Markers + reference

Roldana

2 species · Asteraceae · Asterales

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Species 2
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
trnC-GCA-petN LSC 798 0.0263 1.00 74.0 yes View details
psbC-trnS-TGA LSC 239 0.0460 1.00 71.9 yes View details
psaA-ycf3 LSC 686 0.0204 1.00 70.5 yes View details
ycf3-trnS-GGA LSC 880 0.0193 1.00 69.9 yes View details
rps4-trnT-TGT LSC 341 0.0296 0.89 58.4 yes View details
clpP LSC 2011 0.0159 1.00 61.6 yes View details
psbB-psbT LSC 195 0.0052 0.99 49.7 yes View details
ycf1 SSC 5037 0.0064 1.00 56.3 yes View details
rpl32-ndhF SSC 1065 0.0181 0.98 58.3 yes View details
psbI-trnS-GCT LSC 140 0.0441 0.97 80.5 yes View details
psbT-psbN LSC 69 0.1875 0.93 76.7 yes View details
ndhI-ndhG SSC 361 0.0277 1.00 69.7 yes View details
rps18-rpl20 LSC 317 0.0285 1.00 69.5 yes View details
trnK-TTT LSC 35 0.0571 1.00 69.0 yes View details
trnQ-TTG-psbK LSC 356 0.0225 1.00 66.6 yes View details
petN-psbM LSC 507 0.0138 1.00 64.7 yes View details
rps16 LSC 1092 0.0083 1.00 63.8 yes View details
accD-psaI LSC 688 0.0087 1.00 63.8 yes View details
atpH-atpF LSC 389 0.0154 1.00 63.2 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_p1 trnK-TTT GACAATGGGTTGCACAATGG GAAAGCCGTGTGCAATGAAA 138 1.000 79.4
trnK-TTT_p2 trnK-TTT ACAATGGGTTGCACAATGGA GAAAGCCGTGTGCAATGAAA 137 1.000 77.8
trnK-TTT_p3 trnK-TTT GACAATGGGTTGCACAATGG GGCTTGGGGAGGGATTTTTA 107 1.000 76.5
trnK-TTT_p4 trnK-TTT GACAATGGGTTGCACAATGG ATGAAAAATGCAAGCACGGC 124 1.000 76.1
trnK-TTT_p5 trnK-TTT GACAATGGGTTGCACAATGG AAGCCGTGTGCAATGAAAAA 136 1.000 75.8
rps16_p1 rps16 TCGTTTGATTAGGGTAAAGTTCCT GTCTATGTACCGAGCGAACC 1196–1199 1.000 46.9
rps16_p2 rps16 TCGTTTGATTAGGGTAAAGTTCCT CCGAGCGAACCAATGACTAT 1187–1190 1.000 46.1
rps16_p3 rps16 TCGTTTGATTAGGGTAAAGTTCCT TCTATGTACCGAGCGAACCA 1195–1198 1.000 45.9
rps16_p4 rps16 TCGTTTGATTAGGGTAAAGTTCCT ATGTACCGAGCGAACCAATG 1192–1195 1.000 45.1
rps16_p5 rps16 TCGTTTGATTAGGGTAAAGTTCC GTCTATGTACCGAGCGAACC 1196–1199 1.000 44.2
trnQ-TTG-psbK_p1 trnQ-TTG-psbK GTTGCCTTACCACTTGGCTA GGGCAATTTGGCGAAGAAAA 458 1.000 78.5
trnQ-TTG-psbK_p2 trnQ-TTG-psbK TTGCCTTACCACTTGGCTAC GGGCAATTTGGCGAAGAAAA 457 1.000 78.5
trnQ-TTG-psbK_p3 trnQ-TTG-psbK GTTGCCTTACCACTTGGCTA CATAGGCTTCGGGCAATTTG 468 1.000 75.8
trnQ-TTG-psbK_p4 trnQ-TTG-psbK TTGCCTTACCACTTGGCTAC CATAGGCTTCGGGCAATTTG 467 1.000 75.8
trnQ-TTG-psbK_p5 trnQ-TTG-psbK TTGCCTTACCACTTGGCTAC ATAGGCTTCGGGCAATTTGG 466 1.000 75.0
psbI-trnS-GCT_p1 psbI-trnS-GCT CGTAATCCAGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 240–256 1.000 77.6
psbI-trnS-GCT_p2 psbI-trnS-GCT CGTAATCCAGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 240–256 1.000 75.2
psbI-trnS-GCT_p3 psbI-trnS-GCT CCTATCCAATGATCCAGGACG ATTGGGAGAGATGGCTGAGT 259–275 1.000 74.3
psbI-trnS-GCT_p4 psbI-trnS-GCT CGTAATCCAGGACGTGAAGA GATGGCTGAGTGGACGAAAG 231–247 1.000 73.5
psbI-trnS-GCT_p5 psbI-trnS-GCT CGTAATCCAGGACGTGAAGA CGAGTTATTCGTACCGAGGG 204 0.500 49.4
trnC-GCA-petN_p1 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 921–926 1.000 80.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 864–869 1.000 80.2
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 882–887 1.000 77.9
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 922–927 1.000 75.3
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 920–925 1.000 74.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 669 1.000 60.2
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 669 1.000 58.6
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 670 1.000 54.3
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 661 1.000 54.3
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 655 1.000 53.5

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
Roldana aschenborniana MK170177.1 151018 View on NCBI ↗
Roldana barba-johannis MK170178.1 151016 View on NCBI ↗