Markers + reference

Balanops

2 species · Balanopaceae · Malpighiales

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Species 2
Genome length 161–161 kb
Candidate markers 262
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 446 0.0090 1.00 55.7 yes View details
trnS-GCU-trnG-UCC LSC 933 0.0156 0.96 64.9 yes View details
trnG-UCC-trnR-UCU LSC 639 0.0309 0.86 78.3 yes View details
psbC-trnS-UGA LSC 221 0.0317 1.00 64.0 yes View details
psbZ-trnG-GCC LSC 466 0.0172 1.00 65.8 yes View details
psbE-petL LSC 1412 0.0095 0.97 54.5 yes View details
ndhF SSC 2253 0.0067 0.99 47.2 yes View details
rpl32-trnL-UAG SSC 1117 0.0136 0.99 67.5 yes View details
psaC SSC 246 0.0122 1.00 44.9 yes View details
rps15-ycf1 SSC 405 0.0205 0.97 57.6 yes View details
ycf1 SSC 5706 0.0060 1.00 41.9 yes View details
psbI-trnS-GCU LSC 137 0.0292 1.00 69.1 yes View details
atpF-atpH LSC 619 0.0083 0.98 65.7 yes View details
petA-psbJ LSC 1038 0.0097 0.99 65.4 yes View details
ndhI-ndhA SSC 50 0.0200 1.00 64.0 yes View details
rpl20-rps12 LSC 802 0.0087 1.00 63.8 yes View details
psbM-trnD-GUC LSC 1231 0.0066 0.99 63.4 yes View details
ndhC-trnV-UAC LSC 1541 0.0045 0.86 63.4 yes View details
ndhF-rpl32 SSC 823 0.0061 0.99 63.2 yes View details
rps19-rpl2 IRb 60 0.0167 1.00 62.1 yes View details
petN-psbM LSC 970 0.0021 0.98 62.0 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 512–534 1.000 79.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 526–548 1.000 79.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 525–547 1.000 79.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 527–549 1.000 79.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAGACCTAGCTGCTGTCGAA 508–530 1.000 78.6
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TGGACTAAAGCGTCGGATTG 245–248 1.000 79.1
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT GTGGACTAAAGCGTCGGATT 246–249 1.000 79.1
psbI-trnS-GCU_p3 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TTTCAATTGGGAGAGGTGGC 269–272 1.000 78.4
psbI-trnS-GCU_p4 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT GGTGGCTGAGTGGACTAAAG 255–258 1.000 78.3
psbI-trnS-GCU_p5 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT AGGTGGCTGAGTGGACTAAA 256–259 1.000 77.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAATATTAGCCGAGGGATCCC 1012–1044 1.000 71.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGAATATTAGCCGAGGGATCC 1013–1045 1.000 71.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAATATTAGCCGAGGGATCCC 1011–1043 1.000 71.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGAATATTAGCCGAGGGATCC 1012–1044 1.000 71.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATCAACGGAACCGGAAAGAG GAATATTAGCCGAGGGATCCC 1076–1108 1.000 70.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 650–719 1.000 69.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 653–722 1.000 69.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 656–725 1.000 68.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 659–728 1.000 68.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 654–723 1.000 66.9
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA GGACTGGTTGTTGCATTAGC 703–708 1.000 76.8
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA CGGAGGGAAAAATACGAGGT 768–773 1.000 76.2
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA GAGGCGGAGGGAAAAATACG 772–777 1.000 76.0
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA GCGGAGGGAAAAATACGAGG 769–774 1.000 76.0
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA GGCGGAGGGAAAAATACGAG 770–775 1.000 76.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGTTCCTACTGCCTTTTTGCT 1093–1111 1.000 71.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1114–1132 1.000 69.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGTTCCTACTGCCTTTTTGC 1093–1111 1.000 68.7
petN-psbM_p4 petN-psbM TATGGGGAAGAAGTGGCCTC TGTTCCTACTGCCTTTTTGCT 1033–1051 1.000 66.9
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TTGTTCCTACTGCCTTTTTGC 1094–1112 1.000 66.6

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
Balanops balansae NC_052006.1 160930 View on NCBI ↗
Balanops pedicellata NC_052007.1 160765 View on NCBI ↗