Markers + reference

Papilionanthe

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 148–148 kb
Candidate markers 264
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 836 0.0172 0.97 65.5 yes View details
trnS-GGA-trnG-UCC LSC 1343 0.0268 0.92 69.7 yes View details
atpA LSC 1524 0.0039 1.00 47.7 yes View details
petN-psbM LSC 960 0.0119 0.61 46.0 yes View details
petA-psbJ LSC 986 0.0185 0.99 61.9 yes View details
clpP-psbB LSC 732 0.0418 0.98 70.1 yes View details
rpl16-rps3 LSC 1345 0.0164 1.00 55.6 yes View details
trnN-GUU-ndhI IRb 417 0.0239 0.90 59.0 yes View details
ndhG-rps15 SSC 816 0.0196 0.94 59.7 yes View details
rps15 SSC 276 0.0109 1.00 45.0 yes View details
rps15-ycf1 SSC 464 0.0436 0.99 68.5 yes View details
rpl36-infA LSC 114 0.0268 0.98 69.4 yes View details
psbI-trnS-GGA LSC 151 0.0400 0.99 68.7 yes View details
trnF-GAA-ndhJ LSC 428 0.0169 0.97 67.7 yes View details
atpH-atpI LSC 683 0.0061 0.95 66.8 yes View details
trnT-UGU-trnL-UAA LSC 581 0.0138 1.00 66.3 yes View details
ndhD-psaC SSC 139 0.0288 1.00 66.2 yes View details
rbcL-accD LSC 799 0.0088 0.99 64.4 yes View details
psbB-psbT LSC 375 0.0111 0.96 64.3 yes View details
trnR-UCU-atpA LSC 156 0.0449 1.00 63.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TAAGAAGGGAAGCTCGTTGC ATAAGACCGCGACTGATCCT 269–299 1.000 78.2
trnK-UUU_p2 trnK-UUU TAAGAAGGGAAGCTCGTTGC TATAAGACCGCGACTGATCCT 270–300 1.000 71.5
trnK-UUU_p3 trnK-UUU TAAGAAGGGAAGCTCGTTGC TAAGACCGCGACTGATCCT 268–298 1.000 71.2
trnK-UUU_p4 trnK-UUU TAAGAAGGGAAGCTCGTTGC TAAGACCGCGACTGATCCTG 268–298 1.000 70.6
trnK-UUU_p5 trnK-UUU AAGAAGGGAAGCTCGTTGC ATAAGACCGCGACTGATCCT 268–298 1.000 70.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 932–1031 1.000 82.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 909–1008 1.000 81.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 930–1029 1.000 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 936–1035 1.000 80.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 920–1019 1.000 80.9
psbI-trnS-GGA_p1 psbI-trnS-GGA ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 264–287 1.000 81.5
psbI-trnS-GGA_p2 psbI-trnS-GGA TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 265–288 1.000 81.5
psbI-trnS-GGA_p3 psbI-trnS-GGA ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 265–288 1.000 81.4
psbI-trnS-GGA_p4 psbI-trnS-GGA TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 266–289 1.000 81.4
psbI-trnS-GGA_p5 psbI-trnS-GGA ATCTAATGATCCGGGGCGTA GGGTTCGAATCCCTCTCTCT 214–237 1.000 80.2
trnS-GGA-trnG-UCC_p1 trnS-GGA-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1354–1412 1.000 57.6
trnS-GGA-trnG-UCC_p2 trnS-GGA-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1353–1411 1.000 57.6
trnS-GGA-trnG-UCC_p3 trnS-GGA-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1357–1415 1.000 56.5
trnS-GGA-trnG-UCC_p4 trnS-GGA-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1356–1414 1.000 56.5
trnS-GGA-trnG-UCC_p5 trnS-GGA-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1355–1413 1.000 56.5
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CGGCAGCTCAAATTAAAGCC 804–820 1.000 82.5
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCCTGGTCGTGAAGCTTATC 1067–1083 1.000 81.9
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCTGGTCGTGAAGCTTATCC 1066–1082 1.000 81.9
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GGTCGTGAAGCTTATCCAGG 1063–1079 1.000 81.9
trnR-UCU-atpA_p5 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GGTCGTGAAGCTTATCCAGG 1066–1082 1.000 81.7
atpA_p1 atpA AGCCTTCCAAGCTAACGATG CAAGCCTTACAACGAGCTCT 2104–2117 1.000 80.6
atpA_p2 atpA AGCCTTCCAAGCTAACGATG AATTGAGCGTGAGAGCCAAA 2494–2507 1.000 80.3
atpA_p3 atpA CCTAGCCTTCCAAGCTAACG CAAGCCTTACAACGAGCTCT 2107–2120 1.000 80.3
atpA_p4 atpA ACTAGAACCCTCGGCTTCTT CAAGCCTTACAACGAGCTCT 2427–2440 1.000 80.1
atpA_p5 atpA AGCCTTCCAAGCTAACGATG AGCCATTGAACAGCTCGAAA 2337 0.500 58.9

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
Papilionanthe biswasiana PQ505028.1 148183 View on NCBI ↗
Papilionanthe teres PQ505027.1 148145 View on NCBI ↗