Markers + reference

Pseudostellaria

7 species · Caryophyllaceae · Caryophyllales

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Species 7
Genome length 149–150 kb
Candidate markers 265
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 278 0.0161 0.97 52.1 yes View details
rps16-trnQ-UUG LSC 690 0.0199 0.97 65.9 yes View details
psbI-trnS-GCU LSC 160 0.0424 0.99 79.6 yes View details
trnS-GCU-trnG-UCC LSC 710 0.0166 0.99 69.2 yes View details
ycf4-cemA LSC 542 0.0270 0.97 63.2 yes View details
petA-psbJ LSC 804 0.0169 1.00 54.8 yes View details
psbE-petL LSC 1223 0.0118 1.00 55.4 yes View details
ycf1 IRb 1914 0.0018 1.00 36.2 no View details
ndhF SSC 2232 0.0081 1.00 49.2 yes View details
ndhF-rpl32 SSC 722 0.0206 0.99 62.9 yes View details
rpl32-trnL-UAG SSC 822 0.0225 0.99 73.3 yes View details
ndhA SSC 2052 0.0100 1.00 43.6 yes View details
ycf1 SSC 5493 0.0080 1.00 48.0 yes View details
psaA-ycf3 LSC 985 0.0096 1.00 65.5 yes View details
rps19-trnH-GUG LSC 42 0.2357 0.31 64.9 no View details
trnG-UCC-trnR-UCU LSC 151 0.0259 1.00 63.9 yes View details
trnT-GGU-psbD LSC 1072 0.0110 0.99 63.3 yes View details
trnT-UGU-trnL-UAA LSC 605 0.0128 1.00 62.2 yes View details
psaJ-rpl33 LSC 386 0.0185 0.99 61.8 yes View details
trnK-UUU-rps16 LSC 638 0.0084 1.00 61.5 yes View details
trnE-UUC-trnT-GGU LSC 352 0.0095 1.00 58.7 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 386–418 1.000 84.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 400–432 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 399–431 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 401–433 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC GCGCTAACCTTGGTATGGAA 415–447 1.000 81.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAAAAGGCGCTCAACCTACA 814–823 1.000 81.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AAAAAGGCGCTCAACCTACA 815–824 1.000 81.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 766–775 1.000 80.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 765–774 1.000 80.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GCGCTCAACCTACAGAAACT 808–817 1.000 80.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TAAGGCATCGGGTTTTGGTC 791–835 1.000 85.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 770–814 1.000 85.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACGGATCATGTCCTT ATAGAAATCGAAGTGGGGCG 822–866 1.000 84.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 781–825 1.000 84.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ATAGAAATCGAAGTGGGGCG 801–845 1.000 84.7
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT AAGAGGGAGAGATGGCTGAG 287–294 1.000 80.9
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TTCAAGAGGGAGAGATGGCT 290–297 1.000 80.4
psbI-trnS-GCU_p3 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT CGAGTTATTCGTACCGAGGG 234–241 1.000 80.4
psbI-trnS-GCU_p4 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT CAAGAGGGAGAGATGGCTGA 288–295 1.000 78.5
psbI-trnS-GCU_p5 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TCAAGAGGGAGAGATGGCTG 289–296 1.000 78.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG CGGAATAGTAATCAAACCGGGA 844–994 1.000 69.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG TCGGAATAGTAATCAAACCGGG 845–995 1.000 69.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CGGAATAGTAATCAAACCGGGA 843–993 1.000 68.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TCGGAATAGTAATCAAACCGGG 844–994 1.000 68.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG CGGAATAGTAATCAAACCGGG 844–994 1.000 65.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 211–239 1.000 70.8
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 214–242 1.000 70.6
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 217–245 1.000 70.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 220–248 1.000 69.8
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 215–243 1.000 68.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Pseudostellaria davidii NC_068228.1 149732 View on NCBI ↗
Pseudostellaria heterantha NC_058231.1 149406 View on NCBI ↗
Pseudostellaria japonica NC_068229.1 149759 View on NCBI ↗
Pseudostellaria longipedicellata NC_039454.1 149626 View on NCBI ↗
Pseudostellaria okamotoi NC_039974.2 149653 View on NCBI ↗
Pseudostellaria palibiniana NC_041166.1 149668 View on NCBI ↗
Pseudostellaria sylvatica NC_087614.1 149581 View on NCBI ↗