Markers + reference

Sonchus

17 species · Asteraceae · Asterales

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Species 17
Genome length 152–152 kb
Candidate markers 264
Primer pairs 65

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
HRV17_pgt001-psbA Genome 401 0.0160 1.00 63.0 yes View details
HRV17_pgt015-HRV17_pgt016 Genome 581 0.0124 0.99 64.8 yes View details
HRV17_pgp043 Genome 69200 0.0027 1.00 44.2 yes View details
rpl32-ndhF Genome 1082 0.0106 0.98 66.5 yes View details
atpA-HRV17_pgt009 Genome 131 0.0257 0.96 66.2 yes View details
petA-psbJ Genome 775 0.0088 1.00 64.6 yes View details
ndhD-ccsA Genome 263 0.0209 1.00 63.4 yes View details
HRV17_pgt017-ndhJ Genome 590 0.0052 1.00 60.9 yes View details
ndhC-HRV17_pgt018 Genome 1215 0.0058 0.99 60.1 yes View details
petN-psbM Genome 483 0.0115 1.00 58.1 yes View details
ycf3-HRV17_pgt014 Genome 920 0.0067 1.00 57.7 yes View details
HRV17_pgt008-rpoB Genome 915 0.0070 1.00 57.6 yes View details
HRV17_pgt005-petN Genome 672 0.0068 0.97 57.1 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
HRV17_pgt001-psbA_p1 HRV17_pgt001-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 519–550 1.000 81.9
HRV17_pgt001-psbA_p2 HRV17_pgt001-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 533–564 1.000 81.7
HRV17_pgt001-psbA_p3 HRV17_pgt001-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 532–563 1.000 81.7
HRV17_pgt001-psbA_p4 HRV17_pgt001-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 534–565 1.000 81.7
HRV17_pgt001-psbA_p5 HRV17_pgt001-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 520–551 1.000 81.4
HRV17_pgt005-petN_p1 HRV17_pgt005-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 729–885 1.000 83.0
HRV17_pgt005-petN_p2 HRV17_pgt005-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 747–903 1.000 80.7
HRV17_pgt005-petN_p3 HRV17_pgt005-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 728–884 1.000 77.0
HRV17_pgt005-petN_p4 HRV17_pgt005-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 737–893 1.000 76.9
HRV17_pgt005-petN_p5 HRV17_pgt005-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 786–942 1.000 76.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 641–649 1.000 63.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 641–649 1.000 61.6
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 642–650 1.000 57.3
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 633–641 1.000 57.3
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 627–635 1.000 56.6
HRV17_pgt008-rpoB_p1 HRV17_pgt008-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 1034–1079 1.000 67.8
HRV17_pgt008-rpoB_p2 HRV17_pgt008-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 993–1038 1.000 67.4
HRV17_pgt008-rpoB_p3 HRV17_pgt008-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 1024–1069 1.000 67.1
HRV17_pgt008-rpoB_p4 HRV17_pgt008-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 1029–1074 1.000 67.0
HRV17_pgt008-rpoB_p5 HRV17_pgt008-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 1024–1069 1.000 66.5
atpA-HRV17_pgt009_p1 atpA-HRV17_pgt009 TACTTCAGGAACAAGCAGCC GCAATGAAAAGCGTCCATTGT 200–240 1.000 75.8
atpA-HRV17_pgt009_p2 atpA-HRV17_pgt009 CATTCACCGAGGAAGCAGAA GCAATGAAAAGCGTCCATTGT 263–303 1.000 75.6
atpA-HRV17_pgt009_p3 atpA-HRV17_pgt009 AAGACATTCACCGAGGAAGC GCAATGAAAAGCGTCCATTGT 267–307 1.000 75.6
atpA-HRV17_pgt009_p4 atpA-HRV17_pgt009 CATTCACCGAGGAAGCAGAA GCAATGAAAAGCGTCCATTG 263–303 1.000 74.8
atpA-HRV17_pgt009_p5 atpA-HRV17_pgt009 AAGACATTCACCGAGGAAGC GCAATGAAAAGCGTCCATTG 267–307 1.000 74.8
ycf3-HRV17_pgt014_p1 ycf3-HRV17_pgt014 CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 967–1036 1.000 76.6
ycf3-HRV17_pgt014_p2 ycf3-HRV17_pgt014 CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTCAA 917–986 1.000 76.3
ycf3-HRV17_pgt014_p3 ycf3-HRV17_pgt014 CATTTATCCGCGATCTAGGCA GGATTCGAACCCTCGGTAAG 955–1024 1.000 76.0
ycf3-HRV17_pgt014_p4 ycf3-HRV17_pgt014 CATTTATCCGCGATCTAGGCA AGTTCCAATGCTACGCCTTC 919–988 1.000 75.8
ycf3-HRV17_pgt014_p5 ycf3-HRV17_pgt014 CATTTATCCGCGATCTAGGCA CCTCGGTAAGCAAAAGCCTA 945–1014 1.000 74.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Sonchus asper NC_048510.1 151849 View on NCBI ↗
Sonchus asper subsp. glaucescens PP190475.1 151853 View on NCBI ↗
Sonchus berteroanus NC_051923.1 152199 View on NCBI ↗
Sonchus bipontini NC_086757.1 152180 View on NCBI ↗
Sonchus brassicifolius NC_051922.1 152263 View on NCBI ↗
Sonchus bupleuroides NC_063469.1 152350 View on NCBI ↗
Sonchus fragilis NC_063468.1 152363 View on NCBI ↗
Sonchus grandifolius NC_063467.1 152254 View on NCBI ↗
Sonchus masguindalii NC_063466.1 152392 View on NCBI ↗
Sonchus megalocarpus NC_063465.1 152246 View on NCBI ↗
Sonchus micranthus NC_051921.1 152327 View on NCBI ↗
Sonchus novae-zelandiae NC_063464.1 152443 View on NCBI ↗
Sonchus pruinatus NC_051920.1 152348 View on NCBI ↗
Sonchus pustulatus NC_063463.1 152027 View on NCBI ↗
Sonchus schweinfurthii NC_086759.1 152292 View on NCBI ↗
Sonchus sinuatus NC_051924.1 152263 View on NCBI ↗
Sonchus tenerrimus NC_063462.1 151923 View on NCBI ↗