Markers + reference

Fordiophyton

11 species · Melastomataceae · Myrtales

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Species 11
Genome length 154–156 kb
Candidate markers 263
Primer pairs 95

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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1065 0.0021 1.00 43.6 yes View details
trnS-GCU-trnR-UCU LSC 1828 0.0129 0.98 68.9 yes View details
rpoB-trnC-GCA LSC 1375 0.0111 0.99 72.8 yes View details
trnE-UUC-trnT-GGU LSC 630 0.0163 1.00 77.1 yes View details
rps4-trnT-UGU LSC 409 0.0180 0.99 70.7 yes View details
ndhC-trnV-UAC LSC 682 0.0252 1.00 71.1 yes View details
rps8-rpl14 LSC 332 0.0253 0.91 78.4 yes View details
ycf1 IRb 1884 0.0019 1.00 44.2 no View details
ndhF-rpl32 SSC 892 0.0230 0.98 80.9 yes View details
rps15 SSC 264 0.0120 1.00 47.8 yes View details
ycf1 SSC 5460 0.0079 1.00 49.8 yes View details
trnH-GUG-psbA LSC 228 0.0447 0.96 80.7 yes View details
petA-psbJ LSC 905 0.0125 1.00 75.5 yes View details
ndhH-rps15 SSC 128 0.0307 0.99 75.5 yes View details
ccsA-ndhD SSC 320 0.0154 0.99 74.8 yes View details
psbZ-trnG-UCC LSC 288 0.0213 0.98 74.4 yes View details
rpl2-trnH-GUG IRa 136 0.0068 1.00 74.1 no View details
rps18-rpl20 LSC 331 0.0190 1.00 73.2 yes View details
rbcL-accD LSC 600 0.0124 0.99 71.6 yes View details
atpF-atpH LSC 517 0.0109 0.97 71.5 yes View details
psaA-ycf3 LSC 596 0.0071 1.00 71.5 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 GCGCTAACCTTGGTATGGAA 322–345 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 336–359 1.000 90.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 335–358 1.000 90.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 337–360 1.000 90.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 272–295 1.000 90.4
psbA_p1 psbA AAACTCGTCTAAATTCAGACT AGAATTCGTGTGCTTGGGAG 1147–1150 1.000 40.9
psbA_p2 psbA AAACTCGTCTAAATTCAGACT AGAGAATTCGTGTGCTTGGG 1149–1152 1.000 40.9
psbA_p3 psbA AAACTCGTCTAAATTCAGACT GAGAATTCGTGTGCTTGGGA 1148–1151 1.000 40.9
psbA_p4 psbA AAACTCGTCTAAATTCAGACT TGGGAGTCCCTGATGATGAA 1133–1136 1.000 40.9
psbA_p5 psbA AAACTCGTCTAAATTCAGACT TTGGGAGTCCCTGATGATGA 1134–1137 1.000 40.9
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1863–1944 1.000 76.2
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1862–1943 1.000 76.2
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACATAGAAGAACTTGCGTCCA 1870–1951 1.000 74.4
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACATAGAAGAACTTGCGTCCA 1869–1950 1.000 74.3
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1864–1945 1.000 74.2
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GGATTGGTTGTCGCTTTAGC 534–634 1.000 81.8
atpF-atpH_p2 atpF-atpH GGCCCAAGGAAAGGAAAGAA GGATTGGTTGTCGCTTTAGC 502–602 0.909 78.7
atpF-atpH_p3 atpF-atpH GGCCCAAGGAAAGGAAAGAA CGGAGGGAAAAATACGAGGT 567–667 0.909 77.3
atpF-atpH_p4 atpF-atpH GGCCCAAGGAAAGGAAAGAA GCGGAGGGAAAAATACGAGG 568–668 0.909 77.1
atpF-atpH_p5 atpF-atpH GGCCCAAGGAAAGGAAAGAA GGCGGAGGGAAAAATACGAG 569–669 0.909 77.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TTCCCTCACTTCCATCCACC CCGGATTTGAACTGGGGAAA 1429–1479 1.000 78.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCACTTCCATCCACCAGCAT CCGGATTTGAACTGGGGAAA 1424–1474 1.000 78.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GACATTCCCTCACTTCCATCC CCGGATTTGAACTGGGGAAA 1433–1483 1.000 78.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTCCCTCACTTCCATCCA CCGGATTTGAACTGGGGAAA 1431–1481 1.000 78.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCTCACTTCCATCCAC CCGGATTTGAACTGGGGAAA 1430–1480 1.000 78.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 655–717 1.000 87.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 634–696 1.000 86.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TGGCGTTACTCTACCACTGA 631–693 1.000 86.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCGATGACTTACGCCTTACC 652–714 1.000 85.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TTGAACCGATGACTTACGCC 657–719 1.000 84.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Fordiophyton cordifolium MK994784.1 155632 View on NCBI ↗
Fordiophyton faberi NC_068147.1 155664 View on NCBI ↗
Fordiophyton huizhouense MK994786.1 155639 View on NCBI ↗
Fordiophyton jinpingense MK994875.1 154430 View on NCBI ↗
Fordiophyton longipes MK994858.1 154928 View on NCBI ↗
Fordiophyton peperomiifolium MK994785.1 154453 View on NCBI ↗
Fordiophyton phamhoangii NC_068163.1 155084 View on NCBI ↗
Fordiophyton repens MK994815.1 154970 View on NCBI ↗
Fordiophyton strictum MK994816.1 155110 View on NCBI ↗
Fordiophyton tereticaule NC_072987.1 155191 View on NCBI ↗
Fordiophyton zhuangiae MK994839.1 155423 View on NCBI ↗