Markers + reference

Physocarpus

2 species · Rosaceae · Rosales

Back to catalogue

Species 2
Genome length 159–159 kb
Candidate markers 268
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 278 0.0000 1.00 31.4 yes View details
rps16 LSC 1158 0.0009 1.00 59.2 yes View details
psbK-psbI LSC 244 0.0041 1.00 54.9 yes View details
atpA LSC 1524 0.0007 1.00 59.1 yes View details
rpoC2 LSC 4314 0.0002 1.00 53.7 yes View details
psbZ-trnG-GCC LSC 490 0.0086 0.95 65.9 yes View details
rbcL LSC 1428 0.0021 1.00 60.0 yes View details
rpl33 LSC 201 0.0000 1.00 23.2 yes View details
rpl20 LSC 354 0.0000 1.00 34.8 yes View details
rpl20-rps12 LSC 788 0.0038 1.00 60.9 yes View details
ndhF-rpl32 SSC 1067 0.0009 0.99 60.1 yes View details
rbcL-accD LSC 638 0.0000 0.96 63.0 yes View details
rpl2-trnH-GUG LSC 347 0.0098 0.88 61.9 no View details
trnF-GAA-ndhJ LSC 743 0.0000 0.98 60.3 yes View details
ycf3-trnS-GGA LSC 903 0.0011 1.00 59.4 yes View details
rpl32-trnL-UAG SSC 935 0.0011 1.00 59.4 yes View details
psbD LSC 1062 0.0009 1.00 59.3 yes View details
petA-psbJ LSC 961 0.0010 1.00 59.3 yes View details
trnT-UGU-trnL-UAA LSC 1181 0.0008 1.00 59.2 yes View details
rpl16 LSC 1394 0.0007 1.00 59.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 394 1.000 78.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 408 1.000 78.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 407 1.000 78.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 409 1.000 78.7
trnH-GUG-psbA_p5 trnH-GUG-psbA TTATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 455 1.000 78.6
rps16_p1 rps16 AGAGGAAATAGCAAAGAACCA TATGTACCGACCGATCCGAT 1308–1309 1.000 45.1
rps16_p2 rps16 AAGAGGAAATAGCAAAGAACCA TATGTACCGACCGATCCGAT 1309–1310 1.000 43.5
rps16_p3 rps16 AGAGGAAATAGCAAAGAACCAA TATGTACCGACCGATCCGAT 1308–1309 1.000 43.5
rps16_p4 rps16 AGAGGAAATAGCAAAGAACCA ACCGACCGATCCGATGATTA 1303–1304 1.000 43.5
rps16_p5 rps16 AGAGGAAATAGCAAAGAACCA TACCGACCGATCCGATGATT 1304–1305 1.000 43.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 381 1.000 72.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 378 1.000 70.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 379 1.000 70.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 380 1.000 70.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 382 1.000 69.9
atpA_p1 atpA TGATGAAGATTCAAAGTAATCACT TAGTCCTTCTACTGCAGGCA 1606–1607 1.000 40.0
atpA_p2 atpA TGATGAAGATTCAAAGTAATCACT GTCCTTCTACTGCAGGCATT 1604–1605 1.000 40.0
atpA_p3 atpA TGATGAAGATTCAAAGTAATCACT AGTCCTTCTACTGCAGGCAT 1605–1606 1.000 40.0
atpA_p4 atpA TTGATGAAGATTCAAAGTAATCACT TAGTCCTTCTACTGCAGGCA 1607–1608 1.000 40.0
atpA_p5 atpA TGATGAAGATTCAAAGTAATCAC TAGTCCTTCTACTGCAGGCA 1606–1607 1.000 40.0
rpoC2_p1 rpoC2 CCGCGTGTACATTCCCATAA AGATCACTTCGGAATGGCAT 200 1.000 71.8
rpoC2_p2 rpoC2 TTCTACCGCGTGTACATTCC AGATCACTTCGGAATGGCAT 205 1.000 70.0
rpoC2_p3 rpoC2 CCGCGTGTACATTCCCATAA TAGATCACTTCGGAATGGCA 201 1.000 66.6
rpoC2_p4 rpoC2 CCGCGTGTACATTCCCATAA ACATCACACATCCTGGATCA 178 1.000 65.8
rpoC2_p5 rpoC2 CCGCGTGTACATTCCCATAA GCCAATCTGGTCTTTCACAA 268 1.000 65.7
psbD_p1 psbD AAAAGAAGGGGCAGTGTACG ACGACCGGCTAAAGCTAAAG 1205 1.000 79.2
psbD_p2 psbD AAAAGAAGGGGCAGTGTACG CGACCGGCTAAAGCTAAAGT 1204 1.000 79.2
psbD_p3 psbD AAAAGAAGGGGCAGTGTACG GAGCACCCAGTAGTTTACCG 1284 1.000 79.2
psbD_p4 psbD GGGGCAGTGTACGAGAAATC ACGACCGGCTAAAGCTAAAG 1198 1.000 77.2
psbD_p5 psbD GGGGCAGTGTACGAGAAATC CGACCGGCTAAAGCTAAAGT 1197 1.000 77.2

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
Physocarpus amurensis NC_065734.1 159110 View on NCBI ↗
Physocarpus opulifolius NC_077593.1 159131 View on NCBI ↗