Markers + reference

Pseudocodon

2 species · Campanulaceae · Asterales

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Species 2
Genome length 184–188 kb
Candidate markers 271
Primer pairs 80

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 11 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-petN LSC 2982 0.0007 0.98 57.5 yes View details
trnfM-CAU-rpl32 LSC 1354 0.0017 0.86 62.1 yes View details
rpoC2-rps2 LSC 249 0.0120 1.00 59.4 yes View details
atpI-atpH LSC 2272 0.0022 1.00 58.4 yes View details
ycf4 LSC 642 0.0016 1.00 59.6 yes View details
ndhF-trnL-UAG SSC 4271 0.0021 0.55 49.1 yes View details
ndhJ-petD LSC 614 0.0016 1.00 59.7 yes View details
petA-psbJ LSC 1034 0.0000 0.99 59.4 yes View details
trnM-CAU-trnfM-CAU LSC 1281 0.0008 1.00 59.2 yes View details
clpP-trnL-UAA LSC 2569 0.0004 1.00 56.7 yes View details
psaC SSC 246 0.0041 1.00 54.8 yes View details
rps14 LSC 303 0.0033 1.00 54.5 yes View details
rpl16-rps3 LSC 176 0.0000 0.99 53.1 yes View details
trnH-GUG-psbA LSC 360 0.0000 0.66 50.4 yes View details
psbA LSC 1080 NA 0.00 46.2 yes View details
psbA-trnQ-UUG LSC 1244 NA 0.00 46.2 yes View details
rps14 LSC 303 0.0000 1.00 33.8 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TCACAATCCACTGCCTTGTC TAACCGGGCTAACCTTGGTA 497 1.000 82.8
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTGTC TTCCCTCTAGACCTAGCTGC 445 1.000 82.6
trnH-GUG-psbA_p3 trnH-GUG-psbA TTCACAATCCACTGCCTTGT TAACCGGGCTAACCTTGGTA 498 1.000 80.7
trnH-GUG-psbA_p4 trnH-GUG-psbA TTCACAATCCACTGCCTTGT TTCCCTCTAGACCTAGCTGC 446 1.000 80.5
trnH-GUG-psbA_p5 trnH-GUG-psbA TCACAATCCACTGCCTTGTC ATTAACCGGGCTAACCTTGG 499 1.000 79.7
psbA_p1 psbA TCACAATCCACTGCCTTGTC TTCGGTAGAGTCAAGTGGGT 1668 0.500 59.1
psbA_p2 psbA TCCGCCCCTCTACTATGTTT TTCGGTAGAGTCAAGTGGGT 1636 0.500 58.6
psbA_p3 psbA TCACAATCCACTGCCTTGTC CCGCGAAAGTCTGCTAGAAT 1648 0.500 58.6
psbA_p4 psbA TCACAATCCACTGCCTTGTC AAGCACGAAAGCGAAGATCT 1943 0.500 58.5
psbA_p5 psbA TCACAATCCACTGCCTTGTC AGCACGAAAGCGAAGATCTT 1942 0.500 58.5
psbA-trnQ-UUG_p1 psbA-trnQ-UUG CGGTTTTCAGGGCTGGTTAT TTGAACCCGGCATATCGAAG 1383 0.500 58.3
psbA-trnQ-UUG_p2 psbA-trnQ-UUG ACCATCCAATGTAAAGGCGG TTGAACCCGGCATATCGAAG 1400 0.500 57.7
psbA-trnQ-UUG_p3 psbA-trnQ-UUG CCATCCAATGTAAAGGCGGT TTGAACCCGGCATATCGAAG 1399 0.500 57.7
psbA-trnQ-UUG_p4 psbA-trnQ-UUG AAGCGACCCCATAAGCTTTC TTGAACCCGGCATATCGAAG 1353 0.500 57.6
psbA-trnQ-UUG_p5 psbA-trnQ-UUG CGGTTTTCAGGGCTGGTTAT CCTGTTGCTACAAACGCATC 1447 0.500 56.7
trnQ-UUG-petN_p1 trnQ-UUG-petN GCTGGTATCACATCTCCGTC CATTGGTCGAAGAGGCTCAG 280 1.000 76.4
trnQ-UUG-petN_p2 trnQ-UUG-petN GTCCGCTGGTATCACATCTC CATTGGTCGAAGAGGCTCAG 284 1.000 76.3
trnQ-UUG-petN_p3 trnQ-UUG-petN GGAGATTGTCCGCTGGTATC CATTGGTCGAAGAGGCTCAG 291 1.000 76.2
trnQ-UUG-petN_p4 trnQ-UUG-petN GCTGGTATCACATCTCCGTC ATTGGTCGAAGAGGCTCAGA 279 1.000 75.6
trnQ-UUG-petN_p5 trnQ-UUG-petN GTCCGCTGGTATCACATCTC ATTGGTCGAAGAGGCTCAGA 283 1.000 75.6
trnfM-CAU-rpl32_p1 trnfM-CAU-rpl32 TCATCGGTTCAAATCCGGTC ATGCCAAAGCTTTTAACGCC 1296–1481 1.000 83.3
trnfM-CAU-rpl32_p2 trnfM-CAU-rpl32 CATCGGTTCAAATCCGGTCT ATGCCAAAGCTTTTAACGCC 1295–1480 1.000 83.3
trnfM-CAU-rpl32_p3 trnfM-CAU-rpl32 TCATCGGTTCAAATCCGGTC AGCCCTTCCCTTTCCAAATC 1269–1454 1.000 82.1
trnfM-CAU-rpl32_p4 trnfM-CAU-rpl32 TCATCGGTTCAAATCCGGTC GAGCCCTTCCCTTTCCAAAT 1270–1455 1.000 82.1
trnfM-CAU-rpl32_p5 trnfM-CAU-rpl32 TCATCGGTTCAAATCCGGTC GCCCTTCCCTTTCCAAATCT 1268–1453 1.000 82.1
rpoC2-rps2_p1 rpoC2-rps2 TCTTCGAGGGGGAAATGAGA AGGTGCCATTTTCGGATTCC 467 1.000 74.3
rpoC2-rps2_p2 rpoC2-rps2 TTCGAGGGGGAAATGAGAGA AGGTGCCATTTTCGGATTCC 465 1.000 74.3
rpoC2-rps2_p3 rpoC2-rps2 TCTTCGAGGGGGAAATGAGA CATGGCCAAAATGAACTCCC 435 1.000 73.1
rpoC2-rps2_p4 rpoC2-rps2 TTCGAGGGGGAAATGAGAGA CATGGCCAAAATGAACTCCC 433 1.000 73.1
rpoC2-rps2_p5 rpoC2-rps2 TCGAGGGGGAAATGAGAGAT AGGTGCCATTTTCGGATTCC 464 1.000 72.5

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
Pseudocodon convolvulaceus NC_060685.1 183616 View on NCBI ↗
Pseudocodon vinciflorus MW336936.1 187634 View on NCBI ↗