Markers + reference

Griffitharia

8 species · Rosaceae · Rosales

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Species 8
Genome length 159–160 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 263 0.0182 1.00 55.7 yes View details
trnK-UUU-rps16 LSC 957 0.0056 0.98 47.4 yes View details
trnR-UCU-atpA LSC 398 0.0169 1.00 61.7 yes View details
atpH-atpI LSC 1195 0.0038 1.00 62.9 yes View details
rpoC1 LSC 2792 0.0015 1.00 35.7 yes View details
trnT-GGU-psbD LSC 1399 0.0029 1.00 46.6 yes View details
psbZ-trnG-GCC LSC 424 0.0073 1.00 59.7 yes View details
rps4-trnT-UGU LSC 397 0.0115 1.00 55.0 yes View details
trnT-UGU-trnL-UAA LSC 1213 0.0024 1.00 50.0 yes View details
trnL-UAA-trnF-GAA LSC 397 0.0050 1.00 37.7 yes View details
ndhC-trnV-UAC LSC 581 0.0082 1.00 63.6 yes View details
rpl36-infA LSC 269 0.0019 1.00 25.5 yes View details
ycf4-cemA LSC 557 0.0027 1.00 60.3 yes View details
ndhF-rpl32 SSC 1061 0.0035 0.98 59.3 yes View details
rpl32-trnL-UAG SSC 1442 0.0028 0.98 57.5 yes View details
psbM-trnD-GUC LSC 1252 0.0019 0.98 55.3 yes View details
accD-psaI LSC 811 0.0044 1.00 54.8 yes View details
rpl33-rps18 LSC 218 0.0082 1.00 54.5 yes View details
clpP LSC 2028 0.0014 1.00 54.5 yes View details
trnC-GCA-petN LSC 935 0.0031 1.00 54.4 yes View details
ndhF SSC 2256 0.0015 1.00 52.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 372–383 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 386–397 1.000 83.2
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 384–394 0.875 78.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 387–397 0.875 77.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 434–444 0.875 77.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGGAACTTCGCCCTAATCAA 1099–1139 1.000 83.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CGGAACTTCGCCCTAATCAA 1095–1135 1.000 82.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 1253–1293 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AACCGTAGTAGGGCTCTACC CGGAACTTCGCCCTAATCAA 1262–1302 1.000 82.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1357–1397 1.000 82.1
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 567–1241 1.000 68.5
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 566–1240 1.000 68.5
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 506–1180 1.000 67.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 567–1241 1.000 64.5
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGGAATGAAAAGCGTCCAT AGACATTTACCGACGAAGCG 568–1242 1.000 64.5
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1278–1292 1.000 81.0
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1244–1258 1.000 81.0
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1308–1322 1.000 80.2
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1274–1288 1.000 80.1
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1245–1259 1.000 79.8
rpoC1_p1 rpoC1 GGTGAACTGGAGAAACCCAA TTTGGCTCTGGAACTGAACC 2952–2964 1.000 77.5
rpoC1_p2 rpoC1 GGTGAACTGGAGAAACCCAA TTGCTCGTTCGAGAACTACG 2975–2987 1.000 77.3
rpoC1_p3 rpoC1 GAAACCCAAAATGACACGGG TTTGGCTCTGGAACTGAACC 2941–2953 1.000 76.9
rpoC1_p4 rpoC1 GGTGAACTGGAGAAACCCAA ACGATCTTTGGCTCTGGAAC 2958–2970 1.000 76.8
rpoC1_p5 rpoC1 GAAACCCAAAATGACACGGG TTGCTCGTTCGAGAACTACG 2964–2976 1.000 76.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGATTTACT 972–1008 1.000 81.5
trnC-GCA-petN_p2 trnC-GCA-petN GTATCATTTTGGCGGCATGG CAGCCCAAGCGAGATTTACT 1024–1060 1.000 81.0
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGTCCACTCCTTCCCCATAC 1030–1066 1.000 80.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GTCCACTCCTTCCCCATACT 1029–1065 1.000 80.7
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG GTCCACTCCTTCCCCATACT 1081–1117 1.000 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Griffitharia atrosanguinea PQ899559.1 159466 View on NCBI ↗
Griffitharia guanii PQ899560.1 159466 View on NCBI ↗
Griffitharia hemsleyi NC_062340.1 159767 View on NCBI ↗
Griffitharia heseltinei OQ100075.1 159982 View on NCBI ↗
Griffitharia needhamii PQ899561.1 160362 View on NCBI ↗
Griffitharia pallescens NC_085660.1 159513 View on NCBI ↗
Griffitharia schwerinii OQ100081.1 159811 View on NCBI ↗
Griffitharia thibetica OQ100077.1 159884 View on NCBI ↗