Markers + reference

Pseudoxandra

2 species · Annonaceae · Magnoliales

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Species 2
Genome length 160–164 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 297 0.0539 1.00 81.7 yes View details
petN-psbM LSC 1122 0.0187 1.00 69.6 yes View details
accD LSC 1941 0.0221 0.95 63.8 yes View details
petA-psbJ LSC 1161 0.0201 0.94 70.1 yes View details
rps18 LSC 570 0.0175 1.00 60.3 yes View details
ycf2-trnL-CAA IRb 1043 0.0182 1.00 69.2 yes View details
trnN-GUU-ndhF IRb 739 0.0522 0.80 72.4 yes View details
rpl32-trnL-UAG SSC 1192 0.0369 0.98 81.2 yes View details
trnL-CAA-ycf2 IRa 1043 0.0182 1.00 69.2 yes View details
ccsA-ndhD SSC 219 0.0467 0.98 70.5 yes View details
petL LSC 96 0.0312 1.00 69.0 yes View details
rps19-rpl2 IRb 70 0.0571 1.00 68.3 yes View details
rbcL-atpB LSC 797 0.0152 0.99 68.1 yes View details
atpI-rps2 LSC 213 0.0192 0.98 65.8 yes View details
pafII-psaI LSC 455 0.0155 0.99 65.3 yes View details
trnT-GGU-psbD LSC 1432 0.0112 1.00 65.2 yes View details
psbM-trnD-GUC LSC 1207 0.0146 0.96 64.4 yes View details
rpl16 LSC 1419 0.0149 0.99 64.2 yes View details
rps16-trnQ-UUG LSC 1709 0.0153 0.99 63.8 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 TCACAATCCACTGCCTTGAG CCTCTAGACCTAGCTGCTGT 381 1.000 81.3
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TGCTGTCGAAGTTCCATCTG 367 1.000 81.3
trnH-GUG-psbA_p3 trnH-GUG-psbA TCACAATCCACTGCCTTGAG GCTGTCGAAGTTCCATCTGT 366 1.000 81.3
trnH-GUG-psbA_p4 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TTCCCTCTAGACCTAGCTGC 384 1.000 81.2
trnH-GUG-psbA_p5 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TAGACCTAGCTGCTGTCGAA 377 1.000 80.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1777–1782 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAATGGAAATGGTGGGTGCA GAGGTTCGAATCCTTCCGTC 1823–1828 1.000 78.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATGGAAATGGTGGGTGCAA GAGGTTCGAATCCTTCCGTC 1822–1827 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1781–1786 1.000 78.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGCAGATCTTGTCCT GAGGTTCGAATCCTTCCGTC 1799–1804 1.000 78.2
atpI-rps2_p1 atpI-rps2 ATGGACTTGGAAACCCCCTA TTTCGATTCCAGCCAACGAT 426–431 1.000 80.3
atpI-rps2_p2 atpI-rps2 GAAATGCTGGCCTACTTCCA TTTCGATTCCAGCCAACGAT 396–401 1.000 79.9
atpI-rps2_p3 atpI-rps2 AAATGCTGGCCTACTTCCAC TTTCGATTCCAGCCAACGAT 395–400 1.000 79.7
atpI-rps2_p4 atpI-rps2 ATGGACTTGGAAACCCCCTA AGAGCCTCAGTCCGATTGAT 400–405 1.000 79.5
atpI-rps2_p5 atpI-rps2 TTCCACACCGGATAGATCGT TTTCGATTCCAGCCAACGAT 381–386 1.000 79.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTCT 1284–1308 1.000 70.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTC 1284–1308 1.000 70.1
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCGTTGTTCATTCT 1223–1247 1.000 68.7
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCGTTGTTCATTC 1223–1247 1.000 68.6
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TTGCTACTGCGTTGTTCATTC 1285–1309 1.000 67.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAACGCAGTAGCA AGTTCAATCGGTCAGAGCAC 1276–1320 1.000 73.2
psbM-trnD-GUC_p2 psbM-trnD-GUC GAATGAACAACGCAGTAGCA AGTTCAATCGGTCAGAGCAC 1275–1319 1.000 73.1
psbM-trnD-GUC_p3 psbM-trnD-GUC GAATGAACAACGCAGTAGCAA AGTTCAATCGGTCAGAGCAC 1275–1319 1.000 70.8
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAACGCAGTAGC AGTTCAATCGGTCAGAGCAC 1276–1320 1.000 70.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGAACAACGCAGTAGCAA AGTTCAATCGGTCAGAGCAC 1274–1318 1.000 69.3
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1582 1.000 78.3
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1596 1.000 78.2
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1585 1.000 78.1
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1599 1.000 78.0
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1598 1.000 77.8

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
Pseudoxandra lucida NC_088523.1 159829 View on NCBI ↗
Pseudoxandra spiritus-sancti NC_088524.1 163708 View on NCBI ↗