Markers + reference

Syringa

31 species · Oleaceae · Lamiales

Back to catalogue

Species 31
Genome length 155–161 kb
Candidate markers 272
Primer pairs 65

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 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 747 0.0607 0.96 71.7 yes View details
accD LSC 1893 0.0964 0.83 65.8 yes View details
ycf2 IRb 5898 0.0198 1.00 51.4 yes View details
ycf1 SSC 1896 0.1172 0.73 61.3 yes View details
ycf1 SSC 5403 0.0474 0.98 68.5 yes View details
ycf2 IRa 5898 0.0192 1.00 51.0 no View details
psbZ-trnG-GCC LSC 328 0.0336 0.99 69.7 yes View details
trnH-GUG-psbA LSC 431 0.0489 1.00 68.4 yes View details
ycf4 LSC 570 0.0558 1.00 63.7 yes View details
trnK-UUU-rps16 LSC 885 0.0183 1.00 62.3 yes View details
psaA-ycf3 LSC 726 0.0205 0.98 60.9 yes View details
rpl32-trnL-UAG SSC 860 0.0249 1.00 60.3 yes View details
clpP LSC 2031 0.0295 0.99 60.1 yes View details
trnI-CAU-ycf2 IRb 437 0.0377 1.00 60.0 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GAAGCTCCATCTACAAATGG 312–518 1.000 57.0
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GAAGCTCCATCTACAAATGG 313–519 1.000 56.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG GAAGCTCCATCTACAAATGG 305–511 1.000 55.4
trnH-GUG-psbA_p4 trnH-GUG-psbA GCCTTAATCCACTTGGCTACA GAAGCTCCATCTACAAATGG 310–516 1.000 52.0
trnH-GUG-psbA_p5 trnH-GUG-psbA TGCCTTAATCCACTTGGCTAC GAAGCTCCATCTACAAATGG 311–517 1.000 52.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATTCCTCGCTTCATCCA GGTGCTCAACCTACAGGAAC 1045–1062 1.000 85.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 997–1014 1.000 85.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 996–1013 1.000 85.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GGTGCTCAACCTACAGGAAC 1011–1028 1.000 84.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 1006–1023 1.000 84.2
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG AATCGAACCCGCATCTTCTC 478–512 1.000 89.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG GAATCGAACCCGCATCTTCT 479–513 1.000 89.7
psbZ-trnG-GCC_p3 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC AATCGAACCCGCATCTTCTC 476–510 1.000 89.3
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC GAATCGAACCCGCATCTTCT 477–511 1.000 89.3
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GGGTTAGTCTTTCTGGTGGG AATCGAACCCGCATCTTCTC 413–447 1.000 87.6
psaA-ycf3_p1 psaA-ycf3 CTTCTGGTTCCGGCGAAC GGAAACAGGCTATAGCGCTT 819–1572 1.000 71.0
psaA-ycf3_p2 psaA-ycf3 CTTCTGGTTCCGGCGAAC ATTGGTTGAAGATCACGGGG 771–1524 1.000 70.8
psaA-ycf3_p3 psaA-ycf3 CTTCTGGTTCCGGCGAAC TGGTTTGATCAAGCAGCTGA 844–1597 1.000 69.1
psaA-ycf3_p4 psaA-ycf3 CTTCTGGTTCCGGCGAAC AGGCTATAGCGCTTACTCCT 813–1566 1.000 69.1
psaA-ycf3_p5 psaA-ycf3 CTTCTGGTTCCGGCGAAC TTGGAAACAGGCTATAGCGC 821–1574 1.000 68.7
rbcL-accD_p1 rbcL-accD ACTACAGTTCGGTGGAGGAA ACGACCCCTCCAACTATGAA 1056–1420 1.000 91.5
rbcL-accD_p2 rbcL-accD TTGAATGCTACTGCGGGTAC ACGACCCCTCCAACTATGAA 1535–1899 1.000 91.4
rbcL-accD_p3 rbcL-accD TCTTCACATTCACCGTGCAA ACGACCCCTCCAACTATGAA 1383–1747 1.000 91.3
rbcL-accD_p4 rbcL-accD TTCTTCACATTCACCGTGCA ACGACCCCTCCAACTATGAA 1384–1748 1.000 91.3
rbcL-accD_p5 rbcL-accD GAGGCTAGCAAATGGAGTCC ACGACCCCTCCAACTATGAA 962–1008 0.774 78.2
accD_p1 accD CCCGGATTCCCACAAAAGAA GCCGGAAATACTAGGCCTAC 2397–2906 0.774 78.7
accD_p2 accD CCCGGATTCCCACAAAAGAA CGACCCAACAGGAAGGAATT 2320–2500 0.387 61.0
accD_p3 accD AGTGAAGTCTTACCCCGGAT CGACCCAACAGGAAGGAATT 2333–2513 0.387 59.6
accD_p4 accD TGAAAACTCGGCCCAATCTT CGACCCAACAGGAAGGAATT 2800–2977 0.387 58.7
accD_p5 accD TTGAAAACTCGGCCCAATCT CGACCCAACAGGAAGGAATT 2801–2978 0.387 58.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (31)

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

Species Accession Length (bp) Link
Syringa emodi PZ239408.1 156687 View on NCBI ↗
Syringa fauriei NC_082162.1 155421 View on NCBI ↗
Syringa josikaea PZ239407.1 157244 View on NCBI ↗
Syringa julianae OP514744.1 160278 View on NCBI ↗
Syringa komarowii PZ239424.1 157069 View on NCBI ↗
Syringa komarowii subsp. reflexa PZ239405.1 157164 View on NCBI ↗
Syringa laciniata PZ239406.1 155414 View on NCBI ↗
Syringa mairei MT656596.1 157315 View on NCBI ↗
Syringa oblata NC_057990.1 155569 View on NCBI ↗
Syringa oblata subsp. dilatata OP514742.1 155602 View on NCBI ↗
Syringa oblata var. alba ON920512.1 155648 View on NCBI ↗
Syringa patula var. kamibayashii OP514747.1 158021 View on NCBI ↗
Syringa patula var. venosa OP514748.1 158473 View on NCBI ↗
Syringa pinetorum OP531898.1 157131 View on NCBI ↗
Syringa pinnatifolia NC_041119.1 155326 View on NCBI ↗
Syringa protolaciniata OP514741.1 155501 View on NCBI ↗
Syringa pubescens OP514750.1 159034 View on NCBI ↗
Syringa pubescens subsp. microphylla PZ239423.1 160544 View on NCBI ↗
Syringa pubescens subsp. patula PZ239414.1 155641 View on NCBI ↗
Syringa pubescens var. potaninii OP514749.1 158988 View on NCBI ↗
Syringa reticulata subsp. amurensis PZ239409.1 156337 View on NCBI ↗
Syringa reticulata subsp. pekinensis OP514736.1 156131 View on NCBI ↗
Syringa sweginzowii PZ239416.1 157128 View on NCBI ↗
Syringa tigerstedtii PZ239415.1 157181 View on NCBI ↗
Syringa tomentella PZ239426.1 157130 View on NCBI ↗
Syringa tomentella subsp. yunnanensis NC_042468.1 156822 View on NCBI ↗
Syringa vulgaris NC_036987.1 155616 View on NCBI ↗
Syringa wolfii NC_049090.1 156517 View on NCBI ↗
Syringa wolfii var. hirsuta OP531905.1 156630 View on NCBI ↗
Syringa x chinensis PZ239410.1 155414 View on NCBI ↗
Syringa x chinensis f. saugeana OP514751.1 155414 View on NCBI ↗