Markers + reference

Platanus

3 species · Platanaceae · Proteales

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Species 3
Genome length 162–162 kb
Candidate markers 280
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 9 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1107 0.0042 1.00 45.1 yes View details
atpF LSC 1322 0.0020 1.00 43.6 yes View details
atpF-atpH LSC 589 0.0103 0.98 54.0 yes View details
trnT-GGU-psbD LSC 1747 0.0023 1.00 47.4 yes View details
trnT-UGU-trnL-UAA LSC 1419 0.0061 1.00 47.8 yes View details
ndhC-trnV-UAC LSC 2266 0.0027 1.00 44.7 yes View details
rbcL-accD LSC 859 0.0031 1.00 48.3 yes View details
rpl33-rps18 LSC 297 0.0090 1.00 45.7 yes View details
ycf1 IRb 345 0.0000 1.00 19.7 yes View details
ndhF SSC 2247 0.0018 1.00 34.3 yes View details
ndhD SSC 1503 0.0013 1.00 44.5 yes View details
ycf1 SSC 5748 0.0013 0.99 41.3 no View details
ycf1-ndhF SSC 78 0.0940 1.00 75.0 yes View details
trnS-GCU-trnG-UCC LSC 1263 0.0016 0.97 50.1 yes View details
trnL-UAG-ccsA SSC 105 0.0129 0.98 49.5 yes View details
trnH-GUG-psbA LSC 500 0.0014 0.96 48.7 yes View details
rpoB-trnC-GCA LSC 1221 0.0006 0.98 48.6 yes View details
atpH-atpI LSC 1160 0.0023 1.00 47.7 yes View details
ycf3-trnS-GGA LSC 889 0.0022 1.00 47.7 yes View details
psaA-ycf3 LSC 656 0.0020 1.00 47.5 yes View details
accD-psaI LSC 632 0.0011 1.00 47.4 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
trnH-GUG-psbA_p1 trnH-GUG-psbA ATTGAATGATGGGCGAACGA CAACCGTGCTAACCTTGGTA 667–686 1.000 80.8
trnH-GUG-psbA_p2 trnH-GUG-psbA ATTGAATGATGGGCGAACGA ATCAACCGTGCTAACCTTGG 669–688 1.000 80.8
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 603–622 1.000 80.3
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 617–636 1.000 80.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 616–635 1.000 80.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1231–1255 1.000 77.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1230–1254 1.000 77.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GGTGCTCAACCTACAGGAAC 1246–1270 1.000 77.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 1240–1264 1.000 76.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 1217–1241 1.000 75.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGAAACCGGAAAGAGAGGGA TCGGAGTATGAATCAAACCGA 1407–1444 1.000 64.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TCGGAGTATGAATCAAACCGA 1353–1390 1.000 64.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGAAACCGGAAAGAGAGGGA TGAATCAAACCGAAAGATCCCT 1399–1436 1.000 63.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TGAATCAAACCGAAAGATCCCT 1345–1382 1.000 63.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGAAACCGGAAAGAGAGGGA TCGGAGTATGAATCAAACCGAA 1407–1444 1.000 62.5
atpF_p1 atpF GCTCGAAGGGTTACCATGAG AGGGCGAAGTGATACAAAAAGA 1463–1468 1.000 63.9
atpF_p2 atpF GCTCGAAGGGTTACCATGAG GGGCGAAGTGATACAAAAAGA 1462–1467 1.000 60.3
atpF_p3 atpF GCTCGAAGGGTTACCATGAG AGGGCGAAGTGATACAAAAAG 1463–1468 1.000 60.2
atpF_p4 atpF ACTAATTTCGTCGGCTCGAA AGGGCGAAGTGATACAAAAAGA 1476–1481 1.000 59.2
atpF_p5 atpF CGAAGGGTTACCATGAGTGT AGGGCGAAGTGATACAAAAAGA 1460–1465 1.000 58.3
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA ATTTATGGACTGGTCGTGGC 684–691 1.000 81.5
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 712–719 1.000 80.8
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA TCGTGGCATTAGCGCTTTTA 671–678 1.000 79.7
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 699–706 1.000 78.9
atpF-atpH_p5 atpF-atpH AGTGACCCAAGGAAACGAAA ATTTATGGACTGGTCGTGGC 683–690 1.000 76.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCCG 1247–1248 1.000 78.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1217–1218 1.000 78.5
atpH-atpI_p3 atpH-atpI GGCAGAAATCAGTGGGTTCA TTTTGCAACTTTAGCTGCCG 1236–1237 1.000 78.5
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCCG 1303–1304 1.000 78.3
atpH-atpI_p5 atpH-atpI GATACCTTCTACGGCTTGGC TTTTGCAACTTTAGCTGCCG 1332–1333 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Platanus occidentalis NC_008335.1 161791 View on NCBI ↗
Platanus orientalis NC_073535.1 161717 View on NCBI ↗
Platanus x hispanica MZ128519.1 161717 View on NCBI ↗