Markers + reference

Vietsenia

2 species · Melastomataceae · Myrtales

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Species 2
Genome length 157–157 kb
Candidate markers 264
Primer pairs 115

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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 430 0.0242 0.96 66.5 yes View details
rps16 LSC 1051 0.0202 0.99 57.4 yes View details
rps16-trnQ-UUG LSC 991 0.0192 1.00 63.1 yes View details
trnS-GCU-trnR-UCU LSC 1802 0.0117 1.00 65.1 yes View details
atpF-atpH LSC 527 0.0282 0.94 64.9 yes View details
rpoB-trnC-GCA LSC 1465 0.0153 0.89 68.0 yes View details
trnE-UUC-trnT-GGU LSC 989 0.0126 0.96 67.4 yes View details
trnL-UAA-trnF-GAA LSC 301 0.0287 0.93 66.1 yes View details
rbcL-accD LSC 605 0.0287 0.98 65.5 yes View details
petA-psbJ LSC 899 0.0200 1.00 70.3 yes View details
ndhF-rpl32 SSC 930 0.0261 0.95 64.6 yes View details
ndhE SSC 306 0.0033 1.00 40.6 yes View details
ndhG-ndhI SSC 413 0.0291 1.00 57.1 yes View details
psaC-ndhE SSC 232 0.0431 1.00 74.4 yes View details
trnH-GUG-psbA LSC 220 0.0273 1.00 68.2 yes View details
ndhI-ndhA SSC 96 0.0444 0.94 67.6 yes View details
rpl14-rpl16 LSC 147 0.0210 0.97 67.1 yes View details
petG-trnW-CCA LSC 139 0.0299 0.96 66.9 yes View details
trnD-GUC-trnY-GUA LSC 478 0.0109 0.96 66.7 yes View details
psbE-petL LSC 1133 0.0080 0.99 64.0 yes View details
psbK-psbI LSC 380 0.0160 0.98 62.9 yes View details
psaI-pafII LSC 446 0.0094 0.96 62.1 yes View details
ccsA-ndhD SSC 350 0.0253 0.90 61.9 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 115 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 337–375 1.000 80.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 351–389 1.000 80.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 350–388 1.000 80.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 352–390 1.000 80.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 287–325 1.000 80.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTTCTTGAAAAGGGTGCGC 542–558 1.000 80.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTTCTTGAAAAGGGTGCGC 541–557 1.000 80.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTTTCTTGAAAAGGGTGCGC 551–567 1.000 79.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTTCAAAAGGGCGGGGG 499–515 1.000 79.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTTCAAAAGGGCGGGGG 500–516 1.000 79.2
rps16_p1 rps16 CCTTTCAGGATCAGTCGTGG CATACCAGTTAAACCCCGGG 1638 0.500 59.5
rps16_p2 rps16 TCAGGATCAGTCGTGGTCTT CATACCAGTTAAACCCCGGG 1634 0.500 59.0
rps16_p3 rps16 TTCAGGATCAGTCGTGGTCT CATACCAGTTAAACCCCGGG 1635 0.500 59.0
rps16_p4 rps16 AAAGCCGAGTACTCTACCGT CATACCAGTTAAACCCCGGG 1543 0.500 58.3
rps16_p5 rps16 AAGCCGAGTACTCTACCGTT CATACCAGTTAAACCCCGGG 1542 0.500 58.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1056–1064 1.000 74.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1059–1067 1.000 72.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TAAGAATCCACGGACGATCC GAGGTTCGAATCCTTCCGTC 1092–1100 1.000 71.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 1060–1068 1.000 69.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 1086–1094 1.000 69.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTATTCGTCACGCCCGG 518–524 1.000 71.8
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTATTCGTCACGCCCGG 515–521 1.000 69.8
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTATTCGTCACGCCCGG 516–522 1.000 69.8
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTATTCGTCACGCCCGG 517–523 1.000 69.8
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGGATTACGTCCTGGATCAT 500–506 1.000 69.3
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1915–1927 1.000 69.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1914–1926 1.000 69.5
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACATAGAAGAACTTGCGTCCA 1922–1934 1.000 67.6
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACATAGAAGAACTTGCGTCCA 1921–1933 1.000 67.6
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1916–1928 1.000 67.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Vietsenia poilanei NC_068157.1 156737 View on NCBI ↗
Vietsenia scaposa NC_068160.1 156736 View on NCBI ↗