Markers + reference

Phryma

2 species · Phrymaceae · Lamiales

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Species 2
Genome length 153–153 kb
Candidate markers 268
Primer pairs 105

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 11 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 538 0.0039 0.95 56.5 yes View details
rps16-trnQ-UUG LSC 1190 0.0017 0.97 62.4 yes View details
trnS-GGA-rps4 LSC 325 0.0100 0.92 62.7 yes View details
clpP1 LSC 1966 0.0041 1.00 60.2 yes View details
rps19 LSC 279 0.0036 1.00 43.2 yes View details
rpl2 IRb 1492 0.0000 1.00 25.8 no View details
ndhF SSC 2244 0.0013 1.00 48.2 yes View details
ndhD SSC 1503 0.0013 1.00 45.0 yes View details
ndhA SSC 2172 0.0014 1.00 52.1 yes View details
ndhH SSC 1182 0.0042 1.00 60.7 yes View details
rpl2 IRa 1492 0.0000 1.00 25.8 yes View details
rpl2-trnH-GUG IRa 74 0.0714 0.76 79.3 no View details
ndhC-trnV-UAC LSC 1173 0.0026 0.99 61.1 yes View details
accD-psaI LSC 618 0.0016 0.99 60.6 yes View details
trnS-GCU-trnG-UCC LSC 708 0.0028 1.00 60.4 yes View details
ycf1 IRb 753 0.0027 1.00 60.3 yes View details
rpoB-trnC-GCA LSC 1204 0.0025 1.00 60.2 yes View details
trnK-UUU-rps16 LSC 906 0.0022 1.00 60.1 yes View details
trnT-UGU-trnL-UAA LSC 599 0.0017 1.00 59.7 yes View details
rpl16 LSC 1279 0.0008 1.00 59.7 yes View details
cemA LSC 690 0.0014 1.00 59.6 yes View details
ycf1 SSC 5112 0.0008 1.00 52.9 no 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 TTCCCTCTAGACCTAGCTGC 578–604 1.000 82.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 592–618 1.000 82.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 591–617 1.000 82.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 593–619 1.000 82.2
trnH-GUG-psbA_p5 trnH-GUG-psbA TAGACAATCATGGGCGAACG TTCCCTCTAGACCTAGCTGC 669 0.500 58.9
trnK-UUU_p1 trnK-UUU TTCGTGTCAACCAATCCCAA CTTTGTTGAAGGTTGAAATTTGA 2746–2747 1.000 40.1
trnK-UUU_p2 trnK-UUU TTCGTGTCAACCAATCCCAA TTGTTGAAGGTTGAAATTTGA 2744–2745 1.000 40.1
trnK-UUU_p3 trnK-UUU TCGTGTCAACCAATCCCAAT CTTTGTTGAAGGTTGAAATTTGA 2745–2746 1.000 40.1
trnK-UUU_p4 trnK-UUU TTCGTGTCAACCAATCCCAA TTTGTTGAAGGTTGAAATTTGA 2745–2746 1.000 40.1
trnK-UUU_p5 trnK-UUU TCGTGTCAACCAATCCCAAT TTGTTGAAGGTTGAAATTTGA 2743–2744 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 1028–1029 1.000 65.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 1027–1028 1.000 65.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GTGCTCAACCCACAGGAAC 1042–1043 1.000 64.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCCACAGGAACT 1027–1028 1.000 64.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGGAACT 1026–1027 1.000 64.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCACAAGGGATCATGTCCT GAAATTCAAATGGGGCGTGG 1333–1343 1.000 81.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACAAGGGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1275–1285 1.000 81.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTCAAATGGGGCGTGG 1311–1321 1.000 80.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1253–1263 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATTCAAATGGGGCGTGG 1322–1332 1.000 80.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCTTTAACT 814 1.000 52.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCTTTAACT 813 1.000 52.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 777 1.000 51.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 776 1.000 51.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCTTTAACT 868 1.000 50.9
trnG-UCC_p1 trnG-UCC CAATCCGACGCTTTAGTCCA AAGCAATCAAGTGCCTTGGA 1833–1840 1.000 80.3
trnG-UCC_p2 trnG-UCC AATCCGACGCTTTAGTCCAC AAGCAATCAAGTGCCTTGGA 1832–1839 1.000 80.3
trnG-UCC_p3 trnG-UCC CAATCCGACGCTTTAGTCCA CCAAGCAGCTCCTCTTACAG 2112–2119 1.000 80.1
trnG-UCC_p4 trnG-UCC AATCCGACGCTTTAGTCCAC CCAAGCAGCTCCTCTTACAG 2111–2118 1.000 80.0
trnG-UCC_p5 trnG-UCC TATTTTGATGGCCCGACCTG AAGCAATCAAGTGCCTTGGA 1587–1594 1.000 79.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Phryma leptostachya PQ443460.1 153325 View on NCBI ↗
Phryma leptostachya subsp. asiatica NC_042727.1 153167 View on NCBI ↗