Markers + reference

Medinilla

5 species · Melastomataceae · Myrtales

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Species 5
Genome length 155–156 kb
Candidate markers 263
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0046 1.00 49.6 yes View details
trnS-GCU-trnR-UCU LSC 1798 0.0207 1.00 69.4 yes View details
trnR-UCU-atpA LSC 300 0.0339 0.99 70.5 yes View details
trnE-UUC-trnT-GGU LSC 883 0.0247 0.98 64.6 yes View details
trnT-GGU-psbD LSC 1209 0.0201 1.00 65.7 yes View details
trnT-UGU-trnL-UAA LSC 842 0.0232 0.99 75.7 yes View details
ndhC-trnV-UAC LSC 712 0.0278 1.00 71.4 yes View details
petA-psbJ LSC 921 0.0168 0.98 61.6 yes View details
clpP LSC 2166 0.0121 1.00 54.0 yes View details
rpl22 LSC 438 0.0381 0.99 70.7 yes View details
ycf1 IRb 1818 0.0032 1.00 45.5 no View details
ndhF-rpl32 SSC 621 0.1533 0.96 87.3 yes View details
ycf1 SSC 5421 0.0140 1.00 54.2 yes View details
ndhD-psaC SSC 141 0.0553 1.00 89.8 yes View details
trnH-GUG-psbA LSC 229 0.0721 0.99 77.4 yes View details
psbM-trnD-GUC LSC 734 0.0136 0.99 71.7 yes View details
rps8-rpl14 LSC 291 0.0353 1.00 71.3 yes View details
psbZ-trnG-UCC LSC 302 0.0359 1.00 70.3 yes View details
ndhB-trnL-CAA IRa 629 0.0103 0.95 70.0 yes View details
trnL-CAA-ndhB IRb 629 0.0099 0.94 69.8 yes View details
rps12-clpP LSC 187 0.0321 1.00 69.4 yes View details
petL-petG LSC 188 0.0330 1.00 68.0 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 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 GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 344–355 1.000 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCCTCTAGACCTAGCTGCAT 297 0.200 46.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCCTCTAGACCTAGCTGCAT 311 0.200 46.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCCTCTAGACCTAGCTGCAT 310 0.200 46.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCCTCTAGACCTAGCTGCAT 312 0.200 46.9
psbA_p1 psbA AAACTCGTCTAAATTCAGACT TGGGAGTCCCTGATGATGAA 1133 1.000 40.7
psbA_p2 psbA AAACTCGTCTAAATTCAGACT TTGGGAGTCCCTGATGATGA 1134 1.000 40.7
psbA_p3 psbA AAAACTCGTCTAAATTCAGACT TGGGAGTCCCTGATGATGAA 1134 1.000 40.7
psbA_p4 psbA AAAACTCGTCTAAATTCAGACT TTGGGAGTCCCTGATGATGA 1135 1.000 40.7
psbA_p5 psbA AAAAACTCGTCTAAATTCAGACT TGGGAGTCCCTGATGATGAA 1135 1.000 40.7
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1847–1912 1.000 75.6
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1846–1911 1.000 75.6
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1848–1913 1.000 73.6
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AAGAACTTGCGTCCAATAGGA 1847–1912 1.000 73.6
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AGCAATCCGACGCTTTAGTC AGAACTTGCGTCCAATAGGA 1849–1914 1.000 72.8
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACAGATGGAACGTTTTGGACT 346–354 1.000 65.6
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACAGATGGAACGTTTTGGAC 346–354 1.000 61.4
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA ACAGATGGAACGTTTTGGACT 345–353 1.000 60.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AACAGATGGAACGTTTTGGAC 347–355 1.000 59.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CAGATGGAACGTTTTGGACT 345–353 1.000 59.1
psbM-trnD-GUC_p1 psbM-trnD-GUC TCACTTTGACTCACGGTTTT TCAATTGGTTAGAGCACCGC 852–918 1.000 61.1
psbM-trnD-GUC_p2 psbM-trnD-GUC TCACTTTGACTCACGGTTTTT TCAATTGGTTAGAGCACCGC 852–918 1.000 59.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AATCACTTTGACTCACGGTT TCAATTGGTTAGAGCACCGC 854–920 1.000 59.2
psbM-trnD-GUC_p4 psbM-trnD-GUC ATCACTTTGACTCACGGTTT TCAATTGGTTAGAGCACCGC 853–919 1.000 59.2
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 798–864 1.000 59.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGGATCAGGGAATTCTTGGG CAAGACTACGGAATCGGCAA 1310–1638 1.000 87.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGGATCAGGGAATTCTTGGG AACAAGACTACGGAATCGGC 1312–1640 1.000 87.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCATTTCATGGCGGATCAGG CAAGACTACGGAATCGGCAA 1321–1649 1.000 87.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGGATCAGGGAATTCTTGGG GAACCGATGACTTACGCCTT 930–1233 1.000 87.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCATTTCATGGCGGATCAGG GAACCGATGACTTACGCCTT 941–1244 1.000 87.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Medinilla amplectens MK994882.1 155529 View on NCBI ↗
Medinilla beamanii MK994880.1 155271 View on NCBI ↗
Medinilla fengii MK994809.1 155841 View on NCBI ↗
Medinilla petelotii MK994847.1 155673 View on NCBI ↗
Medinilla tapete-magicum NC_081464.1 155602 View on NCBI ↗