Markers + reference

Uncaria

8 species · Rubiaceae · Gentianales

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Species 8
Genome length 155–155 kb
Candidate markers 266
Primer pairs 105

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 288 0.0491 0.92 72.6 yes View details
rps16-trnQ-UUG LSC 1264 0.0167 0.99 59.5 yes View details
trnG-GCC-trnR-UCU LSC 187 0.0424 1.00 77.0 yes View details
atpH-atpI LSC 1015 0.0154 1.00 56.7 yes View details
trnT-UGU-trnL-UAA LSC 743 0.0173 0.99 66.3 yes View details
ndhC-trnV-UAC LSC 1182 0.0131 0.90 59.5 yes View details
petA-psbJ LSC 1002 0.0187 0.99 60.8 yes View details
ycf1 IRb 1140 0.0010 1.00 34.1 no View details
ndhF-rpl32 SSC 810 0.0162 1.00 61.1 yes View details
rpl32-trnL-UAG SSC 850 0.0196 0.98 65.6 yes View details
ccsA-psaC SSC 1868 0.0094 1.00 52.6 yes View details
ycf1 SSC 5625 0.0105 1.00 43.8 yes View details
psbE-petL LSC 1085 0.0128 0.99 60.6 yes View details
psbK-psbI LSC 421 0.0140 1.00 60.0 yes View details
trnT-GGU-psbD LSC 1332 0.0068 0.96 59.9 yes View details
trnC-GCA-petN LSC 856 0.0131 1.00 59.2 yes View details
trnK-UUU-rps16 LSC 845 0.0127 1.00 58.7 yes View details
petN-psbM LSC 1043 0.0066 0.95 57.5 yes View details
ycf4-cemA LSC 849 0.0111 0.98 57.1 yes View details
trnS-UGA-psbZ LSC 340 0.0075 1.00 56.5 yes View details
psbM-trnD-GUC LSC 892 0.0097 1.00 56.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 335–358 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTTGGCTACATCCG TCCCTCTAGACCTAGCTGCT 334–357 1.000 83.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCCTCTAGACCTAGCTGCTA 333–356 1.000 81.7
trnH-GUG-psbA_p4 trnH-GUG-psbA TAATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 336–359 1.000 79.7
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG ACTTCCCTCTAGACCTAGCTG 337–360 1.000 78.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 857–975 1.000 83.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 856–974 1.000 83.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GGTGCTCAACCTACAGGAAC 872–990 1.000 82.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 866–984 1.000 82.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 843–961 1.000 81.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1334–1367 1.000 83.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1348–1381 1.000 81.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1338–1371 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1364–1397 1.000 78.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1326–1359 1.000 78.4
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT CCCTTTATTCTTCACGCCCA 568–580 1.000 82.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG CCCTTTATTCTTCACGCCCA 563–575 1.000 82.2
psbK-psbI_p3 psbK-psbI ATGCCAGTCATACCTGTCCT CCCTTTATTCTTCACGCCCA 602–614 1.000 81.5
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT CCCTTTATTCTTCACGCCCA 560–572 1.000 80.2
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT CCCTTTATTCTTCACGCCCA 561–573 1.000 80.2
trnG-GCC_p1 trnG-GCC ATTAGCAATCCGCCGCTTTA AGGAGCAAATGGACCGTTTT 1766–1845 1.000 86.1
trnG-GCC_p2 trnG-GCC ACTCAGCCATCTCTCCCAAT AGGAGCAAATGGACCGTTTT 1742–1821 1.000 85.6
trnG-GCC_p3 trnG-GCC ATTAGCAATCCGCCGCTTTA TTGCCCAATTTGCCTCTGAT 2063–2142 1.000 84.8
trnG-GCC_p4 trnG-GCC ATTAGCAATCCGCCGCTTTA CTTTGCCCAATTTGCCTCTG 2065–2144 1.000 84.6
trnG-GCC_p5 trnG-GCC GCAAGGAAGGGCTATTTCCA AGGAGCAAATGGACCGTTTT 1294–1349 1.000 83.8
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 254–269 1.000 73.4
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 257–272 1.000 73.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 260–275 1.000 72.6
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 263–278 1.000 72.3
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 258–273 1.000 70.9

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
Uncaria hirsuta NC_064964.1 155138 View on NCBI ↗
Uncaria homomalla NC_085791.1 154860 View on NCBI ↗
Uncaria lancifolia NC_085792.1 154798 View on NCBI ↗
Uncaria macrophylla NC_064966.1 155138 View on NCBI ↗
Uncaria rhynchophylla NC_053701.1 154870 View on NCBI ↗
Uncaria rhynchophylloides NC_085793.1 155010 View on NCBI ↗
Uncaria sessilifructus NC_064965.1 155177 View on NCBI ↗
Uncaria sinensis NC_085794.1 154907 View on NCBI ↗