Markers + reference

Debregeasia

3 species · Urticaceae · Rosales

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Species 3
Genome length 156–156 kb
Candidate markers 263
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 252 0.0212 1.00 71.6 yes View details
psbK-psbI LSC 487 0.0055 1.00 36.4 yes View details
rpoB-trnC-GCA LSC 1166 0.0057 1.00 60.7 yes View details
trnT-GGU-psbD LSC 1322 0.0045 1.00 42.5 yes View details
accD-psaI LSC 726 0.0065 0.99 66.6 yes View details
petA-psbJ LSC 971 0.0069 1.00 62.5 yes View details
ccsA SSC 957 0.0028 1.00 33.3 yes View details
rps15-ycf1 SSC 402 0.0083 1.00 47.4 yes View details
ycf1 SSC 5733 0.0038 1.00 45.4 yes View details
ndhD-psaC SSC 106 0.0220 1.00 67.0 yes View details
trnK-UUU-rps16 LSC 819 0.0024 1.00 62.8 yes View details
psaA-ycf3 LSC 743 0.0045 1.00 62.3 yes View details
ndhF-rpl32 SSC 1219 0.0044 1.00 61.6 yes View details
psaJ-rpl33 LSC 443 0.0060 1.00 61.4 yes View details
trnS-GCU-trnG-UCC LSC 680 0.0039 1.00 61.0 yes View details
trnE-UUC-trnT-GGU LSC 653 0.0031 1.00 60.7 yes View details
rpl16 LSC 1434 0.0014 1.00 60.4 yes View details
trnC-GCA-petN LSC 908 0.0022 1.00 60.2 yes View details
rbcL LSC 1449 0.0023 1.00 60.2 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 100 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 CCTCTAGACCTAGCTGCTGT 303–398 1.000 84.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 306–401 1.000 84.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 317–412 1.000 83.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 316–411 1.000 83.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 318–413 1.000 83.8
trnK-UUU_p1 trnK-UUU ACTGAAATGAATTAACAGGTTCGG TGTGCCGTACAATTCAATCTCT 2807–2808 1.000 40.3
trnK-UUU_p2 trnK-UUU CTGAAATGAATTAACAGGTTCGGA TGTGCCGTACAATTCAATCTCT 2806–2807 1.000 40.3
trnK-UUU_p3 trnK-UUU TGAAATGAATTAACAGGTTCGGA TGTGCCGTACAATTCAATCTCT 2805–2806 1.000 40.3
trnK-UUU_p4 trnK-UUU ACTGAAATGAATTAACAGGTTCGG TGTGCCGTACAATTCAATCTC 2807–2808 1.000 40.3
trnK-UUU_p5 trnK-UUU CTGAAATGAATTAACAGGTTCGGA TGTGCCGTACAATTCAATCTC 2806–2807 1.000 40.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAGGCGGGTGT 898–917 1.000 80.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAGGCGGGTGT 897–916 1.000 80.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ATTTCAAAGAAGGCGGGTGT 907–926 1.000 79.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAGAAGGCGGGTGTTTT 894–913 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGAAGGCGGGTGTTT 895–914 1.000 78.7
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGCCCCGGATCATTAGATA 612–613 1.000 79.5
psbK-psbI_p2 psbK-psbI CTTTTGTTTGGCAAGCTGCT TACGCCCCGGATCATTAGAT 613–614 1.000 79.5
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 607–608 1.000 79.5
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 608–609 1.000 79.5
psbK-psbI_p5 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTACGCCCCGGATCATTAGA 614–615 1.000 77.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TAATCAACTCAAGGGACCCC 788–791 1.000 68.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TAATCAACTCAAGGGACCCC 787–790 1.000 68.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TAATCAACTCAAGGGACCCC 842–845 1.000 67.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTAATCAACTCAAGGGACCCC 789–792 1.000 66.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTAATCAACTCAAGGGACCCC 788–791 1.000 66.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TAAGCCCCGATCAATGAACC CCGGATTTGAACTGGGGAAA 1304–1321 1.000 78.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCCCCGATCAATGAACCTAC CCGGATTTGAACTGGGGAAA 1301–1318 1.000 77.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TAAGCCCCGATCAATGAACC TTGTTAATCAGGCGACACCC 1322–1339 1.000 77.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGTTAAGCCCCGA CCGGATTTGAACTGGGGAAA 1314–1331 1.000 77.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCTGTTAAGCCCCG CCGGATTTGAACTGGGGAAA 1315–1332 1.000 77.2

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
Debregeasia longifolia NC_087757.1 155938 View on NCBI ↗
Debregeasia saeneb NC_062311.1 155780 View on NCBI ↗
Debregeasia squamata MN189959.1 156065 View on NCBI ↗