Markers + reference

Tashiroea

6 species · Melastomataceae · Myrtales

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Species 6
Genome length 156–156 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

12 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 1062 0.0041 1.00 40.5 yes View details
rps16-trnQ-UUG LSC 1021 0.0191 0.96 62.1 yes View details
trnR-UCU-atpA LSC 306 0.0160 0.99 58.8 yes View details
rpoB-trnC-GCA LSC 1445 0.0135 0.97 58.6 yes View details
trnC-GCA-ndhJ LSC 887 0.0158 0.98 53.5 yes View details
ndhC-trnV-UAC LSC 609 0.0203 0.98 72.8 yes View details
accD-psaI LSC 847 0.0205 0.99 58.4 yes View details
rps8-rpl14 LSC 324 0.0395 0.83 66.7 yes View details
ycf1 IRb 1899 0.0004 1.00 33.2 no View details
ndhF SSC 2244 0.0103 1.00 58.3 yes View details
ndhF-rpl32 SSC 935 0.0253 0.97 67.5 yes View details
ycf1 SSC 5613 0.0093 0.98 49.9 yes View details
trnH-GUG-psbA LSC 229 0.0631 0.97 71.3 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0105 0.99 67.4 yes View details
psbT-psbN LSC 72 0.0565 1.00 62.0 yes View details
rbcL-accD LSC 629 0.0132 0.95 60.8 yes View details
matK-trnK-UUU LSC 760 0.0124 0.99 60.4 yes View details
rpl2-trnH-GUG IRa 136 0.0049 0.99 60.4 no View details
trnT-GGU-psbD LSC 1213 0.0117 0.99 60.2 yes View details
ndhD-psaC SSC 142 0.0312 0.99 57.8 yes View details
psbM-trnD-GUC LSC 740 0.0148 0.98 57.6 yes View details
psbE-petL LSC 1131 0.0103 0.99 57.6 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 GCTGTTGAAGTTCCATCTACA 278–281 1.000 63.9
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCTGTTGAAGTTCCATCTACA 291–294 1.000 63.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCTGTTGAAGTTCCATCTACA 292–295 1.000 63.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCTGTTGAAGTTCCATCTACA 293–296 1.000 63.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGTTGAAGTTCCATCTACAA 278–281 1.000 61.8
psbA_p1 psbA GATCCACTTGGCTACATCCG AACACAAAACTACTGGCCGT 2046–2049 1.000 81.1
psbA_p2 psbA GATCCACTTGGCTACATCCG ACAAAACTACTGGCCGTGTT 2043–2046 1.000 81.1
psbA_p3 psbA CAATCCACTGCCTTGATCCA AACACAAAACTACTGGCCGT 2060–2063 1.000 81.0
psbA_p4 psbA CAATCCACTGCCTTGATCCA ACAAAACTACTGGCCGTGTT 2057–2060 1.000 81.0
psbA_p5 psbA AATCCACTGCCTTGATCCAC ACAAAACTACTGGCCGTGTT 2056–2059 1.000 81.0
trnK-UUU_p1 trnK-UUU AGGAAATGAGTTCACAAAACACA ATCCAACCAAACATTGCCAA 2688–2715 1.000 42.8
trnK-UUU_p2 trnK-UUU AGGAAATGAGTTCACAAAACACA TCCAACCAAACATTGCCAAT 2687–2714 1.000 42.8
trnK-UUU_p3 trnK-UUU AGGAAATGAGTTCACAAAACACA TCCAACCAAACATTGCCAATT 2687–2714 1.000 42.8
trnK-UUU_p4 trnK-UUU AGGAAATGAGTTCACAAAACACAA ATCCAACCAAACATTGCCAA 2688–2715 1.000 42.8
trnK-UUU_p5 trnK-UUU AGGAAATGAGTTCACAAAACACAA TCCAACCAAACATTGCCAAT 2687–2714 1.000 42.8
matK-trnK-UUU_p1 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA AACGGTAGAGTACTCGGCTT 832–841 1.000 78.3
matK-trnK-UUU_p2 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA ACGGTAGAGTACTCGGCTTT 831–840 1.000 78.3
matK-trnK-UUU_p3 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA TTGGGTTGCTAACTCAACGG 847–856 1.000 76.4
matK-trnK-UUU_p4 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA GGGTTGCTAACTCAACGGTA 845–854 1.000 75.9
matK-trnK-UUU_p5 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGAT ACGGTAGAGTACTCGGCTTT 831–840 1.000 73.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGAAAATGGCAGCAACATGC TAGAGCAGCTTGCCAAACAA 1896–1968 1.000 84.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGAAAATGGCAGCAACATGC TTAGAGCAGCTTGCCAAACA 1897–1969 1.000 84.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACATGCCCCCTTTTATGCT TAGAGCAGCTTGCCAAACAA 1883–1955 0.833 77.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACATGCCCCCTTTTATGCTT TAGAGCAGCTTGCCAAACAA 1882–1954 0.833 77.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACATGCCCCCTTTTATGCTT TTAGAGCAGCTTGCCAAACA 1883–1955 0.833 77.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACCGAGGAAGCAGAA 394–409 1.000 70.7
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACCGAGGAAGC 398–413 1.000 70.6
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCGAGGAAGCAGAATCCATT 388–403 1.000 68.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACCGAGGAAGCAGAATC 392–407 1.000 68.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GACATTCACCGAGGAAGCAG 396–411 1.000 66.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Tashiroea biglandularis MK994829.1 156298 View on NCBI ↗
Tashiroea okinawensis MK994873.1 156023 View on NCBI ↗
Tashiroea quadrangularis MK994802.1 156005 View on NCBI ↗
Tashiroea sessilifolia MK994824.1 156104 View on NCBI ↗
Tashiroea sinensis MK994837.1 155893 View on NCBI ↗
Tashiroea yaeyamensis MK994870.1 156147 View on NCBI ↗