Markers + reference

Olea

23 species · Oleaceae · Lamiales

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Species 23
Genome length 155–156 kb
Candidate markers 262
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 884 0.0141 1.00 55.8 yes View details
trnS(GCU)-trnG(GCC) LSC 707 0.0153 0.99 63.9 yes View details
psbM-trnD(GUC) LSC 647 0.0151 1.00 65.3 yes View details
atpB-rbcL LSC 785 0.0118 1.00 56.4 yes View details
ndhF SSC 2217 0.0077 1.00 48.6 yes View details
ndhF-rpl32 SSC 479 0.0170 0.99 55.6 yes View details
rpl32-trnL(UAG) SSC 859 0.0125 1.00 57.8 yes View details
rps15-trnN(GUU) SSC 6329 0.0089 1.00 48.5 yes View details
rpl2-psbA LSC 607 0.0216 1.00 71.9 no View details
psbI-trnS(GCU) LSC 126 0.0397 0.97 68.3 yes View details
ycf4-cemA LSC 873 0.0096 0.99 67.3 yes View details
ndhC-trnM(CAU) LSC 1947 0.0070 1.00 62.6 yes View details
rps2-rpoC2 LSC 208 0.0188 1.00 61.0 yes View details
psbE-petL LSC 1166 0.0079 1.00 59.4 yes View details
atpH-atpI LSC 1082 0.0089 0.99 59.3 yes View details
rps16-trnQ(UUG) LSC 1257 0.0093 0.99 57.2 yes View details
atpA-atpF LSC 62 0.0273 1.00 56.6 yes View details
ycf3-trnS(GGA) LSC 796 0.0046 0.99 56.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 CGAATTCCTCGCTTCATCCA AAAAGGGTATGTTGCTGCCA 1602–1713 1.000 86.5
trnK-rps16_p2 trnK-rps16 CGAATTCCTCGCTTCATCCA TCTATCCCAATGAGCCGTCT 1133–1229 1.000 86.2
trnK-rps16_p3 trnK-rps16 CGAATTCCTCGCTTCATCCA GCCGTACGAGGAGAAAACTT 1189–1285 1.000 86.1
trnK-rps16_p4 trnK-rps16 TTCCGTTCCACGAATTCGAA AAAAGGGTATGTTGCTGCCA 1751–1862 1.000 85.6
trnK-rps16_p5 trnK-rps16 CGAATTCCTCGCTTCATCCA CCCAGAACAAGGAAAGACCC 1587–1589 0.087 42.3
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) CGGATCTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1336–1759 1.000 82.1
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) ATCTGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1333–1756 1.000 82.1
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1322–1745 1.000 81.7
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) CCACAACGGATCTGTCCTTC GAGGTTCGAATCCTTCCGTC 1342–1765 1.000 80.6
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) GGATCTGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1335–1758 1.000 80.0
psbI-trnS(GCU)_p1 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 211–223 1.000 84.5
psbI-trnS(GCU)_p2 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 212–224 1.000 84.5
psbI-trnS(GCU)_p3 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 230–242 1.000 83.7
psbI-trnS(GCU)_p4 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 211–223 1.000 82.2
psbI-trnS(GCU)_p5 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 212–224 1.000 82.1
trnS(GCU)-trnG(GCC)_p1 trnS(GCU)-trnG(GCC) CAATCCGACGCTTTAGTCCA AGACCGAAAGACCCTTTAACT 798–831 1.000 68.3
trnS(GCU)-trnG(GCC)_p2 trnS(GCU)-trnG(GCC) AATCCGACGCTTTAGTCCAC AGACCGAAAGACCCTTTAACT 797–830 1.000 68.3
trnS(GCU)-trnG(GCC)_p3 trnS(GCU)-trnG(GCC) ATCAACGGAACCGGAAAGAG AGACCGAAAGACCCTTTAACT 862–895 1.000 67.0
trnS(GCU)-trnG(GCC)_p4 trnS(GCU)-trnG(GCC) CATCAACGGAACCGGAAAGA AGACCGAAAGACCCTTTAACT 863–896 1.000 66.2
trnS(GCU)-trnG(GCC)_p5 trnS(GCU)-trnG(GCC) TCATCAACGGAACCGGAAAG AGACCGAAAGACCCTTTAACT 864–897 1.000 66.2
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG TGTTGGGAGCGATGAAAGAA 210–229 1.000 77.4
atpA-atpF_p2 atpA-atpF ATGCCATCGCCTACTTGAAG ATGTTGGGAGCGATGAAAGA 211–230 1.000 75.6
atpA-atpF_p3 atpA-atpF ATGCCATCGCCTACTTGAAG CATGTTGGGAGCGATGAAAG 212–231 1.000 75.2
atpA-atpF_p4 atpA-atpF CAATGCCATCGCCTACTTGA TGTTGGGAGCGATGAAAGAA 212–231 1.000 75.1
atpA-atpF_p5 atpA-atpF ATGCCATCGCCTACTTGAAG ATATTGGCATGTTGGGAGCG 219–228 0.957 74.0
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1203–1216 1.000 80.5
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TCCCTGTCATGTTCCTTGGA 1288–1301 1.000 80.0
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TCCCTGTCATGTTCCTTGGA 1292–1305 1.000 80.0
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TCCCTGTCATGTTCCTTGGA 1213–1226 1.000 79.9
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1220–1233 1.000 79.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Olea brachiata MT560006.1 155109 View on NCBI ↗
Olea caudatilimba MT560027.1 155568 View on NCBI ↗
Olea dioica NC_086554.1 155138 View on NCBI ↗
Olea europaea NC_013707.2 155888 View on NCBI ↗
Olea europaea subsp. cuspidata NC_015604.1 155862 View on NCBI ↗
Olea europaea subsp. europaea NC_015401.1 155875 View on NCBI ↗
Olea europaea subsp. guanchica MT560020.1 155899 View on NCBI ↗
Olea europaea subsp. maroccana NC_015623.1 155896 View on NCBI ↗
Olea exasperata NC_036985.1 155897 View on NCBI ↗
Olea guangxiensis MT560009.1 155149 View on NCBI ↗
Olea hainanensis MT560010.1 155236 View on NCBI ↗
Olea lancea NC_042278.1 155863 View on NCBI ↗
Olea laxiflora MT560011.1 155340 View on NCBI ↗
Olea neriifolia MT560012.1 155248 View on NCBI ↗
Olea paniculata NC_042460.1 155720 View on NCBI ↗
Olea parvilimba MT560013.1 155121 View on NCBI ↗
Olea perrieri NC_042375.1 155912 View on NCBI ↗
Olea rosea MT560014.1 155226 View on NCBI ↗
Olea salicifolia MT560016.1 154997 View on NCBI ↗
Olea tetragonoclada MT560018.1 155246 View on NCBI ↗
Olea tsoongii NC_042461.1 155237 View on NCBI ↗
Olea woodiana subsp. woodiana NC_015608.1 155942 View on NCBI ↗
Olea yuennanensis NC_086553.1 155193 View on NCBI ↗