Markers + reference

Garcinia

19 species · Clusiaceae · Malpighiales

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Species 19
Genome length 156–158 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 511 0.0639 0.90 82.5 yes View details
trnS-GCU-trnG-UCC LSC 1025 0.0255 0.99 66.5 yes View details
trnG-UCC-trnR-UCU LSC 718 0.0367 0.92 75.2 yes View details
atpH-atpI LSC 1263 0.0266 0.96 70.9 yes View details
psbZ-trnG-GCC LSC 903 0.0327 0.96 66.3 yes View details
ndhC-trnV-UAC LSC 593 0.0427 0.89 66.7 yes View details
atpB-rbcL LSC 752 0.0339 0.98 72.4 yes View details
rbcL-accD LSC 997 0.0267 0.96 62.9 yes View details
psbK-psbI LSC 411 0.0374 0.94 71.2 yes View details
ccsA-ndhD SSC 304 0.0416 0.98 70.1 yes View details
ndhF-trnL-UAG SSC 612 0.0289 0.96 69.2 yes View details
psbE-petL LSC 974 0.0257 0.97 67.5 yes View details
rps8-rpl14 LSC 311 0.0380 0.93 67.5 yes View details
rps16 LSC 1124 0.0252 1.00 67.2 yes View details
rpl22-rps19 LSC 108 0.0724 0.95 66.9 yes View details
trnP-UGG-psaJ LSC 501 0.0224 1.00 66.7 yes View details
trnT-UGU-trnL-UAA LSC 470 0.0270 0.99 65.9 yes View details
trnT-GGU-psbD LSC 1050 0.0190 0.97 64.9 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 385–580 0.947 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC TTCCCTCTAGACCTAGCTGC 390–585 0.947 84.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CCTTGATCCACTTGGCTACA TTCCCTCTAGACCTAGCTGC 389–584 0.947 83.0
trnH-GUG-psbA_p4 trnH-GUG-psbA GCGCATGATGGATTCACAAT TTCCCTCTAGACCTAGCTGC 415–610 0.947 83.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ATTGCCTTGATCCACTTGGC TTCCCTCTAGACCTAGCTGC 393–588 0.947 82.8
rps16_p1 rps16 AAATTGAGTCGCACGCTACA GAGGTTCGAATCCTTCCGTC 2152–2373 0.789 79.8
rps16_p2 rps16 AAATTGAGTCGCACGCTACA CGGCGGAAATTGACGAAAAA 2282–2478 0.684 73.9
rps16_p3 rps16 ATTTCCGTAAAAATCCGCGC GAGGTTCGAATCCTTCCGTC 1604–1665 0.526 66.6
rps16_p4 rps16 ATTTCCGTAAAAATCCGCGC TCCCAGAGCATACCGAGAAT 1586–1647 0.526 66.6
rps16_p5 rps16 ATTTCCGTAAAAATCCGCGC CGGCGGAAATTGACGAAAAA 1717–1778 0.263 54.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 504–531 1.000 91.0
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 505–532 1.000 91.0
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 506–533 1.000 89.2
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 501–528 1.000 89.0
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 502–529 1.000 89.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTAGTCCACTCAGCCACC TACCACTAAACTATACCCGC 1040–1189 1.000 57.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTAGTCCACTCAGCCACC TTACCACTAAACTATACCCGC 1041–1190 1.000 56.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TTTAGTCCACTCAGCCACCT TACCACTAAACTATACCCGC 1039–1188 1.000 56.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TTTAGTCCACTCAGCCACCT TTACCACTAAACTATACCCGC 1040–1189 1.000 55.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CTTTAGTCCACTCAGCCACC TTTACCACTAAACTATACCCGC 1042–1191 1.000 54.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 705–880 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 708–883 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 711–886 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 714–889 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 709–884 1.000 72.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCATGGAAGGGCATCATTGA 1275–1336 1.000 90.2
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCATGGAAGGGCATCATTG 1276–1337 1.000 90.2
atpH-atpI_p3 atpH-atpI AGCGGCAGAAATCAATGGAT CCATGGAAGGGCATCATTGA 1267–1328 1.000 90.1
atpH-atpI_p4 atpH-atpI AGCGGCAGAAATCAATGGAT TCCATGGAAGGGCATCATTG 1268–1329 1.000 90.1
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTGCAACTTTAGCTGCTGC 1309–1370 1.000 89.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Garcinia anomala MW582313.1 156774 View on NCBI ↗
Garcinia aristata PP228198.1 157933 View on NCBI ↗
Garcinia bracteata (nom. inval.) PV110184.1 156773 View on NCBI ↗
Garcinia brasiliensis PX781195.1 158062 View on NCBI ↗
Garcinia celebica PP191178.1 156698 View on NCBI ↗
Garcinia esculenta NC_085365.1 155853 View on NCBI ↗
Garcinia gummi-gutta NC_047250.1 156202 View on NCBI ↗
Garcinia hanburyi PV110183.1 156539 View on NCBI ↗
Garcinia humilis PX644754.1 157642 View on NCBI ↗
Garcinia indica PP179384.1 157826 View on NCBI ↗
Garcinia madruno PP179383.1 158062 View on NCBI ↗
Garcinia mangostana NC_036341.1 158179 View on NCBI ↗
Garcinia oblongifolia NC_050384.1 156577 View on NCBI ↗
Garcinia paucinervis NC_056905.1 157702 View on NCBI ↗
Garcinia pedunculata NC_048983.1 157688 View on NCBI ↗
Garcinia schomburgkiana PP191179.1 156990 View on NCBI ↗
Garcinia subelliptica NC_059006.1 158356 View on NCBI ↗
Garcinia xanthochymus NC_069300.1 157688 View on NCBI ↗
Garcinia yunnanensis PP073962.1 158155 View on NCBI ↗