Markers + reference

Leptopus

2 species · Phyllanthaceae · Malpighiales

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Species 2
Genome length 155–155 kb
Candidate markers 263
Primer pairs 100

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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 426 0.0414 0.96 79.7 yes View details
trnK-UUU-trnQ-UUG LSC 2252 0.0132 0.94 69.0 yes View details
rpoB-trnC-GCA LSC 1021 0.0128 0.99 67.0 yes View details
trnF-GAA-ndhJ LSC 727 0.0152 1.00 67.9 yes View details
trnM-CAU-atpE LSC 289 0.0285 0.97 58.8 yes View details
petA-psbJ LSC 1151 0.0149 0.99 58.9 yes View details
rps8 LSC 405 0.0148 1.00 52.0 yes View details
rps19 LSC 279 0.0072 1.00 43.2 yes View details
ycf1 IRb 1921 0.0010 1.00 46.5 no View details
ndhA SSC 2201 0.0085 0.96 65.7 yes View details
ycf1 SSC 5718 0.0091 0.99 44.2 yes View details
rps19-rpl2 IRb 57 0.1304 0.81 83.4 yes View details
atpA-atpF LSC 56 0.0566 0.95 71.9 yes View details
psbI-trnS-GCU LSC 137 0.0229 0.96 69.8 yes View details
petG-trnW-CCA LSC 129 0.0236 0.98 66.0 yes View details
petN-psbM LSC 497 0.0086 0.94 65.9 yes View details
rpl2-trnH-GUG IRa 216 0.0312 0.89 65.4 no View details
rbcL-accD LSC 764 0.0040 0.98 63.5 yes View details
psbL-psbF LSC 26 0.0385 1.00 62.8 yes View details
trnD-GUC-trnY-GUA LSC 414 0.0122 0.99 62.5 yes View details
ndhG-ndhI SSC 240 0.0167 1.00 62.5 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 100 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 TGTCGAAGCTCCATCCACTA 467–475 1.000 83.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGTCGAAGCTCCATCCACTA 481–489 1.000 83.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGTCGAAGCTCCATCCACTA 480–488 1.000 83.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TGTCGAAGCTCCATCCACTA 482–490 1.000 83.0
trnH-GUG-psbA_p5 trnH-GUG-psbA TGATTATGGGCGAATGACGG TGTCGAAGCTCCATCCACTA 528–536 1.000 82.6
trnK-UUU_p1 trnK-UUU CATCAGAGACTCCCAAGCAC TGCATAGCCTAAAAGCCAAGA 2988 0.500 48.9
trnK-UUU_p2 trnK-UUU TCATCAGAGACTCCCAAGCA TGCATAGCCTAAAAGCCAAGA 2989 0.500 48.6
trnK-UUU_p3 trnK-UUU CAGAGACTCCCAAGCACAAA TGCATAGCCTAAAAGCCAAGA 2985 0.500 47.0
trnK-UUU_p4 trnK-UUU ATCAGAGACTCCCAAGCACA TGCATAGCCTAAAAGCCAAGA 2987 0.500 46.3
trnK-UUU_p5 trnK-UUU CATCAGAGACTCCCAAGCAC TGCATAGCCTAAAAGCCAAG 2988 0.500 44.5
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2199–2311 1.000 83.0
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2198–2310 1.000 83.0
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 2185–2297 1.000 80.7
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT AAATAAAAATGGGGCGTGGC 2256–2368 1.000 80.5
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT AAATAAAAATGGGGCGTGGC 2255–2367 1.000 80.5
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TGGACTAAAGCGTCGGATTG 227–233 1.000 80.8
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GTGGACTAAAGCGTCGGATT 228–234 1.000 80.8
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GACTAAAGCGTCGGATTGCT 225–231 1.000 78.0
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TTTGGGAGAGATGGCTGAGT 246–252 1.000 77.9
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA CTGAGTGGACTAAAGCGTCG 232–238 1.000 77.7
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG ATTGGCATATTTGGGGCGAT 208–211 1.000 82.6
atpA-atpF_p2 atpA-atpF CCCCGCCATTACTTCATCAA ATTGGCATATTTGGGGCGAT 245–248 1.000 82.1
atpA-atpF_p3 atpA-atpF ATGCCATCGCCTACTTGAAG GAAGCGGATCAGTTTCGAGT 454–457 1.000 81.2
atpA-atpF_p4 atpA-atpF CCCCGCCATTACTTCATCAA GAAGCGGATCAGTTTCGAGT 491–494 1.000 81.0
atpA-atpF_p5 atpA-atpF AATTCCCCCGCCATTACTTC GAAGCGGATCAGTTTCGAGT 496–499 1.000 80.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCCCGTTTTTATCCCTGAG TTTCGTGTCTTGACTAGGCG 1121–1130 1.000 80.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCCCGTTTTTATCCCTGAG CCGGATTTGAACTGGGGAAA 1097–1106 1.000 80.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCGTTTTTATCCCTGAGCA TTTCGTGTCTTGACTAGGCG 1119–1128 1.000 80.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCGTTTTTATCCCTGAGCA CCGGATTTGAACTGGGGAAA 1095–1104 1.000 80.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCCCGTTTTTATCCCTGAG GTGTCTTGACTAGGCGACAC 1117–1126 1.000 78.7

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
Leptopus chinensis NC_063630.1 154600 View on NCBI ↗
Leptopus cordifolius NC_058615.1 155027 View on NCBI ↗