Markers + reference

Pseudodissochaeta

2 species · Melastomataceae · Myrtales

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Species 2
Genome length 157–157 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 0.0009 1.00 47.0 yes View details
trnS-GCU-trnR-UCU LSC 1836 0.0094 0.98 57.0 yes View details
atpF-atpH LSC 618 0.0131 0.99 54.7 yes View details
rpoB-trnC-GCA LSC 1469 0.0165 0.99 61.8 yes View details
trnE-UUC-trnT-GGU LSC 1079 0.0091 0.91 59.3 yes View details
ndhJ LSC 477 0.0063 1.00 45.0 yes View details
accD-psaI LSC 744 0.0202 1.00 67.4 yes View details
psaI-ycf4 LSC 439 0.0190 0.96 64.8 yes View details
petA-psbJ LSC 885 0.0148 0.84 68.7 yes View details
rpl22 LSC 414 0.0121 1.00 48.2 yes View details
ndhF SSC 2172 0.0064 1.00 47.2 yes View details
ndhF-rpl32 SSC 827 0.0157 1.00 67.8 yes View details
trnH-GUG-psbA LSC 202 0.0594 1.00 82.4 yes View details
ndhK-ndhC LSC 61 0.0345 0.95 76.9 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0339 1.00 68.4 yes View details
trnK-UUU LSC 37 0.0270 1.00 65.3 yes View details
ndhC-trnV-UAC LSC 502 0.0140 1.00 64.9 yes View details
petB-petD LSC 1018 0.0050 0.97 64.1 yes View details
rpl2-trnH-GUG IRa 136 0.0000 1.00 63.6 no View details
psbI-trnS-GCU LSC 66 0.0303 1.00 63.5 yes View details
psbE-petL LSC 1142 0.0062 1.00 62.7 yes View details
psaA-ycf3 LSC 596 0.0067 1.00 62.5 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 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 CCTCTAGACCTAGCTGCTGT 269–276 1.000 82.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 319–326 1.000 81.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 333–340 1.000 81.5
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 332–339 1.000 81.5
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 334–341 1.000 81.5
psbA_p1 psbA AAACTCGTCTAAATTCAGACT AGAATTCGTGTGCTTGGGAG 1147 1.000 40.1
psbA_p2 psbA AAACTCGTCTAAATTCAGACT AGAGAATTCGTGTGCTTGGG 1149 1.000 40.1
psbA_p3 psbA AAACTCGTCTAAATTCAGACT GAGAATTCGTGTGCTTGGGA 1148 1.000 40.1
psbA_p4 psbA AAACTCGTCTAAATTCAGACT TGGGAGTCCCTGATGATGAA 1133 1.000 40.1
psbA_p5 psbA AAACTCGTCTAAATTCAGACT TTGGGAGTCCCTGATGATGA 1134 1.000 40.1
trnK-UUU_p1 trnK-UUU CCTTTCAGGATCAGTCGTGG CAACCAAACGTTGCCAATTT 159 1.000 66.2
trnK-UUU_p2 trnK-UUU TCAGGATCAGTCGTGGTCTT CAACCAAACGTTGCCAATTT 155 1.000 65.8
trnK-UUU_p3 trnK-UUU TTCAGGATCAGTCGTGGTCT CAACCAAACGTTGCCAATTT 156 1.000 65.8
trnK-UUU_p4 trnK-UUU CCTTTCAGGATCAGTCGTGG CAACCAAACGTTGCCAATTTT 159 1.000 64.2
trnK-UUU_p5 trnK-UUU TCAGGATCAGTCGTGGTCTT CAACCAAACGTTGCCAATTTT 155 1.000 63.7
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCCGGACGTGACGAATA TTTTTCGTACCGAGGGTTCG 123 1.000 72.4
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCCGGACGTGACGAATAA TTTTTCGTACCGAGGGTTCG 122 1.000 72.4
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCCGGACGTGACGAAT TTTTTCGTACCGAGGGTTCG 124 1.000 72.4
psbI-trnS-GCU_p4 psbI-trnS-GCU AATCCCGGACGTGACGAATA CCTAAAGCGTCGGATTGCTA 157 1.000 72.1
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCCGGACGTGACGAATAA CCTAAAGCGTCGGATTGCTA 156 1.000 72.1
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAACTTGCGTCCAATAGGA 2004–2011 1.000 69.1
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU TAGCAATCCGACGCTTTAGG AGAACTTGCGTCCAATAGGA 1953–1960 1.000 68.6
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA ACATAGAAGAACTTGCGTCCA 2011–2018 1.000 67.2
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AAGAACTTGCGTCCAATAGGA 2005–2012 1.000 67.1
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU TAGCAATCCGACGCTTTAGG ACATAGAAGAACTTGCGTCCA 1960–1967 1.000 66.7
atpF-atpH_p1 atpF-atpH AAAGGAAAGAATCGGTTAGAT CTGTTATTTGCGAATCCCTTTGT 669–673 1.000 42.0
atpF-atpH_p2 atpF-atpH AAAGGAAAGAATCGGTTAGAT TGTTATTTGCGAATCCCTTTGT 668–672 1.000 42.0
atpF-atpH_p3 atpF-atpH AAAGGAAAGAATCGGTTAGAT TGTTATTTGCGAATCCCTTTGTT 668–672 1.000 42.0
atpF-atpH_p4 atpF-atpH AAAGGAAAGAATCGGTTAGAT ATTTGCGAATCCCTTTGTTT 664–668 1.000 42.0
atpF-atpH_p5 atpF-atpH AAAGGAAAGAATCGGTTAGAT CTGTTATTTGCGAATCCCTTTG 669–673 1.000 42.0

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
Pseudodissochaeta lanceata MK994850.1 156790 View on NCBI ↗
Pseudodissochaeta septentrionalis MK994778.1 156580 View on NCBI ↗