Markers + reference

Thunia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 160–160 kb
Candidate markers 273
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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 29.9 yes View details
rps16 LSC 1165 0.0017 0.99 60.4 yes View details
trnS-GCU-trnG-GCC LSC 1113 0.0009 1.00 59.4 yes View details
atpI LSC 744 0.0000 1.00 31.8 yes View details
rpoC1 LSC 2816 0.0004 1.00 56.2 yes View details
rpoB-trnC-GCA LSC 1419 0.0000 1.00 36.2 yes View details
trnC-GCA-petN LSC 886 0.0011 1.00 59.4 yes View details
trnE-UUC-trnT-GGU LSC 1362 0.0007 1.00 59.6 yes View details
ndhK LSC 795 0.0013 1.00 44.8 yes View details
accD-psaI LSC 745 0.0094 1.00 64.2 yes View details
psbB-psbT LSC 592 0.0017 1.00 59.6 yes View details
ndhJ-ndhK LSC 81 0.0123 1.00 59.4 yes View details
ndhF-rpl32 SSC 1075 0.0009 1.00 59.3 yes View details
psbE-petL LSC 1186 0.0008 1.00 59.2 yes View details
rps16-trnQ-UUG LSC 1106 0.0000 1.00 58.8 yes View details
atpF LSC 1516 0.0000 1.00 58.8 yes View details
petA-psbJ LSC 1067 0.0000 1.00 58.8 yes View details
petD LSC 1376 0.0000 1.00 58.8 yes View details
rpl16 LSC 1695 0.0000 1.00 58.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGGGGATTGCTATCTTCAA GTGCTTGGGAGTCCTTGAAA 1158 1.000 65.3
psbA_p2 psbA TTGGGGGATTGCTATCTTCA GTGCTTGGGAGTCCTTGAAA 1159 1.000 65.3
psbA_p3 psbA TGGGGGATTGCTATCTTCAA AATACGTGTGCTTGGGAGTC 1165 1.000 64.7
psbA_p4 psbA TTGGGGGATTGCTATCTTCA AATACGTGTGCTTGGGAGTC 1166 1.000 64.7
psbA_p5 psbA ACAAGATATTGGGGGATTGCT GTGCTTGGGAGTCCTTGAAA 1167 1.000 64.0
rps16_p1 rps16 GGTACTAGTTACCCTATCCTT TGTATCGGTTCAGCCAATGA 1272–1280 1.000 40.6
rps16_p2 rps16 GGTACTAGTTACCCTATCCTT GTATCGGTTCAGCCAATGACT 1271–1279 1.000 40.6
rps16_p3 rps16 GGTACTAGTTACCCTATCCTTT TGTATCGGTTCAGCCAATGA 1272–1280 1.000 40.6
rps16_p4 rps16 GGTACTAGTTACCCTATCCTTT GTATCGGTTCAGCCAATGACT 1271–1279 1.000 40.6
rps16_p5 rps16 GGTACTAGTTACCCTATCCTTTT TGTATCGGTTCAGCCAATGA 1272–1280 1.000 40.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GACCAAATCAAAATGGGGCG 1262–1263 1.000 79.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 1201–1202 1.000 79.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GACCAAATCAAAATGGGGCG 1239–1240 1.000 78.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GACCAAATCAAAATGGGGCG 1260–1261 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GACCAAATCAAAATGGGGCG 1250–1251 1.000 78.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1181–1182 1.000 51.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1180–1181 1.000 51.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1183–1184 1.000 50.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1184–1185 1.000 50.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1182–1183 1.000 50.7
atpF_p1 atpF GCTCGAAGGGTTCCCATTAG CGGAGCGATACAAAAAGAACTC 1680–1687 1.000 62.0
atpF_p2 atpF GCTCGAAGGGTTCCCATTAG CGGAGCGATACAAAAAGAACT 1680–1687 1.000 61.2
atpF_p3 atpF AGCTCGAAGGGTTCCCATTA CGGAGCGATACAAAAAGAACTC 1681–1688 1.000 59.0
atpF_p4 atpF AGCTCGAAGGGTTCCCATTA CGGAGCGATACAAAAAGAACT 1681–1688 1.000 58.2
atpF_p5 atpF GCTCGAAGGGTTCCCATTAG CGGAGCGATACAAAAAGAAC 1680–1687 1.000 57.1
atpI_p1 atpI TCTTCTCCAACCCAGTGGAT AGTTCGATTTCTGTTAGAGGACA 854 1.000 49.9
atpI_p2 atpI TTCTTCTCCAACCCAGTGGA AGTTCGATTTCTGTTAGAGGACA 855 1.000 48.7
atpI_p3 atpI TGAAACCCCTGCATTGCTTA AGTTCGATTTCTGTTAGAGGACA 829 1.000 47.8
atpI_p4 atpI ATTGAAACCCCTGCATTGCT AGTTCGATTTCTGTTAGAGGACA 831 1.000 47.4
atpI_p5 atpI TCTTCTCCAACCCAGTGGAT AGTTCGATTTCTGTTAGAGGACAA 854 1.000 46.9

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
Thunia alba NC_056197.1 159948 View on NCBI ↗
Thunia pulchra PP190469.1 160031 View on NCBI ↗