:intergenic
TGTGAAAGTCTAAAATGTGA+TGG 0.629705 6_1:-90089632 Msa0897730:CDS
TGTGAAGATTCAAAGTGTGA+TGG 0.647633 6_1:-90089581 Msa0897730:CDS
GGTGGTGAAGGATTCTTCTG+AGG 0.647882 6_1:+90089449 None:intergenic
GTAGGTATGATGTCACATGA+TGG 0.671048 6_1:+90089298 None:intergenic
TGTGACAACAAGAAGTGTGA+TGG 0.671842 6_1:-90089533 Msa0897730:CDS
ACATGATGGAGCAAGTCTCG+GGG 0.673679 6_1:+90089312 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAGACTTTCACATTTT+GGG + chr6_1:90089396-90089415 None:intergenic 20.0%
!! CATTTTAGACTTTCACATTT+TGG + chr6_1:90089397-90089416 None:intergenic 25.0%
! TCATAAACAACCTTACAATA+AGG + chr6_1:90089694-90089713 None:intergenic 25.0%
! TGTGAAAGTCTAAAATGTGA+TGG - chr6_1:90089400-90089419 Msa0897730:CDS 30.0%
TAAACAACCTTACAATAAGG+TGG + chr6_1:90089691-90089710 None:intergenic 30.0%
TGTGAAGATTCAAAGTGTGA+TGG - chr6_1:90089451-90089470 Msa0897730:CDS 35.0%
AAAGTGTGATGGTAAGTGTA+AGG - chr6_1:90089462-90089481 Msa0897730:CDS 35.0%
AAGTGTGATGGTAAGTGTAA+GGG - chr6_1:90089463-90089482 Msa0897730:CDS 35.0%
CCTTACAATAAGGTGGATAA+GGG + chr6_1:90089684-90089703 None:intergenic 35.0%
ACCTTACAATAAGGTGGATA+AGG + chr6_1:90089685-90089704 None:intergenic 35.0%
! TGTCACGACTTGAGTTGTAA+TGG - chr6_1:90089355-90089374 Msa0897730:CDS 40.0%
! TGTGACAACAAGAAGTGTGA+TGG - chr6_1:90089499-90089518 Msa0897730:CDS 40.0%
CATTGAGGACATTGTTGGAT+GGG + chr6_1:90089607-90089626 None:intergenic 40.0%
GATATGGAGCGTAGCATTTA+GGG + chr6_1:90089639-90089658 None:intergenic 40.0%
CCCTTATCCACCTTATTGTA+AGG - chr6_1:90089681-90089700 Msa0897730:CDS 40.0%
! GCATGTCGTAGTGTTTTGCA+AGG - chr6_1:90089319-90089338 Msa0897730:CDS 45.0%
CCATTGAGGACATTGTTGGA+TGG + chr6_1:90089608-90089627 None:intergenic 45.0%
CCATCCAACAATGTCCTCAA+TGG - chr6_1:90089605-90089624 Msa0897730:CDS 45.0%
TGCACCATTGAGGACATTGT+TGG + chr6_1:90089612-90089631 None:intergenic 45.0%
CGATATGGAGCGTAGCATTT+AGG + chr6_1:90089640-90089659 None:intergenic 45.0%
CAAGGTGGATAAGGTCGATA+TGG + chr6_1:90089655-90089674 None:intergenic 45.0%
GGGTTAGAACAAGGTGGATA+AGG + chr6_1:90089664-90089683 None:intergenic 45.0%
GGATAAGGGTTAGAACAAGG+TGG + chr6_1:90089670-90089689 None:intergenic 45.0%
GGTGGATAAGGGTTAGAACA+AGG + chr6_1:90089673-90089692 None:intergenic 45.0%
! TCACATGATGGAGCAAGTCT+CGG + chr6_1:90089725-90089744 None:intergenic 45.0%
GTAGGTGTAGGAGGCTTCTT+AGG + chr6_1:90089544-90089563 None:intergenic 50.0%
! TTCTTCTGAGGAGGTGTAGG+AGG + chr6_1:90089574-90089593 None:intergenic 50.0%
! GGATTCTTCTGAGGAGGTGT+AGG + chr6_1:90089577-90089596 None:intergenic 50.0%
! GGTGAAGGATTCTTCTGAGG+AGG + chr6_1:90089583-90089602 None:intergenic 50.0%
GGTGGTGAAGGATTCTTCTG+AGG + chr6_1:90089586-90089605 None:intergenic 50.0%
CATTGTTGGATGGGTGGTGA+AGG + chr6_1:90089598-90089617 None:intergenic 50.0%
TGAGGACATTGTTGGATGGG+TGG + chr6_1:90089604-90089623 None:intergenic 50.0%
TTAGGGCATGTGCACCATTG+AGG + chr6_1:90089622-90089641 None:intergenic 50.0%
! ACATGATGGAGCAAGTCTCG+GGG + chr6_1:90089723-90089742 None:intergenic 50.0%
! CACATGATGGAGCAAGTCTC+GGG + chr6_1:90089724-90089743 None:intergenic 50.0%
GGTGTAGGAGGCTTCTTAGG+AGG + chr6_1:90089541-90089560 None:intergenic 55.0%
GGCTTCTCAGTAGGTGTAGG+AGG + chr6_1:90089553-90089572 None:intergenic 55.0%
GGAGGCTTCTCAGTAGGTGT+AGG + chr6_1:90089556-90089575 None:intergenic 55.0%
GGTGTAGGAGGCTTCTCAGT+AGG + chr6_1:90089562-90089581 None:intergenic 55.0%
! GGAGGCTTCTTAGGAGGTGC+AGG + chr6_1:90089535-90089554 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 90089310 90089744 90089310 ID=Msa0897730;Name=Msa0897730
chr6_1 mRNA 90089310 90089744 90089310 ID=Msa0897730-mRNA-1;Parent=Msa0897730;Name=Msa0897730-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|-1|0|1|-1|1|1|0|144
chr6_1 exon 90089310 90089744 90089310 ID=Msa0897730-mRNA-1:exon:15373;Parent=Msa0897730-mRNA-1
chr6_1 CDS 90089310 90089744 90089310 ID=Msa0897730-mRNA-1:cds;Parent=Msa0897730-mRNA-1
Gene Sequence

>Msa0897730

ATGATAGAAGCATGTCGTAGTGTTTTGCAAGGTACTTGCATCAAGTGTCACGACTTGAGTTGTAATGGAAAATGTAATAAATGCCCAAAATGTGAAAGTCTAAAATGTGATGGCAAACATTGTGTCACAATTTGCTTTAAATGTGAAGATTCAAAGTGTGATGGTAAGTGTAAGGGTAATTGCTGCAATTGTGACAACAAGAAGTGTGATGGTTGTACACTTCCTGCACCTCCTAAGAAGCCTCCTACACCTACTGAGAAGCCTCCTACACCTCCTCAGAAGAATCCTTCACCACCCATCCAACAATGTCCTCAATGGTGCACATGCCCTAAATGCTACGCTCCATATCGACCTTATCCACCTTGTTCTAACCCTTATCCACCTTATTGTAAGGTTGTTTATGAACAAAACCCCGAGACTTGCTCCATCATGTGA
Protein sequence

>Msa0897730

MIEACRSVLQGTCIKCHDLSCNGKCNKCPKCESLKCDGKHCVTICFKCEDSKCDGKCKGNCCNCDNKKCDGCTLPAPPKKPPTPTEKPPTPPQKNPSPPIQQCPQWCTCPKCYAPYRPYPPCSNPYPPYCKVVYEQNPETCSIM*