Markers + reference

Paracalia

2 species · Asteraceae · Asterales

Back to catalogue

Species 2
Genome length 151–151 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-TTT-rps16 LSC 835 0.0146 0.98 68.8 yes View details
rps16 LSC 1104 0.0073 1.00 57.0 yes View details
rpoB LSC 3183 0.0066 1.00 45.3 yes View details
rpoC1 LSC 2821 0.0053 1.00 59.1 yes View details
atpH-atpF LSC 389 0.0180 1.00 64.7 yes View details
psaA-ycf3 LSC 687 0.0146 1.00 63.9 yes View details
trnT-TGT-trnL-TAA LSC 623 0.0113 1.00 65.4 yes View details
trnM-CAT-atpE LSC 207 0.0386 1.00 70.1 yes View details
accD-psaI LSC 681 0.0147 1.00 67.2 yes View details
ycf1 SSC 5007 0.0050 1.00 55.4 yes View details
rpoC2-rps2 LSC 221 0.0182 1.00 63.4 yes View details
psbE-petL LSC 1227 0.0057 1.00 62.0 yes View details
rbcL-accD LSC 521 0.0077 1.00 61.4 yes View details
ndhK LSC 678 0.0044 1.00 61.3 yes View details
rps16-trnQ-TTG LSC 977 0.0031 0.99 61.2 yes View details
trnC-GCA-petN LSC 807 0.0025 0.99 60.8 yes View details
ycf15-trnV-GAC IRb 680 0.0029 1.00 60.4 yes View details
trnV-GAC-ycf15 IRa 680 0.0029 1.00 60.4 yes View details
rpl2 IRb 1487 0.0027 1.00 60.3 yes View details
rpl2 IRa 1487 0.0027 1.00 60.3 no 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
trnK-TTT_p1 trnK-TTT GACAATGGGTTGCACAATGG TCAAATGATGGGTTCGTTGGA 2895–2920 1.000 71.6
trnK-TTT_p2 trnK-TTT ACAATGGGTTGCACAATGGA TCAAATGATGGGTTCGTTGGA 2894–2919 1.000 69.9
trnK-TTT_p3 trnK-TTT GACAATGGGTTGCACAATGG TTTCCGTCCCATAGGTTTGA 2933–2956 1.000 68.3
trnK-TTT_p4 trnK-TTT GACAATGGGTTGCACAATGG TCATCGTGATAAGCAGCTCT 2958–2981 1.000 68.3
trnK-TTT_p5 trnK-TTT GACAATGGGTTGCACAATGG CAAATGATGGGTTCGTTGGA 2894–2919 1.000 67.3
trnK-TTT-rps16_p1 trnK-TTT-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 964–971 1.000 78.4
trnK-TTT-rps16_p2 trnK-TTT-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 963–970 1.000 78.4
trnK-TTT-rps16_p3 trnK-TTT-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1049–1056 1.000 77.7
trnK-TTT-rps16_p4 trnK-TTT-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 1048–1055 1.000 77.6
trnK-TTT-rps16_p5 trnK-TTT-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 979–986 1.000 77.6
rps16_p1 rps16 TGAATAGAGCAAGAAAAGAAGGA GTCTATGTACCGAGCGAACC 1302–1307 1.000 40.6
rps16_p2 rps16 AGAGCAAGAAAAGAAGGAAA GTCTATGTACCGAGCGAACC 1297–1302 1.000 40.6
rps16_p3 rps16 TGAATAGAGCAAGAAAAGAAGGA CCGAGCGAACCAATGACTAT 1293–1298 1.000 40.6
rps16_p4 rps16 AGAGCAAGAAAAGAAGGAAA CCGAGCGAACCAATGACTAT 1288–1293 1.000 40.6
rps16_p5 rps16 TGAATAGAGCAAGAAAAGAAGGA TCTATGTACCGAGCGAACCA 1301–1306 1.000 40.6
rps16-trnQ-TTG_p1 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1043–1050 1.000 79.0
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AGAATAAGAATCCACGCCGG GAGGTTCGAATCCTTCCGTC 1075–1082 1.000 78.2
rps16-trnQ-TTG_p3 rps16-trnQ-TTG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1058–1065 1.000 77.2
rps16-trnQ-TTG_p4 rps16-trnQ-TTG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1057–1064 1.000 77.2
rps16-trnQ-TTG_p5 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1047–1054 1.000 74.3
trnC-GCA-petN_p1 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 925–930 1.000 79.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 868–873 1.000 78.8
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 886–891 1.000 76.6
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 926–931 1.000 74.0
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 924–929 1.000 73.1
rpoB_p1 rpoB CCGAACACGAGGGAAAGATT GCTCGCTAATGAGTACTGCA 285 1.000 79.0
rpoB_p2 rpoB AGATTCAGGGGCTCTTGCTA GCTCGCTAATGAGTACTGCA 308 1.000 78.7
rpoB_p3 rpoB TAGATTCAGGGGCTCTTGCT GCTCGCTAATGAGTACTGCA 309 1.000 78.7
rpoB_p4 rpoB CAAGCGGCTCTAGATTCAGG GCTCGCTAATGAGTACTGCA 319 1.000 78.5
rpoB_p5 rpoB CCAAGCGGCTCTAGATTCAG GCTCGCTAATGAGTACTGCA 320 1.000 78.5

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
Paracalia jungioides NC_062449.1 151014 View on NCBI ↗
Paracalia pentamera NC_063116.1 151139 View on NCBI ↗