Markers + reference

Macodes

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 153–153 kb
Candidate markers 275
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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 623 0.0129 0.99 53.3 yes View details
rps16 LSC 1237 0.0162 1.00 56.2 yes View details
trnS-GCU-trnG-GCC LSC 501 0.0265 0.98 67.3 yes View details
rpoB-trnC-GCA LSC 1086 0.0185 1.00 60.1 yes View details
trnT-GGU-psbD LSC 1028 0.0182 0.96 67.6 yes View details
trnT-UGU-trnL-UAA LSC 947 0.0160 0.99 60.0 yes View details
rbcL-accD LSC 796 0.0165 0.99 55.9 yes View details
psbB-psbT LSC 334 0.0218 0.96 57.9 yes View details
rpl32-trnL-UAG SSC 881 0.0299 0.99 71.2 yes View details
psaC SSC 246 0.0041 1.00 40.4 yes View details
ndhD-psaC SSC 129 0.0465 1.00 74.4 yes View details
rpl33-rps18 LSC 159 0.0323 0.97 73.4 yes View details
rpl22-psbA LSC 88 0.0247 0.92 70.5 no View details
psaJ-rpl33 LSC 592 0.0139 0.97 69.3 yes View details
rpl36-infA LSC 126 0.0505 0.79 67.9 yes View details
psbN-psbH LSC 120 0.0435 0.96 67.3 yes View details
ndhF-rpl32 SSC 168 0.0370 0.96 65.9 yes View details
trnE-UUC-trnT-GGU LSC 402 0.0233 0.96 65.2 yes View details
atpB-rbcL LSC 837 0.0085 0.98 65.2 yes View details
rpl14-rpl16 LSC 122 0.0168 0.98 64.5 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 TTTTATTTGAACTTTGGTATGGA TCATATCTACACTTCATCTTTATCT 2980–2984 1.000 41.1
trnK-UUU_p2 trnK-UUU TTTTTATTTGAACTTTGGTATGGA TCATATCTACACTTCATCTTTATCT 2981–2985 1.000 41.1
trnK-UUU_p3 trnK-UUU ATTTGAACTTTGGTATGGATTAA TCATATCTACACTTCATCTTTATCT 2976–2980 1.000 41.1
trnK-UUU_p4 trnK-UUU TTATTTGAACTTTGGTATGGATT TCATATCTACACTTCATCTTTATCT 2978–2982 1.000 41.1
trnK-UUU_p5 trnK-UUU TTTATTTGAACTTTGGTATGGAT TCATATCTACACTTCATCTTTATCT 2979–2983 1.000 41.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAAAGACAACGAATTCCGG 1298–1303 1.000 80.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 1297–1302 1.000 80.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCGATCCCGAAGAGAAGGAA 889–893 1.000 79.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 888–892 1.000 79.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT GCAAAGACAACGAATTCCGG 1383–1388 1.000 78.9
rps16_p1 rps16 AGAATTACACAAAGATAGGTACT TGTATCGGTTCAGTCAATGGT 1350–1356 1.000 41.7
rps16_p2 rps16 AAGAATTACACAAAGATAGGTACT TGTATCGGTTCAGTCAATGGT 1351–1357 1.000 41.7
rps16_p3 rps16 AGAATTACACAAAGATAGGTACT TGTATCGGTTCAGTCAATGGTT 1350–1356 1.000 41.7
rps16_p4 rps16 AAAGAATTACACAAAGATAGGTACT TGTATCGGTTCAGTCAATGGT 1352–1358 1.000 41.7
rps16_p5 rps16 AAGAATTACACAAAGATAGGTACT TGTATCGGTTCAGTCAATGGTT 1351–1357 1.000 41.7
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 560–570 1.000 54.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 559–569 1.000 54.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GTTATCAGGGGAGTCGGAGA ACGAATCACACTTTTACCACT 627–637 1.000 54.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGTTATCAGGGGAGTCGGAG ACGAATCACACTTTTACCACT 628–638 1.000 54.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 562–572 1.000 53.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCTGTCAAGCCCCG TAAAGGATTTGCAGTCCCCC 1234–1336 1.000 75.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCTGTCAAGCCCCG CGACACCCAGATTCGAACTG 1258–1360 1.000 74.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCTGTCAAGCCCCG ATAAAGGATTTGCAGTCCCCC 1235–1337 1.000 71.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTTCTGTCAAGCCCCGATTA TAAAGGATTTGCAGTCCCCC 1230–1332 1.000 71.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTCTGTCAAGCCCCGATTA CGACACCCAGATTCGAACTG 1254–1356 1.000 70.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 491–506 1.000 82.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 470–485 1.000 82.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 467–482 1.000 82.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 469–484 1.000 81.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGAAAAAGCCCCTTATCGG 515–530 1.000 81.2

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
Macodes petola MW589527.1 153048 View on NCBI ↗
Macodes sanderiana MW589528.1 153116 View on NCBI ↗