Markers + reference

Anerincleistus

7 species · Melastomataceae · Myrtales

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Species 7
Genome length 157–157 kb
Candidate markers 262
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0090 1.00 51.9 yes View details
rps16 LSC 1063 0.0095 1.00 53.3 yes View details
trnS-GCU-trnR-UCU LSC 1819 0.0104 1.00 66.1 yes View details
rps2 LSC 714 0.0115 1.00 49.4 yes View details
rpoC2 LSC 4140 0.0086 1.00 47.5 yes View details
rpoC1 LSC 2777 0.0058 1.00 50.9 yes View details
trnS-UGA-psbZ LSC 377 0.0225 1.00 62.1 yes View details
psbZ-trnG-UCC LSC 296 0.0280 1.00 69.8 yes View details
atpE LSC 423 0.0128 1.00 37.7 yes View details
petL-petG LSC 187 0.0331 1.00 59.7 yes View details
rps19 LSC 279 0.0133 1.00 48.9 yes View details
ndhF-rpl32 SSC 986 0.0250 0.98 72.4 yes View details
trnH-GUG-psbA LSC 254 0.0590 0.92 72.2 yes View details
rbcL-accD LSC 628 0.0122 0.98 70.6 yes View details
ndhD-psaC SSC 142 0.0314 1.00 70.1 yes View details
petD-rpoA LSC 234 0.0301 1.00 67.7 yes View details
petN-psbM LSC 351 0.0130 1.00 67.1 yes View details
rpl2-trnH-GUG IRa 136 0.0077 1.00 65.3 no View details
trnT-UGU-trnL-UAA LSC 908 0.0101 0.90 62.9 yes View details
accD-psaI LSC 856 0.0091 0.98 61.8 yes View details
ycf2-trnL-CAA IRb 635 0.0061 1.00 61.6 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 100 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 TGTTGAAGTTCCATCTACAAATGG 279–304 1.000 54.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGTTGAAGTTCCATCTACAAATGG 293–318 1.000 54.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGTTGAAGTTCCATCTACAAATGG 292–317 1.000 54.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TGTTGAAGTTCCATCTACAAATGG 294–319 1.000 54.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TGTTGAAGTTCCATCTACAAATGG 308–333 1.000 52.0
psbA_p1 psbA GATCCACTTGGCTACATCCG AACACAAAACTACTGGCCGT 2050–2075 0.857 76.8
psbA_p2 psbA GATCCACTTGGCTACATCCG ACAAAACTACTGGCCGTGTT 2047–2072 0.857 76.8
psbA_p3 psbA CAATCCACTGCCTTGATCCA AACACAAAACTACTGGCCGT 2064–2089 0.857 76.7
psbA_p4 psbA CAATCCACTGCCTTGATCCA ACAAAACTACTGGCCGTGTT 2061–2086 0.857 76.7
psbA_p5 psbA AATCCACTGCCTTGATCCAC ACAAAACTACTGGCCGTGTT 2060–2085 0.857 76.7
rps16_p1 rps16 CCTTTCAGGATCAGTCGTGG ATTTAACCCGCTCAGTCAGC 2019–2095 1.000 81.9
rps16_p2 rps16 TCAGGATCAGTCGTGGTCTT ATTTAACCCGCTCAGTCAGC 2015–2091 1.000 81.4
rps16_p3 rps16 TTCAGGATCAGTCGTGGTCT ATTTAACCCGCTCAGTCAGC 2016–2092 1.000 81.4
rps16_p4 rps16 CGACCCCCATTCTGATTCTG ATTTAACCCGCTCAGTCAGC 2179 0.143 43.3
rps16_p5 rps16 TCGACCCCCATTCTGATTCT ATTTAACCCGCTCAGTCAGC 2180 0.143 42.7
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1922–1963 1.000 71.2
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1921–1962 1.000 71.2
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACATAGAAGAACTTGCGTCCA 1929–1970 1.000 69.3
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACATAGAAGAACTTGCGTCCA 1928–1969 1.000 69.3
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1923–1964 1.000 69.2
rps2_p1 rps2 GGCTCACGTCTCGAATGAAT TCTGTTACCGCGCTATCCTA 1807–1832 1.000 81.8
rps2_p2 rps2 GGCTCACGTCTCGAATGAAT CGAGTTTTAGCCAAAGCAGC 1718–1743 1.000 81.8
rps2_p3 rps2 TTCTCCAATCTGGGTTTGGC TCTGTTACCGCGCTATCCTA 1824–1849 0.714 68.6
rps2_p4 rps2 GGCTCACGTCTCGAATGAAT TTCCGTCGGAACAATTGGTT 1256–1259 0.714 68.3
rps2_p5 rps2 TTCTCCAATCTGGGTTTGGC TTCCGTCGGAACAATTGGTT 1273–1276 0.714 68.3
rpoC2_p1 rpoC2 AGTTCCGTGATTTTGGTGGT GGTTTGGTTCGAGCTTTCCT 192 1.000 76.9
rpoC2_p2 rpoC2 AGTTCCGTGATTTTGGTGGT TGGTTTGGTTCGAGCTTTCC 193 1.000 74.6
rpoC2_p3 rpoC2 ATGTGCGAATAGTTCCGTGA GGTTTGGTTCGAGCTTTCCT 202 1.000 74.3
rpoC2_p4 rpoC2 TGTGCGAATAGTTCCGTGAT GGTTTGGTTCGAGCTTTCCT 201 1.000 74.3
rpoC2_p5 rpoC2 AGTTCCGTGATTTTGGTGGT ACAAATGGTTTGGTTCGAGC 198 1.000 73.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Anerincleistus bracteatus MK994899.1 156862 View on NCBI ↗
Anerincleistus bullatus MK994897.1 156823 View on NCBI ↗
Anerincleistus macrophyllus NC_068182.1 156737 View on NCBI ↗
Anerincleistus phyllagathoides MK994917.1 156884 View on NCBI ↗
Anerincleistus quintuplinervis NC_068180.1 157115 View on NCBI ↗
Anerincleistus sertuliferum MK994888.1 157069 View on NCBI ↗
Anerincleistus setulosus MK994881.1 156523 View on NCBI ↗