Markers + reference

Bredia

27 species · Melastomataceae · Myrtales

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Species 27
Genome length 155–156 kb
Candidate markers 257
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0025 1.00 36.1 yes View details
rps16-trnQ-UUG LSC 992 0.0165 0.99 71.5 yes View details
trnS-GCU-trnR-UCU LSC 1804 0.0098 1.00 62.5 yes View details
petN-psbM LSC 363 0.0195 0.99 67.0 yes View details
ndhC-trnV-UAC LSC 742 0.0170 0.99 70.5 yes View details
rps8 LSC 405 0.0085 1.00 37.3 yes View details
ndhF-rpl32 SSC 905 0.0173 0.96 71.4 yes View details
ccsA-psaC SSC 1974 0.0111 0.99 53.1 yes View details
psaC SSC 246 0.0058 1.00 26.9 yes View details
ycf1 SSC 5508 0.0077 1.00 48.2 yes View details
trnH-GUG-psbA LSC 231 0.0533 0.97 90.9 yes View details
rpl2-trnH-GUG IRa 136 0.0074 1.00 68.9 no View details
psbE-petL LSC 1141 0.0079 0.98 67.7 yes View details
ndhK-ndhC LSC 54 0.0428 1.00 66.7 yes View details
psbK-psbI LSC 373 0.0138 1.00 64.0 yes View details
psaJ-rpl33 LSC 532 0.0112 1.00 63.7 yes View details
psbM-trnD-GUC LSC 729 0.0084 1.00 63.4 yes View details
trnE-UUC-trnT-GGU LSC 978 0.0094 0.99 62.3 yes View details
petA-psbJ LSC 903 0.0114 1.00 61.7 yes View details
rpl14-rps3 LSC 1734 0.0069 1.00 60.6 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 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 342–437 1.000 90.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 356–451 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 355–450 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 357–452 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 292–387 0.963 89.0
psbA_p1 psbA AAACTCGTCTAAATTCAGACT AGAATTCGTGTGCTTGGGAG 1147 1.000 41.2
psbA_p2 psbA AAACTCGTCTAAATTCAGACT AGAGAATTCGTGTGCTTGGG 1149 1.000 41.2
psbA_p3 psbA AAACTCGTCTAAATTCAGACT GAGAATTCGTGTGCTTGGGA 1148 1.000 41.2
psbA_p4 psbA AAACTCGTCTAAATTCAGACT TGGGAGTCCCTGATGATGAA 1133 1.000 41.2
psbA_p5 psbA AAACTCGTCTAAATTCAGACT TTGGGAGTCCCTGATGATGA 1134 1.000 41.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1037–1079 1.000 82.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1040–1082 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 1041–1083 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 1067–1109 1.000 77.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 1039–1081 1.000 77.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTATTCGTCACGCCCGG 512–527 1.000 79.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTATTCGTCACGCCCGG 509–524 1.000 77.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTATTCGTCACGCCCGG 510–525 1.000 77.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTATTCGTCACGCCCGG 511–526 1.000 77.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGGATTACGTCCTGGATCAT 494–509 1.000 76.8
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTATGTCCT 1866–1917 1.000 52.7
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTATGTCCT 1865–1916 1.000 52.7
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTATGTCCTATCCA 1860–1911 1.000 52.5
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTATGTCCTATCCA 1859–1910 1.000 52.5
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACCAAAGGTTTAGAAGACCTATGT 1871–1922 1.000 52.1
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA AAACCGTGAGTCAAGGTGAT 441–471 1.000 82.1
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA AACCGTGAGTCAAGGTGATT 440–470 1.000 82.1
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAACCGTGAGTCAAGGTGA 463 0.037 35.8
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG AAAACCGTGAGTCAAGGTGA 469 0.037 34.3
petN-psbM_p5 petN-psbM GGCTGCTTTAATGGTCGTCT AAAACCGTGAGTCAAGGTGA 454 0.037 33.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (27)

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

Species Accession Length (bp) Link
Bredia bullata NC_071759.1 155960 View on NCBI ↗
Bredia changii MK994827.1 156066 View on NCBI ↗
Bredia dulanica MK994834.1 155219 View on NCBI ↗
Bredia enchengensis PQ068595.1 155665 View on NCBI ↗
Bredia esquirolii PQ068596.1 155986 View on NCBI ↗
Bredia esquirolii var. cordata PQ068620.1 155961 View on NCBI ↗
Bredia fordii PQ068625.1 156191 View on NCBI ↗
Bredia fordii var. micrantha PQ068653.1 156169 View on NCBI ↗
Bredia gibba MK994835.1 155896 View on NCBI ↗
Bredia gracilis MK994796.1 155894 View on NCBI ↗
Bredia guidongensis MK994801.1 155853 View on NCBI ↗
Bredia hirsuta MK994833.1 155713 View on NCBI ↗
Bredia hirsuta var. rotundifolia MK994822.1 155744 View on NCBI ↗
Bredia hispida NC_068184.1 155943 View on NCBI ↗
Bredia latisepala PQ068663.1 156090 View on NCBI ↗
Bredia longearistata PQ068667.1 156104 View on NCBI ↗
Bredia longiloba MK994825.1 156166 View on NCBI ↗
Bredia longiradiosa var. pulchella MK994806.1 155871 View on NCBI ↗
Bredia microphylla MK994828.1 156193 View on NCBI ↗
Bredia oldhamii MK994821.1 155885 View on NCBI ↗
Bredia plagiopetala MK994797.1 156270 View on NCBI ↗
Bredia reniformis NC_068183.1 156203 View on NCBI ↗
Bredia repens PQ068691.1 155983 View on NCBI ↗
Bredia scandens MK994823.1 155733 View on NCBI ↗
Bredia tuberculata PQ068697.1 155927 View on NCBI ↗
Bredia violacea NC_068153.1 156220 View on NCBI ↗
Bredia yunnanensis PQ068710.1 155979 View on NCBI ↗