Markers + reference

Downingia

2 species · Campanulaceae · Asterales

Back to catalogue

Species 2
Genome length 133–137 kb
Candidate markers 270
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ORF213 LSC 642 0.2694 0.42 71.5 yes View details
ORF342 LSC 1029 0.4627 0.83 80.3 yes View details
ORF175 IRb 528 0.4529 0.72 75.7 no View details
ycf1 SSC 6924 0.1883 0.97 75.5 yes View details
ORF441 SSC 1326 0.3209 0.95 83.4 yes View details
ORF175 IRa 528 0.4517 0.73 75.8 yes View details
psbM-trnD (GUC) LSC 921 0.0929 0.93 84.4 yes View details
trnT (GGU)-psbD LSC 1081 0.1156 0.98 82.7 yes View details
trnS (GCU)-trnG (UCC) LSC 653 0.1130 0.99 82.6 yes View details
trnA (UGC)-rrn23 IRb 148 0.0878 1.00 82.6 yes View details
rrn23-trnA (UGC) IRa 148 0.0878 1.00 82.6 yes View details
psbA-rbcL LSC 823 0.1123 0.98 82.0 yes View details
trnT (UGU)-trnL (UAA) LSC 665 0.1002 0.98 81.8 yes View details
trnK (UUU)-rps16 LSC 511 0.1242 0.96 81.5 yes View details
cemA-pafII LSC 841 0.1130 0.98 81.2 yes View details
pafI-trnS (GGA) LSC 896 0.1217 0.98 81.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-rbcL_p1 psbA-rbcL CGTCTCTCTAAAATTGCAGTCA ATTTGAGTTTGCCGCAATGG 877–908 1.000 60.4
psbA-rbcL_p2 psbA-rbcL CGTCTCTCTAAAATTGCAGTCA TGAGTTTGCCGCAATGGATA 874–905 1.000 60.1
psbA-rbcL_p3 psbA-rbcL CGTCTCTCTAAAATTGCAGTCA AGTTTGCCGCAATGGATACT 872–903 1.000 60.0
psbA-rbcL_p4 psbA-rbcL CGTCTCTCTAAAATTGCAGTCA GAGTTTGCCGCAATGGATAC 873–904 1.000 57.2
psbA-rbcL_p5 psbA-rbcL CGTCTCTCTAAAATTGCAGTCAT ATTTGAGTTTGCCGCAATGG 877–908 1.000 56.2
trnK (UUU)-rps16_p1 trnK (UUU)-rps16 ATCCATTGGACCCAACCCTA ACGGTAACTATTCGTGTGCC 1336 0.500 60.0
trnK (UUU)-rps16_p2 trnK (UUU)-rps16 TATCCATTGGACCCAACCCT ACGGTAACTATTCGTGTGCC 1337 0.500 60.0
trnK (UUU)-rps16_p3 trnK (UUU)-rps16 CCTTACCCGTATTCAGGCAC ACGGTAACTATTCGTGTGCC 1478 0.500 59.6
trnK (UUU)-rps16_p4 trnK (UUU)-rps16 ATCCATTGGACCCAACCCTA CTCTCACCGAAATCAGGAGC 1105 0.500 59.4
trnK (UUU)-rps16_p5 trnK (UUU)-rps16 TATCCATTGGACCCAACCCT CTCTCACCGAAATCAGGAGC 1106 0.500 59.4
ORF213_p1 ORF213 TTCGGGAGCGAACATCAATT ACCGGCCCAATCAAAAATCT 980–1409 1.000 90.6
ORF213_p2 ORF213 ATTCTTGCAAGGGATAGCCG TGGGCGCTAATTGCAATTTG 1713 0.500 59.7
ORF213_p3 ORF213 ATTCTTGCAAGGGATAGCCG ACCGGCCCAATCAAAAATCT 1625 0.500 59.3
ORF213_p4 ORF213 TTCGGGAGCGAACATCAATT TGGGCGCTAATTGCAATTTG 1497 0.500 59.1
ORF213_p5 ORF213 TTTTCGAAGCTCGCTTCCTT TGGGCGCTAATTGCAATTTG 1520 0.500 59.0
trnS (GCU)-trnG (UCC)_p1 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 776–808 1.000 58.6
trnS (GCU)-trnG (UCC)_p2 trnS (GCU)-trnG (UCC) ACGAAAACGGAAAGAGAGGG ACGAATCACACTTTTACCACT 782–814 1.000 58.4
trnS (GCU)-trnG (UCC)_p3 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 779–811 1.000 57.5
trnS (GCU)-trnG (UCC)_p4 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 778–810 1.000 57.5
trnS (GCU)-trnG (UCC)_p5 trnS (GCU)-trnG (UCC) ACGAAAACGGAAAGAGAGGG GAACGAATCACACTTTTACCACT 784–816 1.000 57.3
ORF342_p1 ORF342 ACAGCCGTACCATTAACGTC ACTTCGTCCCCAGACTACAA 1780 0.500 60.0
ORF342_p2 ORF342 ACAGCCGTACCATTAACGTC TTCGTCCCCAGACTACAAGT 1778 0.500 60.0
ORF342_p3 ORF342 CACGAACAGCCGTACCATTA ACTTCGTCCCCAGACTACAA 1785 0.500 59.9
ORF342_p4 ORF342 CACGAACAGCCGTACCATTA TTCGTCCCCAGACTACAAGT 1783 0.500 59.9
ORF342_p5 ORF342 ACAGCCGTACCATTAACGTC GGTGCAGAGTCAAAAAGGGA 1630 0.500 59.8
psbM-trnD (GUC)_p1 psbM-trnD (GUC) ACTGCCAGAATATTGACTTCCA AGATCCCTTAGTTCCCTGGG 1019–1035 1.000 68.0
psbM-trnD (GUC)_p2 psbM-trnD (GUC) ACTGCCAGAATATTGACTTCCA TTCAATTGGTCAGAGCACCG 992–1008 1.000 66.0
psbM-trnD (GUC)_p3 psbM-trnD (GUC) ACTGCCAGAATATTGACTTCCA TCCCTTAGTTCCCTGGGATT 1016–1032 1.000 64.2
psbM-trnD (GUC)_p4 psbM-trnD (GUC) AACTGCCAGAATATTGACTTCCA AGATCCCTTAGTTCCCTGGG 1020–1036 1.000 64.0
psbM-trnD (GUC)_p5 psbM-trnD (GUC) ACTGCCAGAATATTGACTTCCA CCCTTAGTTCCCTGGGATTG 1015–1031 1.000 63.8

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
Downingia cuspidata NC_035359.1 136733 View on NCBI ↗
Downingia elegans NC_035360.1 132649 View on NCBI ↗