Markers + reference

Paulownia

8 species · Paulowniaceae · Lamiales

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Species 8
Genome length 155–155 kb
Candidate markers 272
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 488 0.0142 0.91 58.1 yes View details
trnK(UUU)-rps16 LSC 890 0.0135 1.00 55.8 yes View details
trnS(GCU)-trnG(UCC) LSC 636 0.0061 1.00 53.0 yes View details
petN-psbM LSC 986 0.0073 1.00 54.9 yes View details
psbM-trnD(GUC) LSC 538 0.0107 1.00 47.0 yes View details
ycf3 LSC 1964 0.0026 1.00 45.4 yes View details
accD-psaI LSC 728 0.0076 0.98 54.0 yes View details
rpl22 LSC 459 0.0015 1.00 28.2 yes View details
ycf1 IRb 1071 0.0013 1.00 33.2 no View details
ccsA-ndhD SSC 309 0.0169 0.82 57.7 yes View details
ycf1 SSC 5583 0.0018 1.00 27.5 yes View details
trnG(GCC)-tRNA-fM(CAU) LSC 185 0.0147 0.99 62.8 yes View details
psbT-psbN LSC 60 0.0375 1.00 60.6 yes View details
ycf3-trnS(GGA) LSC 848 0.0037 1.00 52.6 yes View details
trnT(UGU)-trnL(UAA) LSC 705 0.0038 1.00 48.5 yes View details
trnR(UCU)-atpA LSC 108 0.0112 1.00 48.1 yes View details
trnR(ACG)-trnN(GUU) IRb 579 0.0032 1.00 48.0 yes View details
trnN(GUU)-trnR(ACG) IRa 579 0.0032 1.00 48.0 yes View details
trnT(GGU)-psbD LSC 1268 0.0027 1.00 47.3 yes View details
petA-psbJ LSC 1012 0.0008 0.99 47.0 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
trnH(GUG)-psbA_p1 trnH(GUG)-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 374–567 1.000 84.8
trnH(GUG)-psbA_p2 trnH(GUG)-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 388–581 1.000 84.7
trnH(GUG)-psbA_p3 trnH(GUG)-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 387–580 1.000 84.7
trnH(GUG)-psbA_p4 trnH(GUG)-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 389–582 1.000 84.7
trnH(GUG)-psbA_p5 trnH(GUG)-psbA GATCCACTTGGCTACATCCG TGGAAGTTATGCACGAACGT 406–599 1.000 84.0
trnK(UUU)-rps16_p1 trnK(UUU)-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 1013–1019 1.000 69.5
trnK(UUU)-rps16_p2 trnK(UUU)-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 1012–1018 1.000 69.5
trnK(UUU)-rps16_p3 trnK(UUU)-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCCACAGGAACT 1012–1018 1.000 68.7
trnK(UUU)-rps16_p4 trnK(UUU)-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGGAACT 1011–1017 1.000 68.7
trnK(UUU)-rps16_p5 trnK(UUU)-rps16 TCTAGCCGCACTTAAAAGCC GTGCTCAACCCACAGGAAC 1027–1033 1.000 68.6
trnS(GCU)-trnG(UCC)_p1 trnS(GCU)-trnG(UCC) CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 689–705 1.000 55.1
trnS(GCU)-trnG(UCC)_p2 trnS(GCU)-trnG(UCC) AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 688–704 1.000 55.1
trnS(GCU)-trnG(UCC)_p3 trnS(GCU)-trnG(UCC) CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 692–708 1.000 54.0
trnS(GCU)-trnG(UCC)_p4 trnS(GCU)-trnG(UCC) CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 691–707 1.000 54.0
trnS(GCU)-trnG(UCC)_p5 trnS(GCU)-trnG(UCC) AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 690–706 1.000 54.0
trnR(UCU)-atpA_p1 trnR(UCU)-atpA AAAAATCGGAATGAACGGCG TTCAGGAACAAATGGACCGG 241–245 1.000 78.5
trnR(UCU)-atpA_p2 trnR(UCU)-atpA GAACGGCGTCCATTGTCTAA TTCAGGAACAAATGGACCGG 229–233 1.000 78.4
trnR(UCU)-atpA_p3 trnR(UCU)-atpA ACGGCGTCCATTGTCTAATG TTCAGGAACAAATGGACCGG 227–231 1.000 77.9
trnR(UCU)-atpA_p4 trnR(UCU)-atpA AACGGCGTCCATTGTCTAAT TTCAGGAACAAATGGACCGG 228–232 1.000 77.5
trnR(UCU)-atpA_p5 trnR(UCU)-atpA AAAAATCGGAATGAACGGCG AGGAACAAATGGACCGGTTT 238–242 1.000 76.3
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA AGTTCCTACCGCTTTTCTACT 1074–1084 1.000 60.4
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT AGTTCCTACCGCTTTTCTACT 1072–1082 1.000 60.4
petN-psbM_p3 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCT 1079–1089 1.000 60.3
petN-psbM_p4 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCT 1081–1091 1.000 60.2
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG AGTTCCTACCGCTTTTCTACT 1071–1081 1.000 59.8
psbM-trnD(GUC)_p1 psbM-trnD(GUC) AGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 663–671 1.000 57.7
psbM-trnD(GUC)_p2 psbM-trnD(GUC) AGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 655–663 1.000 57.6
psbM-trnD(GUC)_p3 psbM-trnD(GUC) AAGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 656–664 1.000 56.0
psbM-trnD(GUC)_p4 psbM-trnD(GUC) AGCGGTAGGAACTAGAATGAA TTCAATTGGTCAGAGCACCG 655–663 1.000 56.0
psbM-trnD(GUC)_p5 psbM-trnD(GUC) AAGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 664–672 1.000 55.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Paulownia catalpifolia NC_045084.1 154743 View on NCBI ↗
Paulownia coreana NC_031435.1 154545 View on NCBI ↗
Paulownia elongata NC_045085.1 154611 View on NCBI ↗
Paulownia fargesii NC_045086.1 154506 View on NCBI ↗
Paulownia fortunei NC_045087.1 154612 View on NCBI ↗
Paulownia kawakamii NC_045088.1 154746 View on NCBI ↗
Paulownia taiwaniana NC_045083.1 154646 View on NCBI ↗
Paulownia tomentosa NC_031436.1 154540 View on NCBI ↗