Markers + reference

Pittosporum

15 species · Pittosporaceae · Apiales

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Species 15
Genome length 153–154 kb
Candidate markers 258
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 820 0.0046 1.00 61.6 yes View details
rps16-trnQ-UUG LSC 909 0.0035 1.00 51.1 yes View details
trnS-GCU-trnT-CGU LSC 761 0.0040 1.00 53.8 yes View details
trnT-UGU-trnL-UAA LSC 747 0.0100 1.00 55.3 yes View details
ndhC-trnV-UAC LSC 1143 0.0041 0.99 58.4 yes View details
rps18 LSC 306 0.0009 1.00 27.2 yes View details
petB-petD LSC 883 0.0036 1.00 46.7 yes View details
ndhF-trnL-UAG SSC 2203 0.0027 1.00 57.8 yes View details
ndhD SSC 1512 0.0008 1.00 35.5 yes View details
ycf1 SSC 5670 0.0015 1.00 43.1 yes View details
psbE-petL LSC 1196 0.0035 0.99 62.3 yes View details
trnE-UUC-trnT-CGU LSC 718 0.0033 1.00 61.8 yes View details
rpl33-rps18 LSC 173 0.0139 1.00 58.9 yes View details
trnT-CGU-psbD LSC 1393 0.0019 1.00 57.6 yes View details
accD-psaI LSC 708 0.0034 1.00 56.7 yes View details
ndhD-psaC SSC 122 0.0194 1.00 56.2 yes View details
petA-psbJ LSC 1029 0.0026 1.00 56.0 yes View details
petD-rps11 LSC 1258 0.0017 1.00 55.1 yes View details
rpoC1 LSC 2880 0.0011 1.00 55.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ACTCCCAAGCACACGAATTT ACGGTTTGATTGCCTTGTCT 2846–2854 1.000 80.7
trnK-UUU_p2 trnK-UUU CGATTCTCGGTGCTGGTTAT ACGGTTTGATTGCCTTGTCT 2957–2965 1.000 79.0
trnK-UUU_p3 trnK-UUU GTACAGACGATTCTCGGTGC ACGGTTTGATTGCCTTGTCT 2964–2972 1.000 77.2
trnK-UUU_p4 trnK-UUU GACTCCCAAGCACACGAATT ACGGTTTGATTGCCTTGTCT 2847–2855 1.000 77.1
trnK-UUU_p5 trnK-UUU ACTCCCAAGCACACGAATTT CAACGGTTTGATTGCCTTGT 2848–2856 1.000 76.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCTTCGCTTCATCCA TCCTTGAAAAAGGGGCTCAG 970–979 1.000 79.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCCTTGAAAAAGGGGCTCAG 922–931 1.000 78.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCCTTGAAAAAGGGGCTCAG 921–930 1.000 78.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TCCTTGAAAAAGGGGCTCAG 1007–1016 1.000 77.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TCCTTGAAAAAGGGGCTCAG 1006–1015 1.000 77.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 982–1256 1.000 79.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CATCGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1000–1274 1.000 78.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 997–1271 1.000 77.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 996–1270 1.000 77.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACATCGGATCGTGTCCTTC GAGGTTCGAATCCTTCCGTC 1002–1276 1.000 76.8
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCACT 817–855 1.000 73.8
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCAC 817–855 1.000 73.8
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 866–904 1.000 72.7
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCAC 866–904 1.000 72.6
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU ATTAGCAATCCGCCGCTTTA AACGAATCGCACTTTTACCAC 818–856 1.000 71.5
rpoC1_p1 rpoC1 TCCGGAATTCTCGTCCTAGT ACGATCTTTGGCTCTGGAAC 2984–2998 1.000 76.5
rpoC1_p2 rpoC1 TCCGGAATTCTCGTCCTAGT CGATCTTTGGCTCTGGAACT 2983–2997 1.000 74.1
rpoC1_p3 rpoC1 CGTCCTAGTTGAACCGGAGA ACGATCTTTGGCTCTGGAAC 2973–2987 1.000 73.3
rpoC1_p4 rpoC1 CTCGTCCTAGTTGAACCGGA ACGATCTTTGGCTCTGGAAC 2975–2989 1.000 73.3
rpoC1_p5 rpoC1 TCGTCCTAGTTGAACCGGAG ACGATCTTTGGCTCTGGAAC 2974–2988 1.000 73.3
trnE-UUC-trnT-CGU_p1 trnE-UUC-trnT-CGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 813–833 1.000 83.7
trnE-UUC-trnT-CGU_p2 trnE-UUC-trnT-CGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 850–870 1.000 83.6
trnE-UUC-trnT-CGU_p3 trnE-UUC-trnT-CGU TTTCGTAGTACCCTACCCCC GGCGTTACTCTACCGTTGAG 825–845 1.000 82.9
trnE-UUC-trnT-CGU_p4 trnE-UUC-trnT-CGU CGTTGCCTCCTTGAAAGAGA GGCGTTACTCTACCGTTGAG 788–808 1.000 82.9
trnE-UUC-trnT-CGU_p5 trnE-UUC-trnT-CGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 791–811 1.000 82.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Pittosporum brevicalyx NC_058267.1 153388 View on NCBI ↗
Pittosporum crispulum NC_068008.1 153667 View on NCBI ↗
Pittosporum daphniphylloides var. adaphniphylloides ON254202.1 153721 View on NCBI ↗
Pittosporum illicioides PP506677.1 153610 View on NCBI ↗
Pittosporum kerrii NC_046847.1 153581 View on NCBI ↗
Pittosporum kunmingense NC_068009.1 153538 View on NCBI ↗
Pittosporum merrillianum NC_068010.1 153629 View on NCBI ↗
Pittosporum napaulense NC_068011.1 153612 View on NCBI ↗
Pittosporum paniculiferum NC_068012.1 153477 View on NCBI ↗
Pittosporum parvicapsulare NC_068013.1 153727 View on NCBI ↗
Pittosporum perryanum NC_068014.1 153636 View on NCBI ↗
Pittosporum serpentinum NC_084331.1 153292 View on NCBI ↗
Pittosporum tobira NC_057165.1 153754 View on NCBI ↗
Pittosporum trigonocarpum NC_068015.1 153639 View on NCBI ↗
Pittosporum truncatum NC_068016.1 153722 View on NCBI ↗