Markers + reference

Petrocodon

5 species · Gesneriaceae · Lamiales

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Species 5
Genome length 153–154 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 308 0.0689 1.00 77.7 yes View details
trnK-UUU-rps16 LSC 806 0.0190 1.00 58.8 yes View details
trnS-GCU-trnG-UCC LSC 850 0.0168 1.00 63.1 yes View details
trnG-UCC-trnR-UCU LSC 209 0.0817 1.00 78.4 yes View details
rpoB-trnC-GCA LSC 978 0.0183 1.00 63.4 yes View details
psbE-petL LSC 909 0.0165 1.00 58.7 yes View details
petD LSC 1240 0.0105 1.00 54.2 yes View details
ycf1 IRb 779 0.0008 1.00 26.1 no View details
ndhF-rpl32 SSC 715 0.0193 1.00 61.5 yes View details
rpl32-trnL-UAG SSC 866 0.0177 1.00 63.0 yes View details
ycf1 SSC 5358 0.0142 1.00 49.9 yes View details
psbI-trnS-GCU LSC 116 0.0491 1.00 77.3 yes View details
atpA-atpF LSC 64 0.0783 0.98 74.4 yes View details
rps16-trnQ-UUG LSC 1077 0.0167 1.00 70.7 yes View details
ccsA-ndhD SSC 251 0.0239 1.00 67.8 yes View details
ycf3-trnS-GGA LSC 851 0.0112 1.00 67.0 yes View details
trnA-UGC-rrn23 IRb 152 0.0289 0.97 64.6 yes View details
trnE-UUC-trnT-GGU LSC 688 0.0118 1.00 63.0 yes View details
clpP-psbB LSC 455 0.0092 1.00 62.6 yes View details
ndhC-trnV-UAC LSC 1054 0.0160 1.00 62.3 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 100 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 TCAGTGCTATGCATGGTTCC 688–760 1.000 87.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 702–774 1.000 87.0
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 687–759 1.000 87.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 701–773 1.000 87.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 703–775 1.000 87.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT GCCGTACGAGGAGAAAACTT 1201–1207 1.000 82.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT TCTATCCCAATGAGCCGTCT 1145–1151 1.000 82.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT AGCCGTCTATCGAATCGTTG 1133–1139 1.000 81.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT TCGATCCCGAAGAGAAGGAA 1103–1109 1.000 81.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT CCGTCTATCGAATCGTTGCA 1131–1137 1.000 81.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1146–1168 1.000 84.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1129–1151 1.000 84.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1147–1169 1.000 83.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1144–1166 1.000 82.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1143–1165 1.000 82.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTATTCGTACCGAGGGTTCG 176–179 1.000 71.6
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTCGAATCCCTCTCTTTCCG 160–163 1.000 71.3
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGTTCGAATCCCTCTCTTT 163–166 1.000 70.2
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGTTCGAATCCCTCTCTTTC 163–166 1.000 70.2
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGTTCGAATCCCTCTCTTTCC 162–165 1.000 70.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 863–912 1.000 46.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC AGAACGAATCACACTTTTACCAC 866–915 1.000 46.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC GAACGAATCACACTTTTACCACT 865–914 1.000 46.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC AGGGTTAAAAGAACGAATCACAC 875–924 1.000 46.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC GGGTTAAAAGAACGAATCACACT 874–923 1.000 46.8
trnG-UCC_p1 trnG-UCC TCCCCACGAAAAACGCTTAT AGGGACCGGTTTCTACTTCA 1276–1289 1.000 83.1
trnG-UCC_p2 trnG-UCC TCCCCACGAAAAACGCTTAT GGAACATAGGGACCGGTTTC 1283–1296 1.000 82.9
trnG-UCC_p3 trnG-UCC TCCCCACGAAAAACGCTTAT GAGGAAGCAGAAGCCCTTTT 1318–1331 1.000 82.4
trnG-UCC_p4 trnG-UCC TATCTCCCCACGAAAAACGC AGGGACCGGTTTCTACTTCA 1280–1293 1.000 82.4
trnG-UCC_p5 trnG-UCC TATCTCCCCACGAAAAACGC GGAACATAGGGACCGGTTTC 1287–1300 1.000 82.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Petrocodon coriaceifolius NC_065790.1 153292 View on NCBI ↗
Petrocodon gracilis PQ636880.1 153547 View on NCBI ↗
Petrocodon hancei PQ636881.1 153294 View on NCBI ↗
Petrocodon longitubus NC_068074.1 152958 View on NCBI ↗
Petrocodon multiflorus NC_065791.1 153227 View on NCBI ↗