AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0112850

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0112850 MtrunA17_Chr1g0163201 71.429 77 22 0 45 121 317 393 7.21e-32 115
Msa0112850 MtrunA17_Chr1g0163111 63.750 80 29 0 42 121 150 229 3.12e-31 110
Msa0112850 MtrunA17_Chr1g0163151 62.500 80 30 0 42 121 143 222 6.64e-31 109
Msa0112850 MtrunA17_Chr1g0163181 63.636 77 28 0 45 121 354 430 4.81e-28 105
Msa0112850 MtrunA17_Chr1g0163131 52.632 76 32 2 47 120 233 306 1.14e-17 76.6
Msa0112850 MtrunA17_Chr6g0476171 49.180 61 31 0 60 120 185 245 1.44e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATGCACCAAAGAGATTTA+TGG 0.245600 1_3:+28368626 Msa0112850:intron
ATGGGTTTGCTCCTGGCTTA+TGG 0.276895 1_3:+28368423 Msa0112850:CDS
CCTCTTTCCATAAATCTCTT+TGG 0.284821 1_3:-28368633 None:intergenic
GAAGAAAGCAAAGTGGAAAT+TGG 0.294808 1_3:+28368771 Msa0112850:CDS
CTTTGCCATGGGTTTGCTCC+TGG 0.300951 1_3:+28368416 None:intergenic
CAGCTCCTGGCAAATTTGTT+AGG 0.346344 1_3:-28368491 None:intergenic
GGCAAATTGCAATTACAAAC+TGG 0.389806 1_3:-28368447 None:intergenic
CAATTTGCCAGGGGTTTCCC+TGG 0.409346 1_3:+28368461 Msa0112850:CDS
AAAATTGTGGAGTTGAAAAT+GGG 0.422112 1_3:+28368666 Msa0112850:CDS
GTGTTTAAAGTTTCCATTGT+GGG 0.433176 1_3:+28368834 Msa0112850:CDS
GTTTGTAATTGCAATTTGCC+AGG 0.458528 1_3:+28368450 Msa0112850:CDS
CGTGGTTGTCAGTTCAGTAA+AGG 0.468915 1_3:+28368732 Msa0112850:CDS
ATGCTCCTGGCATTATTCCC+TGG 0.469201 1_3:+28368514 Msa0112850:CDS
AACTGACAACCACGAATACT+AGG 0.474382 1_3:-28368723 None:intergenic
ATTTATTATCCTAGTATTCG+TGG 0.474870 1_3:+28368714 Msa0112850:CDS
TTGCCAGGAGCTGATGCTCC+TGG 0.505150 1_3:+28368501 Msa0112850:CDS
CCAAAGAGATTTATGGAAAG+AGG 0.511759 1_3:+28368633 Msa0112850:CDS
TACAAACTGGACCATAAGCC+AGG 0.521680 1_3:-28368434 None:intergenic
ATGCCAGGAGCATCAGCTCC+TGG 0.533308 1_3:-28368504 None:intergenic
AATTTGTTAGGAGTAATGCC+AGG 0.536073 1_3:-28368479 None:intergenic
GTTGTCAGTTCAGTAAAGGT+TGG 0.536590 1_3:+28368736 Msa0112850:CDS
TTACTCCTAACAAATTTGCC+AGG 0.555544 1_3:+28368486 Msa0112850:CDS
GAAATACTTGTCTCCTAGAG+CGG 0.589908 1_3:+28368793 Msa0112850:CDS
ATTTGTTAGGAGTAATGCCA+GGG 0.610060 1_3:-28368478 None:intergenic
TTTGTAATTGCAATTTGCCA+GGG 0.616575 1_3:+28368451 Msa0112850:CDS
ATTTATGGAAGAAAGCAAAG+TGG 0.622753 1_3:+28368764 Msa0112850:CDS
TTGTAATTGCAATTTGCCAG+GGG 0.628207 1_3:+28368452 Msa0112850:CDS
AAATTGTGGAGTTGAAAATG+GGG 0.628496 1_3:+28368667 Msa0112850:CDS
AATTGTGGAGTTGAAAATGG+GGG 0.632867 1_3:+28368668 Msa0112850:CDS
AGTAATGCCAGGGAAACCCC+TGG 0.634189 1_3:-28368468 None:intergenic
ATAAGCCAGGAGCAAACCCA+TGG 0.650838 1_3:-28368421 None:intergenic
ATTGTGGAGTTGAAAATGGG+GGG 0.654265 1_3:+28368669 Msa0112850:CDS
TGTGTTTAAAGTTTCCATTG+TGG 0.655197 1_3:+28368833 Msa0112850:CDS
TATAAGGTTCTATCCCACAA+TGG 0.669677 1_3:-28368847 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATGTATAAATGTTATTT+TGG + chr1_3:28368591-28368610 Msa0112850:intron 10.0%
!! TAAAGGTTGGAAAAAATTTA+TGG + chr1_3:28368749-28368768 Msa0112850:CDS 20.0%
! AAAAATTGTGGAGTTGAAAA+TGG + chr1_3:28368665-28368684 Msa0112850:CDS 25.0%
! AAAATTGTGGAGTTGAAAAT+GGG + chr1_3:28368666-28368685 Msa0112850:CDS 25.0%
! ATTTATTATCCTAGTATTCG+TGG + chr1_3:28368714-28368733 Msa0112850:CDS 25.0%
TTTGTAATTGCAATTTGCCA+GGG + chr1_3:28368451-28368470 Msa0112850:CDS 30.0%
AAATTGTGGAGTTGAAAATG+GGG + chr1_3:28368667-28368686 Msa0112850:CDS 30.0%
ATTTATGGAAGAAAGCAAAG+TGG + chr1_3:28368764-28368783 Msa0112850:CDS 30.0%
! TGTGTTTAAAGTTTCCATTG+TGG + chr1_3:28368833-28368852 Msa0112850:CDS 30.0%
! GTGTTTAAAGTTTCCATTGT+GGG + chr1_3:28368834-28368853 Msa0112850:CDS 30.0%
GGCAAATTGCAATTACAAAC+TGG - chr1_3:28368450-28368469 None:intergenic 35.0%
GTTTGTAATTGCAATTTGCC+AGG + chr1_3:28368450-28368469 Msa0112850:CDS 35.0%
TTGTAATTGCAATTTGCCAG+GGG + chr1_3:28368452-28368471 Msa0112850:CDS 35.0%
! ATTTGTTAGGAGTAATGCCA+GGG - chr1_3:28368481-28368500 None:intergenic 35.0%
!! AATTTGTTAGGAGTAATGCC+AGG - chr1_3:28368482-28368501 None:intergenic 35.0%
TTACTCCTAACAAATTTGCC+AGG + chr1_3:28368486-28368505 Msa0112850:CDS 35.0%
GAATGCACCAAAGAGATTTA+TGG + chr1_3:28368626-28368645 Msa0112850:intron 35.0%
CCTCTTTCCATAAATCTCTT+TGG - chr1_3:28368636-28368655 None:intergenic 35.0%
CCAAAGAGATTTATGGAAAG+AGG + chr1_3:28368633-28368652 Msa0112850:CDS 35.0%
AGGATGTCGTGAAAAAATTG+TGG + chr1_3:28368653-28368672 Msa0112850:CDS 35.0%
AATTGTGGAGTTGAAAATGG+GGG + chr1_3:28368668-28368687 Msa0112850:CDS 35.0%
GAAGAAAGCAAAGTGGAAAT+TGG + chr1_3:28368771-28368790 Msa0112850:CDS 35.0%
! AGAAATCTTGCGTTTTGCCA+GGG - chr1_3:28368534-28368553 None:intergenic 40.0%
! AAGAAATCTTGCGTTTTGCC+AGG - chr1_3:28368535-28368554 None:intergenic 40.0%
ATTGTGGAGTTGAAAATGGG+GGG + chr1_3:28368669-28368688 Msa0112850:CDS 40.0%
AACTGACAACCACGAATACT+AGG - chr1_3:28368726-28368745 None:intergenic 40.0%
GTTGTCAGTTCAGTAAAGGT+TGG + chr1_3:28368736-28368755 Msa0112850:CDS 40.0%
GAAATACTTGTCTCCTAGAG+CGG + chr1_3:28368793-28368812 Msa0112850:CDS 40.0%
! TTTTCTCATCAATCCGCTCT+AGG - chr1_3:28368809-28368828 None:intergenic 40.0%
TACAAACTGGACCATAAGCC+AGG - chr1_3:28368437-28368456 None:intergenic 45.0%
! CAGCTCCTGGCAAATTTGTT+AGG - chr1_3:28368494-28368513 None:intergenic 45.0%
! TTTTGCCAGGGAATAATGCC+AGG - chr1_3:28368522-28368541 None:intergenic 45.0%
TGAAAATGGGGGGACAATCA+TGG + chr1_3:28368679-28368698 Msa0112850:CDS 45.0%
CGTGGTTGTCAGTTCAGTAA+AGG + chr1_3:28368732-28368751 Msa0112850:CDS 45.0%
! ATGGGTTTGCTCCTGGCTTA+TGG + chr1_3:28368423-28368442 Msa0112850:CDS 50.0%
ATGCTCCTGGCATTATTCCC+TGG + chr1_3:28368514-28368533 Msa0112850:CDS 50.0%
CAATTTGCCAGGGGTTTCCC+TGG + chr1_3:28368461-28368480 Msa0112850:CDS 55.0%
AGTAATGCCAGGGAAACCCC+TGG - chr1_3:28368471-28368490 None:intergenic 55.0%
TTGCCAGGAGCTGATGCTCC+TGG + chr1_3:28368501-28368520 Msa0112850:CDS 60.0%
!! ATGCCAGGAGCATCAGCTCC+TGG - chr1_3:28368507-28368526 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 28368423 28368860 28368423 ID=Msa0112850;Name=Msa0112850
chr1_3 mRNA 28368423 28368860 28368423 ID=Msa0112850-mRNA-1;Parent=Msa0112850;Name=Msa0112850-mRNA-1;_AED=0.62;_eAED=0.62;_QI=0|0|0|0.5|1|1|2|0|121
chr1_3 exon 28368423 28368554 28368423 ID=Msa0112850-mRNA-1:exon:9340;Parent=Msa0112850-mRNA-1
chr1_3 exon 28368627 28368860 28368627 ID=Msa0112850-mRNA-1:exon:9341;Parent=Msa0112850-mRNA-1
chr1_3 CDS 28368423 28368554 28368423 ID=Msa0112850-mRNA-1:cds;Parent=Msa0112850-mRNA-1
chr1_3 CDS 28368627 28368860 28368627 ID=Msa0112850-mRNA-1:cds;Parent=Msa0112850-mRNA-1
Gene Sequence

>Msa0112850

ATGGGTTTGCTCCTGGCTTATGGTCCAGTTTGTAATTGCAATTTGCCAGGGGTTTCCCTGGCATTACTCCTAACAAATTTGCCAGGAGCTGATGCTCCTGGCATTATTCCCTGGCAAAACGCAAGATTTCTTAATGCACCAAAGAGATTTATGGAAAGAGGATGTCGTGAAAAAATTGTGGAGTTGAAAATGGGGGGACAATCATGGTTCGTAAAAGTGATTTATTATCCTAGTATTCGTGGTTGTCAGTTCAGTAAAGGTTGGAAAAAATTTATGGAAGAAAGCAAAGTGGAAATTGGAAATACTTGTCTCCTAGAGCGGATTGATGAGAAAAAGTATGTGTTTAAAGTTTCCATTGTGGGATAG
Protein sequence

>Msa0112850

MGLLLAYGPVCNCNLPGVSLALLLTNLPGADAPGIIPWQNARFLNAPKRFMERGCREKIVELKMGGQSWFVKVIYYPSIRGCQFSKGWKKFMEESKVEIGNTCLLERIDEKKYVFKVSIVG*