Markers + reference

Couepia

10 species · Chrysobalanaceae · Malpighiales

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Species 10
Genome length 162–162 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 398 0.0176 1.00 57.6 yes View details
trnS-GCU-trnG-GCC LSC 964 0.0072 1.00 58.3 yes View details
trnG-GCC-trnR-UCU LSC 758 0.0059 0.98 62.6 yes View details
trnR-UCU-atpA LSC 282 0.0158 1.00 62.2 yes View details
rbcL-accD LSC 818 0.0038 0.99 59.6 yes View details
psaJ-rpl33 LSC 527 0.0095 0.97 65.5 yes View details
psbB LSC 1527 0.0003 1.00 44.0 yes View details
rpl16 LSC 1483 0.0025 1.00 57.5 yes View details
ndhF-rpl32 SSC 1123 0.0090 1.00 69.1 yes View details
ndhD SSC 1503 0.0015 1.00 43.2 yes View details
ndhC-trnV-UAC LSC 1189 0.0026 0.95 61.6 yes View details
rpl20-rps12 LSC 841 0.0033 0.98 60.3 yes View details
psbM-trnD-GUC LSC 1014 0.0028 0.98 59.5 yes View details
psbZ-trnG-UCC LSC 710 0.0031 1.00 59.4 yes View details
atpA-atpF LSC 67 0.0193 1.00 58.9 yes View details
trnE-UUC-trnT-GGU LSC 677 0.0036 0.97 58.5 yes View details
rpl36-rps8 LSC 537 0.0032 1.00 58.0 yes View details
atpH-atpI LSC 1201 0.0024 1.00 57.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 524–547 1.000 80.5
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 525–548 1.000 80.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 525–548 1.000 80.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 526–549 1.000 79.8
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 517–540 1.000 78.9
trnK-UUU_p1 trnK-UUU TCGATCTTATCTAACTAGATTCAGCA TGGTTTGATTGTCTAGCGTGA 2847–2855 1.000 40.6
trnK-UUU_p2 trnK-UUU CGATCTTATCTAACTAGATTCAGCA TGGTTTGATTGTCTAGCGTGA 2846–2854 1.000 40.6
trnK-UUU_p3 trnK-UUU CGATCTTATCTAACTAGATTCAGCAG TGGTTTGATTGTCTAGCGTGA 2846–2854 1.000 40.6
trnK-UUU_p4 trnK-UUU TCGATCTTATCTAACTAGATTCAGC TGGTTTGATTGTCTAGCGTGA 2847–2855 1.000 40.6
trnK-UUU_p5 trnK-UUU TCGATCTTATCTAACTAGATTCAGCA TGGTTTGATTGTCTAGCGTG 2847–2855 1.000 40.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAATAGTTATTCCCCGAGGG 1036–1126 1.000 58.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAATAGTTATTCCCCGAGGG 1035–1125 1.000 58.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATCAACGGAACCGGAAAGAG GAATAGTTATTCCCCGAGGG 1100–1190 1.000 57.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 990–1080 1.000 56.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 989–1079 1.000 56.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 787–902 1.000 68.4
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 790–905 1.000 68.2
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 793–908 1.000 67.7
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 796–911 1.000 67.5
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 791–906 1.000 66.0
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT ATTCGGGAACAGATGGAACG 387–434 1.000 84.9
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT CGGGAACAGATGGAACGTTT 384–431 1.000 81.3
trnR-UCU-atpA_p3 trnR-UCU-atpA TTTGGAATGGAAAAGCGTCC ATTCGGGAACAGATGGAACG 394–441 1.000 78.2
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT AAACATTCACCGAAGAGGCG 428–475 1.000 78.1
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT GCTATTCGGGAACAGATGGA 390–437 1.000 77.8
atpA-atpF_p1 atpA-atpF TACTAATCTCGTCGGCTCGA TATTGGCATGTTTGGAGCGA 135–139 1.000 80.7
atpA-atpF_p2 atpA-atpF CCGTCGCCTACTTGAAGTAC TATTGGCATGTTTGGAGCGA 217–221 1.000 80.5
atpA-atpF_p3 atpA-atpF GTCGCCTACTTGAAGTACGG TATTGGCATGTTTGGAGCGA 215–219 1.000 80.5
atpA-atpF_p4 atpA-atpF TAATCTCGTCGGCTCGAATG TATTGGCATGTTTGGAGCGA 132–136 1.000 79.4
atpA-atpF_p5 atpA-atpF ACTTGAAGTACGGTACCGGT TATTGGCATGTTTGGAGCGA 208–212 1.000 78.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Couepia caryophylloides NC_030547.1 161887 View on NCBI ↗
Couepia grandiflora NC_030548.1 162090 View on NCBI ↗
Couepia guianensis NC_024063.1 162125 View on NCBI ↗
Couepia ovalifolia NC_030549.1 161926 View on NCBI ↗
Couepia paraensis NC_030550.1 161924 View on NCBI ↗
Couepia paraensis subsp. cerradoana KX180057.1 162063 View on NCBI ↗
Couepia polyandra NC_030551.1 162045 View on NCBI ↗
Couepia rankiniae NC_030552.1 162045 View on NCBI ↗
Couepia sandwithii NC_030553.1 162065 View on NCBI ↗
Couepia subcordata NC_030554.1 162019 View on NCBI ↗