Markers + reference

Ochagavia

2 species · Bromeliaceae · Poales

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Species 2
Genome length 158–163 kb
Candidate markers 270
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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ LSC 1525 0.0163 0.96 71.5 yes View details
trnS-trnR LSC 2293 0.0133 0.69 61.7 yes View details
atpF LSC 1389 0.0079 1.00 48.8 yes View details
trnF-ndhJ LSC 763 0.0162 0.89 58.2 yes View details
atpB-rbcL LSC 796 0.0138 1.00 66.7 yes View details
psbE-petL LSC 1488 0.0135 1.00 57.4 yes View details
ndhF-rpl32 SSC 1117 0.0204 0.61 56.6 yes View details
psaC-ndhE SSC 387 0.0284 1.00 65.0 yes View details
ndhE SSC 306 0.0065 1.00 41.5 yes View details
ycf1 SSC 5598 0.0084 1.00 48.6 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
psbC-trnS LSC 137 0.0511 1.00 73.4 yes View details
atpH-atpI LSC 1024 0.0091 0.97 67.0 yes View details
ndhI-ndhA SSC 88 0.0227 1.00 65.6 yes View details
petB-petD LSC 889 0.0090 1.00 64.4 yes View details
accD-psaI LSC 922 0.0087 1.00 64.1 yes View details
rps8-rpl14 IRb 154 0.0195 1.00 63.7 yes View details
trnK-rps16 LSC 695 0.0144 1.00 62.9 yes View details
petA-psbJ LSC 1093 0.0064 1.00 62.6 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
trnK-rps16_p1 trnK-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 804 1.000 78.1
trnK-rps16_p2 trnK-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 803 1.000 78.1
trnK-rps16_p3 trnK-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 790 1.000 75.8
trnK-rps16_p4 trnK-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGGAAC 815 1.000 74.9
trnK-rps16_p5 trnK-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 813 1.000 73.6
rps16-trnQ_p1 rps16-trnQ CAGCCGATCATGTCCTTCAA GAAATCAAAATGGGGCGTGG 1620–1675 1.000 83.5
rps16-trnQ_p2 rps16-trnQ GCCGATCATGTCCTTCAAGT GAAATCAAAATGGGGCGTGG 1618–1673 1.000 83.5
rps16-trnQ_p3 rps16-trnQ AATCCACAGCCGATCATGTC GAAATCAAAATGGGGCGTGG 1626–1681 1.000 83.4
rps16-trnQ_p4 rps16-trnQ CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1562–1617 1.000 83.1
rps16-trnQ_p5 rps16-trnQ GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1560–1615 1.000 83.1
trnS-trnR_p1 trnS-trnR GAGAAAGCGGAAAGAGAGGG AGAAGACCTCTGTCCTATCCA 1753–2424 1.000 68.3
trnS-trnR_p2 trnS-trnR ATTAGCAATCCGCCGCTTTA AGAAGACCTCTGTCCTATCCA 1698–2369 1.000 68.1
trnS-trnR_p3 trnS-trnR GAGAAAGCGGAAAGAGAGGG AGGTTTAGAAGACCTCTGTCCT 1759–2430 1.000 67.6
trnS-trnR_p4 trnS-trnR ATTAGCAATCCGCCGCTTTA AGGTTTAGAAGACCTCTGTCCT 1704–2375 1.000 67.4
trnS-trnR_p5 trnS-trnR AGAAAGCGGAAAGAGAGGGA AGAAGACCTCTGTCCTATCCA 1752–2423 1.000 65.6
atpF_p1 atpF CGCTCCTGGAAAGTAGTCAC GGACTGCTTTGAGGATGAGG 2410–2416 1.000 80.2
atpF_p2 atpF CGCTCCTGGAAAGTAGTCAC ATTTCTGCCGCTTCCGTTAT 2792–2798 1.000 80.2
atpF_p3 atpF CGCTCCTGGAAAGTAGTCAC TTGCCGTTTCCTTCTTCGAA 2481–2487 1.000 80.1
atpF_p4 atpF CGCTCCTGGAAAGTAGTCAC GTTGTGGCATTAGCGCTTTT 2600–2606 1.000 80.0
atpF_p5 atpF CGCTCCTGGAAAGTAGTCAC TGAGACTCCAGGAAGGACTG 2424–2430 1.000 79.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1061–1081 1.000 81.3
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 1117–1137 1.000 80.6
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA CGAATCCATGGAGGGTCATC 1077–1097 1.000 80.4
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1062–1082 1.000 80.2
atpH-atpI_p5 atpH-atpI GAAGCAAGTCCTACAGCCAA CGAATCCATGGAGGGTCATC 1091–1111 1.000 80.1
rpoC1-rpoB_p1 rpoC1-rpoB GGTAGGATTTTGTTGGCCCA TTGCTCGTTCGAGAACTACG 205 1.000 79.5
rpoC1-rpoB_p2 rpoC1-rpoB AGGTAGGATTTTGTTGGCCC TTGCTCGTTCGAGAACTACG 206 1.000 78.2
rpoC1-rpoB_p3 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TTGCTCGTTCGAGAACTACG 239 1.000 77.1
rpoC1-rpoB_p4 rpoC1-rpoB GGTAGGATTTTGTTGGCCCA TTCGATTGCTCGTTCGAGAA 210 1.000 77.1
rpoC1-rpoB_p5 rpoC1-rpoB GGTAGGATTTTGTTGGCCCA TTTCGATTGCTCGTTCGAGA 211 1.000 77.1

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
Ochagavia carnea NC_045386.1 162835 View on NCBI ↗
Ochagavia elegans NC_045385.1 158163 View on NCBI ↗