Markers + reference

Coelogyne

52 species · Orchidaceae · Asparagales

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Species 52
Genome length 157–160 kb
Candidate markers 276
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1121 0.0298 1.00 79.3 yes View details
rpoB-trnC-GCA LSC 1497 0.0197 0.96 72.6 yes View details
trnE-UUC-trnT-GGU LSC 1382 0.0243 0.98 81.5 yes View details
trnF-GAA-ndhJ LSC 646 0.0352 1.00 82.6 yes View details
atpB-rbcL LSC 1069 0.0332 0.97 81.9 yes View details
psbB-psbT LSC 475 0.0453 1.00 81.2 yes View details
ycf1 IRb 1035 0.0053 1.00 55.2 no View details
ndhF-rpl32 SSC 982 0.0373 1.00 78.4 yes View details
psaC-ndhE SSC 888 0.0342 0.99 87.6 yes View details
ycf1 SSC 5532 0.0238 1.00 67.2 yes View details
ndhA SSC 2208 0.0123 1.00 80.4 yes View details
rpl32-trnL-UAG SSC 573 0.0293 0.99 76.4 yes View details
psbE-petL LSC 1170 0.0143 1.00 75.6 yes View details
trnT-UGU-trnL-UAA LSC 610 0.0177 0.99 75.2 yes View details
atpF-atpH LSC 157 0.0206 1.00 74.5 yes View details
petA-psbJ LSC 1096 0.0213 0.98 73.1 yes View details
rpl20-rps12 LSC 736 0.0095 1.00 73.0 yes View details
rps19-psbA IRa 245 0.0555 0.92 72.9 no View details
matK-trnK-UUU LSC 1087 0.0265 0.99 72.8 yes View details
ycf4-cemA LSC 749 0.0171 1.00 72.8 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TCGCGACGAGAATGGAATTT AAAGAGTGATTGGGTTGCGA 784–950 0.904 86.0
trnK-UUU_p2 trnK-UUU TCGCGACGAGAATGGAATTT AAGAGTGATTGGGTTGCGAA 783–949 0.904 86.0
trnK-UUU_p3 trnK-UUU TCGCGACGAGAATGGAATTT AGAGTGATTGGGTTGCGAAA 782–948 0.904 86.0
trnK-UUU_p4 trnK-UUU ACTAATCGCGACGAGAATGG AAGAGTGATTGGGTTGCGAA 788–954 0.904 85.0
trnK-UUU_p5 trnK-UUU ACTAATCGCGACGAGAATGG AGAGTGATTGGGTTGCGAAA 787–953 0.904 85.0
matK-trnK-UUU_p1 matK-trnK-UUU TCGCGACGAGAATGGAATTT ATCCGGGTTGCTAACTCAAC 1341–1513 1.000 91.1
matK-trnK-UUU_p2 matK-trnK-UUU TCGCGACGAGAATGGAATTT TGACAATGGCGTCTCAAACA 1508–1671 0.981 90.9
matK-trnK-UUU_p3 matK-trnK-UUU TCGCGACGAGAATGGAATTT TTGGCTCTTTCCTTCGCTTT 1545–1603 0.962 90.3
matK-trnK-UUU_p4 matK-trnK-UUU ACTAATCGCGACGAGAATGG TTGGCTCTTTCCTTCGCTTT 1550–1608 0.962 89.3
matK-trnK-UUU_p5 matK-trnK-UUU TCGCGACGAGAATGGAATTT ATCCCCATTCCCTATTGGCT 1445–2278 0.962 89.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GACCAAATCAAAATGGGGCG 1005–1301 1.000 90.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 944–1240 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 948–1244 1.000 89.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CAAATCAAAATGGGGCGTGG 1002–1298 1.000 88.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CCAAATCAAAATGGGGCGTG 1003–1299 1.000 88.7
atpF-atpH_p1 atpF-atpH TAAACTCGAAACTCCCAGCG ATTTATGGACTGGTCGTGGC 251–292 1.000 91.1
atpF-atpH_p2 atpF-atpH CCCGCGGAAACAAAAGAATC ATTTATGGACTGGTCGTGGC 80–260 0.981 90.7
atpF-atpH_p3 atpF-atpH TAAACTCGAAACTCCCAGCG GGTCGTGGCATTAGCTCTTT 240–281 1.000 89.3
atpF-atpH_p4 atpF-atpH CCCGCGGAAACAAAAGAATC GGTCGTGGCATTAGCTCTTT 208–2278 0.981 89.0
atpF-atpH_p5 atpF-atpH CGCGGAAACAAAAGAATCGG ATTTATGGACTGGTCGTGGC 80–258 0.962 87.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 1494–1680 1.000 86.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT TAAAGGATTTGCAGTCCCCC 1495–1681 1.000 83.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG ATAAAGGATTTGCAGTCCCCC 1495–1681 1.000 82.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTTCCGTCAAGCCCTGATTA TAAAGGATTTGCAGTCCCCC 1490–1676 1.000 82.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GAAATTCTTCCGTCAAGCCC TAAAGGATTTGCAGTCCCCC 1496–1682 1.000 80.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1099–1556 1.000 90.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 1078–1535 1.000 90.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 1075–1532 1.000 90.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1077–1534 1.000 89.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1096–1553 1.000 89.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (52)

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

Species Accession Length (bp) Link
Coelogyne alba PP190464.1 160127 View on NCBI ↗
Coelogyne apoensis OR687508.1 160175 View on NCBI ↗
Coelogyne articulata NC_050859.1 160114 View on NCBI ↗
Coelogyne barbata NC_050858.1 160093 View on NCBI ↗
Coelogyne bulleyia NC_052739.1 159581 View on NCBI ↗
Coelogyne cantonensis NC_067981.1 158786 View on NCBI ↗
Coelogyne carnea PP190458.1 159560 View on NCBI ↗
Coelogyne chinensis NC_067982.1 159122 View on NCBI ↗
Coelogyne convallariae PP190454.1 160009 View on NCBI ↗
Coelogyne cootesii OR687509.1 159908 View on NCBI ↗
Coelogyne corymbosa NC_062713.1 159012 View on NCBI ↗
Coelogyne cristata PP190443.1 159789 View on NCBI ↗
Coelogyne flaccida NC_063910.1 160433 View on NCBI ↗
Coelogyne fusca PP190463.1 160083 View on NCBI ↗
Coelogyne gardneriana PP190452.1 160089 View on NCBI ↗
Coelogyne imbricata NC_048955.1 159292 View on NCBI ↗
Coelogyne kouytcheensis NC_050285.1 159729 View on NCBI ↗
Coelogyne leveilleana NC_067983.1 159353 View on NCBI ↗
Coelogyne longipes PP216492.1 160024 View on NCBI ↗
Coelogyne magna PP190472.1 159659 View on NCBI ↗
Coelogyne mandarinorum PP190473.1 159486 View on NCBI ↗
Coelogyne missionariorum NC_067984.1 159029 View on NCBI ↗
Coelogyne nervosa PP190442.1 159833 View on NCBI ↗
Coelogyne niana NC_067985.1 159078 View on NCBI ↗
Coelogyne nitida PP216499.1 159872 View on NCBI ↗
Coelogyne occultata PP216495.1 160019 View on NCBI ↗
Coelogyne odoratissima PP216488.1 160114 View on NCBI ↗
Coelogyne pallida NC_067986.1 159171 View on NCBI ↗
Coelogyne pallidiflavens PP190449.1 158583 View on NCBI ↗
Coelogyne panchaseensis PP190466.1 159293 View on NCBI ↗
Coelogyne peltastes PP190453.1 160318 View on NCBI ↗
Coelogyne porrecta OR687513.1 160078 View on NCBI ↗
Coelogyne prolifera PQ157938.1 160180 View on NCBI ↗
Coelogyne protracta NC_067987.1 159781 View on NCBI ↗
Coelogyne punctulata PP190462.1 159887 View on NCBI ↗
Coelogyne rochussenii OR687506.1 159592 View on NCBI ↗
Coelogyne rubra PP190448.1 160219 View on NCBI ↗
Coelogyne salmonicolor PP190471.1 159439 View on NCBI ↗
Coelogyne sanderae PP216485.1 160244 View on NCBI ↗
Coelogyne sanderiana PP190455.1 160124 View on NCBI ↗
Coelogyne schultesii PP190468.1 160087 View on NCBI ↗
Coelogyne spathacea PP190446.1 158720 View on NCBI ↗
Coelogyne speciosa PP190444.1 159510 View on NCBI ↗
Coelogyne sulphurea OR687501.1 160280 View on NCBI ↗
Coelogyne teleensis PP190445.1 159888 View on NCBI ↗
Coelogyne tricallosa PQ723627.1 159244 View on NCBI ↗
Coelogyne trinervis PP190441.1 160127 View on NCBI ↗
Coelogyne uncata PQ723628.1 157476 View on NCBI ↗
Coelogyne uniflora NC_052740.1 159341 View on NCBI ↗
Coelogyne ventricosa NC_067988.1 159418 View on NCBI ↗
Coelogyne viscosa PP216487.1 160097 View on NCBI ↗
Coelogyne wenshanica NC_067989.1 159070 View on NCBI ↗