AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0038760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0038760 MtrunA17_Chr1g0202541 86.458 96 12 1 1 95 41 136 2.03e-40 130
Msa0038760 MtrunA17_Chr1g0202581 81.053 95 16 1 1 95 40 132 3.84e-33 111
Msa0038760 MtrunA17_Chr1g0204291 81.053 95 16 1 1 95 40 132 7.01e-33 110
Msa0038760 MtrunA17_Chr1g0202561 71.000 100 23 4 1 95 41 139 3.40e-25 91.7
Msa0038760 MtrunA17_Chr6g0469571 48.936 94 37 2 1 94 41 123 1.27e-13 61.6
Msa0038760 MtrunA17_Chr6g0469551 47.872 94 38 2 1 94 41 123 4.01e-13 60.5
Msa0038760 MtrunA17_Chr6g0469591 47.872 94 38 2 1 94 41 123 2.11e-12 58.5
Msa0038760 MtrunA17_Chr6g0469681 47.368 95 40 3 1 94 41 126 3.24e-12 58.2
Msa0038760 MtrunA17_Chr6g0469651 44.444 99 43 2 1 94 41 132 3.66e-11 55.5
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 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGATCCTCTTCAACGCTTA+TGG 0.283035 1_1:+68249747 None:intergenic
ATTAATCCTTTCGTGCTCTA+TGG 0.313770 1_1:-68249826 Msa0038760:CDS
ATTCATCTGATGATTATTAC+AGG 0.361033 1_1:+68249792 None:intergenic
ACGAAAGGATTAATTATCAT+TGG 0.419156 1_1:+68249835 None:intergenic
AGCTTAGCCACTACAAGTAC+TGG 0.428511 1_1:+68249967 None:intergenic
TAGATGATGACACAGCCATT+AGG 0.441354 1_1:+68249727 None:intergenic
TGGGTCGGTATCTCCTACTA+AGG 0.446407 1_1:+68249987 None:intergenic
GACAAGAAAATGACCTTAGT+AGG 0.452020 1_1:-68250000 None:intergenic
TTCAGTTGGACCAGCTAAAG+TGG 0.482641 1_1:-68249917 Msa0038760:CDS
GCACGGTGGTATGAATTGTA+TGG 0.520307 1_1:+68249769 None:intergenic
CATGCAGAAATACTTTCAGT+TGG 0.545738 1_1:-68249931 Msa0038760:CDS
CCGTGCCATAAGCGTTGAAG+AGG 0.546888 1_1:-68249752 Msa0038760:CDS
TACTTGTAGTGGCTAAGCTA+AGG 0.547972 1_1:-68249963 Msa0038760:CDS
TGATGATTATTACAGGTAGT+AGG 0.548716 1_1:+68249799 None:intergenic
AGCGTTGAAGAGGATCCTAA+TGG 0.594188 1_1:-68249742 Msa0038760:CDS
CCTCTTCAACGCTTATGGCA+CGG 0.607325 1_1:+68249752 None:intergenic
GGTGTACCATAGAGCACGAA+AGG 0.612408 1_1:+68249820 None:intergenic
GCTTAGCCACTACAAGTACT+GGG 0.632143 1_1:+68249968 None:intergenic
AGCCACTACAAGTACTGGGT+CGG 0.650008 1_1:+68249972 None:intergenic
TACCGACCCAGTACTTGTAG+TGG 0.655849 1_1:-68249974 Msa0038760:CDS
CTTCAACGCTTATGGCACGG+TGG 0.735189 1_1:+68249755 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTTTTTATCATCTTTTTT+AGG + chr1_1:68249840-68249859 None:intergenic 15.0%
!! TAAAAAAGATGATAAAAAGA+AGG - chr1_1:68249839-68249858 Msa0038760:CDS 15.0%
! ACGAAAGGATTAATTATCAT+TGG + chr1_1:68249885-68249904 None:intergenic 25.0%
! ATTCATCTGATGATTATTAC+AGG + chr1_1:68249928-68249947 None:intergenic 25.0%
TGATGATTATTACAGGTAGT+AGG + chr1_1:68249921-68249940 None:intergenic 30.0%
CATGCAGAAATACTTTCAGT+TGG - chr1_1:68249786-68249805 Msa0038760:CDS 35.0%
! TCTTTCTTTTCCACTTTAGC+TGG + chr1_1:68249813-68249832 None:intergenic 35.0%
ATTAATCCTTTCGTGCTCTA+TGG - chr1_1:68249891-68249910 Msa0038760:CDS 35.0%
TACTTGTAGTGGCTAAGCTA+AGG - chr1_1:68249754-68249773 Msa0038760:CDS 40.0%
TAGATGATGACACAGCCATT+AGG + chr1_1:68249993-68250012 None:intergenic 40.0%
GCTTAGCCACTACAAGTACT+GGG + chr1_1:68249752-68249771 None:intergenic 45.0%
AGCTTAGCCACTACAAGTAC+TGG + chr1_1:68249753-68249772 None:intergenic 45.0%
TTCAGTTGGACCAGCTAAAG+TGG - chr1_1:68249800-68249819 Msa0038760:CDS 45.0%
GCACGGTGGTATGAATTGTA+TGG + chr1_1:68249951-68249970 None:intergenic 45.0%
AGGATCCTCTTCAACGCTTA+TGG + chr1_1:68249973-68249992 None:intergenic 45.0%
! AGCGTTGAAGAGGATCCTAA+TGG - chr1_1:68249975-68249994 Msa0038760:CDS 45.0%
TGGGTCGGTATCTCCTACTA+AGG + chr1_1:68249733-68249752 None:intergenic 50.0%
TACCGACCCAGTACTTGTAG+TGG - chr1_1:68249743-68249762 Msa0038760:CDS 50.0%
!! AGCCACTACAAGTACTGGGT+CGG + chr1_1:68249748-68249767 None:intergenic 50.0%
GGTGTACCATAGAGCACGAA+AGG + chr1_1:68249900-68249919 None:intergenic 50.0%
CCTCTTCAACGCTTATGGCA+CGG + chr1_1:68249968-68249987 None:intergenic 50.0%
CTTCAACGCTTATGGCACGG+TGG + chr1_1:68249965-68249984 None:intergenic 55.0%
!! CCGTGCCATAAGCGTTGAAG+AGG - chr1_1:68249965-68249984 Msa0038760:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 68249726 68250013 68249726 ID=Msa0038760;Name=Msa0038760
chr1_1 mRNA 68249726 68250013 68249726 ID=Msa0038760-mRNA-1;Parent=Msa0038760;Name=Msa0038760-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|95
chr1_1 exon 68249726 68250013 68249726 ID=Msa0038760-mRNA-1:exon:22234;Parent=Msa0038760-mRNA-1
chr1_1 CDS 68249726 68250013 68249726 ID=Msa0038760-mRNA-1:cds;Parent=Msa0038760-mRNA-1
Gene Sequence

>Msa0038760

ATGACCTTAGTAGGAGATACCGACCCAGTACTTGTAGTGGCTAAGCTAAGGAAGTTATGTCATGCAGAAATACTTTCAGTTGGACCAGCTAAAGTGGAAAAGAAAGATGAACCTAAAAAAGATGATAAAAAGAAGGAAGATGATAAGAAAGATTCACCAATGATAATTAATCCTTTCGTGCTCTATGGTACACCTACTACCTGTAATAATCATCAGATGAATCCATACAATTCATACCACCGTGCCATAAGCGTTGAAGAGGATCCTAATGGCTGTGTCATCATCTAA
Protein sequence

>Msa0038760

MTLVGDTDPVLVVAKLRKLCHAEILSVGPAKVEKKDEPKKDDKKKEDDKKDSPMIINPFVLYGTPTTCNNHQMNPYNSYHRAISVEEDPNGCVII*