Markers + reference

Maesa

3 species · Primulaceae · Ericales

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Species 3
Genome length 157–157 kb
Candidate markers 264
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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1491 0.0086 0.98 65.9 yes View details
trnT-UGU-trnL-UAA LSC 1079 0.0075 0.98 61.7 yes View details
trnL-UAA-trnF-GAA LSC 379 0.0158 1.00 54.7 yes View details
ndhC-trnV-UAC LSC 1144 0.0087 1.00 56.5 yes View details
psbE-petL LSC 1115 0.0100 0.99 64.0 yes View details
psaJ-rpl33 LSC 459 0.0058 0.99 47.6 yes View details
ycf1 SSC 5592 0.0067 1.00 53.2 yes View details
trnL-UAG-rpl32 SSC 432 0.0216 1.00 61.7 yes View details
ndhF SSC 2241 0.0067 1.00 47.0 yes View details
rps2-rpoC2 LSC 220 0.0199 0.99 66.7 yes View details
trnK-UUU-rps16 LSC 848 0.0056 0.98 65.0 yes View details
atpA-atpF LSC 54 0.0123 1.00 64.6 yes View details
infA-rps8 LSC 126 0.0160 0.99 64.3 yes View details
atpH-atpI LSC 1061 0.0063 0.99 63.4 yes View details
ndhD-ccsA SSC 241 0.0166 1.00 63.1 yes View details
atpF-atpH LSC 387 0.0103 1.00 62.7 yes View details
rbcL-accD LSC 611 0.0044 1.00 61.8 yes View details
accD-psaI LSC 758 0.0044 1.00 61.6 yes View details
psbK-psbI LSC 415 0.0081 0.99 61.2 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AACCTACAGAAACGGTTCGG 998–1008 1.000 80.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AACCTACAGAAACGGTTCGG 999–1009 1.000 80.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC AACCTACAGAAACGGTTCGG 1003–1013 1.000 80.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AACCTACAGAAACGGTTCGG 1001–1011 1.000 80.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA TGCTCAACCTACAGAAACGG 1003–1013 1.000 80.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1571–1659 1.000 81.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1554–1642 1.000 80.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1572–1660 1.000 80.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1568–1656 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG CAATTTAAATGGGGCGTGGC 1628–1638 0.667 65.2
psbK-psbI_p1 psbK-psbI CAAGCTGCCGTAAGTTTTCG ACGCCCTGGATCGTTAGATA 524–529 1.000 81.1
psbK-psbI_p2 psbK-psbI CAAGCTGCCGTAAGTTTTCG TACGCCCTGGATCGTTAGAT 525–530 1.000 81.1
psbK-psbI_p3 psbK-psbI CAAGCTGCCGTAAGTTTTCG TTACGCCCTGGATCGTTAGA 526–531 1.000 79.3
psbK-psbI_p4 psbK-psbI GCAAGCTGCCGTAAGTTTTC ACGCCCTGGATCGTTAGATA 525–530 1.000 78.9
psbK-psbI_p5 psbK-psbI GCAAGCTGCCGTAAGTTTTC TACGCCCTGGATCGTTAGAT 526–531 1.000 78.9
atpA-atpF_p1 atpA-atpF TTCGTCGGCTCGAATAGTTG AGGTGCTCTAGGAACTCTGA 182–190 1.000 73.3
atpA-atpF_p2 atpA-atpF TTCGTCGGCTCGAATAGTTG TTACGTACCATCAGTGCCAA 136–144 1.000 71.9
atpA-atpF_p3 atpA-atpF TTCGTCGGCTCGAATAGTTG TTTACGTACCATCAGTGCCA 137–145 1.000 71.9
atpA-atpF_p4 atpA-atpF TTCGTCGGCTCGAATAGTTG AAGGTGCTCTAGGAACTCTGA 183–191 1.000 71.1
atpA-atpF_p5 atpA-atpF TTCGTCGGCTCGAATAGTTG AGGTGCTCTAGGAACTCTGAA 182–190 1.000 71.1
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GGACTGGTTGTAGCATTAGCA 497–509 1.000 73.0
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGACTGGTTGTAGCATTAGC 498–510 1.000 73.0
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCGGAGGGGAAAATACGAG 563–575 1.000 72.8
atpF-atpH_p4 atpF-atpH CCAGTAGCCCAAAGAAACGA GGACTGGTTGTAGCATTAGCA 470–482 1.000 72.6
atpF-atpH_p5 atpF-atpH CCAGTAGCCCAAAGAAACGA GCGGAGGGGAAAATACGAG 536–548 1.000 72.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT AAGCGGCATTCAAGCTCTTA 1163–1169 1.000 79.9
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT AAGCGGCATTCAAGCTCTTA 1219–1225 1.000 79.3
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA AAGCGGCATTCAAGCTCTTA 1164–1170 1.000 78.8
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC AAGCGGCATTCAAGCTCTTA 1223–1229 1.000 78.7
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AAGCGGCATTCAAGCTCTTA 1178–1184 1.000 78.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Maesa cavinervis PV662410.1 156743 View on NCBI ↗
Maesa hupehensis NC_062126.1 157005 View on NCBI ↗
Maesa japonica NC_079854.1 157189 View on NCBI ↗