Markers + reference

Pontederia

26 species · Pontederiaceae · Commelinales

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Species 26
Genome length 102–164 kb
Candidate markers 270
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1498 0.1140 0.86 76.9 yes View details
atpH-atpI LSC 1764 0.0686 0.87 76.9 yes View details
trnT-UGU-trnL-UAA LSC 1149 0.0885 0.91 84.8 yes View details
ndhC-trnV-UAC LSC 2047 0.0842 0.47 75.0 yes View details
accD-psaI LSC 1444 0.0498 0.92 80.7 yes View details
rps15-ycf1 SSC 546 0.0942 0.80 74.9 yes View details
petA-psbJ LSC 1195 0.0445 0.93 90.7 yes View details
psaI-ycf4 LSC 392 0.0483 1.00 88.4 yes View details
psaJ-rpl33 LSC 621 0.0505 0.91 87.4 yes View details
psaC-ndhE SSC 657 0.0558 0.94 84.9 yes View details
rpl32-trnL-UAG SSC 592 0.0621 0.97 83.6 yes View details
rps16-trnQ-UUG LSC 1481 0.0414 0.94 82.3 yes View details
trnF-GAA-ndhJ LSC 690 0.0270 0.98 75.8 yes View details
rpoB-trnC-GCA LSC 1175 0.0241 0.96 74.2 yes View details
petD-rpoA LSC 174 0.0515 1.00 74.2 yes View details
ndhF-rpl32 SSC 888 0.0316 0.99 73.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1127–1604 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1131–1608 1.000 85.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1119–1596 1.000 85.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1126–1603 1.000 84.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTTTTGGTCCCGTTATTCG 1147–1624 1.000 83.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 1024–2151 0.962 50.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC AGAACGAATCACACTTTTACCAC 1027–2154 0.962 50.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC GAACGAATCACACTTTTACCACT 1026–2153 0.962 50.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC AACGAATCACACTTTTACCACT 1025–2152 0.962 50.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC TACCACTAAACTATACCCGC 1010–2137 0.962 50.5
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA CCATGGAGGGTCATCATTGA 1150–2484 0.923 79.8
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TCCATGGAGGGTCATCATTG 1151–2485 0.923 79.8
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC CCATGGAGGGTCATCATTGA 1167–2501 0.923 78.9
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC TCCATGGAGGGTCATCATTG 1168–2502 0.923 78.9
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG CCATGGAGGGTCATCATTGA 1162–2496 0.923 78.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTTCCATCATTCCGGAGCA GCGACACCCAGATTTGAACT 1265–1360 0.923 79.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTTCCATCATTCCGGAGCAT GCGACACCCAGATTTGAACT 1264–1359 0.923 79.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTTCCATCATTCCGGAGCA TAAAGGATTTGCAGTCCCCC 1240–1335 0.923 78.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTTCCATCATTCCGGAGCAT TAAAGGATTTGCAGTCCCCC 1239–1334 0.923 78.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTTCCATCATTCCGGAGCAT CCTTACCACTTGGCCATGTC 1218–1313 0.923 78.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AGAGAAAAAGCCGGCTATCG ACCAATTTCGCCATATCCCC 1107–1531 0.923 88.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA AGAGAAAAAGCCGGCTATCG TAGCGTCTACCAATTTCGCC 1115–1539 0.923 87.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1056–1480 0.923 87.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GAGTCGAACCGATGACCATC ACCAATTTCGCCATATCCCC 1087–1511 0.923 87.6
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1064–1488 0.923 87.3
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATAGGTTGGCCCCTACGTAA 776–811 0.962 88.6
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AAAGTTGGATAGGTTGGCCC 784–819 0.962 88.2
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GATAGGTTGGCCCCTACGTA 777–812 0.923 86.2
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CGGGAAATAGTCGGGATAGC ATAGGTTGGCCCCTACGTAA 824–859 0.962 86.1
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TAGGTTGGCCCCTACGTAAG 775–810 0.923 84.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (26)

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

Species Accession Length (bp) Link
Pontederia africana NC_063314.1 161387 View on NCBI ↗
Pontederia australasica NC_063307.1 159728 View on NCBI ↗
Pontederia azurea PQ010072.1 161650 View on NCBI ↗
Pontederia cordata NC_044968.1 162234 View on NCBI ↗
Pontederia cordata var. cordata PQ010095.1 102266 View on NCBI ↗
Pontederia cordata var. lancifolia PQ010096.1 125842 View on NCBI ↗
Pontederia crassipes NC_046773.1 161783 View on NCBI ↗
Pontederia cyanea PQ010091.1 160108 View on NCBI ↗
Pontederia diversifolia PQ010074.1 161052 View on NCBI ↗
Pontederia elata NC_063308.1 162195 View on NCBI ↗
Pontederia gigantea PQ010097.1 162544 View on NCBI ↗
Pontederia hastata NC_063309.1 161848 View on NCBI ↗
Pontederia heterosperma PQ010075.1 161824 View on NCBI ↗
Pontederia korsakowii NC_063310.1 161816 View on NCBI ↗
Pontederia meyeri PQ010076.1 161032 View on NCBI ↗
Pontederia natans PQ010077.1 161559 View on NCBI ↗
Pontederia ovalis PQ010098.1 163172 View on NCBI ↗
Pontederia paniculata NC_063305.1 161862 View on NCBI ↗
Pontederia paradoxa PQ010079.1 161396 View on NCBI ↗
Pontederia plantaginea NC_063311.1 162090 View on NCBI ↗
Pontederia reflexa PQ010099.1 163986 View on NCBI ↗
Pontederia rotundifolia PQ010100.1 161642 View on NCBI ↗
Pontederia subovata PQ010101.1 162023 View on NCBI ↗
Pontederia triflora PQ010102.1 162089 View on NCBI ↗
Pontederia vaginalis NC_063312.1 162071 View on NCBI ↗
Pontederia valida NC_063313.1 162239 View on NCBI ↗