Markers + reference

Cathetus

2 species · Phyllanthaceae · Malpighiales

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Species 2
Genome length 146–156 kb
Candidate markers 262
Primer pairs 95

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 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 427 0.1316 0.93 80.0 yes View details
trnK-UUU-rps16 LSC 1249 0.0592 0.91 77.7 yes View details
rps16-trnQ-UUG LSC 930 0.2327 0.56 74.5 yes View details
psbM-trnD-GUC LSC 1143 0.0573 0.99 78.3 yes View details
psbZ-trnG-GCC LSC 609 0.0874 0.94 88.0 yes View details
ndhF-rpl32 SSC 937 0.0623 0.38 64.7 yes View details
rpl32-trnL-UAG SSC 780 0.0770 0.85 79.6 yes View details
rps15-ycf1 SSC 382 0.1181 1.00 74.5 yes View details
ycf1 SSC 5676 0.0589 0.97 70.1 yes View details
trnG-UCC-trnR-UCU LSC 267 0.1167 0.96 82.6 yes View details
trnS-GCU-trnG-UCC LSC 772 0.0517 0.98 82.5 yes View details
accD-psaI LSC 601 0.0420 0.95 81.7 yes View details
psbK-psbI LSC 454 0.0692 0.92 80.6 yes View details
psaA-ycf3 LSC 700 0.0433 0.99 79.2 yes View details
rpl36-rps8 LSC 110 0.1009 0.99 77.9 yes View details
trnD-GUC-trnY-GUA LSC 417 0.0539 0.98 77.6 yes View details
trnM-rps14 LSC 165 0.0446 0.95 77.6 yes View details
trnE-UUC-trnT-GGU LSC 1058 0.0381 0.94 77.3 yes View details
ndhC-trnV-UAC LSC 1019 0.0450 0.92 76.9 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 GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 543–582 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 557–596 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 556–595 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 558–597 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 879–918 1.000 86.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGGGTATGGACGAGTTTGTT CGCTTTAACCACACGCAATT 1320–1368 1.000 87.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGGGTATGGACGAGTTTGTT CCCAATGAGCCGTTTATCGA 1526–1574 1.000 87.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGGGTATGGACGAGTTTGTT TCCCAATGAGCCGTTTATCG 1527–1575 1.000 87.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGGGTATGGACGAGTTTGTT GCCGTACGAGGAGAAAACTT 1586–1636 1.000 86.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CATCTCCCCCTTGTAGTGGA CGCTTTAACCACACGCAATT 1705–1754 1.000 86.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCCCCCGAAAAAGAAATCA CTTACAGCAGCTTGCCAAAC 1776 0.500 59.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG CTTACAGCAGCTTGCCAAAC 1592 0.500 59.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGAATCCACAACCGATCGTG CTTACAGCAGCTTGCCAAAC 1611 0.500 59.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGCCCCCGAAAAAGAAATCA GAGGTTCGAATCCTTCCGTC 1194 0.500 59.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1010 0.500 59.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 539–574 1.000 87.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 540–575 1.000 87.2
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 541–576 1.000 85.4
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 536–571 1.000 85.2
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 537–572 1.000 85.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAACCGAGAGATCCCTTAAC 878–907 1.000 67.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAACCGAGAGATCCCTTAAC 877–906 1.000 67.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAACCGAGAGATCCCTTAACT 878–907 1.000 66.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAACCGAGAGATCCCTTAACT 877–906 1.000 66.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGAACCGGAAAGAGAGGGAT TGAACCGAGAGATCCCTTAAC 936–965 1.000 65.4
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 347–382 1.000 72.1
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 350–385 1.000 71.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 353–388 1.000 71.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 356–391 1.000 71.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 351–386 1.000 69.6

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
Cathetus clarkei OR683690.1 155810 View on NCBI ↗
Cathetus virgatus PV944218.1 146299 View on NCBI ↗