Markers + reference

Physospermopsis

8 species · Apiaceae · Apiales

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Species 8
Genome length 156–157 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 374 0.0591 0.93 74.6 yes View details
rps16-trnQ-UUG LSC 1230 0.0278 0.96 70.9 yes View details
trnG-UCC-trnR-UCU LSC 259 0.0914 0.88 81.8 yes View details
trnE-UUC-trnT-GGU LSC 803 0.0309 0.98 72.1 yes View details
trnT-GGU-psbD LSC 1422 0.0235 0.97 68.7 yes View details
trnS-UGA-psbZ LSC 375 0.0342 0.98 70.4 yes View details
trnT-UGU-trnL-UAA LSC 792 0.0278 0.98 69.2 yes View details
ndhC-trnV-UAC LSC 725 0.0432 0.96 79.3 yes View details
ndhF-rpl32 SSC 1206 0.0262 0.99 65.1 yes View details
rpl32-trnL-UAG SSC 951 0.0280 0.95 71.0 yes View details
atpF-atpH LSC 384 0.0338 0.98 73.8 yes View details
rps2-rpoC2 LSC 218 0.0334 0.97 68.3 yes View details
rps12-clpP LSC 158 0.0266 0.93 68.2 yes View details
trnS-GCU-trnG-UCC LSC 732 0.0240 0.98 67.5 yes View details
atpH-atpI LSC 764 0.0208 0.99 66.5 yes View details
ndhG-ndhI SSC 410 0.0320 0.98 65.9 yes View details
psbM-trnD-GUC LSC 680 0.0179 1.00 65.4 yes View details
trnK-UUU-rps16 LSC 910 0.0244 0.98 64.7 yes View details
petN-psbM LSC 1096 0.0203 0.99 64.4 yes View details
trnF-GAA-ndhJ LSC 418 0.0347 0.94 64.2 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 100 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 AGCTCCATCTACAAATGGGT 395–421 1.000 76.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTCCATCTACAAATGGGT 409–435 1.000 76.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTCCATCTACAAATGGGT 408–434 1.000 76.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTCCATCTACAAATGGGT 410–436 1.000 76.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AAGCTCCATCTACAAATGGGT 396–422 1.000 74.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG TGCTGCCATTTTGGAAGGAT 1660–1715 1.000 87.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TGCTGCCATTTTGGAAGGAT 1659–1714 1.000 87.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG TGCTGCCATTTTGGAAGGAT 1608–1663 1.000 87.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 1246–1308 1.000 87.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1245–1307 1.000 87.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 1304–1685 1.000 81.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC TCGGAGGTTCGAATCCTTTC 1319–1700 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG TCGGAGGTTCGAATCCTTTC 1318–1699 1.000 79.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TCGGAGGTTCGAATCCTTTC 1296–1677 1.000 76.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC TCGGAGGTTCGAATCCTTTC 1303–1684 1.000 75.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGGTTACTAGAACGAATCA 617–809 1.000 67.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGGTTACTAGAACGAATCAC 617–809 1.000 67.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGGTTACTAGAACGAATCA 612–804 1.000 67.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AGGGGGTTACTAGAACGAATCA 618–810 1.000 66.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGGTTACTAGAACGAATCAC 612–804 1.000 66.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 292–354 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 295–357 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 298–360 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 301–363 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 296–358 1.000 72.9
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAAGAAACGA GCCTGGTTGTAGCATTAGCA 464–486 1.000 85.3
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 491–513 1.000 84.3
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAAGAAACGA TGGCCTGGTTGTAGCATTAG 466–488 1.000 83.9
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 493–515 1.000 82.9
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAAGAAACGA CGGAGGGAAAAATACGAGGT 530–552 1.000 80.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Physospermopsis alepidioides MW202266.1 156167 View on NCBI ↗
Physospermopsis delavayi OP425129.1 156222 View on NCBI ↗
Physospermopsis handelii PQ551029.1 155868 View on NCBI ↗
Physospermopsis kingdon-wardii MW202268.1 156166 View on NCBI ↗
Physospermopsis muliensis MW202269.1 156376 View on NCBI ↗
Physospermopsis obtusiuscula PP530889.1 156218 View on NCBI ↗
Physospermopsis rubrinervis PQ551030.1 155672 View on NCBI ↗
Physospermopsis shaniana MW202273.1 157059 View on NCBI ↗