Markers + reference

Trichoglottis

7 species · Orchidaceae · Asparagales

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Species 7
Genome length 149–150 kb
Candidate markers 266
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1076 0.0218 1.00 63.1 yes View details
trnE-UUC-trnT-GGU LSC 887 0.0226 1.00 63.5 yes View details
trnT-GGU-psbD LSC 1015 0.0169 0.98 54.0 yes View details
accD-psaI LSC 905 0.0141 1.00 53.7 yes View details
clpP-psbB LSC 802 0.0244 0.99 71.7 yes View details
trnN-GUU-rpl32 SSC 979 0.0307 1.00 70.5 yes View details
rpl32-trnL-UAG SSC 602 0.0188 1.00 64.0 yes View details
psaC-ndhE SSC 685 0.0241 1.00 60.9 yes View details
atpB-rbcL LSC 928 0.0109 0.97 58.5 yes View details
trnR-UCU-atpA LSC 205 0.0216 1.00 56.8 yes View details
rps16-trnQ-UUG LSC 869 0.0107 1.00 56.1 yes View details
petA-psbJ LSC 958 0.0084 1.00 55.2 yes View details
atpH-atpI LSC 623 0.0082 1.00 54.8 yes View details
rpoB-trnC-GCA LSC 1643 0.0087 1.00 54.4 yes View details
matK-trnK-UUU LSC 1149 0.0108 1.00 54.3 yes View details
psbB-psbT LSC 367 0.0149 1.00 51.8 yes View details
ndhI-rps15 SSC 146 0.0189 1.00 51.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU CGGATATAGGAAGTTTTGTTGCC TCCGGGTTGCTAACTCAATG 1249–1301 1.000 57.4
matK-trnK-UUU_p2 matK-trnK-UUU CGGATATAGGAAGTTTTGTTGCC CGGGTTGCTAACTCAATGGT 1247–1299 1.000 56.8
matK-trnK-UUU_p3 matK-trnK-UUU GCGGATATAGGAAGTTTTGTTGC TCCGGGTTGCTAACTCAATG 1250–1302 1.000 55.5
matK-trnK-UUU_p4 matK-trnK-UUU CGGATATAGGAAGTTTTGTTGCC GATCCGGGTTGCTAACTCAA 1251–1303 1.000 55.1
matK-trnK-UUU_p5 matK-trnK-UUU CGGATATAGGAAGTTTTGTTGCC TTGATCCGGGTTGCTAACTC 1253–1305 1.000 55.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 954–969 1.000 82.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GACCAAAAAGAAATGGGGCG 1015–1030 1.000 81.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 931–946 1.000 81.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GACCAAAAAGAAATGGGGCG 992–1007 1.000 81.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 952–967 1.000 81.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1132–1338 1.000 58.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1131–1337 1.000 58.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1135–1341 1.000 57.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1134–1340 1.000 57.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1133–1339 1.000 57.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCGAAGAAGCTGAAACCCTT 275–304 1.000 73.2
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CCGAAGAAGCTGAAACCCTT 310–339 1.000 69.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA CCGAAGAAGCTGAAACCCTT 274–303 1.000 67.6
trnR-UCU-atpA_p4 trnR-UCU-atpA ATGGATAGGACAGAGGTCTTCT CCGAAGAAGCTGAAACCCTT 311–340 1.000 65.9
trnR-UCU-atpA_p5 trnR-UCU-atpA AGGACAGAGGTCTTCTAAACC CCGAAGAAGCTGAAACCCTT 305–334 1.000 65.4
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 792–827 1.000 79.9
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 741–776 1.000 79.9
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 720–755 1.000 79.4
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 740–775 1.000 79.3
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 719–754 1.000 78.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA CCGGGGATAAAGGATTTGCA 1572–1738 1.000 76.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC CCGGGGATAAAGGATTTGCA 1573–1739 1.000 76.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA ACCGGGGATAAAGGATTTGC 1573–1739 1.000 76.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC ACCGGGGATAAAGGATTTGC 1574–1740 1.000 76.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA TCGAACCGGGGATAAAGGAT 1577–1743 1.000 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Trichoglottis cirrhifera NC_083135.1 149442 View on NCBI ↗
Trichoglottis ionosma NC_083136.1 149841 View on NCBI ↗
Trichoglottis lanceolaria NC_083137.1 149467 View on NCBI ↗
Trichoglottis latisepala MN124432.1 149402 View on NCBI ↗
Trichoglottis orchidea NC_083138.1 149449 View on NCBI ↗
Trichoglottis philippinensis MN124404.1 149663 View on NCBI ↗
Trichoglottis subviolacea NC_083139.1 149439 View on NCBI ↗