Markers + reference

Heptapleurum

14 species · Araliaceae · Apiales

Back to catalogue

Species 14
Genome length 156–157 kb
Candidate markers 264
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-TTG LSC 1765 0.0099 0.99 54.1 yes View details
trnS-GCT-trnR-TCT LSC 1675 0.0096 1.00 45.5 yes View details
trnE-TTC-trnT-GGT LSC 822 0.0116 0.96 54.2 yes View details
petB LSC 1432 0.0089 1.00 40.2 yes View details
ycf1 IRb 1515 0.0055 1.00 35.1 no View details
ndhF SSC 2226 0.0057 1.00 40.1 yes View details
ycf1 SSC 5634 0.0142 1.00 45.2 yes View details
rpoB-trnC-GCA LSC 1275 0.0039 1.00 58.2 yes View details
psbE-petL LSC 1153 0.0075 1.00 54.9 yes View details
rpl16-rps3 LSC 1110 0.0065 1.00 54.5 yes View details
ndhC-trnM-CAT LSC 1848 0.0079 1.00 52.4 yes View details
rpl32-trnL-TAG SSC 819 0.0094 1.00 52.2 yes View details
ycf3-trnS-GGA LSC 859 0.0069 1.00 51.4 yes View details
rpl20-rps12 LSC 775 0.0056 1.00 50.8 yes View details
psbA-trnK-UUU LSC 219 0.0148 0.98 50.7 yes View details
ndhF-rpl32 SSC 1198 0.0074 0.99 50.5 yes View details
psaA-ycf3 LSC 722 0.0030 0.99 50.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GAAAGCCGTGTGCAATGAAA 415–422 1.000 80.6
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTAGTTCCGGGTTCGAATCC 330–337 1.000 80.6
psbA-trnK-UUU_p3 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC GAAAGCCGTGTGCAATGAAA 416–423 1.000 80.1
psbA-trnK-UUU_p4 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTAGTTCCGGGTTCGAATCC 331–338 1.000 80.1
psbA-trnK-UUU_p5 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT TTTGGGGAGGGGTTTTTACC 382–389 1.000 78.8
rps16-trnQ-TTG_p1 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1263–1838 1.000 85.0
rps16-trnQ-TTG_p2 rps16-trnQ-TTG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1278–1853 1.000 83.1
rps16-trnQ-TTG_p3 rps16-trnQ-TTG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1277–1852 1.000 83.1
rps16-trnQ-TTG_p4 rps16-trnQ-TTG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1334–1909 1.000 82.0
rps16-trnQ-TTG_p5 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1267–1842 1.000 80.3
trnS-GCT-trnR-TCT_p1 trnS-GCT-trnR-TCT ATCTAATGATCCGGGGCGTA CGCGGTGGAAGAACAGATAA 2354–2389 1.000 82.8
trnS-GCT-trnR-TCT_p2 trnS-GCT-trnR-TCT TATCTAATGATCCGGGGCGT CGCGGTGGAAGAACAGATAA 2355–2390 1.000 82.8
trnS-GCT-trnR-TCT_p3 trnS-GCT-trnR-TCT ATTAGCAATCCGCCGCTTTA CGCGGTGGAAGAACAGATAA 2127–2155 1.000 82.7
trnS-GCT-trnR-TCT_p4 trnS-GCT-trnR-TCT ATTAGCAATCCGCCGCTTTA CGTTTCCAGAGTGGGATCTG 2325–2353 1.000 82.5
trnS-GCT-trnR-TCT_p5 trnS-GCT-trnR-TCT ATCTAATGATCCGGGGCGTA CGTTTCCAGAGTGGGATCTG 2552–2587 1.000 82.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CTTACCACTCGGCCATATCG 1361–1407 1.000 82.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CCGGATTTGAACTGGGGAAA 1401–1447 1.000 82.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CTTACCACTCGGCCATATCG 1289–1335 1.000 81.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCGGATTTGAACTGGGGAAA 1329–1375 1.000 81.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AAAAGGATTTGCAGTCCCCC 1383–1429 1.000 80.3
trnE-TTC-trnT-GGT_p1 trnE-TTC-trnT-GGT CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 902–934 1.000 84.2
trnE-TTC-trnT-GGT_p2 trnE-TTC-trnT-GGT TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 939–971 1.000 84.1
trnE-TTC-trnT-GGT_p3 trnE-TTC-trnT-GGT CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 867–899 1.000 83.7
trnE-TTC-trnT-GGT_p4 trnE-TTC-trnT-GGT TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 904–936 1.000 83.5
trnE-TTC-trnT-GGT_p5 trnE-TTC-trnT-GGT TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 880–912 1.000 83.5
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 886–916 1.000 80.7
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TATGGCGCTTACTCCTGGTA 858–888 1.000 80.5
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT CGATCAAGCCGCTGAGTATT 888–918 1.000 79.9
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TTGAAGATCACGAGGCGTTT 815–845 1.000 79.9
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TTGGTTGAAGATCACGAGGC 819–849 1.000 79.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Heptapleurum actinophyllum NC_049889.1 156675 View on NCBI ↗
Heptapleurum arboricola NC_085755.1 156704 View on NCBI ↗
Heptapleurum aromaticum PX591082.1 156703 View on NCBI ↗
Heptapleurum capituliferum PX591090.1 156092 View on NCBI ↗
Heptapleurum delavayi NC_022813.1 156341 View on NCBI ↗
Heptapleurum ellipticum PX591083.1 156713 View on NCBI ↗
Heptapleurum farinosum PX591086.1 156710 View on NCBI ↗
Heptapleurum fastigiatum PX591087.1 156654 View on NCBI ↗
Heptapleurum heptaphyllum NC_029764.1 156685 View on NCBI ↗
Heptapleurum longifolium PX591088.1 156632 View on NCBI ↗
Heptapleurum rhynchocarpum PX591091.1 156095 View on NCBI ↗
Heptapleurum rigidum PX591089.1 156654 View on NCBI ↗
Heptapleurum rugosum PX591084.1 156629 View on NCBI ↗
Heptapleurum sibayakense PX591085.1 156551 View on NCBI ↗