Markers + reference

Muehlenbeckia

4 species · Polygonaceae · Caryophyllales

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Species 4
Genome length 163–163 kb
Candidate markers 267
Primer pairs 110

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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 856 0.0183 0.99 64.6 yes View details
rps16-trnQ-UUG LSC 1584 0.0222 0.95 66.0 yes View details
trnS-GCU-trnG-GCC LSC 1208 0.0299 0.99 74.2 yes View details
psbM-trnD-GUC LSC 1045 0.0190 1.00 65.4 yes View details
trnT-GGU-psbD LSC 1455 0.0146 1.00 64.8 yes View details
rps4-trnT-UGU LSC 578 0.0228 1.00 67.2 yes View details
ndhC-trnV-UAC LSC 631 0.0246 0.98 63.9 yes View details
atpB-rbcL LSC 849 0.0245 0.98 69.0 yes View details
rpl33-rps18 LSC 517 0.0252 0.97 67.2 yes View details
ndhA SSC 2200 0.0128 1.00 62.4 yes View details
trnL-UAG-rpl32 SSC 756 0.0261 0.99 67.8 yes View details
rpl32-ndhF SSC 985 0.0163 1.00 58.2 yes View details
trnH-GUG-psbA LSC 210 0.0397 1.00 79.2 yes View details
ndhI-ndhG SSC 347 0.0240 0.99 70.8 yes View details
petN-psbM LSC 1176 0.0162 1.00 69.9 yes View details
ndhD-ccsA SSC 210 0.0419 0.99 68.9 yes View details
atpF-atpH LSC 436 0.0160 0.98 68.6 yes View details
ycf3-trnS-GGA LSC 918 0.0158 1.00 66.6 yes View details
accD-psaI LSC 745 0.0211 0.99 65.8 yes View details
trnE-UUC-trnT-GGU LSC 890 0.0178 0.99 64.6 yes View details
trnY-GUA-trnE-UUC LSC 70 0.0310 1.00 64.3 yes View details
trnT-UGU-trnL-UAA LSC 496 0.0192 1.00 64.0 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 110 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 GCGCTAACCTTGGTATGGAA 325–349 1.000 82.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 339–363 1.000 82.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 338–362 1.000 82.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 340–364 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC GCGCTAACCTTGGTATGGAA 354–378 1.000 79.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA CGCTCAACCTACTGGAACTG 1026–1043 1.000 80.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC CGCTCAACCTACTGGAACTG 1027–1044 1.000 80.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT CGCTCAACCTACTGGAACTG 1029–1046 1.000 80.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AACTCTACCGATGGTGTGGA CGCTCAACCTACTGGAACTG 1046–1063 1.000 80.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA TTCGCCCTAATGAAACGACA 967–984 1.000 79.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1594–1649 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1597–1652 1.000 77.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 1598–1653 1.000 75.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 1624–1679 1.000 74.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 1596–1651 1.000 74.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 527–1331 1.000 59.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA ACGAATCACACTTTTACCACT 497–1301 1.000 58.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 530–1334 1.000 58.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 529–1333 1.000 58.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA GAACGAATCACACTTTTACCACT 499–1303 1.000 57.3
atpF-atpH_p1 atpF-atpH TTAAATCCGAAACTCCCCGC GCAGAGGGGAAAATACGAGG 609–620 1.000 80.9
atpF-atpH_p2 atpF-atpH CCCGGGGAAACGAAAGAATC GCAGAGGGGAAAATACGAGG 576–587 1.000 75.9
atpF-atpH_p3 atpF-atpH TTAAATCCGAAACTCCCCGC CCGAAGCAGAGGGGAAAATA 614–625 1.000 75.6
atpF-atpH_p4 atpF-atpH TTAAATCCGAAACTCCCCGC AGCAGAGGGGAAAATACGAG 610–621 1.000 73.4
atpF-atpH_p5 atpF-atpH CCCGGGGAAACGAAAGAAT GCAGAGGGGAAAATACGAGG 576–587 1.000 73.1
petN-psbM_p1 petN-psbM CCCTTTCACTCGTCGTATGG AAAACGGTCAGCCAAAACAA 1231–1238 1.000 73.9
petN-psbM_p2 petN-psbM CCTTTCACTCGTCGTATGGG AAAAACGGTCAGCCAAAACA 1231–1238 1.000 73.9
petN-psbM_p3 petN-psbM CCTTTCACTCGTCGTATGGG AAAACGGTCAGCCAAAACAA 1230–1237 1.000 73.9
petN-psbM_p4 petN-psbM CTTTCACTCGTCGTATGGGG AAAAACGGTCAGCCAAAACA 1230–1237 1.000 73.9
petN-psbM_p5 petN-psbM CTTTCACTCGTCGTATGGGG AAAACGGTCAGCCAAAACAA 1229–1236 1.000 73.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Muehlenbeckia australis NC_059029.1 163407 View on NCBI ↗
Muehlenbeckia axillaris NC_059030.1 163435 View on NCBI ↗
Muehlenbeckia gracillima NC_059031.1 163434 View on NCBI ↗
Muehlenbeckia gunnii NC_059032.1 163182 View on NCBI ↗