Markers + reference

Heliconia

5 species · Heliconiaceae · Zingiberales

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Species 5
Genome length 162–162 kb
Candidate markers 269
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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0023 1.00 30.4 yes View details
rps16-trnQ-UUG LSC 1715 0.0082 1.00 59.8 yes View details
trnS-GCU-trnG-GCC LSC 1659 0.0139 0.99 63.1 yes View details
atpF-atpH LSC 515 0.0099 0.99 64.5 yes View details
trnT-GGU-psbD LSC 1103 0.0102 1.00 52.1 yes View details
trnT-UGU-trnL-UAA LSC 838 0.0197 1.00 68.6 yes View details
petA-psbJ LSC 1008 0.0081 1.00 55.2 yes View details
ccsA-ndhD SSC 283 0.0249 0.99 61.8 yes View details
psaC-ndhE SSC 924 0.0171 0.91 63.7 yes View details
rps15-ycf1 SSC 399 0.0291 0.98 61.8 yes View details
trnH-GUG-psbA LSC 425 0.0395 1.00 78.4 no View details
trnH-GUG-rpl2 IRb 43 0.0744 1.00 68.7 yes View details
rpl2-trnH-GUG IRa 43 0.0744 1.00 68.7 yes View details
trnK-UUU-rps16 LSC 743 0.0095 1.00 66.2 yes View details
trnR-ACG-trnN-GUU IRb 573 0.0091 1.00 65.5 yes View details
trnN-GUU-trnR-ACG IRa 573 0.0091 1.00 65.5 yes View details
atpH-atpI LSC 1229 0.0076 1.00 65.2 yes View details
trnL-UAG-ccsA SSC 89 0.0337 1.00 64.1 yes View details
psbM-trnD-GUC LSC 1023 0.0090 1.00 64.0 yes View details
psaJ-rpl33 LSC 571 0.0079 1.00 63.6 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 ATGTATGTTGTGCGCAAAAA CATAGGGAAAGTCGTGTGCA 1562–1567 1.000 56.9
psbA_p2 psbA ATGTATGTTGTGCGCAAAAA ACATAGGGAAAGTCGTGTGC 1563–1568 1.000 56.9
psbA_p3 psbA ATGTATGTTGTGCGCAAAAA AATACGTGTGCTTGGGAGTC 1238–1243 1.000 56.8
psbA_p4 psbA CAAACAAAGTAGCAATACCCCA CATAGGGAAAGTCGTGTGCA 1529–1534 1.000 55.2
psbA_p5 psbA CAAACAAAGTAGCAATACCCCA AATACGTGTGCTTGGGAGTC 1205–1210 1.000 55.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAGGAACT 843–863 1.000 73.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAGGAACT 842–862 1.000 73.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAGGAACT 829–849 1.000 70.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAGGAACT 854–874 1.000 69.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAGGGCGCTCAAC 853–873 1.000 69.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1799–1806 1.000 80.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GTGCCAACCGGTAAAAATGG 1864–1871 1.000 80.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GTGCCAACCGGTAAAAATGG 1862–1869 1.000 80.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1797–1804 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GTGCCAACCGGTAAAAATGG 1870–1877 1.000 80.7
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACTGAGAGACCCCTTAACT 1764–1862 1.000 59.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC TCAAGTAATCAGAGCGAGCG AACTGAGAGACCCCTTAACT 1830–1928 1.000 58.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AAACTGAGAGACCCCTTAACT 1765–1863 1.000 58.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA AACTGAGAGACCCCTTAACT 1812–1910 1.000 57.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TCAAGTAATCAGAGCGAGCG AAACTGAGAGACCCCTTAACT 1831–1929 1.000 57.0
atpF-atpH_p1 atpF-atpH CAGTGTCCCAAGGAAACGAA AATTTACGGACTGGTCGTGG 598–617 1.000 82.1
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AATTTACGGACTGGTCGTGG 626–645 1.000 81.4
atpF-atpH_p3 atpF-atpH CAGTGTCCCAAGGAAACGAA TCGTGGCATTAGCGCTTTTA 584–603 1.000 80.8
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 612–631 1.000 80.0
atpF-atpH_p5 atpF-atpH CAGTGTCCCAAGGAAACGAA CGTGGCATTAGCGCTTTTAT 583–602 1.000 76.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 1318–1373 1.000 76.8
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 1290–1345 1.000 76.8
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TAGGTGAATCCATGGAGGGT 1346–1401 1.000 76.2
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACGTTAGCCGC 1374–1429 1.000 76.1
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACGTTAGCCGC 1319–1374 1.000 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Heliconia bihai NC_086671.1 161745 View on NCBI ↗
Heliconia caribaea NC_086670.1 161908 View on NCBI ↗
Heliconia collinsiana NC_020362.1 161907 View on NCBI ↗
Heliconia orthotricha NC_086669.1 161689 View on NCBI ↗
Heliconia tortuosa NC_086672.1 161672 View on NCBI ↗