AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene69741

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69741.t1 MTR_3g080890 41.176 153 29 6 1 111 1 134 5.45e-19 77.0
MS.gene69741.t1 MTR_1g021965 55.769 52 23 0 23 74 28 79 4.99e-13 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAAGGTTGCCAAAGAAATT+TGG 0.150495 3.4:-77024880 MS.gene69741:CDS
CATGTTGTCCCAAATTTCTT+TGG 0.218353 3.4:+77024871 None:intergenic
CATGCCAACGACGGAAATTA+TGG 0.246928 3.4:+77024993 None:intergenic
TACGTTATCTGATTTACGTT+TGG 0.342657 3.4:-77024918 MS.gene69741:CDS
AATTTCTTTGGCAACCTTGT+AGG 0.347836 3.4:+77024883 None:intergenic
CAAGGTTGCCAAAGAAATTT+GGG 0.359776 3.4:-77024879 MS.gene69741:CDS
ACTTCAATTCTGGAAACGTC+TGG 0.392283 3.4:+77025025 None:intergenic
ACAACATGAAAGTTTGTTGT+TGG 0.456822 3.4:-77024856 MS.gene69741:CDS
TAGGTGACCGCTGTCGGAGG+AGG 0.490184 3.4:+77025061 None:intergenic
AAGGCCATAATTTCCGTCGT+TGG 0.491561 3.4:-77024997 MS.gene69741:CDS
CCTTCAATTCTTAAAGGAGT+TGG 0.497366 3.4:+77024774 None:intergenic
GGATGTTTACTGTTCCTACA+AGG 0.517229 3.4:-77024897 MS.gene69741:CDS
ACAATCTAAGGAATTATGGC+TGG 0.522622 3.4:-77025148 None:intergenic
CTTCACACTGCTAGACATCC+AGG 0.527754 3.4:-77024963 MS.gene69741:CDS
TTTGCATAGGTGACCGCTGT+CGG 0.542339 3.4:+77025055 None:intergenic
ATAACGTAGAAAGAAGTGTA+TGG 0.548593 3.4:+77024933 None:intergenic
CTTCAATTCTGGAAACGTCT+GGG 0.550347 3.4:+77025026 None:intergenic
GAAGTGTATGGCGACAAACC+TGG 0.551944 3.4:+77024945 None:intergenic
TACTGATCCTCCTCCGACAG+CGG 0.564869 3.4:-77025068 MS.gene69741:CDS
TCTGTGATGACAAATGAAAG+AGG 0.575820 3.4:-77024827 MS.gene69741:CDS
GAGGATCAGTAGCAACAACA+AGG 0.606584 3.4:+77025080 None:intergenic
GCATAGGTGACCGCTGTCGG+AGG 0.620658 3.4:+77025058 None:intergenic
TGACAATAAGAAGAATGTCT+CGG 0.627026 3.4:-77025110 MS.gene69741:CDS
AGATGCGTTCATGCCAACGA+CGG 0.660184 3.4:+77024984 None:intergenic
AGGATCAGTAGCAACAACAA+GGG 0.691715 3.4:+77025081 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TACGTTATCTGATTTACGTT+TGG - chr3.4:77024999-77025018 MS.gene69741:CDS 30.0%
TGACAATAAGAAGAATGTCT+CGG - chr3.4:77024807-77024826 MS.gene69741:CDS 30.0%
! ATAACGTAGAAAGAAGTGTA+TGG + chr3.4:77024987-77025006 None:intergenic 30.0%
! TCCAGAATTGAAGTTTTTGA+AGG - chr3.4:77024901-77024920 MS.gene69741:CDS 30.0%
!! ACAACATGAAAGTTTGTTGT+TGG - chr3.4:77025061-77025080 MS.gene69741:CDS 30.0%
AATTTCTTTGGCAACCTTGT+AGG + chr3.4:77025037-77025056 None:intergenic 35.0%
ACAAGGTTGCCAAAGAAATT+TGG - chr3.4:77025037-77025056 MS.gene69741:CDS 35.0%
CAAGGTTGCCAAAGAAATTT+GGG - chr3.4:77025038-77025057 MS.gene69741:CDS 35.0%
CATGTTGTCCCAAATTTCTT+TGG + chr3.4:77025049-77025068 None:intergenic 35.0%
GCCTTCAAAAACTTCAATTC+TGG + chr3.4:77024905-77024924 None:intergenic 35.0%
TCTGTGATGACAAATGAAAG+AGG - chr3.4:77025090-77025109 MS.gene69741:CDS 35.0%
AGGATCAGTAGCAACAACAA+GGG + chr3.4:77024839-77024858 None:intergenic 40.0%
GGATGTTTACTGTTCCTACA+AGG - chr3.4:77025020-77025039 MS.gene69741:CDS 40.0%
! ACTTCAATTCTGGAAACGTC+TGG + chr3.4:77024895-77024914 None:intergenic 40.0%
! CTTCAATTCTGGAAACGTCT+GGG + chr3.4:77024894-77024913 None:intergenic 40.0%
AAGGCCATAATTTCCGTCGT+TGG - chr3.4:77024920-77024939 MS.gene69741:CDS 45.0%
CATGCCAACGACGGAAATTA+TGG + chr3.4:77024927-77024946 None:intergenic 45.0%
GAGGATCAGTAGCAACAACA+AGG + chr3.4:77024840-77024859 None:intergenic 45.0%
! GTCTGGGAACTGTTTTGCAT+AGG + chr3.4:77024878-77024897 None:intergenic 45.0%
AGATGCGTTCATGCCAACGA+CGG + chr3.4:77024936-77024955 None:intergenic 50.0%
CTTCACACTGCTAGACATCC+AGG - chr3.4:77024954-77024973 MS.gene69741:CDS 50.0%
GAAGTGTATGGCGACAAACC+TGG + chr3.4:77024975-77024994 None:intergenic 50.0%
TTTGCATAGGTGACCGCTGT+CGG + chr3.4:77024865-77024884 None:intergenic 50.0%
TACTGATCCTCCTCCGACAG+CGG - chr3.4:77024849-77024868 MS.gene69741:CDS 55.0%
GCATAGGTGACCGCTGTCGG+AGG + chr3.4:77024862-77024881 None:intergenic 65.0%
TAGGTGACCGCTGTCGGAGG+AGG + chr3.4:77024859-77024878 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 77024784 77025155 77024784 ID=MS.gene69741
chr3.4 mRNA 77024784 77025155 77024784 ID=MS.gene69741.t1;Parent=MS.gene69741
chr3.4 exon 77024784 77025155 77024784 ID=MS.gene69741.t1.exon1;Parent=MS.gene69741.t1
chr3.4 CDS 77024784 77025155 77024784 ID=cds.MS.gene69741.t1;Parent=MS.gene69741.t1
Gene Sequence

>MS.gene69741

ATGGCTGGAGATGATTCTAACAATGACAATAAGAAGAATGTCTCGGACTCTACCCTTGTTGTTGCTACTGATCCTCCTCCGACAGCGGTCACCTATGCAAAACAGTTCCCAGACGTTTCCAGAATTGAAGTTTTTGAAGGCCATAATTTCCGTCGTTGGCATGAACGCATCTTCACACTGCTAGACATCCAGGTTTGTCGCCATACACTTCTTTCTACGTTATCTGATTTACGTTTGGATGTTTACTGTTCCTACAAGGTTGCCAAAGAAATTTGGGACAACATGAAAGTTTGTTGTTGGAAACTATCTGTGATGACAAATGAAAGAGGACAAAGAAATCAAAGTGCAGATTATCACTACCAACTCCTTTAA
Protein sequence

>MS.gene69741.t1

MAGDDSNNDNKKNVSDSTLVVATDPPPTAVTYAKQFPDVSRIEVFEGHNFRRWHERIFTLLDIQVCRHTLLSTLSDLRLDVYCSYKVAKEIWDNMKVCCWKLSVMTNERGQRNQSADYHYQLL