Markers + reference

Gypsophila

4 species · Caryophyllaceae · Caryophyllales

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Species 4
Genome length 152–153 kb
Candidate markers 266
Primer pairs 100

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 31.3 yes View details
trnS-GCU-trnG-UCC LSC 818 0.0064 0.99 65.3 yes View details
pafI LSC 2098 0.0014 1.00 55.8 yes View details
ndhC-trnV-UAC LSC 961 0.0010 1.00 45.7 yes View details
rpl16 LSC 1388 0.0029 1.00 55.0 yes View details
ycf2 IRb 6411 0.0009 1.00 53.2 yes View details
ycf1 IRb 1917 0.0003 1.00 48.7 no View details
ndhF SSC 2253 0.0024 1.00 44.5 yes View details
ndhD SSC 1503 0.0027 1.00 45.6 yes View details
ycf1 SSC 5667 0.0021 1.00 39.7 yes View details
ycf2 IRa 6411 0.0009 1.00 53.2 no View details
trnE-UUC-trnT-GGU LSC 645 0.0047 1.00 65.0 yes View details
petA-psbJ LSC 989 0.0027 1.00 63.8 yes View details
rps16-trnQ-UUG LSC 735 0.0029 1.00 63.6 yes View details
petN-psbM LSC 1161 0.0032 1.00 60.9 yes View details
trnF-GAA-ndhJ LSC 766 0.0033 1.00 60.9 yes View details
rpoA LSC 1032 0.0026 1.00 60.5 yes View details
psbE-petL LSC 1090 0.0009 0.99 60.1 yes View details
accD LSC 1431 0.0017 1.00 60.0 yes View details
clpP1 LSC 2123 0.0014 0.99 59.4 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
psbA_p1 psbA TGCTCCGTTACTTTGACTTTCA ACACGGGCATATAAGGCATG 1261–1262 1.000 61.6
psbA_p2 psbA TGCTCCGTTACTTTGACTTTCA CACGGGCATATAAGGCATGT 1260–1261 1.000 61.6
psbA_p3 psbA TGCTCCGTTACTTTGACTTTCA GACACGGGCATATAAGGCAT 1262–1263 1.000 60.9
psbA_p4 psbA GCTCCGTTACTTTGACTTTCA ACACGGGCATATAAGGCATG 1260–1261 1.000 59.1
psbA_p5 psbA GCTCCGTTACTTTGACTTTCA CACGGGCATATAAGGCATGT 1259–1260 1.000 59.1
trnK-UUU_p1 trnK-UUU GCCTTATATGCCCGTGTCAA ACGAATCTGTTGTATTGGTGT 2851–2861 0.750 42.3
trnK-UUU_p2 trnK-UUU ACATGCCTTATATGCCCGTG ACGAATCTGTTGTATTGGTGT 2855–2865 0.750 41.7
trnK-UUU_p3 trnK-UUU CATGCCTTATATGCCCGTGT ACGAATCTGTTGTATTGGTGT 2854–2864 0.750 41.7
trnK-UUU_p4 trnK-UUU ATGCCTTATATGCCCGTGTC ACGAATCTGTTGTATTGGTGT 2853–2863 0.750 41.1
trnK-UUU_p5 trnK-UUU TGCCCGTGTCAACCAATATT ACGAATCTGTTGTATTGGTGT 2843–2853 0.750 40.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 825–851 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 836–862 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCATCGGGTTTTGGT 826–852 1.000 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTGGTAAGGCATCGGGTTTT 829–855 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTAAGGCATCGGGTTTTG 828–854 1.000 77.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG TCAAACCGGTAGACCCCTTA 983–1117 1.000 78.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AACCGGTAGACCCCTTAACT 980–1114 1.000 78.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AATCAAACCGGTAGACCCCT 985–1119 1.000 78.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG ATCAAACCGGTAGACCCCTT 984–1118 1.000 78.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TCAAACCGGTAGACCCCTTA 982–1116 1.000 78.2
trnG-UCC_p1 trnG-UCC TCGGTGTTCGACAAAAGTGA AGTGTTCTGAAAAAGAAATCGGA 896–903 1.000 43.2
trnG-UCC_p2 trnG-UCC ATGTCCAGTTTCGGTGTTCG AGTGTTCTGAAAAAGAAATCGGA 906–913 1.000 41.7
trnG-UCC_p3 trnG-UCC TCGGTGTTCGACAAAAGTGA GTGTTCTGAAAAAGAAATCGGA 895–902 1.000 40.4
trnG-UCC_p4 trnG-UCC TCGGTGTTCGACAAAAGTGA AGTGTTCTGAAAAAGAAATCGG 896–903 1.000 40.4
trnG-UCC_p5 trnG-UCC TCGGTGTTCGACAAAAGTGA AGTGTTCTGAAAAAGAAATCGGAT 896–903 1.000 40.4
petN-psbM_p1 petN-psbM TCGTATGGGGAAGAAGTGGA GCTACTGCGCTCTTCATTCT 1265–1322 1.000 78.0
petN-psbM_p2 petN-psbM ATTGTAAGTCTCGCTTGGGC GCTACTGCGCTCTTCATTCT 1323–1380 1.000 77.8
petN-psbM_p3 petN-psbM TCGTATGGGGAAGAAGTGGA TTGCTACTGCGCTCTTCATT 1267–1324 1.000 77.7
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC TTGCTACTGCGCTCTTCATT 1325–1382 1.000 77.5
petN-psbM_p5 petN-psbM CGTATGGGGAAGAAGTGGAC GCTACTGCGCTCTTCATTCT 1264–1321 1.000 77.4

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
Gypsophila huashanensis NC_067946.1 152457 View on NCBI ↗
Gypsophila licentiana PQ047136.1 152676 View on NCBI ↗
Gypsophila oldhamiana NC_058757.1 152675 View on NCBI ↗
Gypsophila patrinii NC_087609.1 152681 View on NCBI ↗