Markers + reference

Adenophora

10 species · Campanulaceae · Asterales

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Species 10
Genome length 160–186 kb
Candidate markers 285
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbB-rpl20 Genome 3278 0.0797 0.99 74.3 yes View details
psbJ-ndhC Genome 2822 0.0639 0.98 77.4 yes View details
trnC-GCA-petN Genome 2092 0.0963 0.92 80.9 yes View details
psbJ-ycf3 Genome 2392 0.0932 0.99 81.5 yes View details
ycf3-rpoB Genome 1792 0.0868 0.47 65.5 yes View details
ndhB-trnI-CAU Genome 2397 0.0576 0.72 84.5 yes View details
ndhF-rpl32 Genome 1900 0.0787 0.99 79.8 yes View details
trnT-UGU-psbJ Genome 2926 0.0385 0.99 80.5 yes View details
rps12-ycf3 Genome 932 0.0502 0.89 77.9 yes View details
rpoA-petD Genome 1184 0.0438 0.99 73.2 yes View details
psbT-psbB Genome 228 0.0196 1.00 67.2 yes View details
trnV-GAC-psbJ Genome 733 0.0242 0.99 63.0 yes View details
petG-petL Genome 191 0.0200 0.93 61.0 yes View details
ndhE-ndhF Genome 106 0.0352 0.98 60.2 yes View details
ycf1 Genome 6540 0.0204 0.99 57.9 yes View details
ycf1 Genome 6540 0.0314 0.00 35.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoA-petD_p1 rpoA-petD AGTTCGGGATTTATTTACCGCA CCCATTTCGTCGTCCAGTAG 1334–1349 0.900 67.1
rpoA-petD_p2 rpoA-petD AGTTCGGGATTTATTTACCGCA TTGGTTGGGTATTGGTGCAA 1277–1292 0.900 67.1
rpoA-petD_p3 rpoA-petD AGTTCGGGATTTATTTACCGCA TTTGGTTGGGTATTGGTGCA 1278–1293 0.900 67.1
rpoA-petD_p4 rpoA-petD AGTTCGGGATTTATTTACCGCA CAGTAGCGACAACCGTCTTT 1320–1335 0.900 66.0
rpoA-petD_p5 rpoA-petD GTTCGGGATTTATTTACCGCA CCCATTTCGTCGTCCAGTAG 1333–1348 0.900 65.6
psbT-psbB_p1 psbT-psbB GAACTTTTGGCGGCTCTCTA GCTCAAGTCGAATTTGGAGC 360–383 1.000 82.1
psbT-psbB_p2 psbT-psbB GAACTTTTGGCGGCTCTCTA GGTGCTAGAACCCTCTTCAG 414–437 1.000 80.6
psbT-psbB_p3 psbT-psbB AACTTTTGGCGGCTCTCTAA GCTCAAGTCGAATTTGGAGC 359–382 1.000 78.4
psbT-psbB_p4 psbT-psbB ACTTTTGGCGGCTCTCTAAA GCTCAAGTCGAATTTGGAGC 358–381 1.000 78.4
psbT-psbB_p5 psbT-psbB ACTTTTGGCGGCTCTCTAAA GGTGCTAGAACCCTCTTCAG 412–435 1.000 76.8
psbB-rpl20_p1 psbB-rpl20 GTGAAATCGGTAGACACGCT TGCGTCGATTAAAAGCTCGA 1493–1495 0.200 56.4
psbB-rpl20_p2 psbB-rpl20 TGAAATCGGTAGACACGCTG TGCGTCGATTAAAAGCTCGA 1492–1494 0.200 56.4
psbB-rpl20_p3 psbB-rpl20 GTGAAATCGGTAGACACGCT CGACAGCGTCTTGATGAAGA 1317 0.100 43.8
psbB-rpl20_p4 psbB-rpl20 GTGAAATCGGTAGACACGCT CTCGACAGCGTCTTGATGAA 1319 0.100 43.8
psbB-rpl20_p5 psbB-rpl20 GTGAAATCGGTAGACACGCT TCGACAGCGTCTTGATGAAG 1318 0.100 43.8
petG-petL_p1 petG-petL TCAAAGGTCCAACTGATCGC TAGCTCCTTCATGCCTACGA 396–411 1.000 83.3
petG-petL_p2 petG-petL TCAAAGGTCCAACTGATCGC GGGTTTCTACTAGCGGCTTT 362–377 1.000 81.2
petG-petL_p3 petG-petL TCAAAGGTCCAACTGATCGC ATCGGGCTGAGCAAAATACG 320–335 1.000 79.3
petG-petL_p4 petG-petL TCAAAGGTCCAACTGATCGC AGCTCCTTCATGCCTACGAT 395–410 1.000 79.2
petG-petL_p5 petG-petL TCAAAGGTCCAACTGATCGC TTTCGGGTTTCTACTAGCGG 366–381 1.000 79.0
psbJ-ndhC_p1 psbJ-ndhC ATTCCGGATTGGGTTCATCC GGGGCTAATACTCCCGAAAG 1412–2946 0.300 56.7
psbJ-ndhC_p2 psbJ-ndhC ATTCCGGATTGGGTTCATCC GGGGGCTAATACTCCCGAAA 1413–2947 0.300 54.2
psbJ-ndhC_p3 psbJ-ndhC ATTCCGGATTGGGTTCATCC AATGGGGGCTAATACTCCCG 1416–2950 0.300 53.6
psbJ-ndhC_p4 psbJ-ndhC ATTCCGGATTGGGTTCATCC GGGGGCTAATACTCCCGAA 1413–2947 0.300 51.8
psbJ-ndhC_p5 psbJ-ndhC ATTCCGGATTGGGTTCATCC ATGGGGGCTAATACTCCCG 1415–2949 0.300 51.3
trnT-UGU-psbJ_p1 trnT-UGU-psbJ GATGGTCATCGGTTCGAGTC ATTCTGGATTGGGTTCATCC 900–2984 0.400 40.4
trnT-UGU-psbJ_p2 trnT-UGU-psbJ GATGGTCATCGGTTCGAGTC TCCTATTCTGGATTGGGTTCA 904–2988 0.400 40.2
trnT-UGU-psbJ_p3 trnT-UGU-psbJ GATGGTCATCGGTTCGAGTC AGTTCCTATTCTGGATTGGGT 907–2991 0.400 40.1
trnT-UGU-psbJ_p4 trnT-UGU-psbJ GATGGTCATCGGTTCGAGTC AGTTCCTATTCTGGATTGGGTTC 907–2991 0.400 39.1
trnT-UGU-psbJ_p5 trnT-UGU-psbJ GATGGTCATCGGTTCGAGTC GTTCCTATTCTGGATTGGGTTCA 906–2990 0.400 38.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Adenophora divaricata NC_036221.1 176331 View on NCBI ↗
Adenophora kayasanensis MZ365443.1 169433 View on NCBI ↗
Adenophora koreana PV339537.1 175721 View on NCBI ↗
Adenophora lamarckii PZ309718.1 169439 View on NCBI ↗
Adenophora maximowicziana PZ309719.1 182584 View on NCBI ↗
Adenophora nikoensis PZ309720.1 186376 View on NCBI ↗
Adenophora palustris PZ309721.1 178166 View on NCBI ↗
Adenophora polyantha PZ309722.1 173897 View on NCBI ↗
Adenophora racemosa MT012303.1 169344 View on NCBI ↗
Adenophora stricta NC_036223.1 159759 View on NCBI ↗