Markers + reference

Danxiaorchis

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 85–88 kb
Candidate markers 129
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 129 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps2-trnC-GCA LSC 3043 0.0049 1.00 58.5 yes View details
trnC-GCA-trnE-UUC LSC 1553 0.0068 0.95 58.3 yes View details
clpP-rps11 LSC 2437 0.0109 0.98 62.2 yes View details
psaC-rps7 SSC 1207 0.0078 0.85 56.0 yes View details
ycf1-rpl32 SSC 1649 0.0032 0.57 54.7 yes View details
rpl22-matK LSC 1261 0.0079 1.00 63.3 no View details
trnL-UAA LSC 50 0.0400 1.00 72.6 yes View details
rps3-rpl22 IRb 43 0.0233 1.00 65.9 yes View details
rps7-rps12 SSC 58 0.0172 1.00 62.4 yes View details
accD LSC 1482 0.0021 0.99 61.4 yes View details
trnG-GCC LSC 65 0.0154 1.00 61.3 yes View details
rps16 LSC 1053 0.0038 0.99 61.1 yes View details
trnD-GUC-petN LSC 986 0.0064 0.96 61.1 yes View details
trnV-GAC-rrn16S SSC 213 0.0142 1.00 61.1 yes View details
rpl16 LSC 1676 0.0036 1.00 60.9 yes View details
rrn4.5S-rrn5S SSC 212 0.0142 1.00 60.6 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 TCATGATTCTTGTGTTCCCT TGGTTCAGTAAATGACTATTCATGA 1183–1189 1.000 40.7
rps16_p2 rps16 TCATGATTCTTGTGTTCCCTT TGGTTCAGTAAATGACTATTCATGA 1183–1189 1.000 40.7
rps16_p3 rps16 TTCATGATTCTTGTGTTCCCT TGGTTCAGTAAATGACTATTCATGA 1184–1190 1.000 40.7
rps16_p4 rps16 TCATGATTCTTGTGTTCCCT TGTATTGGTTCAGTAAATGACT 1188–1194 1.000 40.7
rps16_p5 rps16 TCATGATTCTTGTGTTCCCTTTC TGGTTCAGTAAATGACTATTCATGA 1183–1189 1.000 40.7
rps2-trnC-GCA_p1 rps2-trnC-GCA GAGCACTCGAGCAGTTTCTT ACGTCAAGTAACACCAAGAGT 217 1.000 65.3
rps2-trnC-GCA_p2 rps2-trnC-GCA TGTTGAATCCGGTACCAACC ACGTCAAGTAACACCAAGAGT 302 1.000 65.0
rps2-trnC-GCA_p3 rps2-trnC-GCA CCAACCGGTATAATTCCCCC ACGTCAAGTAACACCAAGAGT 288 1.000 64.3
rps2-trnC-GCA_p4 rps2-trnC-GCA GTAGAGCACTCGAGCAGTTT ACGTCAAGTAACACCAAGAGT 220 1.000 64.1
rps2-trnC-GCA_p5 rps2-trnC-GCA AGCACTCGAGCAGTTTCTTG ACGTCAAGTAACACCAAGAGT 216 1.000 63.0
trnC-GCA-trnE-UUC_p1 trnC-GCA-trnE-UUC CCAGTTCGAATCTGGGTGTT GTCGCCTCCTTGAAAGAGAG 1625–1690 1.000 82.6
trnC-GCA-trnE-UUC_p2 trnC-GCA-trnE-UUC CCAGTTCGAATCTGGGTGTT TCCACAGCCAACTCACTTTC 1679–1744 1.000 82.3
trnC-GCA-trnE-UUC_p3 trnC-GCA-trnE-UUC CCAGTTCGAATCTGGGTGTT TCGCCTCCTTGAAAGAGAGA 1624–1689 1.000 82.1
trnC-GCA-trnE-UUC_p4 trnC-GCA-trnE-UUC CCAGTTCGAATCTGGGTGTT TGTCCTGAACCACTAGACGA 1604–1669 1.000 80.5
trnC-GCA-trnE-UUC_p5 trnC-GCA-trnE-UUC AGTTCGAATCTGGGTGTTGC GTCGCCTCCTTGAAAGAGAG 1623–1688 1.000 80.3
trnD-GUC-petN_p1 trnD-GUC-petN AGTTCAATCGGTCAGAGCAC TAGTAAGTCTCGCTTGGGCT 1092–1135 1.000 81.6
trnD-GUC-petN_p2 trnD-GUC-petN AGTTCAATCGGTCAGAGCAC TAGTATGGGGAAGGAGTGGG 1035–1078 1.000 79.1
trnD-GUC-petN_p3 trnD-GUC-petN AGTTCAATCGGTCAGAGCAC ATAGTAAGTCTCGCTTGGGC 1093–1136 1.000 75.7
trnD-GUC-petN_p4 trnD-GUC-petN GTTCAATCGGTCAGAGCACC TAGTAAGTCTCGCTTGGGCT 1091–1134 1.000 74.9
trnD-GUC-petN_p5 trnD-GUC-petN AGTTCAATCGGTCAGAGCAC TCGCTTGGGCTGCTTTAAA 1083–1126 1.000 74.6
trnG-GCC_p1 trnG-GCC ACGCATCAGGAACGAAGAAA AGTCAACTATACTGACAGAATCT 125 1.000 40.6
trnG-GCC_p2 trnG-GCC ACGCATCAGGAACGAAGAAA ACTACTGTATTCACTACTATGCA 164 1.000 40.5
trnG-GCC_p3 trnG-GCC TATGTGTGGACATATGCGGC AGTCAACTATACTGACAGAATCT 147 1.000 40.5
trnG-GCC_p4 trnG-GCC GTACGCATCAGGAACGAAGA ACTACTGTATTCACTACTATGCA 166 1.000 40.5
trnG-GCC_p5 trnG-GCC TATGTGTGGACATATGCGGC ACTACTGTATTCACTACTATGCA 186 1.000 40.4
trnL-UAA_p1 trnL-UAA GACGAGAATAAAGAGAGAGTCCC AGCGAGGAAGTAAAATGGGC 145 1.000 53.7
trnL-UAA_p2 trnL-UAA GACGAGAATAAAGAGAGAGTCCC GCGAGGAAGTAAAATGGGCT 144 1.000 53.7
trnL-UAA_p3 trnL-UAA GGACGAGAATAAAGAGAGAGTCC AGCGAGGAAGTAAAATGGGC 146 1.000 53.7
trnL-UAA_p4 trnL-UAA GGACGAGAATAAAGAGAGAGTCC GCGAGGAAGTAAAATGGGCT 145 1.000 53.7
trnL-UAA_p5 trnL-UAA CGAGAATAAAGAGAGAGTCCCA GCGAGGAAGTAAAATGGGCT 142 1.000 53.1

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
Danxiaorchis mangdangshanensis NC_086587.1 85273 View on NCBI ↗
Danxiaorchis singchiana NC_048523.1 87931 View on NCBI ↗