Markers + reference

Aristolochia

39 species · Aristolochiaceae · Piperales

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Species 39
Genome length 159–161 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 763 0.0804 0.96 84.0 yes View details
rps16-trnQ-UUG LSC 545 0.0644 0.96 80.7 yes View details
trnS-GCU-trnG-UCC LSC 873 0.0597 0.96 82.9 yes View details
atpH-atpI LSC 1251 0.0403 0.97 78.7 yes View details
trnT-UGU-trnL-UAA LSC 894 0.0657 0.91 84.6 yes View details
petA-psbJ LSC 1119 0.0470 0.97 81.5 yes View details
rpl33-rps18 LSC 348 0.1158 0.81 72.8 yes View details
rps15-trnN-GUU SSC 6381 0.0322 1.00 69.7 yes View details
trnC-GCA-petN LSC 1188 0.0389 0.99 82.8 yes View details
ndhF-rpl32 SSC 896 0.0438 0.98 81.8 yes View details
matK-trnK-UUU LSC 829 0.0515 0.92 81.3 yes View details
trnF-GAA-ndhJ LSC 753 0.0372 0.98 78.6 yes View details
atpF-atpH LSC 540 0.0464 0.96 76.6 yes View details
psbA-trnK-UUU LSC 295 0.0464 0.99 76.0 yes View details
rpl32-trnL-UAG SSC 631 0.0386 0.99 75.4 yes View details
ycf3-trnS-GGA LSC 907 0.0333 0.97 75.0 yes View details
ndhC-trnV-UAC LSC 1249 0.0369 0.97 74.7 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
psbA-trnK-UUU_p1 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA ACTCCATCCGACTAGTTCCG 364–411 1.000 87.0
psbA-trnK-UUU_p2 psbA-trnK-UUU CATCAAAACGCCGAACCATC ACTCCATCCGACTAGTTCCG 443–490 1.000 86.3
psbA-trnK-UUU_p3 psbA-trnK-UUU AAACGCCGAACCATCCAATA ACTCCATCCGACTAGTTCCG 438–485 1.000 86.2
psbA-trnK-UUU_p4 psbA-trnK-UUU AAAGACGGTTCTCAGTGCTG ACTCCATCCGACTAGTTCCG 417–464 1.000 86.1
psbA-trnK-UUU_p5 psbA-trnK-UUU GATCATCAAAACGCCGAACC ACTCCATCCGACTAGTTCCG 446–493 1.000 85.7
trnK-UUU_p1 trnK-UUU TGGATCCATTTGTTATTTCGGA CTCCACGGTCCATAAGTTTGT 2845–2985 0.564 32.1
trnK-UUU_p2 trnK-UUU TCCATTTGTTATTTCGGATCGA CTCCACGGTCCATAAGTTTGT 2853–2998 0.487 29.3
trnK-UUU_p3 trnK-UUU TCCATTTGTTATTTCGGATCGA TCCACGGTCCATAAGTTTGT 2852–2997 0.487 29.3
trnK-UUU_p4 trnK-UUU TCCATTTGTTATTTCGGATCGA TCTCCACGGTCCATAAGTTTG 2854–2999 0.487 29.3
trnK-UUU_p5 trnK-UUU GGATCCATTTGTTATTTCGGATCG CTCCACGGTCCATAAGTTTGT 2876–2984 0.385 24.5
matK-trnK-UUU_p1 matK-trnK-UUU GGGAGCATCTTGTATCCAGC GGGCAATCCCGCTTATTGTA 1777–2659 0.846 84.8
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGGCTCCAGAGGATGT GGGCAATCCCGCTTATTGTA 1989–2871 0.795 83.3
matK-trnK-UUU_p3 matK-trnK-UUU AGGCTCCAGAGGATGTTGAT GGGCAATCCCGCTTATTGTA 1985–2867 0.795 82.7
matK-trnK-UUU_p4 matK-trnK-UUU TCAAGAAAGGCTCCAGAGGA GGGCAATCCCGCTTATTGTA 1992–2874 0.769 82.3
matK-trnK-UUU_p5 matK-trnK-UUU TCAAGAAAGGCTCCAGAGGA TCCGGGTTGCTAACTCAATG 1542–1965 0.769 80.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA TCGAGTTAATCAAACAAAGTCCA 755–1292 1.000 52.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCGAGTTAATCAAACAAAGTCCA 754–1291 0.974 51.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA TCGAGTTAATCAAACAAAGTCCA 752–1289 0.974 51.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC TCGAGTTAATCAAACAAAGTCCA 751–1288 0.974 51.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT TCGAGTTAATCAAACAAAGTCCA 753–1290 0.974 51.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 465–728 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 469–732 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 467–730 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GGTTTTGGTCCCGTTATTCG 485–748 1.000 78.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCTTTCTACCACAT GAGGTTCGAATCCTTCCGTC 467–730 1.000 78.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TACCACTAAACTATACCCGC 695–1032 1.000 56.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TTACCACTAAACTATACCCGC 696–1033 1.000 55.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TACCACTAAACTATACCCGC 690–1027 0.974 54.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TTTACCACTAAACTATACCCGC 697–1034 1.000 53.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TTACCACTAAACTATACCCGC 691–1028 0.974 53.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (39)

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

Species Accession Length (bp) Link
Aristolochia arborea PX868665.1 158842 View on NCBI ↗
Aristolochia bambusifolia PX868655.1 160030 View on NCBI ↗
Aristolochia contorta NC_036152.1 160576 View on NCBI ↗
Aristolochia dabieshanensis NC_080311.1 159635 View on NCBI ↗
Aristolochia debilis NC_036153.1 159793 View on NCBI ↗
Aristolochia delavayi MW413320.1 160344 View on NCBI ↗
Aristolochia fulvicoma NC_080372.1 159806 View on NCBI ↗
Aristolochia gigantea NC_080373.1 160594 View on NCBI ↗
Aristolochia griffithii NC_080309.1 160125 View on NCBI ↗
Aristolochia hainanensis NC_061937.1 159764 View on NCBI ↗
Aristolochia howii PX868686.1 159898 View on NCBI ↗
Aristolochia hyperxantha PX868658.1 159558 View on NCBI ↗
Aristolochia kaempferi NC_041452.1 159612 View on NCBI ↗
Aristolochia kunmingensis NC_041451.1 160051 View on NCBI ↗
Aristolochia littoralis NC_080308.1 160610 View on NCBI ↗
Aristolochia liukiuensis PX868657.1 159605 View on NCBI ↗
Aristolochia macrophylla NC_041453.1 160493 View on NCBI ↗
Aristolochia manshuriensis NC_046766.1 160182 View on NCBI ↗
Aristolochia mollissima NC_041457.1 159653 View on NCBI ↗
Aristolochia moupinensis NC_041454.1 159374 View on NCBI ↗
Aristolochia neolongifolia NC_080310.1 159634 View on NCBI ↗
Aristolochia ovatifolia PX868688.1 159951 View on NCBI ↗
Aristolochia panamensis PX868650.1 160004 View on NCBI ↗
Aristolochia plagiostoma PX868687.1 159886 View on NCBI ↗
Aristolochia pulvinata PX868679.1 159988 View on NCBI ↗
Aristolochia reticulata PX868652.1 160180 View on NCBI ↗
Aristolochia ringens PP786657.1 160942 View on NCBI ↗
Aristolochia salvadorensis PX868663.1 158837 View on NCBI ↗
Aristolochia serpentaria PX868651.1 160129 View on NCBI ↗
Aristolochia shimadae PX868656.1 159638 View on NCBI ↗
Aristolochia tagala NC_041455.1 159308 View on NCBI ↗
Aristolochia thwaitesii PX868676.1 159919 View on NCBI ↗
Aristolochia tomentosa PX868653.1 160474 View on NCBI ↗
Aristolochia tricaudata PX868664.1 159185 View on NCBI ↗
Aristolochia tubiflora NC_041456.1 160520 View on NCBI ↗
Aristolochia veracruzana PX868670.1 159124 View on NCBI ↗
Aristolochia versicolor PX868691.1 159704 View on NCBI ↗
Aristolochia westlandii PX868672.1 159796 View on NCBI ↗
Aristolochia zhuhaiensis PX868671.1 160024 View on NCBI ↗