Markers + reference

Rhizophora

3 species · Rhizophoraceae · Malpighiales

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Species 3
Genome length 164–164 kb
Candidate markers 267
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 LSC 255 0.0444 0.18 38.8 yes View details
trnK-UUU-trnQ-UUG LSC 1502 0.0128 0.93 70.8 yes View details
trnC-GCA-petN LSC 1246 0.0405 0.86 85.0 yes View details
trnE-UUC-trnT-GGU LSC 1290 0.0348 0.76 77.5 yes View details
trnM-CAU-psbD LSC 2361 0.0073 0.94 58.8 yes View details
psbZ-trnG-GCC LSC 1086 0.0465 0.98 90.4 yes View details
psbB-psbT LSC 746 0.0204 0.48 50.8 yes View details
rps19 LSC 279 0.0024 1.00 29.1 no View details
rpl32-trnL-TAG SSC 1616 0.0074 0.95 59.8 yes View details
atpA-atpF LSC 55 0.0128 0.95 64.8 yes View details
ndhF-rpl32 SSC 1028 0.0021 0.94 64.4 yes View details
atpF-atpH LSC 650 0.0052 0.98 63.9 yes View details
psaA-ycf3 LSC 829 0.0049 0.98 63.8 yes View details
trnR-UCU-atpA LSC 476 0.0044 0.96 62.2 yes View details
trnL-TAG-ccsA SSC 134 0.0308 0.97 62.2 yes View details
rps15-ycf1 SSC 527 0.0027 0.95 61.4 yes View details
rps3 LSC 678 0.0039 1.00 61.3 yes View details
psbE-petL LSC 1402 0.0014 1.00 60.0 yes View details
ndhA SSC 2195 0.0036 1.00 59.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps19_p1 rps19 GGGCCCCAATTGGTAGAAAA GCCCATAATCACTTCGCTCA 620 0.333 52.5
rps19_p2 rps19 GGGCCCCAATTGGTAGAAAA GTCGTTCGCCCATAATCACT 627 0.333 52.4
rps19_p3 rps19 TTGATTCTTCGTCGCCGTAG GCCCATAATCACTTCGCTCA 528 0.333 52.2
rps19_p4 rps19 TTGATTCTTCGTCGCCGTAG GTCGTTCGCCCATAATCACT 535 0.333 52.1
rps19_p5 rps19 GGGCCCCAATTGGTAGAAAA CACTTCGCTCATAACCCCAA 611 0.333 52.0
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1573–2104 1.000 83.2
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1572–2103 1.000 83.2
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 1559–2090 1.000 80.8
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 1584–2115 1.000 79.9
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 1582–2113 1.000 78.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTTCGGCTTCAGGAACAAGT 522–611 1.000 66.5
trnR-UCU-atpA_p2 trnR-UCU-atpA TTCGAATTGAAAAGCGTCCA TTTCGGCTTCAGGAACAAGT 585–674 1.000 66.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGAAGAAGCAGAAGCCCTTT 574–663 1.000 65.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACCGAAGAAGCAGAAGC 579–668 1.000 65.1
trnR-UCU-atpA_p5 trnR-UCU-atpA TTCGAATTGAAAAGCGTCCA CGAAGAAGCAGAAGCCCTTT 637–726 1.000 64.8
atpA-atpF_p1 atpA-atpF AATCTCATCGGCTCGAATGG TGGTATGTTTGGGGCAATGA 115–119 1.000 77.2
atpA-atpF_p2 atpA-atpF TCATCGGCTCGAATGGTTAC TGGTATGTTTGGGGCAATGA 111–115 1.000 76.9
atpA-atpF_p3 atpA-atpF CCGTCGCCTACTTGAAGTAC TGGTATGTTTGGGGCAATGA 201–205 1.000 76.3
atpA-atpF_p4 atpA-atpF GTCGCCTACTTGAAGTACGG TGGTATGTTTGGGGCAATGA 199–203 1.000 76.3
atpA-atpF_p5 atpA-atpF TCGCCTACTTGAAGTACGGT TGGTATGTTTGGGGCAATGA 198–202 1.000 73.4
atpF-atpH_p1 atpF-atpH GCCAATGACCCAAAGAAACG TGGTTGTGGCATTAGCACTT 737–789 1.000 81.3
atpF-atpH_p2 atpF-atpH ATTAAGCCCGAAACTCCCAG TGGTTGTGGCATTAGCACTT 763–815 1.000 78.4
atpF-atpH_p3 atpF-atpH GGCCAATGACCCAAAGAAAC TGGTTGTGGCATTAGCACTT 738–790 1.000 78.2
atpF-atpH_p4 atpF-atpH GCCAATGACCCAAAGAAACG CTGGTTGTGGCATTAGCACT 738–790 1.000 77.7
atpF-atpH_p5 atpF-atpH GCCAATGACCCAAAGAAACG CGGAGGGAAAAATACGAGGT 806–858 1.000 75.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCAGTTCAAATCCGGG AGCCCAAGCGAGACTTACTA 1139–1301 1.000 86.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCAGTTCAAATCCGGG TGCCCCATACTACGAGTGAA 1188–1350 1.000 86.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCAGTTCAAATCCGGG ACTTCTGCCCCATACTACGA 1193–1355 1.000 86.3
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCAGTTCAAATCCGGG TTCTGCCCCATACTACGAGT 1191–1353 1.000 86.3
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCAGTTCAAATCCGGG CACTTCTGCCCCATACTACG 1194–1356 1.000 85.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Rhizophora apiculata NC_057465.1 164343 View on NCBI ↗
Rhizophora mucronata MZ959046.1 164474 View on NCBI ↗
Rhizophora stylosa NC_042819.1 164475 View on NCBI ↗