Markers + reference

Triphora

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 152–154 kb
Candidate markers 258
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1194 0.0213 0.98 60.8 yes View details
rps16-trnQ-UUG LSC 748 0.0337 0.95 78.5 yes View details
trnS-GCU-trnG-UCC LSC 845 0.0302 0.98 75.8 yes View details
trnE-UUC-trnT-GGU LSC 863 0.0256 0.95 63.4 yes View details
atpB-rbcL LSC 854 0.0244 0.96 61.5 yes View details
accD-psaI LSC 771 0.0270 0.91 63.1 yes View details
petA-psbJ LSC 941 0.0269 0.99 61.9 yes View details
psaJ-rpl33 LSC 655 0.0349 0.96 77.1 yes View details
clpP LSC 2493 0.0139 0.95 63.1 yes View details
clpP-psbB LSC 931 0.0213 0.91 74.4 yes View details
rpl16 LSC 1916 0.0324 0.95 67.3 yes View details
rps15 SSC 279 0.0397 0.99 62.5 yes View details
rps15-psaC IRa 300 0.0705 0.99 70.4 yes View details
rps8-rpl14 LSC 231 0.0519 1.00 73.9 yes View details
psbI-trnS-GCU LSC 169 0.0617 0.96 73.7 yes View details
atpH-atpI LSC 645 0.0176 0.97 71.8 yes View details
trnM-CAU-atpE LSC 175 0.0629 1.00 71.6 yes View details
petN-psbM LSC 811 0.0200 0.99 71.5 yes View details
psbC-trnS-UGA LSC 136 0.0376 0.98 70.8 yes View details
psbL-psbF LSC 22 0.0455 1.00 70.8 yes View details
infA-rps8 LSC 58 0.0517 1.00 70.7 yes View details
psbE-petL LSC 1122 0.0210 0.98 69.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 GGAATATAAAACAAACTTTGAAGAAAG ACGGTTCCAAAATAAAATGAGAGG 1263–1309 1.000 42.9
rps16_p2 rps16 GGAATATAAAACAAACTTTGAAGAAAG AAATTGCATACGGTTCCAAA 1272–1318 1.000 42.8
rps16_p3 rps16 GGAATATAAAACAAACTTTGAAGAAAG AATTGCATACGGTTCCAAAA 1271–1317 1.000 42.8
rps16_p4 rps16 GGAATATAAAACAAACTTTGAAGAAAG AAATTGCATACGGTTCCAAAA 1272–1318 1.000 42.8
rps16_p5 rps16 GGAATATAAAACAAACTTTGAAGAAAG ATTGCATACGGTTCCAAAAT 1270–1316 1.000 42.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC ACAGGTTTTGGTCCCGTTAC 845–867 1.000 84.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 822–844 1.000 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACAGGTTTTGGTCCCGTTAC 822–844 1.000 84.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT ACAGGTTTTGGTCCCGTTAC 843–865 1.000 84.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC TCTTTTAGGAATGGGGCGTG 881–903 1.000 83.8
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCTGGGCGTGAAGAAAA TGGACTAAAGCGTCGGATTG 264–269 1.000 82.8
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCTGGGCGTGAAGAAAAA TGGACTAAAGCGTCGGATTG 263–268 1.000 82.8
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCCTGGGCGTGAAGAAAAA GTGGACTAAAGCGTCGGATT 264–269 1.000 82.8
psbI-trnS-GCU_p4 psbI-trnS-GCU AATCCTGGGCGTGAAGAAAA GTGGACTAAAGCGTCGGATT 265–270 1.000 82.7
psbI-trnS-GCU_p5 psbI-trnS-GCU CCTGGGCGTGAAGAAAAAGA TGGACTAAAGCGTCGGATTG 261–266 1.000 82.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAAATGGAAAGATCCCTTGACT 955–1210 1.000 54.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AGAAATGGAAAGATCCCTTGACT 954–1209 1.000 54.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 914–1169 1.000 54.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 913–1168 1.000 54.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCAAAGGGGTCGGAGAGA AGAAATGGAAAGATCCCTTGACT 1020 0.500 31.4
atpH-atpI_p1 atpH-atpI TACCTTGACCAATCCCAGGT AACTTTGGCTGCGGCTTATA 775–782 1.000 81.8
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 756–763 1.000 81.6
atpH-atpI_p3 atpH-atpI AACGGAAGCAGCAGAAATCA AACTTTGGCTGCGGCTTATA 717–724 1.000 81.6
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 735–742 1.000 81.2
atpH-atpI_p5 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 755–762 1.000 81.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CTTGCGCTTATTGCTACTGC 984–986 1.000 80.2
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGCTCTTCATTT 973–975 1.000 80.2
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TTGCTACTGCGCTCTTCATT 974–976 1.000 80.2
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTCTTCAT 975–977 1.000 78.4
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT GCTTATTGCTACTGCGCTCT 979–981 1.000 77.6

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
Triphora trianthophoros PP812547.1 151898 View on NCBI ↗
Triphora wagneri PP812546.1 153825 View on NCBI ↗