Markers + reference

Mesoamerantha

2 species · Bromeliaceae · Poales

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Species 2
Genome length 160–160 kb
Candidate markers 281
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2223 0.0162 1.00 53.3 yes View details
ndhF-rpl32 SSC 1109 0.0268 0.98 65.1 yes View details
ccsA-ndhD SSC 265 0.0514 0.95 79.6 yes View details
psaC-ndhE SSC 390 0.0308 1.00 69.6 yes View details
ndhA SSC 2152 0.0149 1.00 53.5 yes View details
rps16-trnQ-UUG LSC 1520 0.0195 0.98 65.3 yes View details
trnS-GCU-trnG-UCC LSC 1271 0.0261 0.96 69.4 yes View details
atpF LSC 1395 0.0138 0.98 54.6 yes View details
atpH-atpI LSC 980 0.0290 0.99 73.7 yes View details
trnF-GAA-ndhJ LSC 760 0.0239 0.99 65.6 yes View details
accD-psaI LSC 875 0.0220 0.99 60.5 yes View details
petA-psbJ LSC 1139 0.0186 0.99 57.0 yes View details
trnI-GAU-rrn16S IRb 316 0.0443 1.00 78.3 yes View details
rrn16S-trnI-GAU IRa 316 0.0443 1.00 78.3 yes View details
psbC-trnS-UGA LSC 137 0.0511 1.00 74.3 yes View details
ndhD-psaC SSC 105 0.0952 1.00 72.2 yes View details
petG-trnW-CCA LSC 122 0.0492 1.00 72.2 yes View details
atpF-atpH LSC 179 0.0335 1.00 71.8 yes View details
rpl32-trnL-UAG SSC 788 0.0218 0.99 71.0 yes View details
psaJ-rpl33 LSC 519 0.0179 0.97 70.5 yes View details
ndhC-trnV-UAC LSC 1096 0.0116 0.94 70.0 yes View details
trnV-UAC-trnM-CAU LSC 177 0.0299 0.94 69.1 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhF_p1 ndhF AGAACTTGAATGTAAAAGATTTGT GTATCCTCACGAATCGGACA 166 1.000 42.4
ndhF_p2 ndhF AGAACTTGAATGTAAAAGATTTGT TGTATCCTCACGAATCGGAC 167 1.000 42.4
ndhF_p3 ndhF AGAACTTGAATGTAAAAGATTTGT ATCCTCACGAATCGGACAAT 164 1.000 42.4
ndhF_p4 ndhF AGAACTTGAATGTAAAAGATTTGT CCATGTATCCTCACGAATCGG 170 1.000 42.4
ndhF_p5 ndhF AGAACTTGAATGTAAAAGATTTGT GTATCCTCACGAATCGGACAA 166 1.000 42.4
ndhF-rpl32_p1 ndhF-rpl32 GGAAGAAAAGGTATTATCCACGC GGTGGAAACCGATTTCGCTA 1266–1273 1.000 53.9
ndhF-rpl32_p2 ndhF-rpl32 AGAAAAGGTATTATCCACGCA GGTGGAAACCGATTTCGCTA 1263–1270 1.000 49.4
ndhF-rpl32_p3 ndhF-rpl32 GAAGAAAAGGTATTATCCACGCA GGTGGAAACCGATTTCGCTA 1265–1272 1.000 48.8
ndhF-rpl32_p4 ndhF-rpl32 AAGAAAAGGTATTATCCACGCA GGTGGAAACCGATTTCGCTA 1264–1271 1.000 47.7
ndhF-rpl32_p5 ndhF-rpl32 GTGGAAGAAAAGGTATTATCCACG GGTGGAAACCGATTTCGCTA 1268–1275 1.000 46.4
rpl32-trnL-UAG_p1 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT AGCGTGTCTACCGATTTCAC 852–860 1.000 78.1
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT CAGCGTGTCTACCGATTTCA 853–861 1.000 78.1
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT TTTAGAAGATGCCGCCACTC 912–920 1.000 77.8
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TTCCACCGGGCATTCAAAAA AGCGTGTCTACCGATTTCAC 855–863 1.000 77.6
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TTTCCACCGGGCATTCAAAA AGCGTGTCTACCGATTTCAC 856–864 1.000 77.6
ccsA-ndhD_p1 ccsA-ndhD GGAAAGGTACGAATTCGGCA CCCGATTTCGTTCTCTCGTT 438–450 1.000 82.3
ccsA-ndhD_p2 ccsA-ndhD TGGAAAGGTACGAATTCGGC CCCGATTTCGTTCTCTCGTT 439–451 1.000 82.3
ccsA-ndhD_p3 ccsA-ndhD AGGTACGAATTCGGCACTTG CCCGATTTCGTTCTCTCGTT 434–446 1.000 82.3
ccsA-ndhD_p4 ccsA-ndhD GGAAAGGTACGAATTCGGCA CAGTTGACAAGGTACACGCT 416–428 1.000 81.5
ccsA-ndhD_p5 ccsA-ndhD TGGAAAGGTACGAATTCGGC CAGTTGACAAGGTACACGCT 417–429 1.000 81.5
ndhD-psaC_p1 ndhD-psaC AATTGGCCAAGCTGCAAAAG CTGAAACAACTCGCAGCATG 488 1.000 81.4
ndhD-psaC_p2 ndhD-psaC TTTGACCGCTGTACATTGCT CTGAAACAACTCGCAGCATG 543 1.000 81.3
ndhD-psaC_p3 ndhD-psaC TGTAGCCGAGTAGAGACGTT CTGAAACAACTCGCAGCATG 662 1.000 81.1
ndhD-psaC_p4 ndhD-psaC TTGTAGCCGAGTAGAGACGT CTGAAACAACTCGCAGCATG 663 1.000 81.1
ndhD-psaC_p5 ndhD-psaC ACAACCGCGAATTTCGAGTA CTGAAACAACTCGCAGCATG 507 0.500 59.1
psaC-ndhE_p1 psaC-ndhE TTGCTTGGCTTTACATCCGT TTATAGCCATTGCAGCTGCT 614–627 1.000 78.0
psaC-ndhE_p2 psaC-ndhE ACATCCGTCCCAAGGTATCA TTATAGCCATTGCAGCTGCT 602–615 1.000 77.7
psaC-ndhE_p3 psaC-ndhE CCAATACATCTGTGGGGCAA TTATAGCCATTGCAGCTGCT 579–592 1.000 77.7
psaC-ndhE_p4 psaC-ndhE TTGCTTGGCTTTACATCCGT TATAGCCATTGCAGCTGCTG 613–626 1.000 77.6
psaC-ndhE_p5 psaC-ndhE TTGCTTGGCTTTACATCCGT GTTATAGCCATTGCAGCTGC 615–628 1.000 77.5

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
Mesoamerantha guatemalensis NC_080305.1 160022 View on NCBI ↗
Mesoamerantha malvernii NC_080306.1 160034 View on NCBI ↗