Markers + reference

Quercus

115 species · Fagaceae · Fagales

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Species 115
Genome length 160–162 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 441 0.0314 0.99 67.6 yes View details
trnK-UUU-rps16 LSC 1085 0.0159 0.96 63.5 yes View details
rps16-trnQ-UUG LSC 1602 0.0072 0.94 57.7 yes View details
trnS-GCU-trnG-GCC LSC 973 0.0119 0.92 56.0 yes View details
trnT-GGU-psbD LSC 1635 0.0079 0.99 58.8 yes View details
trnF-GAA-ndhJ LSC 855 0.0102 1.00 62.7 yes View details
rbcL-accD LSC 595 0.0219 0.99 54.0 yes View details
psbE-petL LSC 1343 0.0077 0.99 67.2 yes View details
ycf1 IRb 1074 0.0091 0.98 44.8 no View details
ndhF SSC 2280 0.0078 0.99 48.5 yes View details
ndhF-rpl32 SSC 958 0.0111 0.98 62.7 yes View details
ycf1 SSC 4608 0.0078 1.00 48.7 yes View details
petA-psbJ LSC 1022 0.0096 1.00 69.0 yes View details
ycf4-cemA LSC 631 0.0069 0.99 64.3 yes View details
rpoB-trnC-GCA LSC 1268 0.0076 0.98 62.0 yes View details
ccsA-ndhD SSC 322 0.0082 0.99 61.5 yes View details
psaJ-rpl33 LSC 494 0.0076 1.00 60.7 yes View details
ndhC-trnV-UAC LSC 467 0.0072 0.97 60.3 yes View details
atpF LSC 1334 0.0039 1.00 58.0 yes View details
atpH-atpI LSC 1187 0.0062 0.99 58.0 yes View details
trnM-CAU-atpE LSC 200 0.0167 1.00 57.3 yes View details
psaA-ycf3 LSC 744 0.0032 1.00 57.1 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 GATCCACTTGGCTACATCCG CGTGCTAACCTTGGTATGGA 505–589 1.000 85.5
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 506–590 1.000 85.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCTAACCTTGGTATGGA 519–603 1.000 85.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGTGCTAACCTTGGTATGG 520–604 1.000 85.5
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCTAACCTTGGTATGGA 518–602 1.000 85.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAGACTGATCGACGGACTCT TGTATCGCGCAGGAATCAAA 2251–2520 1.000 89.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGACTGATCGACGGACTCTT TGTATCGCGCAGGAATCAAA 2250–2519 1.000 89.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCCCACACTCTAATGGAGA TGTATCGCGCAGGAATCAAA 2075–2343 1.000 89.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGTTTTGAACCGATCCGCT TGTATCGCGCAGGAATCAAA 1817–2083 0.991 88.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 GATCGACGGACTCTTTAGCC TGTATCGCGCAGGAATCAAA 2245–2514 0.870 83.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GACCATATCCCTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1493–1732 1.000 88.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 1475–1714 1.000 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCATATCCCTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1491–1730 0.965 87.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 1479–1718 1.000 86.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGACCATATCCCTCAAGTCG GAGGTTCGAATCCTTCCGTC 1494–1733 1.000 86.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 952–1067 1.000 81.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 951–1066 1.000 81.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 952–1067 1.000 81.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 951–1066 1.000 81.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TAGTCCACTCAGCCATCTCC ACGAATCGCACTTTTACCACT 939–1054 1.000 79.4
atpF_p1 atpF CACCCGCCATTACTTCATCA GCCAAGCTGTAGAAGGGATC 2064–2167 1.000 87.0
atpF_p2 atpF CACCCGCCATTACTTCATCA ATTTCTGCCGCTTCCGTTAT 2149–2252 1.000 86.9
atpF_p3 atpF CACCCGCCATTACTTCATCA ACACTAACCCATGGGAAGGA 1826–1918 0.991 86.6
atpF_p4 atpF CACCCGCCATTACTTCATCA CCATGGGAAGGACTGATTGG 1818–1910 0.991 86.4
atpF_p5 atpF CACCCGCCATTACTTCATCA CCCATGGGAAGGACTGATTG 1819–1911 0.991 86.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1206–1293 1.000 86.4
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC TTTTGCAACTTTAGCTGCGG 1291–1378 1.000 86.2
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1176–1263 1.000 86.1
atpH-atpI_p4 atpH-atpI GATCCCTTCTACAGCTTGGC CGAATCCATGGAGGGTCATC 1261–1348 1.000 85.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1207–1294 1.000 85.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (115)

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

Species Accession Length (bp) Link
Quercus acrodonta NC_059815.1 161105 View on NCBI ↗
Quercus acuta NC_054352.1 160533 View on NCBI ↗
Quercus acutissima NC_039429.1 161127 View on NCBI ↗
Quercus agrifolia var. agrifolia OK634019.1 161283 View on NCBI ↗
Quercus aliena NC_026790.1 160921 View on NCBI ↗
Quercus aliena var. acutiserrata MK105452.1 161194 View on NCBI ↗
Quercus aquifolioides NC_026913.1 160415 View on NCBI ↗
Quercus argyrotricha NC_073549.1 160999 View on NCBI ↗
Quercus augustinii PP498794.1 160846 View on NCBI ↗
Quercus austrocochinchinensis NC_083081.1 160768 View on NCBI ↗
Quercus austroglauca NC_069211.1 160913 View on NCBI ↗
Quercus bambusifolia NC_061579.1 160814 View on NCBI ↗
Quercus baronii NC_029490.1 161072 View on NCBI ↗
Quercus bawanglingensis NC_046583.1 161394 View on NCBI ↗
Quercus bella PP471977.1 160798 View on NCBI ↗
Quercus blakei OQ603430.1 160765 View on NCBI ↗
Quercus blakei var. parvifolia OQ603453.1 160816 View on NCBI ↗
Quercus brandisiana OQ603452.1 161914 View on NCBI ↗
Quercus brevicalyx OQ603455.1 160835 View on NCBI ↗
Quercus camusae OR966887.1 161632 View on NCBI ↗
Quercus championii PP465455.1 160811 View on NCBI ↗
Quercus chapensis OQ603434.1 160835 View on NCBI ↗
Quercus chenii NC_039428.1 161117 View on NCBI ↗
Quercus chungii NC_057248.1 160731 View on NCBI ↗
Quercus ciliaris MN199024.1 160842 View on NCBI ↗
Quercus cocciferoides NC_061586.1 160857 View on NCBI ↗
Quercus daimingshanensis PP498796.1 160784 View on NCBI ↗
Quercus delavayi PP465457.1 160926 View on NCBI ↗
Quercus dentata NC_039725.1 161250 View on NCBI ↗
Quercus dentata subsp. stewardii NC_061589.1 161142 View on NCBI ↗
Quercus dinghuensis OQ596301.1 160801 View on NCBI ↗
Quercus disciformis OQ603437.1 160808 View on NCBI ↗
Quercus dolicholepis NC_031357.1 161237 View on NCBI ↗
Quercus edithiae PP471975.1 160933 View on NCBI ↗
Quercus engleriana NC_061593.1 161221 View on NCBI ↗
Quercus fabri NC_061594.1 161227 View on NCBI ↗
Quercus fenchengensis NC_048513.1 161296 View on NCBI ↗
Quercus fleuryi NC_058778.1 160796 View on NCBI ↗
Quercus franchetii OR188394.1 160967 View on NCBI ↗
Quercus gambelii MK105457.1 161213 View on NCBI ↗
Quercus gambleana NC_069210.1 160832 View on NCBI ↗
Quercus gilliana NC_061578.1 160810 View on NCBI ↗
Quercus gilva NC_049876.1 160742 View on NCBI ↗
Quercus glauca NC_036930.1 160798 View on NCBI ↗
Quercus glaucoides NC_061575.1 160765 View on NCBI ↗
Quercus griffithii NC_061614.1 161278 View on NCBI ↗
Quercus guyavifolia NC_061587.1 161131 View on NCBI ↗
Quercus helferiana NC_083082.1 160801 View on NCBI ↗
Quercus hui OQ596303.1 160806 View on NCBI ↗
Quercus hypargyrea NC_061576.1 160778 View on NCBI ↗
Quercus hypophaea OQ603432.1 160549 View on NCBI ↗
Quercus kelloggii NC_062092.1 161119 View on NCBI ↗
Quercus kerrii NC_068858.1 160743 View on NCBI ↗
Quercus kingiana NC_088487.1 161167 View on NCBI ↗
Quercus kiukiangensis OQ603442.1 161276 View on NCBI ↗
Quercus kouangsiensis OQ603425.1 160800 View on NCBI ↗
Quercus lamellosa NC_069845.1 160928 View on NCBI ↗
Quercus langbianensis OQ603428.1 160798 View on NCBI ↗
Quercus litseoides NC_065782.1 160782 View on NCBI ↗
Quercus lobbii OQ603448.1 160846 View on NCBI ↗
Quercus longinux OQ603433.1 160814 View on NCBI ↗
Quercus longispica NC_082110.1 160873 View on NCBI ↗
Quercus macrocalyx OQ603438.1 161269 View on NCBI ↗
Quercus macrocarpa MK105459.1 161236 View on NCBI ↗
Quercus malacotricha MK922348.1 161247 View on NCBI ↗
Quercus marlipoensis NC_088486.1 160995 View on NCBI ↗
Quercus mongolica NC_043858.1 161194 View on NCBI ↗
Quercus mongolica subsp. crispula NC_049877.1 161199 View on NCBI ↗
Quercus monimotricha NC_061577.1 160809 View on NCBI ↗
Quercus morii OQ603431.1 160788 View on NCBI ↗
Quercus myrsinifolia NC_061611.1 160781 View on NCBI ↗
Quercus ningangensis NC_061582.1 160839 View on NCBI ↗
Quercus obovatifolia NC_039972.1 160817 View on NCBI ↗
Quercus oxyodon NC_069209.1 160883 View on NCBI ↗
Quercus oxyphylla NC_061588.1 161131 View on NCBI ↗
Quercus pachyloma NC_068537.1 160778 View on NCBI ↗
Quercus palustris MK105461.1 161284 View on NCBI ↗
Quercus pannosa NC_050963.1 161222 View on NCBI ↗
Quercus patelliformis OQ603423.1 160823 View on NCBI ↗
Quercus phanera OQ603424.1 160814 View on NCBI ↗
Quercus phillyraeoides NC_048488.1 161384 View on NCBI ↗
Quercus poilanei NC_085458.1 160784 View on NCBI ↗
Quercus pseudosemecarpifolia NC_061583.1 160849 View on NCBI ↗
Quercus pubescens subsp. pubescens PP203132.1 161305 View on NCBI ↗
Quercus rehderiana NC_061615.1 161383 View on NCBI ↗
Quercus rex NC_083083.1 160842 View on NCBI ↗
Quercus salicina NC_083127.1 160801 View on NCBI ↗
Quercus saravanensis MW411183.1 160767 View on NCBI ↗
Quercus schottkyana MW450872.1 160746 View on NCBI ↗
Quercus semecarpifolia NC_061613.1 160875 View on NCBI ↗
Quercus semiserrata OR966888.1 161630 View on NCBI ↗
Quercus senescens NC_061590.1 161146 View on NCBI ↗
Quercus serrata NC_061591.1 161169 View on NCBI ↗
Quercus serrata var. brevipetiolata NC_061595.1 161230 View on NCBI ↗
Quercus sessilifolia NC_061581.1 160825 View on NCBI ↗
Quercus shennongii NC_068538.1 160716 View on NCBI ↗
Quercus sichourensis NC_036941.1 160681 View on NCBI ↗
Quercus spinosa NC_026907.1 160825 View on NCBI ↗
Quercus stellata MK105467.1 161214 View on NCBI ↗
Quercus stewardiana MN199023.1 160842 View on NCBI ↗
Quercus suber CM075948.1 161179 View on NCBI ↗
Quercus tarokoensis NC_036370.1 161355 View on NCBI ↗
Quercus tatakaensis NC_061585.1 161346 View on NCBI ↗
Quercus thorelii PP465454.1 160736 View on NCBI ↗
Quercus tiaoloshanica OQ603436.1 160805 View on NCBI ↗
Quercus tungmaiensis NC_036936.1 160702 View on NCBI ↗
Quercus turbinella NC_081467.1 161208 View on NCBI ↗
Quercus utilis NC_061584.1 160854 View on NCBI ↗
Quercus variabilis NC_031356.1 161077 View on NCBI ↗
Quercus virginiana NC_050972.1 161221 View on NCBI ↗
Quercus wislizeni NC_062091.1 161130 View on NCBI ↗
Quercus wutaishanica NC_043857.1 161296 View on NCBI ↗
Quercus x morehus NC_062093.1 161130 View on NCBI ↗
Quercus yonganensis OQ603451.1 160834 View on NCBI ↗
Quercus yunnanensis NC_061592.1 161199 View on NCBI ↗