Markers + reference

Phaius

8 species · Orchidaceae · Asparagales

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Species 8
Genome length 158–158 kb
Candidate markers 279
Primer pairs 100

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 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 845 0.0118 1.00 62.0 yes View details
trnS-GCU-trnG-GCC LSC 1036 0.0092 0.98 52.5 yes View details
ndhC-trnV-UAC LSC 1338 0.0096 0.99 56.0 yes View details
rbcL-accD LSC 863 0.0111 0.98 52.1 yes View details
accD-psaI LSC 830 0.0096 1.00 39.2 yes View details
clpP-psbB LSC 761 0.0230 0.92 71.0 yes View details
psbB-psbT LSC 536 0.0147 1.00 52.6 yes View details
rps8 LSC 396 0.0041 1.00 29.2 yes View details
ndhF-rpl32 SSC 1032 0.0159 0.99 53.9 yes View details
psaC-ndhE SSC 486 0.0319 1.00 57.1 yes View details
matK-trnK-UUU LSC 1099 0.0158 0.96 62.8 yes View details
trnE-UUC-trnT-GGU LSC 698 0.0097 0.94 60.3 yes View details
rps19-psbA IRa 565 0.0045 0.93 59.4 no View details
psbE-petL LSC 1208 0.0071 0.95 55.6 yes View details
petA-psbJ LSC 1048 0.0097 0.98 55.2 yes View details
ndhA SSC 2214 0.0034 1.00 52.8 yes View details
petN-psbM LSC 790 0.0061 0.97 52.7 yes View details
rps8-rpl14 LSC 238 0.0249 0.99 51.5 yes View details
atpB-rbcL LSC 998 0.0073 0.97 50.7 yes View details
trnT-GGU-psbD LSC 935 0.0054 1.00 50.4 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
trnK-UUU_p1 trnK-UUU TCGCGACGAGAATGGAATTT AGTGCCTGATGTGGGAAAAG 1064–1100 1.000 85.4
trnK-UUU_p2 trnK-UUU ACTAATCGCGACGAGAATGG AGTGCCTGATGTGGGAAAAG 1069–1105 1.000 84.4
trnK-UUU_p3 trnK-UUU AATCGCGACGAGAATGGAAT AGTGCCTGATGTGGGAAAAG 1066–1102 1.000 83.6
trnK-UUU_p4 trnK-UUU ATCGCGACGAGAATGGAATT AGTGCCTGATGTGGGAAAAG 1065–1101 1.000 83.6
trnK-UUU_p5 trnK-UUU CAGATGGATGGGATGGGGTA AGTGCCTGATGTGGGAAAAG 1205–1241 1.000 82.7
matK-trnK-UUU_p1 matK-trnK-UUU TCCTTGTAATTCTGCCATTT ATCCGGGTTGCTAACTCAAC 1116–1168 1.000 46.8
matK-trnK-UUU_p2 matK-trnK-UUU TCCTTGTAATTCTGCCATTT AACGGTAGAGTACTCGGCTT 1099–1151 1.000 46.8
matK-trnK-UUU_p3 matK-trnK-UUU TCCTTGTAATTCTGCCATTT ACGGTAGAGTACTCGGCTTT 1098–1150 1.000 46.8
matK-trnK-UUU_p4 matK-trnK-UUU ATCCTTGTAATTCTGCCATT ATCCGGGTTGCTAACTCAAC 1117–1169 1.000 46.8
matK-trnK-UUU_p5 matK-trnK-UUU TCCTTGTAATTCTGCCATTT GATCCGGGTTGCTAACTCAA 1117–1169 1.000 46.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 941–990 1.000 80.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 918–967 1.000 80.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 939–988 1.000 79.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 945–994 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 929–978 1.000 79.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1104–1228 1.000 54.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1103–1227 1.000 54.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1107–1231 1.000 53.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1106–1230 1.000 53.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1105–1229 1.000 53.7
petN-psbM_p1 petN-psbM GGGGAAGAAGTGGGCTTTAG CTTGCGCTTATTGCTACTGC 886–914 1.000 81.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT CTTGCGCTTATTGCTACTGC 949–977 1.000 80.6
petN-psbM_p3 petN-psbM GGGGAAGAAGTGGGCTTTAG ATTGCTACTGCGCTGTTCAT 877–905 1.000 79.7
petN-psbM_p4 petN-psbM TATGGGGAAGAAGTGGGCTT CTTGCGCTTATTGCTACTGC 889–917 1.000 79.4
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 940–968 1.000 79.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 751–870 1.000 83.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 730–849 1.000 83.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 727–846 1.000 83.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 729–848 1.000 83.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU ATGACCAACTTCCTTTCGCA GAACCGATGACTTACGCCTT 801–920 1.000 83.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Phaius antoninae NC_084156.1 158234 View on NCBI ↗
Phaius mishmensis NC_084158.1 158382 View on NCBI ↗
Phaius philippinensis NC_084159.1 157979 View on NCBI ↗
Phaius takeoi NC_084160.1 158296 View on NCBI ↗
Phaius tancarvilleae NC_050866.1 158229 View on NCBI ↗
Phaius tonkinensis PQ300638.1 158429 View on NCBI ↗
Phaius wallichii NC_084161.1 158234 View on NCBI ↗
Phaius wenshanensis PQ300640.1 158415 View on NCBI ↗