Markers + reference

Renanthera

4 species · Orchidaceae · Asparagales

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Species 4
Genome length 145–149 kb
Candidate markers 246
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 246 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 1321 0.0495 0.91 80.2 yes View details
rpoB-trnC-GCA LSC 1809 0.0412 0.88 74.4 yes View details
trnE-UUC-trnT-GGU LSC 882 0.0378 0.91 79.0 yes View details
rbcL-accD LSC 807 0.0392 1.00 75.6 yes View details
clpP-psbB LSC 696 0.0459 0.97 80.1 yes View details
trnN-GUU-rpl32 SSC 816 0.0709 0.91 83.3 yes View details
psaC-rps15 SSC 1850 0.0319 0.98 69.6 yes View details
trnR-UCU-atpA LSC 156 0.0556 1.00 76.3 yes View details
trnF-GAA-trnV-UAC LSC 577 0.0326 1.00 76.1 yes View details
psbT-psbN LSC 62 0.0484 1.00 75.2 yes View details
petD-rpoA LSC 172 0.0446 1.00 74.0 yes View details
psbE-petL LSC 1138 0.0259 1.00 73.5 yes View details
psbB-psbT LSC 391 0.0348 0.94 72.7 yes View details
psbA-trnK-UUU LSC 238 0.0406 1.00 71.2 yes View details
trnG-GCC-trnR-UCU LSC 140 0.0381 0.91 70.4 yes View details
psbM-trnD-GUC LSC 1139 0.0196 0.99 67.4 yes View details
psbI-trnS-GCU LSC 174 0.0326 0.99 67.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTCCATCCGACTAGTTCCG 315–325 1.000 80.5
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTAGTTCCGGGTTCGAGTC 305–315 1.000 78.9
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC GACTAGTTCCGGGTTCGAGT 306–316 1.000 78.9
psbA-trnK-UUU_p4 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ATCCGACTAGTTCCGGGTTC 310–320 1.000 78.4
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT ACTCCATCCGACTAGTTCCG 312–322 1.000 78.3
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA GGGTTCGAATCCCTCTCTCT 211–220 1.000 82.8
psbI-trnS-GCU_p2 psbI-trnS-GCU CTTATCTAACGATCCGGGGC GGGTTCGAATCCCTCTCTCT 231–240 1.000 82.7
psbI-trnS-GCU_p3 psbI-trnS-GCU CTTATCTAACGATCCGGGGC TTCGAATCCCTCTCTCTCCG 228–237 1.000 82.0
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA TTCGAATCCCTCTCTCTCCG 208–217 1.000 82.0
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAAT GGGTTCGAATCCCTCTCTCT 211–220 1.000 77.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 925–1420 1.000 62.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 924–1419 1.000 62.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 928–1423 1.000 61.2
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 927–1422 1.000 61.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 926–1421 1.000 61.2
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 207–220 1.000 70.4
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 210–223 1.000 70.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 213–226 1.000 69.6
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 216–229 1.000 69.4
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCAACGTCGACTATAACCCC AGAAGACCTCTGTCCTATCCA 228–241 1.000 68.6
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CGGCAGCTCAAATTAAAGCC 826–859 1.000 84.7
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCCTGGTCGTGAAGCTTATC 1089–1122 1.000 83.7
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCTGGTCGTGAAGCTTATCC 1088–1121 1.000 83.7
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GGTCGTGAAGCTTATCCAGG 1085–1118 1.000 83.7
trnR-UCU-atpA_p5 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GGTCGTGAAGCTTATCCAGG 1088–1121 1.000 83.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA CCGGGGATAAAGGATTTGCA 1377–1892 1.000 79.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC CCGGGGATAAAGGATTTGCA 1378–1893 1.000 79.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA ACCGGGGATAAAGGATTTGC 1378–1893 1.000 79.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC ACCGGGGATAAAGGATTTGC 1379–1894 1.000 79.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA TCGAACCGGGGATAAAGGAT 1382–1897 1.000 78.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Renanthera citrina NC_066482.1 146255 View on NCBI ↗
Renanthera coccinea NC_066483.1 149007 View on NCBI ↗
Renanthera imschootiana NC_066484.1 144673 View on NCBI ↗
Renanthera philippinensis NC_066485.1 147713 View on NCBI ↗