Markers + reference

Alcantarea

2 species · Bromeliaceae · Poales

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Species 2
Genome length 157–157 kb
Candidate markers 281
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 IRb 279 0.0000 1.00 25.6 yes View details
trnS-GCU-trnG-UCC LSC 1192 0.0025 1.00 60.4 yes View details
rpoC1 LSC 2764 0.0014 1.00 56.9 yes View details
psbC LSC 1422 0.0000 1.00 28.9 yes View details
trnF-GAA-ndhJ LSC 779 0.0026 1.00 52.7 yes View details
petA LSC 963 0.0021 1.00 54.8 yes View details
petA-psbJ LSC 1133 0.0044 1.00 61.4 yes View details
petL-petG LSC 177 0.0000 1.00 29.8 yes View details
rps19 IRa 279 0.0000 1.00 33.8 no View details
psbC-trnS-UGA LSC 137 0.0511 1.00 81.4 yes View details
petG-trnW-CCA LSC 122 0.0328 1.00 71.4 yes View details
rps19-psbA LSC 145 0.0207 1.00 64.4 yes View details
ndhF-rpl32 SSC 453 NA 0.98 62.6 no View details
rbcL-accD LSC 739 0.0028 0.98 62.4 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0169 1.00 62.2 yes View details
rpl16 LSC 1522 0.0027 0.98 62.0 yes View details
trnT-GGU-psbD LSC 1049 0.0029 1.00 60.8 yes View details
rps16 LSC 1080 0.0028 1.00 60.3 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
rps19_p1 rps19 TCTGACCTCCATACTTAGATCGA TCTTCCTTTGTTTGATTCACATCT 429 1.000 40.0
rps19_p2 rps19 TGACCTCCATACTTAGATCGAGA TCTTCCTTTGTTTGATTCACATCT 427 1.000 40.0
rps19_p3 rps19 TCTGACCTCCATACTTAGATCGA TCTTCCTTTGTTTGATTCACA 429 1.000 40.0
rps19_p4 rps19 TGACCTCCATACTTAGATCGAGA TCTTCCTTTGTTTGATTCACA 427 1.000 40.0
rps19_p5 rps19 CTGACCTCCATACTTAGATCGAG TCTTCCTTTGTTTGATTCACATCT 428 1.000 40.0
rps19-psbA_p1 rps19-psbA TCTGACTTTCGCGAGACATG AGCTGTTGTTGAAGCTCCAT 228 1.000 78.6
rps19-psbA_p2 rps19-psbA TCTGACTTTCGCGAGACATG ATGCTCACAACTTCCCCCTA 253 1.000 78.2
rps19-psbA_p3 rps19-psbA CCTACTCTGACTTTCGCGAG AGCTGTTGTTGAAGCTCCAT 233 1.000 77.3
rps19-psbA_p4 rps19-psbA CCTACTCTGACTTTCGCGAG ATGCTCACAACTTCCCCCTA 258 1.000 76.8
rps19-psbA_p5 rps19-psbA TCTGACTTTCGCGAGACATG TAATGCTCACAACTTCCCCC 255 1.000 76.7
trnK-UUU_p1 trnK-UUU ACACCAATGTCAACCAACCT TTTGATAGGGTCGTGCAGTG 2870–2876 1.000 76.0
trnK-UUU_p2 trnK-UUU ACACCAATGTCAACCAACCT GTCGTGCAGTGCAATTCAAT 2861–2867 1.000 74.1
trnK-UUU_p3 trnK-UUU ACACCAATGTCAACCAACCT TGTTTTGATAGGGTCGTGCA 2873–2879 1.000 72.3
trnK-UUU_p4 trnK-UUU ACACCAATGTCAACCAACCT TTTTGATAGGGTCGTGCAGT 2871–2877 1.000 70.0
trnK-UUU_p5 trnK-UUU ACACCAATGTCAACCAACCTT TTTGATAGGGTCGTGCAGTG 2870–2876 1.000 69.6
rps16_p1 rps16 AGCAAGAAAAAGGAAAATGGTGT ACCGGTTGAACCAATGACTA 1271 1.000 43.4
rps16_p2 rps16 AGCAAGAAAAAGGAAAATGGTGT TACCGGTTGAACCAATGACT 1272 1.000 43.4
rps16_p3 rps16 GCAAGAAAAAGGAAAATGGTGTG ACCGGTTGAACCAATGACTA 1270 1.000 43.0
rps16_p4 rps16 GCAAGAAAAAGGAAAATGGTGTG TACCGGTTGAACCAATGACT 1271 1.000 43.0
rps16_p5 rps16 GCAAGAAAAAGGAAAATGGTGT ACCGGTTGAACCAATGACTA 1270 1.000 40.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG AACCGATGGACCCCTTAACT 1359–1372 1.000 77.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACCGATGGACCCCTTAACT 1304–1317 1.000 77.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG AAACCGATGGACCCCTTAAC 1360–1373 1.000 76.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AAACCGATGGACCCCTTAAC 1305–1318 1.000 76.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG ACCGATGGACCCCTTAACTA 1358–1371 1.000 75.7
trnG-UCC_p1 trnG-UCC TTTTCACGATTCCGCTGCTA TCCAAATTGATGACGCATGT 884–885 1.000 63.6
trnG-UCC_p2 trnG-UCC CGATTCCGCTGCTATCTTGA TCCAAATTGATGACGCATGT 878–879 1.000 63.2
trnG-UCC_p3 trnG-UCC ACGATTCCGCTGCTATCTTG TCCAAATTGATGACGCATGT 879–880 1.000 63.2
trnG-UCC_p4 trnG-UCC CACGATTCCGCTGCTATCTT TCCAAATTGATGACGCATGT 880–881 1.000 63.2
trnG-UCC_p5 trnG-UCC TTCACGATTCCGCTGCTATC TCCAAATTGATGACGCATGT 882–883 1.000 63.2

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
Alcantarea nahoumii NC_081513.1 157107 View on NCBI ↗
Alcantarea odorata NC_065162.1 157077 View on NCBI ↗