Markers + reference

Plicosepalus

2 species · Loranthaceae · Santalales

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Species 2
Genome length 120–121 kb
Candidate markers 209
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 9 remaining regions by MarkerSeek score (out of 209 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-matK LSC 624 0.0883 0.91 84.1 yes View details
rpoB-trnC-GCA LSC 843 0.0988 0.72 75.0 yes View details
rpl16 LSC 798 0.1065 0.93 83.1 yes View details
ycf1 SSC 5019 0.0547 0.98 70.9 yes View details
ycf1-psaC SSC 415 0.1217 0.73 72.6 yes View details
ccsA SSC 942 0.0572 0.95 78.6 yes View details
ycf3-trnS-GGA LSC 670 0.0753 0.93 80.9 yes View details
trnS-GGA-rps4 LSC 147 0.0634 0.97 80.2 yes View details
trnY-GUA-trnE-UUC LSC 67 0.0781 0.96 79.1 yes View details
psbM-trnD-GUC LSC 624 0.0681 0.96 78.5 yes View details
atpB-rbcL LSC 766 0.0580 0.95 78.1 yes View details
matK-trnQ-UUG LSC 412 0.0663 0.95 77.0 yes View details
atpI-rps2 LSC 219 0.1121 0.98 76.9 yes View details
psaC-ccsA SSC 190 0.1694 0.96 76.7 yes View details
petN-psbM LSC 491 0.0457 0.85 76.2 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-matK_p1 psbA-matK GGCTTTCACTTTTGCGTCTC AGAAGGTCGTATTTGGTATTTGGA 685–722 1.000 56.9
psbA-matK_p2 psbA-matK CCACAGGCTTTCACTTTTGC AGAAGGTCGTATTTGGTATTTGGA 690–727 1.000 56.0
psbA-matK_p3 psbA-matK CAGGCTTTCACTTTTGCGTC AGAAGGTCGTATTTGGTATTTGGA 687–724 1.000 55.3
psbA-matK_p4 psbA-matK AGGCTTTCACTTTTGCGTCT AGAAGGTCGTATTTGGTATTTGGA 686–723 1.000 54.7
psbA-matK_p5 psbA-matK GGCTTTCACTTTTGCGTCTC GAGAAGGTCGTATTTGGTATTTGG 686–723 1.000 54.5
matK-trnQ-UUG_p1 matK-trnQ-UUG GCATCTTTCACCCAACAACG GGCGTAGTCAAGTGGTAAGG 994–1008 1.000 85.5
matK-trnQ-UUG_p2 matK-trnQ-UUG GCATCTTTCACCCAACAACG GGGCGTAGTCAAGTGGTAAG 995–1009 1.000 85.5
matK-trnQ-UUG_p3 matK-trnQ-UUG CCGAGTTCGCTCTAGGTCTA GGCGTAGTCAAGTGGTAAGG 523 0.500 59.6
matK-trnQ-UUG_p4 matK-trnQ-UUG CCGAGTTCGCTCTAGGTCTA GGGCGTAGTCAAGTGGTAAG 524 0.500 59.6
matK-trnQ-UUG_p5 matK-trnQ-UUG GTTTCCGAGTTCGCTCTAGG GGCGTAGTCAAGTGGTAAGG 527 0.500 59.2
atpI-rps2_p1 atpI-rps2 TGGTGGAACATAATAGAACATCCA CGCAATTTGTGAAGGTCGTT 287–349 1.000 49.5
atpI-rps2_p2 atpI-rps2 TGGTGGAACATAATAGAACATCCA TCGCAATTTGTGAAGGTCGT 288–350 1.000 49.4
atpI-rps2_p3 atpI-rps2 TGGTGGAACATAATAGAACATCCA TTCGCAATTTGTGAAGGTCG 289–351 1.000 47.3
atpI-rps2_p4 atpI-rps2 GGTGGAACATAATAGAACATCCA CGCAATTTGTGAAGGTCGTT 286–348 1.000 47.3
atpI-rps2_p5 atpI-rps2 TGGTGGAACATAATAGAACATCC CGCAATTTGTGAAGGTCGTT 287–349 1.000 47.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCATTTCCATCCCAGAGCAT CCGGATTTGAACTGGGGAAA 717–925 1.000 77.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCATTTCCATCCCAGAGCAT AACTGGGGAAAGGGGATTTG 708–916 1.000 75.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCAGAGCAT ATTTGAACTGGGGAAAGGGG 713–921 1.000 75.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCATTTCCATCCCAGAGCAT TGAACTGGGGAAAGGGGATT 710–918 1.000 74.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCATTTCCATCCCAGAGCAT TTGAACTGGGGAAAGGGGAT 711–919 1.000 74.1
petN-psbM_p1 petN-psbM ATCGCTTGGGCTGCTTTAAT ACGTAAAAACGGCTAGTCAA 562–604 1.000 63.6
petN-psbM_p2 petN-psbM ATCGCTTGGGCTGCTTTAAT TCCTTTACGTAAAAACGGCT 568–610 1.000 63.3
petN-psbM_p3 petN-psbM GTATCGCTTGGGCTGCTTTA ACGTAAAAACGGCTAGTCAA 564–606 1.000 62.7
petN-psbM_p4 petN-psbM GTATCGCTTGGGCTGCTTTA TCCTTTACGTAAAAACGGCT 570–612 1.000 62.4
petN-psbM_p5 petN-psbM TATCGCTTGGGCTGCTTTAA ACGTAAAAACGGCTAGTCAA 563–605 1.000 62.1
psbM-trnD-GUC_p1 psbM-trnD-GUC ATCGCTTGGGCTGCTTTAAT GAACCGATGACTTACGCCTT 1987–2536 1.000 85.3
psbM-trnD-GUC_p2 psbM-trnD-GUC ATCGCTTGGGCTGCTTTAAT CCATGGCGTTACTCTACCAC 1966–2515 1.000 84.9
psbM-trnD-GUC_p3 psbM-trnD-GUC ATCGCTTGGGCTGCTTTAAT TGGCGTTACTCTACCACTGA 1963–2512 1.000 84.7
psbM-trnD-GUC_p4 psbM-trnD-GUC GTATCGCTTGGGCTGCTTTA GAACCGATGACTTACGCCTT 1989–2538 1.000 84.4
psbM-trnD-GUC_p5 psbM-trnD-GUC ATCGCTTGGGCTGCTTTAAT CCGATGACTTACGCCTTACC 1984–2533 1.000 84.1

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
Plicosepalus acaciae NC_068660.1 120181 View on NCBI ↗
Plicosepalus curviflorus NC_068661.1 121086 View on NCBI ↗