Markers + reference

Cinchona

4 species · Rubiaceae · Gentianales

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Species 4
Genome length 155–157 kb
Candidate markers 273
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1449 0.0105 1.00 56.2 yes View details
trnC-GCA-petN LSC 880 0.0121 1.00 60.0 yes View details
trnT-GGU-psbD LSC 1247 0.0100 0.99 62.5 yes View details
ndhC-trnV-UAC LSC 1233 0.0130 0.99 63.3 yes View details
rpl16 LSC 1401 0.0069 1.00 50.7 yes View details
rpl22 IRb 468 0.0053 1.00 37.6 no View details
ndhF SSC 2226 0.0054 1.00 47.8 yes View details
rpl32-trnL-UAG SSC 868 0.0144 0.99 57.0 yes View details
ccsA-ndhD SSC 270 0.0377 1.00 72.7 yes View details
rpl22 IRa 468 0.0256 0.06 45.9 yes View details
rpl16 IRa 15 0.0000 0.00 8.1 no View details
psbK-psbI LSC 415 0.0116 1.00 63.7 yes View details
petB-petD LSC 845 0.0095 1.00 61.9 yes View details
pafI LSC 1977 0.0035 1.00 60.1 yes View details
ndhF-rpl32 SSC 808 0.0078 0.99 59.9 yes View details
rpoB-trnC-GCA LSC 1056 0.0101 1.00 59.8 yes View details
rbcL LSC 1437 0.0016 1.00 59.8 yes View details
trnG-GCC-trnR-UCU LSC 173 0.0096 1.00 59.5 yes View details
psbZ-trnG-GCC LSC 320 0.0031 0.95 59.3 yes View details
atpB LSC 1497 0.0019 1.00 58.2 yes View details
petL-petG LSC 176 0.0104 0.99 57.7 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GATTCCCGCGTGATACACTT CTTTTGACCCCACCCAATCA 1943–2115 1.000 84.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACTTCGGTGCTTCTGAATCC CTTTTGACCCCACCCAATCA 2029–2201 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATTCCCGCGTGATACACTT AGCAGCTTGCCAAACAAAAG 2212–2384 1.000 84.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GATTCCCGCGTGATACACTT CTTACAGCAGCTTGCCAAAC 2217–2389 1.000 84.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGAGTGGTCTTTACCCCCTT CTTTTGACCCCACCCAATCA 2169–2341 1.000 84.0
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTCTTCACGCCCAGGATTAC 558–565 1.000 78.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 553–560 1.000 78.4
psbK-psbI_p3 psbK-psbI ATGCCAGTCATACCTGTCCT TTCTTCACGCCCAGGATTAC 592–599 1.000 77.8
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGCCCAGGATTAC 550–557 1.000 76.4
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTCTTCACGCCCAGGATTAC 551–558 1.000 76.4
trnG-GCC_p1 trnG-GCC ATTAGCAATCCGCCGCTTTA AAGGAGCAAATGGACCGTTT 1729–1744 1.000 81.3
trnG-GCC_p2 trnG-GCC ATTAGCAATCCGCCGCTTTA AGGAGCAAATGGACCGTTTT 1728–1743 1.000 81.3
trnG-GCC_p3 trnG-GCC ATTCAAGCAAGGGCAAGGAA AAGGAGCAAATGGACCGTTT 1326–1330 1.000 80.9
trnG-GCC_p4 trnG-GCC ATTCAAGCAAGGGCAAGGAA AGGAGCAAATGGACCGTTTT 1325–1329 1.000 80.9
trnG-GCC_p5 trnG-GCC ATTCAAGCAAGGGCAAGGAA TTGCCCAATTTGCCTCTGAT 1622–1626 1.000 80.4
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 251–252 1.000 64.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGAAGACCTCTGTCCTATCCA 257–258 1.000 64.6
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 257–258 1.000 63.9
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTCTGTCCT 263–264 1.000 63.9
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TCGACGTCGACTATAACCCT AGAAGACCTCTGTCCTATCCA 272–273 1.000 62.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1139 1.000 72.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AGCCATTCCCTCATTTCCATC CCGGATTTGAACTGGGGAAA 1148 1.000 72.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1144 1.000 72.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCAGGTATTGTAGCCATTCCC CCGGATTTGAACTGGGGAAA 1159 1.000 71.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1138 1.000 71.5
trnC-GCA-petN_p1 trnC-GCA-petN TGTATATCGTTTTGGCGGCA ACTTCTTCCCCACACTACGA 1034–1045 1.000 82.1
trnC-GCA-petN_p2 trnC-GCA-petN TGTATATCGTTTTGGCGGCA TTCTTCCCCACACTACGAGT 1032–1043 1.000 82.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 979–990 1.000 81.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 977–988 1.000 81.7
trnC-GCA-petN_p5 trnC-GCA-petN TGTATATCGTTTTGGCGGCA CACTTCTTCCCCACACTACG 1035–1046 1.000 81.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Cinchona macrocalyx OP946452.1 157062 View on NCBI ↗
Cinchona micrantha PX354551.1 155392 View on NCBI ↗
Cinchona officinalis OP946451.1 156990 View on NCBI ↗
Cinchona pitayensis OR502875.1 155284 View on NCBI ↗