Markers + reference

Holcoglossum

13 species · Orchidaceae · Asparagales

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Species 13
Genome length 146–148 kb
Candidate markers 262
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 1289 0.0479 0.92 80.8 yes View details
trnF-GAA-trnV-UAC LSC 676 0.1052 0.86 91.3 yes View details
clpP-psbB LSC 744 0.0518 0.92 96.1 yes View details
rpl16 LSC 1711 0.0163 0.92 59.6 yes View details
trnN-GUU-rpl32 IRb 753 0.0470 0.94 85.3 yes View details
ndhD SSC 1164 0.0215 0.93 60.6 yes View details
psaC-ndhE SSC 727 0.0388 0.83 65.3 yes View details
psbT-psbN LSC 62 0.0449 1.00 71.5 yes View details
atpB-rbcL LSC 1001 0.0102 0.98 68.2 yes View details
trnE-UUC-trnT-GGU LSC 806 0.0204 0.95 67.9 yes View details
atpH-atpI LSC 648 0.0113 1.00 67.6 yes View details
ccsA-ndhD SSC 288 0.0356 0.93 67.6 yes View details
matK-trnK-UUU LSC 1130 0.0153 1.00 67.3 yes View details
psbK-psbI LSC 493 0.0164 0.99 64.2 yes View details
trnT-GGU-psbD LSC 1036 0.0160 0.97 61.6 yes View details
petN-psbM LSC 837 0.0110 0.93 61.1 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TCCGGGTTGCTAACTCAATG 1171–1306 1.000 79.4
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA CGGGTTGCTAACTCAATGGT 1169–1304 1.000 78.8
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GATCCGGGTTGCTAACTCAA 1173–1308 1.000 77.0
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TTGATCCGGGTTGCTAACTC 1175–1310 1.000 77.0
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGATAT TCCGGGTTGCTAACTCAATG 1171–1306 1.000 75.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 602–629 1.000 86.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 603–630 1.000 86.7
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 604–631 1.000 84.9
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 599–626 1.000 84.6
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 600–627 1.000 84.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 716–1357 1.000 63.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 715–1356 1.000 63.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 719–1360 1.000 62.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 718–1359 1.000 62.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 717–1358 1.000 62.6
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 698–830 1.000 85.4
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 647–779 1.000 85.3
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 626–758 1.000 84.9
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 646–778 1.000 84.7
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 625–757 1.000 84.3
petN-psbM_p1 petN-psbM GGGGCATCATTCACATGGAT ACGTCAAAACAGTCAGCCAA 938–970 1.000 85.5
petN-psbM_p2 petN-psbM GGGGCATCATTCACATGGAT ATTGCTACTGCGCTGTTCAT 990–1022 1.000 85.3
petN-psbM_p3 petN-psbM GGGGCATCATTCACATGGAT TATTGCTACTGCGCTGTTCA 991–1023 1.000 84.3
petN-psbM_p4 petN-psbM GGATAGGGGGCATCATTCAC ACGTCAAAACAGTCAGCCAA 944–976 0.923 80.6
petN-psbM_p5 petN-psbM GGATAGGGGGCATCATTCAC ATTGCTACTGCGCTGTTCAT 996–1028 0.923 80.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 864–974 1.000 86.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 843–953 1.000 86.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 840–950 1.000 86.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 842–952 1.000 86.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 861–971 1.000 85.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Holcoglossum amesianum NC_041511.1 148074 View on NCBI ↗
Holcoglossum flavescens NC_041512.1 146863 View on NCBI ↗
Holcoglossum nagalandense NC_041514.1 146826 View on NCBI ↗
Holcoglossum nujiangense NC_041515.1 146487 View on NCBI ↗
Holcoglossum omeiense NC_064528.1 147653 View on NCBI ↗
Holcoglossum quasipinifolium NC_041516.1 147063 View on NCBI ↗
Holcoglossum rupestre NC_041517.1 147163 View on NCBI ↗
Holcoglossum singchianum MN732560.1 147715 View on NCBI ↗
Holcoglossum sinicum NC_041518.1 145909 View on NCBI ↗
Holcoglossum subulifolium NC_041519.1 146930 View on NCBI ↗
Holcoglossum tsii NC_048459.1 146897 View on NCBI ↗
Holcoglossum wangii NC_041520.1 147170 View on NCBI ↗
Holcoglossum weixiense NC_041521.1 146597 View on NCBI ↗