Markers + reference

Gastrochilus

17 species · Orchidaceae · Asparagales

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Species 17
Genome length 146–149 kb
Candidate markers 260
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 882 0.0202 0.96 65.1 yes View details
rpoB-trnC-GCA LSC 1631 0.0273 0.95 67.6 yes View details
trnE-UUC-trnT-GGU LSC 786 0.0245 0.95 72.3 yes View details
rpl16 LSC 1659 0.0138 0.98 62.8 yes View details
trnN-GUU-rpl32 IRb 509 0.0233 1.00 66.3 yes View details
rpl32-trnL-UAG SSC 588 0.0266 1.00 69.5 yes View details
ccsA-ndhD SSC 263 0.0339 0.88 53.7 yes View details
ndhD SSC 1142 0.0173 0.97 59.8 yes View details
matK-trnK-UUU LSC 1227 0.0333 0.97 74.8 yes View details
psbB-psbT LSC 364 0.0256 1.00 70.8 yes View details
petA-psbJ LSC 950 0.0175 1.00 67.6 yes View details
trnS-GCU-trnG-GCC LSC 1178 0.0174 0.96 65.9 yes View details
psbM-trnD-GUC LSC 1127 0.0137 1.00 64.9 yes View details
ndhC-trnV-UAC LSC 662 0.0176 0.97 63.3 yes View details
psaC-rps15 SSC 1359 0.0159 1.00 62.6 yes View details
rps8-rpl14 LSC 241 0.0246 0.98 62.4 yes View details
psbE-petL LSC 1149 0.0118 1.00 62.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CTTTTCCCACATCAGGCACT ATAAGACCGCGACTGATCCT 335–411 1.000 88.9
trnK-UUU_p2 trnK-UUU TAAGAAGGGAAGCTCGTTGC ATAAGACCGCGACTGATCCT 265–341 1.000 88.8
trnK-UUU_p3 trnK-UUU GACCCTTTTCCCACATCAGG ATAAGACCGCGACTGATCCT 339–415 1.000 88.3
trnK-UUU_p4 trnK-UUU CACATCCGTCTCCAATCCAC ATAAGACCGCGACTGATCCT 412–488 1.000 86.8
trnK-UUU_p5 trnK-UUU CATCCGTCTCCAATCCACAA ATAAGACCGCGACTGATCCT 410–486 1.000 86.3
matK-trnK-UUU_p1 matK-trnK-UUU CCAGATGGATGGGATAGGGT TCCGGGTTGCTAACTCAATG 1685–1784 1.000 89.7
matK-trnK-UUU_p2 matK-trnK-UUU CCAGATGGATGGGATAGGGT CGGGTTGCTAACTCAATGGT 1683–1782 1.000 89.1
matK-trnK-UUU_p3 matK-trnK-UUU CCAGATGGATGGGATAGGGT TCGATCCCGAAGAGAAGGAA 2379–2475 1.000 88.5
matK-trnK-UUU_p4 matK-trnK-UUU CCAGATGGATGGGATAGGGT GCTCAACCCACAGAAACTGT 2270–2366 1.000 87.3
matK-trnK-UUU_p5 matK-trnK-UUU CCAGATGGATGGGATAGGGT GTGCTCAACCCACAGAAACT 2272–2368 1.000 87.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 556–965 1.000 87.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 567–976 1.000 86.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 560–969 1.000 86.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 571–980 1.000 85.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 562–971 1.000 84.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 931–1262 1.000 61.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 930–1261 1.000 61.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 934–1265 1.000 60.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 933–1264 1.000 60.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 932–1263 1.000 60.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA CCGGGGATAAAGGATTTGCA 1819–1985 1.000 89.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA AGTATCGACAGACCTAGCCC 1939–2105 0.941 87.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA GTATCGACAGACCTAGCCCT 1938–2104 0.941 87.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT AGTATCGACAGACCTAGCCC 2378–2544 0.941 85.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT GTATCGACAGACCTAGCCCT 2377–2543 0.941 85.7
psbM-trnD-GUC_p1 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT GTTCGAGCCCCGTCAGTC 1182–1223 1.000 53.1
psbM-trnD-GUC_p2 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA GTTCGAGCCCCGTCAGTC 1181–1222 1.000 52.1
psbM-trnD-GUC_p3 psbM-trnD-GUC AAATGAACAGCGCAGTAGCA GTTCGAGCCCCGTCAGTC 1184–1225 1.000 51.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AATGAACAGCGCAGTAGCAA GTTCGAGCCCCGTCAGTC 1183–1224 1.000 51.3
psbM-trnD-GUC_p5 psbM-trnD-GUC GCGCAGTAGCAATAAAAGCA GTTCGAGCCCCGTCAGTC 1175–1216 1.000 50.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Gastrochilus acinacifolius PP963516.1 148666 View on NCBI ↗
Gastrochilus bellinus MN124427.1 147745 View on NCBI ↗
Gastrochilus bigibbus MN124439.1 147896 View on NCBI ↗
Gastrochilus calceolaris NC_042686.1 148428 View on NCBI ↗
Gastrochilus distichus PP963517.1 148068 View on NCBI ↗
Gastrochilus formosanus MN124435.1 148175 View on NCBI ↗
Gastrochilus fuscopunctatus NC_035830.1 146183 View on NCBI ↗
Gastrochilus gongshanensis MN124438.1 147869 View on NCBI ↗
Gastrochilus guangtungensis MN124428.1 148400 View on NCBI ↗
Gastrochilus japonicus NC_035833.1 147697 View on NCBI ↗
Gastrochilus malipoensis PP963518.1 147171 View on NCBI ↗
Gastrochilus obliquus MN124429.1 147835 View on NCBI ↗
Gastrochilus obovatifolius PP942372.1 146268 View on NCBI ↗
Gastrochilus prionophyllus PP963519.1 147925 View on NCBI ↗
Gastrochilus sinensis NC_080211.1 148020 View on NCBI ↗
Gastrochilus somae MN124436.1 147620 View on NCBI ↗
Gastrochilus yunnanensis PP963520.1 147772 View on NCBI ↗