Markers + reference

Flueggea

2 species · Phyllanthaceae · Malpighiales

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Species 2
Genome length 155–158 kb
Candidate markers 269
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 340 0.1829 0.72 76.1 yes View details
rps16 LSC 1134 0.3299 0.09 58.3 yes View details
trnS-GCU-trnG-UCC LSC 775 0.1718 0.88 90.5 yes View details
psbZ-trnG-GCC LSC 745 0.0557 0.72 77.6 yes View details
ndhC-trnV-UAC LSC 1158 0.0714 0.85 80.7 yes View details
ycf4-cemA LSC 882 0.0248 0.41 57.6 yes View details
psbE-petL LSC 786 0.1326 0.98 95.8 yes View details
trnM-CAU-atpE LSC 246 0.0943 0.99 80.0 yes View details
psaJ-rpl33 LSC 451 0.0431 0.98 77.5 yes View details
rps14-psaB LSC 117 0.1468 0.93 77.1 yes View details
petA-psbJ LSC 1130 0.0324 0.79 76.9 yes View details
rpl14-rpl16 LSC 131 0.0709 0.97 74.6 yes View details
trnS-UGA LSC 90 0.0556 1.00 70.2 yes View details
rpl36-rps8 LSC 493 0.0292 0.97 68.6 yes View details
trnR-ACG-trnN-GUU IRb 647 0.0155 1.00 67.6 yes View details
trnN-GUU-trnR-ACG IRa 647 0.0155 1.00 67.6 yes View details
trnP-UGG-psaJ LSC 453 0.0214 0.93 67.5 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 85 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 313–406 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 327–420 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 326–419 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 328–421 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 316–409 1.000 90.4
rps16_p1 rps16 AAGTGGACTCAGAAAGCCTG AGTCGATCTGGTGGATAGGG 2091 0.500 55.5
rps16_p2 rps16 AAGTGGACTCAGAAAGCCTG GTCGATCTGGTGGATAGGGA 2090 0.500 55.5
rps16_p3 rps16 AAGTGGACTCAGAAAGCCTG AGATTGGCTTGGCAAATCCT 1754 0.500 53.6
rps16_p4 rps16 AAGTGGACTCAGAAAGCCTG TGGCTTGGCAAATCCTTTGA 1750 0.500 53.3
rps16_p5 rps16 AAGTGGACTCAGAAAGCCTG TGGTAGATTGGCTTGGCAAA 1758 0.500 53.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAACCGAGAGATCCCTTAAC 800–881 1.000 74.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAACCGAGAGATCCCTTAAC 799–880 1.000 74.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAACCGAGAGATCCCTTAACT 800–881 1.000 73.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAACCGAGAGATCCCTTAACT 799–880 1.000 73.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGAACCGGAAAGAGAGGGAT TGAACCGAGAGATCCCTTAAC 858–939 1.000 72.6
trnS-UGA_p1 trnS-UGA AGCCTCTAAGGGGTCCAAAT GGGGATTGTACCACGAATCC 860–957 1.000 81.5
trnS-UGA_p2 trnS-UGA AGCCTCTAAGGGGTCCAAAT GGGGGATTGTACCACGAATC 861–958 1.000 81.5
trnS-UGA_p3 trnS-UGA AGCCTCTAAGGGGTCCAAAT CCATGTCCTATTCGGCGAAA 681–710 1.000 81.1
trnS-UGA_p4 trnS-UGA AGCCTCTAAGGGGTCCAAAT CAACTCCTATGGCCATGTCC 693 0.500 59.7
trnS-UGA_p5 trnS-UGA ACCTACTGGACCAGAAGCTT CAACTCCTATGGCCATGTCC 884 0.500 59.5
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTCCTGATGGTTGGTCAAGT CGTCTTCTCCTTGGCAAAGA 704–896 1.000 78.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCA CGTCTTCTCCTTGGCAAAGA 707–899 1.000 76.4
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TCTCCTGATGGTTGGTCAAG CGTCTTCTCCTTGGCAAAGA 705–897 1.000 76.4
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TCTTCTCCTGATGGTTGGTCA CGTCTTCTCCTTGGCAAAGA 708–900 1.000 74.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTCTCCTGATGGTTGGTCAAG CGTCTTCTCCTTGGCAAAGA 706–898 1.000 74.2
rps14-psaB_p1 rps14-psaB AATGGTAAAGGGGCTCCTCT AATTTCCTGGCGCGGATATT 706–714 1.000 83.4
rps14-psaB_p2 rps14-psaB TCCTACCCTCTCCCTCTTCT AATTTCCTGGCGCGGATATT 995 0.500 59.8
rps14-psaB_p3 rps14-psaB TCCTACCCTCTCCCTCTTCT CCCGGCTGGTTAAATGCTAT 1504 0.500 59.8
rps14-psaB_p4 rps14-psaB TCTCCTACCCTCTCCCTCTT AATTTCCTGGCGCGGATATT 997 0.500 59.8
rps14-psaB_p5 rps14-psaB TCTCCTACCCTCTCCCTCTT CCCGGCTGGTTAAATGCTAT 1506 0.500 59.8

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
Flueggea suffruticosa PP078675.1 157547 View on NCBI ↗
Flueggea virosa NC_051502.1 154961 View on NCBI ↗