Markers + reference

Phacellaria

3 species · Amphorogynaceae · Santalales

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Species 3
Genome length 138–139 kb
Candidate markers 244
Primer pairs 80

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 244 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0031 1.00 37.6 yes View details
rps16-trnQ(UUG) LSC 1794 0.0227 0.99 68.6 yes View details
psbM-trnD(GUC) LSC 726 0.0391 1.00 78.7 yes View details
trnD(GUC)-trnY(GUA) LSC 347 0.0793 0.90 82.9 yes View details
rpl32-trnL(UAG) SSC 567 0.0282 1.00 66.5 yes View details
ccsA-psaC SSC 1313 0.0173 1.00 64.5 yes View details
psaC-rps15 SSC 967 0.0368 0.99 73.3 yes View details
trnH(GUG) LSC 70 0.1244 0.96 76.9 no View details
psaA-ycf3 LSC 667 0.0126 0.99 67.2 yes View details
trnT(GGU)-psbD LSC 1175 0.0098 0.99 66.4 yes View details
matK-trnK(UUU) LSC 707 0.0241 1.00 65.9 yes View details
trnF(GAA)-tRNA-Met(CAU) LSC 1025 0.0135 0.99 64.1 yes View details
psbE-petL LSC 1263 0.0111 1.00 64.1 yes View details
rrn4.5-rrn5 IRb 208 0.0128 1.00 61.7 yes View details
rrn5-rrn4.5 IRa 208 0.0128 1.00 61.7 yes View details
trnT(UGU)-trnL(UAA) LSC 521 0.0090 1.00 60.8 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
psbA_p1 psbA ACTTTCAATAACTGGTAAACACT ATAGAGACTGCGTGTGCTTG 1161 1.000 40.3
psbA_p2 psbA ACACTACTACTAAATAAGACGGA ATAGAGACTGCGTGTGCTTG 1143 1.000 40.3
psbA_p3 psbA ACACTACTACTAAATAAGACGGAAG ATAGAGACTGCGTGTGCTTG 1143 1.000 40.3
psbA_p4 psbA AACACTACTACTAAATAAGACGGA ATAGAGACTGCGTGTGCTTG 1144 1.000 40.3
psbA_p5 psbA ACACTACTACTAAATAAGACGGAA ATAGAGACTGCGTGTGCTTG 1143 1.000 40.3
trnK(UUU)_p1 trnK(UUU) AATGGCTTGTGAATGACGGA AGAGTTCTTGCTAGTTCATGT 2706–2785 1.000 46.6
trnK(UUU)_p2 trnK(UUU) ATGGCTTGTGAATGACGGAA AGAGTTCTTGCTAGTTCATGT 2705–2784 1.000 46.6
trnK(UUU)_p3 trnK(UUU) AATGGCTTGTGAATGACGGA AGTAGAGTTCTTGCTAGTTCATGT 2709–2788 1.000 45.1
trnK(UUU)_p4 trnK(UUU) ATGGCTTGTGAATGACGGAA AGTAGAGTTCTTGCTAGTTCATGT 2708–2787 1.000 45.1
trnK(UUU)_p5 trnK(UUU) ATGGCTTGTGAATGACGGAA AGAGTTCTTGCTAGTTCATGTT 2705–2784 1.000 45.0
matK-trnK(UUU)_p1 matK-trnK(UUU) TGTTGCCGATATCTATCTCGT AACGGTAGAGTACTCGGCTT 775–778 0.667 46.7
matK-trnK(UUU)_p2 matK-trnK(UUU) TGTTGCCGATATCTATCTCGT ACGGTAGAGTACTCGGCTTT 774–777 0.667 46.7
matK-trnK(UUU)_p3 matK-trnK(UUU) TGTTGCCGATATCTATCTCGTT AACGGTAGAGTACTCGGCTT 775–778 0.667 44.4
matK-trnK(UUU)_p4 matK-trnK(UUU) TGTTGCCGATATCTATCTCGTT ACGGTAGAGTACTCGGCTTT 774–777 0.667 44.4
matK-trnK(UUU)_p5 matK-trnK(UUU) TGTTGCCGATATCTATCTCGT GGGTTGCTAACTCAACGGTA 788–791 0.667 44.3
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1832–1867 1.000 84.3
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) TGTCCTTCATTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1844–1879 1.000 81.0
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) TCCTTCATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1842–1877 1.000 80.8
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) TTCATTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1839–1874 1.000 80.1
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1836–1871 1.000 79.5
psbM-trnD(GUC)_p1 psbM-trnD(GUC) AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 798–841 1.000 65.4
psbM-trnD(GUC)_p2 psbM-trnD(GUC) TGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 805–848 1.000 64.4
psbM-trnD(GUC)_p3 psbM-trnD(GUC) AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 799–842 1.000 61.2
psbM-trnD(GUC)_p4 psbM-trnD(GUC) TGGAACTAGAATGAACAGTGCA GTTCAATTGGTCAGAGCACC 806–849 1.000 60.2
psbM-trnD(GUC)_p5 psbM-trnD(GUC) GGAACTAGAATGAACAGTGCAG TTCAATTGGTCAGAGCACCG 804–847 1.000 59.7
trnD(GUC)-trnY(GUA)_p1 trnD(GUC)-trnY(GUA) ATGATTGGATTCGTCGGGAC GCAATACGTCTACGCTGGTT 420–473 1.000 85.0
trnD(GUC)-trnY(GUA)_p2 trnD(GUC)-trnY(GUA) ATGATTGGATTCGTCGGGAC GTTGGCAATACGTCTACGCT 424–477 1.000 84.9
trnD(GUC)-trnY(GUA)_p3 trnD(GUC)-trnY(GUA) ATGATTGGATTCGTCGGGAC TTGGCAATACGTCTACGCTG 423–476 1.000 84.9
trnD(GUC)-trnY(GUA)_p4 trnD(GUC)-trnY(GUA) ATGATTGGATTCGTCGGGAC GGGGACGGACTGTAAATTCG 443–496 1.000 84.8
trnD(GUC)-trnY(GUA)_p5 trnD(GUC)-trnY(GUA) ATGATTGGATTCGTCGGGAC GGGACGGACTGTAAATTCGT 442–495 1.000 84.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Phacellaria compressa NC_047407.1 138903 View on NCBI ↗
Phacellaria glomerata NC_047408.1 138684 View on NCBI ↗
Phacellaria rigidula NC_077597.1 138492 View on NCBI ↗