Markers + reference

Omphalogramma

6 species · Primulaceae · Ericales

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Species 6
Genome length 154–154 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1519 0.0149 1.00 60.0 yes View details
petN-psbM LSC 1008 0.0155 0.98 61.7 yes View details
trnT-GGU-psbD LSC 1186 0.0158 1.00 63.5 yes View details
trnS-UGA-psbZ LSC 349 0.0203 0.99 59.8 yes View details
trnT-UGU-trnL-UAA LSC 785 0.0145 1.00 61.3 yes View details
ndhC-trnV-UAC LSC 1121 0.0165 0.99 63.1 yes View details
psbE-petL LSC 1224 0.0171 0.98 63.7 yes View details
rpl36-rps8 LSC 458 0.0226 1.00 70.4 yes View details
ndhF-rpl32 SSC 872 0.0213 1.00 72.9 yes View details
ccsA-ndhD SSC 250 0.0278 0.97 62.3 yes View details
ndhD SSC 1521 0.0082 1.00 51.9 yes View details
ycf1 SSC 5574 0.0147 1.00 51.0 yes View details
trnS-CGA-trnR-UCU LSC 259 0.0225 1.00 72.2 yes View details
atpA-atpF LSC 60 0.0300 0.98 71.0 yes View details
atpF-atpH LSC 381 0.0190 1.00 69.3 yes View details
rps4-trnT-UGU LSC 346 0.0262 1.00 68.8 yes View details
trnF-GAA-ndhJ LSC 674 0.0141 1.00 67.1 yes View details
trnL-UAG-ccsA SSC 106 0.0289 0.99 64.3 yes View details
trnV-GAC-rps12 IRa 1491 0.0035 1.00 62.9 yes View details
rps12-trnV-GAC IRb 1491 0.0034 1.00 62.8 yes View details
trnC-GCA-petN LSC 462 0.0131 1.00 62.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1593–1630 1.000 82.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1595–1632 1.000 81.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1586–1623 1.000 81.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCGAGTCAAGAGCACCTTT GAGGTTCGAATCCTTCCGTC 1657–1694 1.000 81.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1596–1633 1.000 81.0
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG TGGGAATACATTGCGTCCAA 385–400 1.000 81.5
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGGAATACATTGCGTCCAA 388–403 1.000 81.2
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG ATGGGAATACATTGCGTCCA 386–401 1.000 79.6
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG ATGGGAATACATTGCGTCCA 389–404 1.000 79.4
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGGGAATACATTGCGTCCAA 389–404 1.000 79.0
atpA-atpF_p1 atpA-atpF TTCGTCGGCTCGAATAGTTG TTACGTACCATCAGTGCCAA 140–147 1.000 74.6
atpA-atpF_p2 atpA-atpF TTCGTCGGCTCGAATAGTTG TTTACGTACCATCAGTGCCA 141–148 1.000 74.6
atpA-atpF_p3 atpA-atpF TTCGTCGGCTCGAATAGTTG ACGTACCATCAGTGCCAATA 138–145 1.000 72.8
atpA-atpF_p4 atpA-atpF TGCTCAATGCGTTCACGTAT TTACGTACCATCAGTGCCAA 172–179 1.000 72.3
atpA-atpF_p5 atpA-atpF TGCTCAATGCGTTCACGTAT TTTACGTACCATCAGTGCCA 173–180 1.000 72.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGAGGCAGAGGGAAAAATCC 568–571 1.000 78.7
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG CCTGAGGCAGAGGGAAAAAT 570–573 1.000 78.7
atpF-atpH_p3 atpF-atpH CCAGTAGCCCAAAGAAACGA TGAGGCAGAGGGAAAAATCC 541–544 1.000 78.4
atpF-atpH_p4 atpF-atpH CCAGTAGCCCAAAGAAACGA CCTGAGGCAGAGGGAAAAAT 543–546 1.000 78.4
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATCCGAGG 564–567 1.000 77.9
trnC-GCA-petN_p1 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 504–513 1.000 79.0
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGAGTCCACTTCTTCCCCAT 565–574 1.000 77.0
trnC-GCA-petN_p3 trnC-GCA-petN CGGGGGACTGCAAATCTTTT AGCCCAAGCGAGACTTACTA 530–539 1.000 76.7
trnC-GCA-petN_p4 trnC-GCA-petN CGGGGGACTGCAAATCTTTT AGAGTCCACTTCTTCCCCAT 591–600 1.000 74.7
trnC-GCA-petN_p5 trnC-GCA-petN CGGGGGACTGCAAATCTTT AGCCCAAGCGAGACTTACTA 530–539 1.000 74.4
petN-psbM_p1 petN-psbM GGCTCAATTATTCCCCAGCA TTTTCGTTTGATTCGGCGTG 1804–1844 1.000 84.7
petN-psbM_p2 petN-psbM TGGCTCAATTATTCCCCAGC TTTTCGTTTGATTCGGCGTG 1805–1845 1.000 84.7
petN-psbM_p3 petN-psbM GGCTCAATTATTCCCCAGCA ATCGGGAATCCCACTTTTCG 1818–1858 1.000 84.5
petN-psbM_p4 petN-psbM AAGGGGCGGAATTTCGATAC TTTTCGTTTGATTCGGCGTG 1653–1684 0.833 75.9
petN-psbM_p5 petN-psbM AAGGGGCGGAATTTCGATAC ATCGGGAATCCCACTTTTCG 1667–1698 0.833 75.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Omphalogramma delavayi OQ596335.1 153780 View on NCBI ↗
Omphalogramma elegans OQ596338.1 153675 View on NCBI ↗
Omphalogramma forrestii OQ596337.1 153626 View on NCBI ↗
Omphalogramma souliei OQ596339.1 153866 View on NCBI ↗
Omphalogramma tibeticum OQ596334.1 153871 View on NCBI ↗
Omphalogramma vinciflorum OQ596336.1 153833 View on NCBI ↗