Markers + reference

Fontanesia

2 species · Oleaceae · Lamiales

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Species 2
Genome length 156–156 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 450 0.0671 0.96 75.7 yes View details
psbM-trnD-GUC LSC 1051 0.0115 1.00 59.1 yes View details
trnF-GAA-ndhJ LSC 654 0.0154 0.99 68.2 yes View details
ycf4-cemA LSC 879 0.0203 0.84 66.2 yes View details
psbE-petL LSC 1155 0.0156 1.00 59.9 yes View details
psaJ-rpl33 LSC 447 0.0135 1.00 52.7 yes View details
petB LSC 1347 0.0089 1.00 50.0 yes View details
petD LSC 1201 0.0067 1.00 49.7 yes View details
ycf1 IRb 1030 0.0000 1.00 25.1 no View details
ndhF SSC 2217 0.0104 1.00 49.0 yes View details
rpl32-trnL-UAG SSC 840 0.0179 1.00 64.3 yes View details
ycf1 SSC 5571 0.0101 0.99 51.5 yes View details
atpA-atpF LSC 60 0.0508 0.98 82.9 yes View details
ycf1-ndhF SSC 31 0.0968 1.00 80.3 yes View details
trnL-UAG-ccsA SSC 90 0.0333 1.00 69.6 yes View details
trnG-UCC-trnR-UCU LSC 164 0.0305 1.00 65.5 yes View details
rpl33-rps18 LSC 169 0.0244 0.97 65.1 yes View details
trnK-UUU-rps16 LSC 888 0.0102 1.00 65.0 yes View details
trnE-UUC-trnT-GGU LSC 806 0.0075 0.99 63.9 yes View details
rpl16-rps3 LSC 151 0.0199 1.00 63.9 yes View details
ndhF-rpl32 SSC 497 0.0063 0.95 63.8 yes View details
atpH-atpI LSC 1113 0.0081 1.00 63.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TTAGTTATGGGCGAACGACG GAGCTTAGTTTCCGTCTGGG 1202–1206 1.000 82.9
trnH-GUG-psbA_p2 trnH-GUG-psbA TTAGTTATGGGCGAACGACG GAGTGGGAGCTTAGTTTCCG 1208–1212 1.000 82.9
trnH-GUG-psbA_p3 trnH-GUG-psbA TTAGTTATGGGCGAACGACG GGAGCTTAGTTTCCGTCTGG 1203–1207 1.000 82.9
trnH-GUG-psbA_p4 trnH-GUG-psbA TTAGTTATGGGCGAACGACG GGGAGCTTAGTTTCCGTCTG 1204–1208 1.000 82.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GAGCTTAGTTTCCGTCTGGG 1147–1151 1.000 82.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATTCCTCGCTTCATCCA GGTGCTCAACCTACAGGAAC 1060–1082 1.000 79.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1012–1034 1.000 78.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1011–1033 1.000 78.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GGTGCTCAACCTACAGGAAC 1026–1048 1.000 77.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 1021–1043 1.000 77.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 244 1.000 65.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 247 1.000 64.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 250 1.000 64.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 253 1.000 64.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 248 1.000 62.5
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG TTGGGGGCGATGAAAGAAAT 205–206 1.000 79.4
atpA-atpF_p2 atpA-atpF ATGCCATCGCCTACTTGAAG ATATTGACATGTTGGGGGCG 216–217 1.000 78.7
atpA-atpF_p3 atpA-atpF CAATGCCATCGCCTACTTGA TTGGGGGCGATGAAAGAAAT 207–208 1.000 77.0
atpA-atpF_p4 atpA-atpF AATGCCATCGCCTACTTGAA TTGGGGGCGATGAAAGAAAT 206–207 1.000 76.4
atpA-atpF_p5 atpA-atpF CAATGCCATCGCCTACTTGA ATATTGACATGTTGGGGGCG 218–219 1.000 76.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 1248–1249 1.000 78.3
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TCCCTGTCATGTTCCTTGGA 1331–1332 1.000 77.4
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TCCCTGTCATGTTCCTTGGA 1335–1336 1.000 77.4
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TCCCTGTCATGTTCCTTGGA 1249–1250 1.000 77.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1263–1264 1.000 76.8
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 1183–1192 1.000 56.4
psbM-trnD-GUC_p2 psbM-trnD-GUC AGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1175–1184 1.000 56.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1176–1185 1.000 54.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AGCGGTAGGAACTAGAATGAA TTCAATTGGTCAGAGCACCG 1175–1184 1.000 54.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 1184–1193 1.000 54.2

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
Fontanesia philliraeoides MT948191.1 155898 View on NCBI ↗
Fontanesia philliraeoides subsp. fortunei MG255754.1 155992 View on NCBI ↗