Markers + reference

Phragmipedium

5 species · Orchidaceae · Asparagales

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Species 5
Genome length 147–151 kb
Candidate markers 259
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 828 0.0471 0.55 76.4 yes View details
petN-psbM LSC 1050 0.0660 0.58 79.5 yes View details
trnT-UGU-trnL-UAA LSC 1073 0.0413 0.92 78.9 yes View details
atpB-rbcL LSC 1121 0.0420 0.98 78.2 yes View details
rps8-rpl14 LSC 410 0.0823 0.95 78.5 yes View details
rpl22 LSC 399 0.0164 1.00 49.2 yes View details
trnL-CAA-ndhF IRb 1111 0.0320 0.63 54.5 yes View details
rps12-trnV-GAC IRb 2236 0.0244 0.98 67.4 yes View details
trnN-GUU-rpl32 IRb 488 0.0492 0.95 74.9 yes View details
rpl32-trnL-UAG SSC 557 0.0793 0.91 81.2 yes View details
trnV-GAC-rps12 IRa 2236 0.0247 0.98 67.6 yes View details
ndhF-trnL-CAA IRa 1111 0.0320 0.63 54.5 yes View details
psaC-ndhI SSC 596 0.0439 0.93 82.6 yes View details
atpF-atpH LSC 290 0.0559 1.00 80.4 yes View details
rpl33-rps18 LSC 269 0.0670 0.87 78.7 yes View details
psbB-psbT LSC 214 0.0516 1.00 78.5 yes View details
rps19-psbA IRa 214 0.1186 0.97 78.5 no View details
trnL-UAG-ccsA SSC 94 0.2057 1.00 77.3 yes View details
rps3-rpl22 LSC 131 0.1205 0.95 76.0 yes View details
rps16-trnQ-UUG LSC 983 0.0378 0.97 75.8 yes View details
accD-psaI LSC 912 0.0407 0.87 74.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCGAGCTCCACCATATGCTA GAGGTTCGAATCCTTCCGTC 1213–1511 1.000 87.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCGAGCTCCACCATATGCTA CGAAAACTTACGGCAGCTTG 1838–2136 1.000 86.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CGAAAACTTACGGCAGCTTG 1704–2002 1.000 86.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATGGTGGATGGCAGAATCC CGAAAACTTACGGCAGCTTG 1720–2018 1.000 85.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCGAGCTCCACCATATGCTA ATCGAAAACTTACGGCAGCT 1840–2138 1.000 85.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 501–1101 1.000 62.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 500–1100 1.000 62.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTAGTCCACTCAGCCACC ACGAATCACACTTTTACCACT 491–1091 1.000 62.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 504–1104 1.000 61.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 503–1103 1.000 61.7
atpF-atpH_p1 atpF-atpH CCACGGAAACAAAAGAATCGG ATTTATGGACTGGTCGTGGC 370–475 1.000 81.8
atpF-atpH_p2 atpF-atpH CCCACGGAAACAAAAGAATCG ATTTATGGACTGGTCGTGGC 371–476 1.000 81.8
atpF-atpH_p3 atpF-atpH CCACGGAAACAAAAGAATCGG GGTCGTGGCATTAGCTCTTT 359–464 1.000 80.2
atpF-atpH_p4 atpF-atpH CCCACGGAAACAAAAGAATCG GGTCGTGGCATTAGCTCTTT 360–465 1.000 80.1
atpF-atpH_p5 atpF-atpH CACGGAAACAAAAGAATCGGT ATTTATGGACTGGTCGTGGC 369–474 1.000 77.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTTTATTGCTACTGCGCTG 737–1219 1.000 89.8
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTCAAAACAGTCAGCCAA 680–1162 1.000 88.8
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 732–1214 1.000 88.4
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TATTGCTACTGCGCTGTTCA 733–1215 1.000 87.5
petN-psbM_p5 petN-psbM TAGTATGGGGAAGGAGTGGG CGTTTATTGCTACTGCGCTG 680–1162 1.000 87.5
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1123–1448 1.000 87.9
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1131–1456 1.000 87.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 1146–1471 1.000 86.1
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 1137–1462 1.000 86.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CAATCAAGTCCGTAGCGTCT 1143–1468 1.000 85.6
atpB-rbcL_p1 atpB-rbcL AGTCGTGGTATTGCTTCTCA GGTGACATAAGTCCCTCCCT 1171–1506 1.000 76.7
atpB-rbcL_p2 atpB-rbcL AAGTCGTGGTATTGCTTCTCA GGTGACATAAGTCCCTCCCT 1172–1507 1.000 74.6
atpB-rbcL_p3 atpB-rbcL AGTCGTGGTATTGCTTCTCA TGGTGACATAAGTCCCTCCC 1172–1507 1.000 74.3
atpB-rbcL_p4 atpB-rbcL AGTCGTGGTATTGCTTCTCAT GGTGACATAAGTCCCTCCCT 1171–1506 1.000 72.9
atpB-rbcL_p5 atpB-rbcL AAGTCGTGGTATTGCTTCTCA TGGTGACATAAGTCCCTCCC 1173–1508 1.000 72.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Phragmipedium besseae NC_058206.1 147384 View on NCBI ↗
Phragmipedium hirtzii NC_069912.1 151023 View on NCBI ↗
Phragmipedium kovachii NC_058207.1 151238 View on NCBI ↗
Phragmipedium lindenii NC_069910.1 150136 View on NCBI ↗
Phragmipedium longifolium NC_028149.1 151157 View on NCBI ↗