Markers + reference

Tropidia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 161–161 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0019 1.00 46.2 yes View details
rps16-trnQ-UUG LSC 1287 0.0331 0.92 74.9 yes View details
trnS-GCU-trnG-UCC LSC 1287 0.0167 0.88 58.7 yes View details
trnE-UUC-trnT-GGU LSC 1647 0.0177 0.96 65.4 yes View details
trnL-UAA-trnF-GAA LSC 392 0.0918 1.00 86.7 yes View details
trnW-CCA-trnP-UGG LSC 179 0.0578 0.97 85.2 yes View details
clpP LSC 2180 0.0069 1.00 47.7 yes View details
rpl16 LSC 1703 0.0157 0.90 59.4 yes View details
ndhF-rpl32 SSC 823 0.0458 0.98 77.5 yes View details
rpl32-trnL-UAG SSC 823 0.0182 1.00 57.3 yes View details
rpl22-psbA LSC 91 0.1429 0.92 80.0 no View details
atpF-atpH LSC 562 0.0113 0.95 69.1 yes View details
atpB-rbcL LSC 716 0.0168 1.00 68.4 yes View details
petD-rpoA LSC 155 0.0203 0.95 68.4 yes View details
trnH-GUG-rpl2 IRb 43 0.0233 1.00 65.3 yes View details
rpl2-trnH-GUG IRa 43 0.0233 1.00 65.3 yes View details
psaC-ndhE SSC 622 0.0097 0.99 65.1 yes View details
ndhC-trnV-UAC LSC 1390 0.0087 0.99 64.9 yes View details
ndhH-rps15 SSC 114 0.0439 1.00 64.4 yes View details
trnR-ACG-trnN-GUU IRb 547 0.0110 1.00 64.0 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
psbA_p1 psbA TCTTGTATCTTGGGGGATTGC GTGCTTGGGAGTCCTTGAAA 1168 0.500 49.5
psbA_p2 psbA CTTGTATCTTGGGGGATTGCT GTGCTTGGGAGTCCTTGAAA 1167 0.500 49.4
psbA_p3 psbA TCTTGTATCTTGGGGGATTGC CATAGGGAAAGTCGTGTGCA 1425 0.500 48.9
psbA_p4 psbA TCTTGTATCTTGGGGGATTGC AATACGTGTGCTTGGGAGTC 1175 0.500 48.9
psbA_p5 psbA TCTTGTATCTTGGGGGATTGC ACATAGGGAAAGTCGTGTGC 1426 0.500 48.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 1280–1383 1.000 85.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1257–1360 1.000 84.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1278–1381 1.000 84.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 1284–1387 1.000 84.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1268–1371 1.000 84.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1204–1356 1.000 56.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1203–1355 1.000 56.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAATCACACTTTTACCACT 1205–1357 1.000 54.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACGAATCACACTTTTACCACT 1204–1356 1.000 54.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA ACGAATCACACTTTTACCACT 1257–1409 1.000 54.3
atpF-atpH_p1 atpF-atpH TTAACTCGAAACTCCCAGCG AATTTATGGGCTGGTCGTGG 656–684 1.000 81.8
atpF-atpH_p2 atpF-atpH TTAACTCGAAACTCCCAGCG GGTCGTGGCATTAGCTCTTT 644–672 1.000 81.7
atpF-atpH_p3 atpF-atpH TTAACTCGAAACTCCCAGCG ACAATTTATGGGCTGGTCGT 658–686 1.000 79.6
atpF-atpH_p4 atpF-atpH TTAACTCGAAACTCCCAGCG CAATTTATGGGCTGGTCGTG 657–685 1.000 76.9
atpF-atpH_p5 atpF-atpH TAACTCGAAACTCCCAGCGA AATTTATGGGCTGGTCGTGG 655–683 1.000 76.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1751–1824 1.000 82.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 1730–1803 1.000 82.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 1727–1800 1.000 82.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1729–1802 1.000 81.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1748–1821 1.000 81.5
trnL-UAA_p1 trnL-UAA ACTGGATCTTTGTCTCAAAGCA AGCGAGGAATTAAAAGGGGC 1011–1054 1.000 66.4
trnL-UAA_p2 trnL-UAA ACTGGATCTTTGTCTCAAAGCA GCGAGGAATTAAAAGGGGCT 1010–1053 1.000 66.4
trnL-UAA_p3 trnL-UAA CTGGATCTTTGTCTCAAAGCA AGCGAGGAATTAAAAGGGGC 1010–1053 1.000 60.5
trnL-UAA_p4 trnL-UAA CTGGATCTTTGTCTCAAAGCA GCGAGGAATTAAAAGGGGCT 1009–1052 1.000 60.5
trnL-UAA_p5 trnL-UAA ACTGGATCTTTGTCTCAAAGC GCGAGGAATTAAAAGGGGCT 1010–1053 1.000 60.5

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
Tropidia angulosa PV424134.1 161395 View on NCBI ↗
Tropidia nipponica PV424135.1 160801 View on NCBI ↗