Markers + reference

Petrocosmea

8 species · Gesneriaceae · Lamiales

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Species 8
Genome length 152–154 kb
Candidate markers 264
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 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
trnH-GUG-psbA LSC 328 0.0748 0.91 77.3 yes View details
rps16 LSC 1115 0.0144 1.00 59.6 yes View details
trnS-GCU-trnG-UCC LSC 807 0.0262 1.00 74.5 yes View details
ndhC-trnV-UAC LSC 999 0.0192 1.00 67.0 yes View details
petD LSC 1241 0.0143 1.00 58.8 yes View details
ndhF-rpl32 SSC 352 0.0370 0.94 74.1 yes View details
rpl32-trnL-UAG SSC 868 0.0223 1.00 67.6 yes View details
rps15-ycf1 SSC 369 0.0316 1.00 66.7 yes View details
ycf1 SSC 4683 0.0169 1.00 53.3 yes View details
ndhD-psaC SSC 101 0.0685 1.00 80.1 yes View details
ccsA-ndhD SSC 242 0.0406 0.99 73.6 yes View details
atpF-atpH LSC 375 0.0174 1.00 69.7 yes View details
rps16-trnQ-UUG LSC 1060 0.0154 1.00 67.9 yes View details
psbK-psbI LSC 405 0.0240 1.00 66.5 yes View details
ycf3-trnS-GGA LSC 876 0.0154 0.99 65.4 yes View details
trnC-GCA-petN LSC 756 0.0121 1.00 64.6 yes View details
trnK-UUU-rps16 LSC 822 0.0169 1.00 63.9 yes View details
psbI-trnS-GCU LSC 117 0.0296 0.99 63.9 yes View details
psbE-petL LSC 907 0.0119 1.00 63.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA ATCCACTTGGCTACATCCG TCCCTCTAGATCTAGCTGCT 352–393 1.000 61.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ATCCACTTGGCTACATCCGC TCCCTCTAGATCTAGCTGCT 352–393 1.000 61.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CCACTTGGCTACATCCGC TCCCTCTAGATCTAGCTGCT 350–391 1.000 61.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ATCCACTTGGCTACATCCG TTCCCTCTAGATCTAGCTGCT 353–394 1.000 60.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ATCCACTTGGCTACATCCGC TTCCCTCTAGATCTAGCTGCT 353–394 1.000 59.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTCCCGTATCAGGTACT GCCGTACGAGGAGAAAACTT 1276–1484 1.000 85.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTCCCGTATCAGGTACT CAAAGTGTATTACGCGGGGA 1722–1930 0.875 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTCCCGTATCAGGTACT TCAAAGTGTATTACGCGGGG 1723–1931 0.875 81.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGGGTCTTCCAAACCATACC CAAAGTGTATTACGCGGGGA 1456–1664 0.875 81.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGGGTCTTCCAAACCATACC TCAAAGTGTATTACGCGGGG 1457–1665 0.875 81.1
rps16_p1 rps16 TACGAATCGAGCAAGAAGGG AAACATGCTGCTTATTGGCG 1707–1740 0.875 73.8
rps16_p2 rps16 GGATTCGACGGAAGGAATGA AAACATGCTGCTTATTGGCG 1735–1768 0.875 73.6
rps16_p3 rps16 CGGATTCGACGGAAGGAATG AAACATGCTGCTTATTGGCG 1736–1769 0.875 72.0
rps16_p4 rps16 TACGAATCGAGCAAGAAGGG AACATGCTGCTTATTGGCGA 1706–1739 0.875 71.7
rps16_p5 rps16 TACGAATCGAGCAAGAAGGG ACATGCTGCTTATTGGCGAA 1705–1738 0.875 71.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 916–1175 1.000 86.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 899–1158 1.000 85.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 917–1176 1.000 85.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 914–1173 1.000 83.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 913–1172 1.000 83.9
psbK-psbI_p1 psbK-psbI GGGGGATTTTGTGATTGGGT TGGACTAAAGCGTCGGATTG 1008–1042 1.000 85.4
psbK-psbI_p2 psbK-psbI GGGGGATTTTGTGATTGGGT GTGGACTAAAGCGTCGGATT 1009–1043 1.000 85.4
psbK-psbI_p3 psbK-psbI TGGGGGATTTTGTGATTGGG TGGACTAAAGCGTCGGATTG 1009–1043 1.000 85.4
psbK-psbI_p4 psbK-psbI GGGGGATTTTGTGATTGGGT CACTTTTCAGCCCTTCCCTT 1176–1212 1.000 85.3
psbK-psbI_p5 psbK-psbI TGGGGGATTTTGTGATTGGG CACTTTTCAGCCCTTCCCTT 1177–1213 1.000 85.3
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 213–214 1.000 76.2
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 214–215 1.000 76.2
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 232–233 1.000 75.1
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 213–214 1.000 73.9
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 214–215 1.000 73.9

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
Petrocosmea chiwui PQ279899.1 153380 View on NCBI ↗
Petrocosmea duyunensis PQ279898.1 152270 View on NCBI ↗
Petrocosmea forrestii PQ279896.1 153435 View on NCBI ↗
Petrocosmea grandifolia PQ279897.1 153616 View on NCBI ↗
Petrocosmea kerrii var. crinita PQ279903.1 153617 View on NCBI ↗
Petrocosmea minor PQ279901.1 153305 View on NCBI ↗
Petrocosmea pengzhouensis PV750053.1 153088 View on NCBI ↗
Petrocosmea rotundifolia PQ279902.1 153279 View on NCBI ↗