AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044284

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044284.t1 MTR_3g080680 78.788 99 21 0 1 99 101 199 1.10e-54 169
MS.gene044284.t1 MTR_3g082420 52.941 102 44 3 2 99 121 222 9.93e-26 95.5
MS.gene044284.t1 MTR_3g082340 52.941 102 44 3 2 99 122 223 1.70e-25 95.1
MS.gene044284.t1 MTR_8g461300 49.515 103 46 2 2 98 96 198 1.20e-22 87.0
MS.gene044284.t1 MTR_3g083050 43.000 100 49 5 2 100 116 208 9.60e-14 64.3
MS.gene044284.t1 MTR_3g083030 43.000 100 49 5 2 100 139 231 1.17e-13 64.3
MS.gene044284.t1 MTR_3g083150 43.158 95 49 3 6 98 120 211 8.97e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATAGATTCTACCATTAATA+AGG 0.262811 3.3:-68851086 None:intergenic
TGTACCCATGCCCTTATTAA+TGG 0.282280 3.3:+68851075 MS.gene044284:CDS
TGGAGTGTCCTTCGAGAATA+GGG 0.410247 3.3:-68850889 None:intergenic
TTGGAGTGTCCTTCGAGAAT+AGG 0.428317 3.3:-68850890 None:intergenic
GCTTGGAAAGTTGTTAAAGC+AGG 0.466031 3.3:-68851153 None:intergenic
ATAGATTCTACCATTAATAA+GGG 0.476198 3.3:-68851085 None:intergenic
GAGAATAGGGCGAACATCAT+CGG 0.483809 3.3:-68850876 None:intergenic
TTCTACCATTAATAAGGGCA+TGG 0.508172 3.3:-68851080 None:intergenic
AGGCCATGAAACACAAAAGC+TGG 0.508489 3.3:-68851045 None:intergenic
AGGACACTCCAAGCTTGCAT+TGG 0.517715 3.3:+68850901 MS.gene044284:CDS
GTAATAGTCCAATGCAAGCT+TGG 0.525102 3.3:-68850909 None:intergenic
CTTGGAAAGTTGTTAAAGCA+GGG 0.540365 3.3:-68851152 None:intergenic
AACATCATCGGAAATGTGAA+GGG 0.573072 3.3:-68850864 None:intergenic
GAACATCATCGGAAATGTGA+AGG 0.574469 3.3:-68850865 None:intergenic
GAACACAGCATACTTCAGCT+TGG 0.589049 3.3:-68851170 None:intergenic
TCTACCATTAATAAGGGCAT+GGG 0.593250 3.3:-68851079 None:intergenic
AGTTGTTAAAGCAGGGGTGT+CGG 0.599691 3.3:-68851145 None:intergenic
TTGGAAAGTTGTTAAAGCAG+GGG 0.623852 3.3:-68851151 None:intergenic
GATGTTCGCCCTATTCTCGA+AGG 0.637823 3.3:+68850881 MS.gene044284:CDS
GGGCATGGGTACACTTAACA+AGG 0.642669 3.3:-68851065 None:intergenic
TGTTCGAGATAAACAACCTG+TGG 0.664849 3.3:+68851188 MS.gene044284:CDS
ACATCATCGGAAATGTGAAG+GGG 0.674764 3.3:-68850863 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTTCATTATGTTATATTA+GGG + chr3.3:68851021-68851040 MS.gene044284:intron 15.0%
!! AATAGATTCTACCATTAATA+AGG - chr3.3:68851089-68851108 None:intergenic 20.0%
!! AGAAGAACAATTAATTAGTT+TGG - chr3.3:68851005-68851024 None:intergenic 20.0%
!! ATAGATTCTACCATTAATAA+GGG - chr3.3:68851088-68851107 None:intergenic 20.0%
!! CTTCTTCATTATGTTATATT+AGG + chr3.3:68851020-68851039 MS.gene044284:intron 20.0%
!!! CCTGATTACTGTTTTTTTCA+CGG - chr3.3:68850934-68850953 None:intergenic 30.0%
AACATCATCGGAAATGTGAA+GGG - chr3.3:68850867-68850886 None:intergenic 35.0%
CCGTGAAAAAAACAGTAATC+AGG + chr3.3:68850931-68850950 MS.gene044284:CDS 35.0%
CTTGGAAAGTTGTTAAAGCA+GGG - chr3.3:68851155-68851174 None:intergenic 35.0%
TTCTACCATTAATAAGGGCA+TGG - chr3.3:68851083-68851102 None:intergenic 35.0%
TTGGAAAGTTGTTAAAGCAG+GGG - chr3.3:68851154-68851173 None:intergenic 35.0%
! AAGATCATCTTCAGCTTTTG+CGG - chr3.3:68851124-68851143 None:intergenic 35.0%
! TCTACCATTAATAAGGGCAT+GGG - chr3.3:68851082-68851101 None:intergenic 35.0%
ACATCATCGGAAATGTGAAG+GGG - chr3.3:68850866-68850885 None:intergenic 40.0%
GAACATCATCGGAAATGTGA+AGG - chr3.3:68850868-68850887 None:intergenic 40.0%
GCTTGGAAAGTTGTTAAAGC+AGG - chr3.3:68851156-68851175 None:intergenic 40.0%
GTAATAGTCCAATGCAAGCT+TGG - chr3.3:68850912-68850931 None:intergenic 40.0%
TGTACCCATGCCCTTATTAA+TGG + chr3.3:68851075-68851094 MS.gene044284:CDS 40.0%
TGTTCGAGATAAACAACCTG+TGG + chr3.3:68851188-68851207 MS.gene044284:CDS 40.0%
! ATCTTCAGCTTTTGCGGTAA+AGG - chr3.3:68851118-68851137 None:intergenic 40.0%
AGGCCATGAAACACAAAAGC+TGG - chr3.3:68851048-68851067 None:intergenic 45.0%
GAACACAGCATACTTCAGCT+TGG - chr3.3:68851173-68851192 None:intergenic 45.0%
GAGAATAGGGCGAACATCAT+CGG - chr3.3:68850879-68850898 None:intergenic 45.0%
! AGTTGTTAAAGCAGGGGTGT+CGG - chr3.3:68851148-68851167 None:intergenic 45.0%
! GGTCCAGCTTTTGTGTTTCA+TGG + chr3.3:68851042-68851061 MS.gene044284:CDS 45.0%
! TGGAGTGTCCTTCGAGAATA+GGG - chr3.3:68850892-68850911 None:intergenic 45.0%
! TTGGAGTGTCCTTCGAGAAT+AGG - chr3.3:68850893-68850912 None:intergenic 45.0%
!! ATGGCACACTTTTTGACCAC+AGG - chr3.3:68851207-68851226 None:intergenic 45.0%
AGGACACTCCAAGCTTGCAT+TGG + chr3.3:68850901-68850920 MS.gene044284:CDS 50.0%
GATGTTCGCCCTATTCTCGA+AGG + chr3.3:68850881-68850900 MS.gene044284:CDS 50.0%
GGGCATGGGTACACTTAACA+AGG - chr3.3:68851068-68851087 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 68850848 68851239 68850848 ID=MS.gene044284
chr3.3 mRNA 68850848 68851239 68850848 ID=MS.gene044284.t1;Parent=MS.gene044284
chr3.3 exon 68850848 68850952 68850848 ID=MS.gene044284.t1.exon1;Parent=MS.gene044284.t1
chr3.3 CDS 68850848 68850952 68850848 ID=cds.MS.gene044284.t1;Parent=MS.gene044284.t1
chr3.3 exon 68851042 68851239 68851042 ID=MS.gene044284.t1.exon2;Parent=MS.gene044284.t1
chr3.3 CDS 68851042 68851239 68851042 ID=cds.MS.gene044284.t1;Parent=MS.gene044284.t1
Gene Sequence

>MS.gene044284

ATGGGCTGTATCATACCCCTTCACATTTCCGATGATGTTCGCCCTATTCTCGAAGGACACTCCAAGCTTGCATTGGACTATTACCGTGAAAAAAACAGTAATCAGGTTCGATACTAAGAGAATGAATTTTTTTTGTATGTTGTTTATTCATTAACCAAACTAATTAATTGTTCTTCTTCATTATGTTATATTAGGGTCCAGCTTTTGTGTTTCATGGCCTTGTTAAGTGTACCCATGCCCTTATTAATGGTAGAATCTATTACATTACCTTTACCGCAAAAGCTGAAGATGATCTTTCCGACACCCCTGCTTTAACAACTTTCCAAGCTGAAGTATGCTGTGTTCGAGATAAACAACCTGTGGTCAAAAAGTGTGCCATTAAAATCACCTGA
Protein sequence

>MS.gene044284.t1

MGCIIPLHISDDVRPILEGHSKLALDYYREKNSNQGPAFVFHGLVKCTHALINGRIYYITFTAKAEDDLSDTPALTTFQAEVCCVRDKQPVVKKCAIKIT