AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59101


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59101.t1 MTR_1g031740 84.615 143 16 1 1 137 1 143 1.85e-78 230
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGGAGGAGAATCTGGGTTT+TGG 0.221469 1.4:-16166829 None:intergenic
GGAGAGTGGCTGGGTGAAAA+TGG 0.232098 1.4:+16167277 MS.gene59101:CDS
GAAGAAGAAGGAGGAGAATC+TGG 0.270359 1.4:-16166836 None:intergenic
TGGAGGAAGATTGGTTTGTT+TGG 0.288556 1.4:-16166861 None:intergenic
GGTCGACGGGGAAGCTTGTT+TGG 0.309086 1.4:-16166932 None:intergenic
GGAGGAAGATTGGTTTGTTT+GGG 0.355312 1.4:-16166860 None:intergenic
GACCACGATGGATTTGTTCT+TGG 0.365556 1.4:+16167210 MS.gene59101:CDS
TAATGAAGTAGTGGAGTTCT+TGG 0.377298 1.4:-16166906 None:intergenic
ACCACGATGGATTTGTTCTT+GGG 0.379690 1.4:+16167211 MS.gene59101:CDS
GAGAGTGGCTGGGTGAAAAT+GGG 0.391269 1.4:+16167278 MS.gene59101:CDS
GGTGTTAGTGGAGCGAAATC+TGG 0.391808 1.4:-16167305 None:intergenic
ATTAGTAATAAGAATGGGTT+TGG 0.396058 1.4:-16166795 None:intergenic
TTGCTACTTACTGGTGTTAG+TGG 0.404594 1.4:-16167317 None:intergenic
CGAAGATGGTGATGGTCGAC+GGG 0.447807 1.4:-16166945 None:intergenic
GAGGGAAACAGGAGAGTGGC+TGG 0.452230 1.4:+16167267 MS.gene59101:CDS
TCAATTTGCATGAGCGAAGA+TGG 0.459616 1.4:-16166959 None:intergenic
AAGAAGAAGGAGGAGAATCT+GGG 0.467707 1.4:-16166835 None:intergenic
GTTGCATTAGTAATAAGAAT+GGG 0.473568 1.4:-16166800 None:intergenic
GTTTGTTTGGGTGAAGAAGA+AGG 0.476332 1.4:-16166848 None:intergenic
AGTTGCATTAGTAATAAGAA+TGG 0.478851 1.4:-16166801 None:intergenic
TTCTTGGGACAAGTATTTGA+AGG 0.485835 1.4:+16167226 MS.gene59101:CDS
ATTGAACGTGCCCTTGGCGC+TGG 0.500974 1.4:+16166977 MS.gene59101:CDS
ATGCAAATTGAACGTGCCCT+TGG 0.511985 1.4:+16166971 MS.gene59101:CDS
GACAGAGCATACTTGAGGTC+AGG 0.519678 1.4:-16167019 None:intergenic
TGTTATAGGTGATTATGAGT+GGG 0.521671 1.4:+16167402 MS.gene59101:intron
CTCTGAAGCTACCAGCGCCA+AGG 0.529782 1.4:-16166988 None:intergenic
GTTATAGGTGATTATGAGTG+GGG 0.532217 1.4:+16167403 MS.gene59101:intron
GCGAAGATGGTGATGGTCGA+CGG 0.545160 1.4:-16166946 None:intergenic
TCTTGGGACAAGTATTTGAA+GGG 0.567555 1.4:+16167227 MS.gene59101:CDS
GAGTTCTTGGATCTTAGTGA+AGG 0.568920 1.4:-16166893 None:intergenic
CGACGGGGAAGCTTGTTTGG+AGG 0.576924 1.4:-16166929 None:intergenic
AGAGTGGCTGGGTGAAAATG+GGG 0.590303 1.4:+16167279 MS.gene59101:CDS
TCTGAAGCTACCAGCGCCAA+GGG 0.590855 1.4:-16166987 None:intergenic
TTGTTATAGGTGATTATGAG+TGG 0.595225 1.4:+16167401 MS.gene59101:intron
GTTTGGAGGTAATGAAGTAG+TGG 0.605102 1.4:-16166915 None:intergenic
TGTTTGGGTGAAGAAGAAGG+AGG 0.610626 1.4:-16166845 None:intergenic
AGGGAAACAGGAGAGTGGCT+GGG 0.620803 1.4:+16167268 MS.gene59101:CDS
GGCGCTGGTAGCTTCAGAGA+CGG 0.635842 1.4:+16166992 MS.gene59101:CDS
AGCTGAGGGAAACAGGAGAG+TGG 0.671817 1.4:+16167263 MS.gene59101:CDS
GAAGATGGTGATGGTCGACG+GGG 0.719959 1.4:-16166944 None:intergenic
TGCATGAGCGAAGATGGTGA+TGG 0.732147 1.4:-16166953 None:intergenic
TCCCAAGAACAAATCCATCG+TGG 0.736351 1.4:-16167212 None:intergenic
AGACGTAAAGAAGACCACGA+TGG 0.745068 1.4:+16167198 MS.gene59101:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATAACATTATGATGAAT+AGG + chr1.4:16167072-16167091 MS.gene59101:intron 15.0%
!!! CACTTTTAACATTATGAAAT+TGG - chr1.4:16167114-16167133 None:intergenic 20.0%
! AGTTGCATTAGTAATAAGAA+TGG - chr1.4:16166804-16166823 None:intergenic 25.0%
! ATCAAAATCCAGAATGAAAT+TGG - chr1.4:16167139-16167158 None:intergenic 25.0%
! GTTGCATTAGTAATAAGAAT+GGG - chr1.4:16166803-16166822 None:intergenic 25.0%
! TGTTAAAGAGGCAAAAAATA+CGG - chr1.4:16167358-16167377 None:intergenic 25.0%
!! ATTAGTAATAAGAATGGGTT+TGG - chr1.4:16166798-16166817 None:intergenic 25.0%
!!! TATTTTTTGCCTCTTTAACA+AGG + chr1.4:16167358-16167377 MS.gene59101:intron 25.0%
TGTTATAGGTGATTATGAGT+GGG + chr1.4:16167402-16167421 MS.gene59101:intron 30.0%
TTGTTATAGGTGATTATGAG+TGG + chr1.4:16167401-16167420 MS.gene59101:intron 30.0%
!! CATGTCTTTTGCTTTGTTAT+AGG + chr1.4:16167388-16167407 MS.gene59101:intron 30.0%
GTTATAGGTGATTATGAGTG+GGG + chr1.4:16167403-16167422 MS.gene59101:intron 35.0%
TCTTGGGACAAGTATTTGAA+GGG + chr1.4:16167227-16167246 MS.gene59101:CDS 35.0%
TGCTACAATCCTTGTTAAAG+AGG - chr1.4:16167370-16167389 None:intergenic 35.0%
TTCTTGGGACAAGTATTTGA+AGG + chr1.4:16167226-16167245 MS.gene59101:CDS 35.0%
! AAAGTGCTCCAATTTCATTC+TGG + chr1.4:16167128-16167147 MS.gene59101:intron 35.0%
! CTTAGTGAAGGTTTTTGCTT+TGG - chr1.4:16166884-16166903 None:intergenic 35.0%
! TAATGAAGTAGTGGAGTTCT+TGG - chr1.4:16166909-16166928 None:intergenic 35.0%
!!! TTTTTGCTTTGGAGGAAGAT+TGG - chr1.4:16166873-16166892 None:intergenic 35.0%
AAACAGACAGAGCATACTTG+AGG - chr1.4:16167027-16167046 None:intergenic 40.0%
AAGAAGAAGGAGGAGAATCT+GGG - chr1.4:16166838-16166857 None:intergenic 40.0%
GAGTTCTTGGATCTTAGTGA+AGG - chr1.4:16166896-16166915 None:intergenic 40.0%
GTTTGGAGGTAATGAAGTAG+TGG - chr1.4:16166918-16166937 None:intergenic 40.0%
GTTTGTTTGGGTGAAGAAGA+AGG - chr1.4:16166851-16166870 None:intergenic 40.0%
TAACACCAGTAAGTAGCAAC+TGG + chr1.4:16167321-16167340 MS.gene59101:intron 40.0%
TCAATTTGCATGAGCGAAGA+TGG - chr1.4:16166962-16166981 None:intergenic 40.0%
! ACCACGATGGATTTGTTCTT+GGG + chr1.4:16167211-16167230 MS.gene59101:CDS 40.0%
! AGTGAAGGTTTTTGCTTTGG+AGG - chr1.4:16166881-16166900 None:intergenic 40.0%
! TTGCTACTTACTGGTGTTAG+TGG - chr1.4:16167320-16167339 None:intergenic 40.0%
!! GGAGGAAGATTGGTTTGTTT+GGG - chr1.4:16166863-16166882 None:intergenic 40.0%
!! TGGAGGAAGATTGGTTTGTT+TGG - chr1.4:16166864-16166883 None:intergenic 40.0%
AGACGTAAAGAAGACCACGA+TGG + chr1.4:16167198-16167217 MS.gene59101:CDS 45.0%
ATGCAAATTGAACGTGCCCT+TGG + chr1.4:16166971-16166990 MS.gene59101:CDS 45.0%
CAGAAAAAGCTGAGGGAAAC+AGG + chr1.4:16167256-16167275 MS.gene59101:CDS 45.0%
GAAGAAGAAGGAGGAGAATC+TGG - chr1.4:16166839-16166858 None:intergenic 45.0%
GACTGTGCAGAAAAAGCTGA+GGG + chr1.4:16167249-16167268 MS.gene59101:CDS 45.0%
TCCCAAGAACAAATCCATCG+TGG - chr1.4:16167215-16167234 None:intergenic 45.0%
TGTTTGGGTGAAGAAGAAGG+AGG - chr1.4:16166848-16166867 None:intergenic 45.0%
! AAGGAGGAGAATCTGGGTTT+TGG - chr1.4:16166832-16166851 None:intergenic 45.0%
! AGGAGGAGAATCTGGGTTTT+GGG - chr1.4:16166831-16166850 None:intergenic 45.0%
! CGTTACCAGTTGCTACTTAC+TGG - chr1.4:16167329-16167348 None:intergenic 45.0%
! GACCACGATGGATTTGTTCT+TGG + chr1.4:16167210-16167229 MS.gene59101:CDS 45.0%
AGAGTGGCTGGGTGAAAATG+GGG + chr1.4:16167279-16167298 MS.gene59101:CDS 50.0%
GACAGAGCATACTTGAGGTC+AGG - chr1.4:16167022-16167041 None:intergenic 50.0%
GAGAGTGGCTGGGTGAAAAT+GGG + chr1.4:16167278-16167297 MS.gene59101:CDS 50.0%
GGACTGTGCAGAAAAAGCTG+AGG + chr1.4:16167248-16167267 MS.gene59101:CDS 50.0%
GGTGTTAGTGGAGCGAAATC+TGG - chr1.4:16167308-16167327 None:intergenic 50.0%
TGCATGAGCGAAGATGGTGA+TGG - chr1.4:16166956-16166975 None:intergenic 50.0%
! GGAGGAGAATCTGGGTTTTG+GGG - chr1.4:16166830-16166849 None:intergenic 50.0%
AGCTGAGGGAAACAGGAGAG+TGG + chr1.4:16167263-16167282 MS.gene59101:CDS 55.0%
AGGGAAACAGGAGAGTGGCT+GGG + chr1.4:16167268-16167287 MS.gene59101:CDS 55.0%
GGAGAGTGGCTGGGTGAAAA+TGG + chr1.4:16167277-16167296 MS.gene59101:CDS 55.0%
! TCTGAAGCTACCAGCGCCAA+GGG - chr1.4:16166990-16167009 None:intergenic 55.0%
!! CGAAGATGGTGATGGTCGAC+GGG - chr1.4:16166948-16166967 None:intergenic 55.0%
!! GAAGATGGTGATGGTCGACG+GGG - chr1.4:16166947-16166966 None:intergenic 55.0%
!! GCGAAGATGGTGATGGTCGA+CGG - chr1.4:16166949-16166968 None:intergenic 55.0%
ATTGAACGTGCCCTTGGCGC+TGG + chr1.4:16166977-16166996 MS.gene59101:CDS 60.0%
GAGGGAAACAGGAGAGTGGC+TGG + chr1.4:16167267-16167286 MS.gene59101:CDS 60.0%
! CGACGGGGAAGCTTGTTTGG+AGG - chr1.4:16166932-16166951 None:intergenic 60.0%
! GGTCGACGGGGAAGCTTGTT+TGG - chr1.4:16166935-16166954 None:intergenic 60.0%
!! CTCTGAAGCTACCAGCGCCA+AGG - chr1.4:16166991-16167010 None:intergenic 60.0%
!! GGCGCTGGTAGCTTCAGAGA+CGG + chr1.4:16166992-16167011 MS.gene59101:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 16166764 16167447 16166764 ID=MS.gene59101
chr1.4 mRNA 16166764 16167447 16166764 ID=MS.gene59101.t1;Parent=MS.gene59101
chr1.4 exon 16166764 16167029 16166764 ID=MS.gene59101.t1.exon1;Parent=MS.gene59101.t1
chr1.4 CDS 16166764 16167029 16166764 ID=cds.MS.gene59101.t1;Parent=MS.gene59101.t1
chr1.4 exon 16167183 16167328 16167183 ID=MS.gene59101.t1.exon2;Parent=MS.gene59101.t1
chr1.4 CDS 16167183 16167328 16167183 ID=cds.MS.gene59101.t1;Parent=MS.gene59101.t1
chr1.4 exon 16167410 16167447 16167410 ID=MS.gene59101.t1.exon3;Parent=MS.gene59101.t1
chr1.4 CDS 16167410 16167447 16167410 ID=cds.MS.gene59101.t1;Parent=MS.gene59101.t1
Gene Sequence

>MS.gene59101

ATGTTTTGCTTATGCAACAATCTTTCTATAACCAAACCCATTCTTATTACTAATGCAACTCTTCCCCAAAACCCAGATTCTCCTCCTTCTTCTTCACCCAAACAAACCAATCTTCCTCCAAAGCAAAAACCTTCACTAAGATCCAAGAACTCCACTACTTCATTACCTCCAAACAAGCTTCCCCGTCGACCATCACCATCTTCGCTCATGCAAATTGAACGTGCCCTTGGCGCTGGTAGCTTCAGAGACGGTGAACCTGACCTCAAGTATGCTCTGTCTGTTTGAATAAACAACTTATTTTGCAGCTTATTATAACATTATGATGAATAGGCTATTTCTATTCACTACCAATTTCATAATGTTAAAAGTGCTCCAATTTCATTCTGGATTTTGATTTCTCTGCATTTTTTTTTTAAAAGAATGAAGAACGATTCAGACGTAAAGAAGACCACGATGGATTTGTTCTTGGGACAAGTATTTGAAGGGACTGTGCAGAAAAAGCTGAGGGAAACAGGAGAGTGGCTGGGTGAAAATGGGGAGACCAGATTTCGCTCCACTAACACCAGTAAGTAGCAACTGGTAACGACTTTTCCGTATTTTTTGCCTCTTTAACAAGGATTGTAGCATGTCTTTTGCTTTGTTATAGGTGATTATGAGTGGGGAAAAACAGAAGTTATAGAGTAA

Protein sequence

>MS.gene59101.t1

MFCLCNNLSITKPILITNATLPQNPDSPPSSSPKQTNLPPKQKPSLRSKNSTTSLPPNKLPRRPSPSSLMQIERALGAGSFRDGEPDLKMKNDSDVKKTTMDLFLGQVFEGTVQKKLRETGEWLGENGETRFRSTNTSDYEWGKTEVIE