Markers + reference

Monopsis

2 species · Campanulaceae · Asterales

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Species 2
Genome length 167–168 kb
Candidate markers 289
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 289 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ORF100 LSC 303 0.1533 0.50 63.8 yes View details
clpP LSC 720 0.1788 0.97 82.2 yes View details
rps12-rpl20 LSC 747 0.1157 0.99 79.6 yes View details
rpl20 LSC 411 0.1583 0.97 77.9 yes View details
rps18 LSC 465 0.1533 0.88 78.9 yes View details
ycf1 IRb 7596 0.0734 0.96 72.5 no View details
ycf1 IRa 7596 0.0734 0.96 72.5 yes View details
trnI (CAU)-rpl23 IRa 519 0.0938 0.97 79.7 yes View details
rpl23-trnI (CAU) IRb 519 0.0938 0.97 79.7 yes View details
trnM (CAU)-atpE LSC 216 0.1070 1.00 78.8 yes View details
atpH-atpI LSC 1063 0.0461 1.00 77.9 yes View details
psbK-ORF100 LSC 712 0.0651 0.97 77.3 yes View details
trnK (UUU)-ORF148 LSC 179 0.1149 0.97 77.2 yes View details
rpl33-psaJ LSC 378 0.0563 0.99 76.3 yes View details
ndhD-ccsA SSC 270 0.0613 0.97 75.8 yes View details
atpB-rbcL LSC 786 0.0280 1.00 74.8 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TAGGTGAATCCATGGAGGGG 1158–1170 1.000 81.7
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGG 1124–1136 1.000 81.7
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TAGGTGAATCCATGGAGGGG 1140–1152 1.000 80.8
atpH-atpI_p4 atpH-atpI GCGATACCTTCTACAGCCTG TAGGTGAATCCATGGAGGGG 1211–1223 1.000 80.6
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TAGGTGAATCCATGGAGGGG 1125–1137 1.000 80.6
trnM (CAU)-atpE_p1 trnM (CAU)-atpE TATTGCTTTCATACGGCGGG GTCGAGGCTATCAATGCGAT 291–292 1.000 82.7
trnM (CAU)-atpE_p2 trnM (CAU)-atpE GTATTGCTTTCATACGGCGG GTCGAGGCTATCAATGCGAT 292–293 1.000 80.7
trnM (CAU)-atpE_p3 trnM (CAU)-atpE GCGGGAGTCATTGGTTCAAA GTCGAGGCTATCAATGCGAT 276–277 1.000 80.3
trnM (CAU)-atpE_p4 trnM (CAU)-atpE CTTTCATACGGCGGGAGTC GTCGAGGCTATCAATGCGAT 286–287 1.000 77.9
trnM (CAU)-atpE_p5 trnM (CAU)-atpE TATTGCTTTCATACGGCGGG CTCTTCGACGAGCTAGGACA 314–315 1.000 77.8
atpB-rbcL_p1 atpB-rbcL GGAAACCCCAGAACCAGAAG CGTCTCTGTTTGTGGTGACA 846 1.000 80.8
atpB-rbcL_p2 atpB-rbcL AGGACCGGACCAATGATTTG CGTCTCTGTTTGTGGTGACA 899 1.000 80.4
atpB-rbcL_p3 atpB-rbcL ACATCTAGGACCGGACCAAT CGTCTCTGTTTGTGGTGACA 905 1.000 80.0
atpB-rbcL_p4 atpB-rbcL GGAAACCCCAGAACCAGAAG TCGTCTCTGTTTGTGGTGAC 847 1.000 79.6
atpB-rbcL_p5 atpB-rbcL AGGACCGGACCAATGATTTG TCGTCTCTGTTTGTGGTGAC 900 1.000 79.2
psbK-ORF100_p1 psbK-ORF100 CTCGTAGCAAGGGCAGAATT AAGTCGCACGTTGCTTTCTA 1318–1489 1.000 87.6
psbK-ORF100_p2 psbK-ORF100 CTCGTAGCAAGGGCAGAATT TAAGTCGCACGTTGCTTTCT 1319–1490 1.000 87.6
psbK-ORF100_p3 psbK-ORF100 CTCGTAGCAAGGGCAGAATT GATTCGCGCCAAAATAGTGG 962 0.500 58.9
psbK-ORF100_p4 psbK-ORF100 CTTACAGCAGCTTGCCAAAC GATTCGCGCCAAAATAGTGG 1082 0.500 58.7
psbK-ORF100_p5 psbK-ORF100 CTCGTAGCAAGGGCAGAATT CGATTCGCGTCAAAATCGTT 910 0.500 58.6
ORF100_p1 ORF100 CACGTGTCAAAGTCCTAGCA GTTGAGCACCCCTTTCAAGA 1178–1349 1.000 88.0
ORF100_p2 ORF100 ACACGTGTCAAAGTCCTAGC GTTGAGCACCCCTTTCAAGA 1179–1350 1.000 88.0
ORF100_p3 ORF100 ACGTGTCAAAGTCCTAGCAC GTTGAGCACCCCTTTCAAGA 1177–1348 1.000 88.0
ORF100_p4 ORF100 CACGTGTCAAAGTCCTAGCA AAAACCCACTTTCCGAAGCT 1276 0.500 58.3
ORF100_p5 ORF100 ACGTGTCAAAGTCCTAGCAC AAAACCCACTTTCCGAAGCT 1275 0.500 58.3
trnK (UUU)-ORF148_p1 trnK (UUU)-ORF148 CTAGTTCCGGGTTCGAATCC ACCGTGAGATTCAAATCATAGA 235–236 1.000 48.5
trnK (UUU)-ORF148_p2 trnK (UUU)-ORF148 CTAGTTCCGGGTTCGAATCC ACCGTGAGATTCAAATCATAGAT 235–236 1.000 48.5
trnK (UUU)-ORF148_p3 trnK (UUU)-ORF148 CTAGTTCCGGGTTCGAATCC ACCGTGAGATTCAAATCATAG 235–236 1.000 48.5
trnK (UUU)-ORF148_p4 trnK (UUU)-ORF148 ATCCGACTAGTTCCGGGTTC ACCGTGAGATTCAAATCATAGA 241–242 1.000 48.3
trnK (UUU)-ORF148_p5 trnK (UUU)-ORF148 CTTCATCCGACTAGTTCCGG ACCGTGAGATTCAAATCATAGA 245–246 1.000 48.1

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
Monopsis debilis var. debilis MF770616.1 167374 View on NCBI ↗
Monopsis flava NC_036083.1 167534 View on NCBI ↗