Markers + reference

Nordenstamia

3 species · Asteraceae · Asterales

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Species 3
Genome length 151–151 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCT-trnC-GCA LSC 745 0.0170 1.00 69.3 yes View details
psaB LSC 2205 0.0024 1.00 44.6 yes View details
ycf3 LSC 1940 0.0014 1.00 38.1 yes View details
psbE-petL LSC 1230 0.0065 1.00 62.8 yes View details
rps11 LSC 411 0.0308 1.00 51.6 yes View details
ycf1 SSC 5010 0.0027 1.00 54.3 yes View details
ndhA SSC 2149 0.0025 1.00 48.8 yes View details
rpl32-ndhF SSC 1025 0.0075 0.99 63.4 yes View details
ndhF SSC 2226 0.0015 1.00 43.7 yes View details
trnT-GGT-psbD LSC 1126 0.0042 0.99 62.2 yes View details
rps18-rpl20 LSC 297 0.0068 1.00 62.1 yes View details
accD-psaI LSC 681 0.0049 1.00 61.7 yes View details
ycf3-trnS-GGA LSC 877 0.0038 1.00 61.1 yes View details
ndhC-trnV-TAC LSC 757 0.0035 1.00 61.0 yes View details
rpl2-trnH-GTG IRa 116 0.0057 1.00 61.0 no View details
petD LSC 1208 0.0017 1.00 60.6 yes View details
rps12-ycf15 IRb 958 0.0028 1.00 60.5 yes View details
ycf15-rps12 IRa 958 0.0028 1.00 60.5 yes View details
trnK-TTT-rps16 LSC 840 0.0024 1.00 60.3 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
trnK-TTT-rps16_p1 trnK-TTT-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 976 1.000 76.4
trnK-TTT-rps16_p2 trnK-TTT-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 975 1.000 76.4
trnK-TTT-rps16_p3 trnK-TTT-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1061 1.000 75.8
trnK-TTT-rps16_p4 trnK-TTT-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 1060 1.000 75.8
trnK-TTT-rps16_p5 trnK-TTT-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 991 1.000 75.6
trnS-GCT-trnC-GCA_p1 trnS-GCT-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 804–896 1.000 83.4
trnS-GCT-trnC-GCA_p2 trnS-GCT-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 786–878 1.000 81.3
trnS-GCT-trnC-GCA_p3 trnS-GCT-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 740–832 1.000 79.7
trnS-GCT-trnC-GCA_p4 trnS-GCT-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 805–897 1.000 79.2
trnS-GCT-trnC-GCA_p5 trnS-GCT-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 722–814 1.000 77.5
trnG-TCC_p1 trnG-TCC CATTCACCGAGGAAGCAGAA CATCAAGCCGCGATCTGATA 1963–1972 1.000 79.7
trnG-TCC_p2 trnG-TCC AAGACATTCACCGAGGAAGC CATCAAGCCGCGATCTGATA 1967–1976 1.000 79.7
trnG-TCC_p3 trnG-TCC CATTCACCGAGGAAGCAGAA ATTCCTGACGGGTCACTGTA 1383–1405 1.000 79.1
trnG-TCC_p4 trnG-TCC AAGACATTCACCGAGGAAGC ATTCCTGACGGGTCACTGTA 1387–1409 1.000 79.1
trnG-TCC_p5 trnG-TCC CCTCTCGGGGTAGAAGAACA ATTCCTGACGGGTCACTGTA 1543–1565 1.000 78.7
trnT-GGT-psbD_p1 trnT-GGT-psbD TACAGTGACCCGTCAGGAAT GAAACGGTCCCTACGTAACC 1307–1321 1.000 80.7
trnT-GGT-psbD_p2 trnT-GGT-psbD TAACTCAGCGGTAGAGCACT GAAACGGTCCCTACGTAACC 1261–1275 1.000 80.0
trnT-GGT-psbD_p3 trnT-GGT-psbD TAGTACAGTGACCCGTCAGG GAAACGGTCCCTACGTAACC 1310–1324 1.000 79.9
trnT-GGT-psbD_p4 trnT-GGT-psbD TACAGTGACCCGTCAGGAAT GGACCAGCCTACAAAAACGA 1325–1339 1.000 79.8
trnT-GGT-psbD_p5 trnT-GGT-psbD GTGACCCGTCAGGAATTCAA GAAACGGTCCCTACGTAACC 1303–1317 1.000 79.8
psaB_p1 psaB GCTACCAAACTGCTCTACCC GTACAAGGACGTGCTGTAGG 2936 1.000 80.1
psaB_p2 psaB AAGGTTATGAGCCTTGCGAG GTACAAGGACGTGCTGTAGG 2955 1.000 80.0
psaB_p3 psaB GCTACCAAACTGCTCTACCC ACAACATGGGCGTTCTTCTT 2885 1.000 80.0
psaB_p4 psaB TTTGAACCCGTGACCTCAAG GTACAAGGACGTGCTGTAGG 2972 1.000 80.0
psaB_p5 psaB AAGGTTATGAGCCTTGCGAG ACAACATGGGCGTTCTTCTT 2904 1.000 79.9
ycf3_p1 ycf3 TGGTTGGTTCTTCCCAAAGG TCCCGCGAGAAGTAATGAGA 2105–2111 1.000 77.6
ycf3_p2 ycf3 TGGTTGGTTCTTCCCAAAGG GGATCATTTTCCCGCGAGAA 2114–2120 1.000 76.8
ycf3_p3 ycf3 TGGTTGGTTCTTCCCAAAGG ATCATTTTCCCGCGAGAAGT 2112–2118 1.000 76.3
ycf3_p4 ycf3 GGTTGGTTCTTCCCAAAGGA TCCCGCGAGAAGTAATGAGA 2104–2110 1.000 75.2
ycf3_p5 ycf3 TGGTTGGTTCTTCCCAAAGG CCCGCGAGAAGTAATGAGAA 2104–2110 1.000 74.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Nordenstamia cajamarcensis NC_062446.1 150907 View on NCBI ↗
Nordenstamia kingii NC_062447.1 150891 View on NCBI ↗
Nordenstamia repanda MK086040.2 151022 View on NCBI ↗