Markers + reference

Frangula

2 species · Rhamnaceae · Rosales

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Species 2
Genome length 161–161 kb
Candidate markers 268
Primer pairs 80

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 7 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 357 0.0000 1.00 34.9 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
rps16 LSC 1148 0.0009 1.00 59.3 yes View details
rps2 LSC 711 0.0000 1.00 36.7 yes View details
petA-psbJ LSC 1068 0.0000 1.00 40.0 yes View details
psbE-petL LSC 1383 0.0007 1.00 59.2 yes View details
ccsA SSC 966 0.0000 1.00 40.0 yes View details
ccsA-ndhD SSC 276 0.0036 1.00 54.6 yes View details
psaC SSC 246 0.0041 1.00 54.8 yes View details
rpl32-trnL-UAG SSC 1332 0.0000 1.00 59.2 yes View details
psbL LSC 117 0.0085 1.00 57.4 yes View details
rps2-rpoC2 LSC 203 0.0049 1.00 55.3 yes View details
matK LSC 1512 0.0000 1.00 40.0 yes View details
matK-trnK-UUU LSC 741 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 1033 0.0000 1.00 40.0 yes View details
trnS-GCU-trnG-UCC LSC 855 0.0000 1.00 40.0 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 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 GATCCACTTGGCTACATCCG CCGAGCTAACTTGGGTATGG 476 1.000 77.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGAGCTAACTTGGGTATGG 490 1.000 77.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGAGCTAACTTGGGTATGG 489 1.000 77.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGAGCTAACTTGGGTATGG 491 1.000 77.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACTTCCCTCTAGACCTAGCG 429 1.000 76.2
psbA_p1 psbA ACACTAATACCAAAGCGAAGTC TTATGTGCTTGGGAGTCCCT 1138 1.000 49.1
psbA_p2 psbA ACACTAATACCAAAGCGAAGTC TTTATGTGCTTGGGAGTCCC 1139 1.000 47.7
psbA_p3 psbA ACACTAATACCAAAGCGAAGT TTATGTGCTTGGGAGTCCCT 1138 1.000 47.4
psbA_p4 psbA ACACTAATACCAAAGCGAAGT TTTATGTGCTTGGGAGTCCC 1139 1.000 46.0
psbA_p5 psbA ACACTAATACCAAAGCGAAGTC ATTTATGTGCTTGGGAGTCCC 1140 1.000 43.6
matK_p1 matK CATTTCCGTAGTCGCACAAC AAACCCCGTTCAAGTCGAAT 1560 1.000 73.8
matK_p2 matK CATTTCCGTAGTCGCACAAC AACCCCGTTCAAGTCGAATT 1559 1.000 73.8
matK_p3 matK CATTTCCGTAGTCGCACAAC ACCCCGTTCAAGTCGAATTT 1558 1.000 73.8
matK_p4 matK ATTTCCGTAGTCGCACAACC AACCCCGTTCAAGTCGAATT 1558 1.000 73.4
matK_p5 matK ATTTCCGTAGTCGCACAACC ACCCCGTTCAAGTCGAATTT 1557 1.000 73.4
matK-trnK-UUU_p1 matK-trnK-UUU GAGGTCATGCTGCTGAGATC AACGGTAGAGTACTCGGCTT 819 1.000 77.6
matK-trnK-UUU_p2 matK-trnK-UUU GAGGTCATGCTGCTGAGATC ACGGTAGAGTACTCGGCTTT 818 1.000 77.6
matK-trnK-UUU_p3 matK-trnK-UUU ATAGGAGGTCATGCTGCTGA AACGGTAGAGTACTCGGCTT 823 1.000 77.0
matK-trnK-UUU_p4 matK-trnK-UUU ATAGGAGGTCATGCTGCTGA ACGGTAGAGTACTCGGCTTT 822 1.000 77.0
matK-trnK-UUU_p5 matK-trnK-UUU GAGGTCATGCTGCTGAGATC GGGTTGCTAACTCAACGGTA 832 1.000 75.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAAGCGGGGGT 1213 1.000 79.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAAGCGGGGGT 1212 1.000 79.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC TCCTGCAAAAAGGAGCTCAG 1254 1.000 78.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TCCTGCAAAAAGGAGCTCAG 1253 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAAGCGGGGGT 1129 1.000 78.6
rps16_p1 rps16 GCGGGGAATAGCAGAGAAAA CGGCCGAACCAATGACTATT 1324 1.000 77.1
rps16_p2 rps16 GCGGGGAATAGCAGAGAAAA TATTATGTACCGGCCGAACC 1334 1.000 73.2
rps16_p3 rps16 GCGGGGAATAGCAGAGAAAA GCCGAACCAATGACTATTCG 1322 1.000 71.6
rps16_p4 rps16 GCGGGGAATAGCAGAGAAAA TTATTATGTACCGGCCGAACC 1335 1.000 70.9
rps16_p5 rps16 GCGGGGAATAGCAGAGAAAA TATGTACCGGCCGAACCAAT 1331 1.000 70.4

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
Frangula alnus NC_068506.1 161255 View on NCBI ↗
Frangula alnus subsp. alnus PP336749.1 161268 View on NCBI ↗