Markers + reference

Dicliptera

5 species · Acanthaceae · Lamiales

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Species 5
Genome length 151–151 kb
Candidate markers 270
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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 291 0.0027 1.00 31.8 yes View details
rps16 LSC 1159 0.0010 1.00 37.6 yes View details
petN-psbM LSC 973 0.0078 1.00 57.2 yes View details
trnE-UUC-trnT-GGU LSC 608 0.0026 1.00 50.5 yes View details
psbZ-trnG-GCC LSC 289 0.0106 1.00 53.8 yes View details
rps4-trnT-UGU LSC 606 0.0033 0.99 54.6 yes View details
rbcL-accD LSC 745 0.0016 1.00 48.7 yes View details
ndhF SSC 2295 0.0009 1.00 50.6 yes View details
ycf1 SSC 5337 0.0009 1.00 42.9 yes View details
rpl2-trnH-GUG IRa 167 0.0000 1.00 71.2 no View details
ndhA SSC 2097 0.0004 1.00 57.9 yes View details
matK LSC 1509 0.0011 1.00 52.7 yes View details
petB LSC 1356 0.0009 1.00 51.9 yes View details
rpoB-trnC-GCA LSC 1213 0.0007 1.00 51.8 yes View details
atpF LSC 1264 0.0000 1.00 51.5 yes View details
trnT-GGU-psbD LSC 1166 0.0003 1.00 48.8 yes View details
rps16-trnQ-UUG LSC 713 0.0011 1.00 48.4 yes View details
trnS-GCU-trnG-UCC LSC 672 0.0012 1.00 48.4 yes View details
accD-psaI LSC 705 0.0011 1.00 48.4 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 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 GATCCACTTGGCTACATCCG CCCTCTAGATTTAGCTGCTAGC 355 1.000 61.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCCTCTAGATTTAGCTGCTAGC 369 1.000 61.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCCTCTAGATTTAGCTGCTAGC 368 1.000 61.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCCTCTAGATTTAGCTGCTAGC 370 1.000 61.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAATCTTGGTATGGA 406 1.000 59.7
trnK-UUU_p1 trnK-UUU ACTCCCAAGCACACGAAATT TGCAATGGTTTGATTAGCTCG 2740–2749 1.000 66.1
trnK-UUU_p2 trnK-UUU ACTCCCAAGCACACGAAATT GCAATGGTTTGATTAGCTCGT 2739–2748 1.000 66.1
trnK-UUU_p3 trnK-UUU GACTCCCAAGCACACGAAAT TGCAATGGTTTGATTAGCTCG 2741–2750 1.000 62.5
trnK-UUU_p4 trnK-UUU GACTCCCAAGCACACGAAAT GCAATGGTTTGATTAGCTCGT 2740–2749 1.000 62.4
trnK-UUU_p5 trnK-UUU ACTCCCAAGCACACGAAATT TCAGTGCAATGGTTTGATTAGC 2744–2753 1.000 60.7
matK_p1 matK ACGGCTTTCCCTATGTATACA AAGTTTACCTGCTTCCGAGG 1738–1747 1.000 54.7
matK_p2 matK ACGGCTTTCCCTATGTATACA AGTTTACCTGCTTCCGAGGT 1737–1746 1.000 53.2
matK_p3 matK ACGGCTTTCCCTATGTATACA ACCTGCTTCCGAGGTATCTA 1732–1741 1.000 52.5
matK_p4 matK ACGGCTTTCCCTATGTATACA TACCTGCTTCCGAGGTATCT 1733–1742 1.000 52.5
matK_p5 matK CGGCTTTCCCTATGTATACATCA AAGTTTACCTGCTTCCGAGG 1737–1746 1.000 51.6
rps16_p1 rps16 ATTGAAGCTATGGGGCCCTA GAGGTTCGAATCCTTCCGTC 2591–2592 1.000 78.2
rps16_p2 rps16 TTGAAGCTATGGGGCCCTAT GAGGTTCGAATCCTTCCGTC 2590–2591 1.000 78.2
rps16_p3 rps16 AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2342–2343 1.000 78.2
rps16_p4 rps16 AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2341–2342 1.000 78.2
rps16_p5 rps16 CGGTCTTCGAAATCACACCA GAGGTTCGAATCCTTCCGTC 2420–2421 1.000 77.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC GAGGTTCGAATCCTTCCGTC 774–775 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATTCTGCCCTTCAAG GAGGTTCGAATCCTTCCGTC 803–804 1.000 78.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC AAAATTGAAATGGGGCGTGG 832–833 1.000 76.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAACGGATTCTGCCCTTCAA GAGGTTCGAATCCTTCCGTC 804–805 1.000 75.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACGGATTCTGCCCTTCAAG AAAATTGAAATGGGGCGTGG 861–862 1.000 75.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 741 1.000 51.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 740 1.000 51.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGAATATGACCGAAAGAACCT 783 1.000 51.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGAATATGACCGAAAGAACCT 782 1.000 51.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 795 1.000 50.7

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
Dicliptera acuminata MK830556.1 150738 View on NCBI ↗
Dicliptera montana MK833946.1 150689 View on NCBI ↗
Dicliptera mucronata MK848596.1 150720 View on NCBI ↗
Dicliptera peruviana MK833945.1 150811 View on NCBI ↗
Dicliptera ruiziana MK833947.1 150750 View on NCBI ↗