Markers + reference

Acer

134 species · Sapindaceae · Sapindales

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Species 134
Genome length 156–157 kb
Candidate markers 279
Primer pairs 95

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 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 390 0.0279 0.98 67.8 yes View details
trnK-UUU-rps16 LSC 930 0.0210 0.96 64.2 yes View details
atpI-rps2 LSC 460 0.0168 0.94 57.8 yes View details
trnE-UUC-trnT-GGU LSC 761 0.0176 1.00 66.1 yes View details
psbZ-trnG-GCC LSC 568 0.0338 0.99 76.0 yes View details
ndhC-trnV-UAC LSC 924 0.0229 0.96 64.2 yes View details
ycf1 IRb 1299 0.0026 1.00 43.5 no View details
ndhF-rpl32 SSC 739 0.0204 0.99 64.5 yes View details
rpl32-trnL-UAG SSC 1077 0.0304 0.99 74.6 yes View details
ycf1 SSC 5511 0.0119 1.00 52.6 yes View details
ccsA-ndhD SSC 196 0.0467 1.00 71.2 yes View details
rpl22 LSC 489 0.0128 1.00 67.3 yes View details
petA-psbJ LSC 762 0.0156 1.00 66.6 yes View details
trnT-UGU-trnL-UAA LSC 945 0.0130 1.00 66.2 yes View details
rpoB-trnC-GCA LSC 1165 0.0133 0.99 65.3 yes View details
trnM-CAU-psbD LSC 1503 0.0132 0.99 65.1 yes View details
rps16-trnQ-UUG LSC 1089 0.0160 0.98 64.8 yes View details
atpH-atpI LSC 1148 0.0150 1.00 64.8 yes View details
psbK-psbI LSC 370 0.0254 0.99 63.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 403–614 0.993 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 402–613 0.993 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 404–615 0.993 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 389–600 0.985 90.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 342–553 0.985 89.8
trnK-UUU_p1 trnK-UUU CTTATAGCCCCGTGTCAACC TTCGCTGGATTCGCTGTTAT 2820–2976 0.963 87.6
trnK-UUU_p2 trnK-UUU CTTATAGCCCCGTGTCAACC TAATGGGTTCGCTGGATTCG 2827–2983 0.560 72.6
trnK-UUU_p3 trnK-UUU TGACTTATAGCCCCGTGTCA TAATGGGTTCGCTGGATTCG 2830–2986 0.560 71.8
trnK-UUU_p4 trnK-UUU ACTCCCAAGCACACAAACTT TAATGGGTTCGCTGGATTCG 2894–2990 0.530 70.5
trnK-UUU_p5 trnK-UUU GACTCCCAAGCACACAAACT TAATGGGTTCGCTGGATTCG 2895–2991 0.530 69.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1184–1463 0.978 90.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT GCCGTACGAGGAGAAAACTT 1180–1459 0.978 89.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT GCCGTACGAGGAGAAAACTT 1181–1460 0.978 89.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCGATGGTATGGACGAATC GCCGTACGAGGAGAAAACTT 1151–1430 0.851 84.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GCCGTACGAGGAGAAAACTT 1150–1429 0.851 84.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 583–1216 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 598–1231 1.000 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 597–1230 1.000 88.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 587–1220 1.000 85.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 613–1246 1.000 85.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCA 384–449 1.000 56.4
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAGAGTTTGAGAGTAAGCA 381–446 1.000 54.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACAAAGAGTTTGAGAGTAAGCA 382–447 1.000 54.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACAAAGAGTTTGAGAGTAAGCA 383–448 1.000 54.4
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACAAAGAGTTTGAGAGTAAGCA 385–450 1.000 54.2
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCGGCG 1169–1270 1.000 87.0
atpH-atpI_p2 atpH-atpI AACAGAAGCGGCAGAAATCA ACAAGCGGTATTCAAGCTCT 1191–1292 1.000 85.0
atpH-atpI_p3 atpH-atpI ACAGAAGCGGCAGAAATCAG TTTTTGCAACTTTAGCGGCG 1168–1269 1.000 83.4
atpH-atpI_p4 atpH-atpI AGAAGCGGCAGAAATCAGTG TTTTTGCAACTTTAGCGGCG 1166–1267 1.000 83.4
atpH-atpI_p5 atpH-atpI CAGAAGCGGCAGAAATCAGT TTTTTGCAACTTTAGCGGCG 1167–1268 1.000 83.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (134)

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

Species Accession Length (bp) Link
Acer acuminatum MN864496.1 155548 View on NCBI ↗
Acer amplum NC_050668.1 156225 View on NCBI ↗
Acer amplum subsp. catalpifolium NC_041080.1 157349 View on NCBI ↗
Acer argutum NC_056202.1 155990 View on NCBI ↗
Acer barbinerve NC_087593.1 155985 View on NCBI ↗
Acer buergerianum NC_034744.1 156477 View on NCBI ↗
Acer buergerianum subsp. ningpoense KF753631.1 156911 View on NCBI ↗
Acer caesium NC_051955.1 155626 View on NCBI ↗
Acer caesium subsp. giraldii MT648754.1 156039 View on NCBI ↗
Acer calcaratum NC_056203.1 156981 View on NCBI ↗
Acer campbellii NC_087596.1 156815 View on NCBI ↗
Acer campestre NC_056204.1 156310 View on NCBI ↗
Acer cappadocicum NC_051956.1 156313 View on NCBI ↗
Acer cappadocicum subsp. divergens MW067034.1 156330 View on NCBI ↗
Acer cappadocicum subsp. sinicum MW067035.1 156267 View on NCBI ↗
Acer carpinifolium NC_087600.1 155568 View on NCBI ↗
Acer caudatifolium NC_081007.1 156385 View on NCBI ↗
Acer caudatum NC_087602.1 156262 View on NCBI ↗
Acer ceriferum NC_087603.1 157029 View on NCBI ↗
Acer cinnamomifolium NC_056164.1 156227 View on NCBI ↗
Acer circinatum NC_056205.1 156850 View on NCBI ↗
Acer cissifolium NC_049162.1 155997 View on NCBI ↗
Acer coriaceifolium NC_050669.1 155944 View on NCBI ↗
Acer crataegifolium NC_056206.1 156250 View on NCBI ↗
Acer davidii NC_030331.1 157044 View on NCBI ↗
Acer davidii subsp. grosseri OP219530.1 155904 View on NCBI ↗
Acer diabolicum NC_056207.1 156127 View on NCBI ↗
Acer distylum NC_056209.1 155857 View on NCBI ↗
Acer duplicatoserratum var. chinense OP219587.1 156920 View on NCBI ↗
Acer elegantulum NC_056210.1 156834 View on NCBI ↗
Acer erianthum NC_087601.1 156571 View on NCBI ↗
Acer fabri NC_050670.1 157031 View on NCBI ↗
Acer fenzelianum NC_045527.1 157373 View on NCBI ↗
Acer flabellatum NC_050671.1 156472 View on NCBI ↗
Acer glabrum MN864498.1 156373 View on NCBI ↗
Acer granatense NC_056211.1 156206 View on NCBI ↗
Acer grandidentatum NC_056212.1 156089 View on NCBI ↗
Acer griseum NC_034346.1 156857 View on NCBI ↗
Acer heldreichii subsp. trautvetteri NC_056235.1 155874 View on NCBI ↗
Acer henryi NC_049163.1 156325 View on NCBI ↗
Acer hyrcanum NC_056213.1 155910 View on NCBI ↗
Acer japonicum NC_056214.1 156936 View on NCBI ↗
Acer kwangsiense NC_087588.1 156789 View on NCBI ↗
Acer laevigatum NC_042443.1 156905 View on NCBI ↗
Acer lanceolatum NC_087595.1 155727 View on NCBI ↗
Acer laurinum NC_056215.1 156175 View on NCBI ↗
Acer leipoense MZ725939.1 155702 View on NCBI ↗
Acer linganense NC_087598.1 156918 View on NCBI ↗
Acer lobelii NC_056216.1 156388 View on NCBI ↗
Acer longipes NC_049126.1 157137 View on NCBI ↗
Acer lucidum NC_081009.1 155960 View on NCBI ↗
Acer macrophyllum NC_056217.1 155757 View on NCBI ↗
Acer mandshuricum NC_049164.1 156234 View on NCBI ↗
Acer maximowiczii NC_087591.1 156105 View on NCBI ↗
Acer metcalfii NC_087590.1 155769 View on NCBI ↗
Acer miaotaiense NC_030343.1 156595 View on NCBI ↗
Acer micranthum MN864500.1 156399 View on NCBI ↗
Acer miyabei NC_067762.1 156289 View on NCBI ↗
Acer monspessulanum NC_056218.1 156172 View on NCBI ↗
Acer morrisonense NC_029371.1 157197 View on NCBI ↗
Acer negundo NC_051957.1 155910 View on NCBI ↗
Acer nikoense NC_049165.1 155952 View on NCBI ↗
Acer nipponicum MN864502.1 156225 View on NCBI ↗
Acer oblongum NC_056208.1 155917 View on NCBI ↗
Acer oblongum var. concolor OP219601.1 155915 View on NCBI ↗
Acer obtusifolium NC_056219.1 155785 View on NCBI ↗
Acer olivaceum NC_056220.1 156796 View on NCBI ↗
Acer oliverianum NC_051958.1 156890 View on NCBI ↗
Acer opalus NC_056221.1 156145 View on NCBI ↗
Acer opalus subsp. obtusatum MW067057.1 155862 View on NCBI ↗
Acer paihengii MZ934750.1 155967 View on NCBI ↗
Acer palmatum NC_034932.1 157367 View on NCBI ↗
Acer palmatum var. palmatum MN864504.1 157023 View on NCBI ↗
Acer pauciflorum NC_056222.1 156957 View on NCBI ↗
Acer paxii NC_056223.1 156066 View on NCBI ↗
Acer pectinatum NC_050672.1 156147 View on NCBI ↗
Acer pensylvanicum NC_056224.1 156077 View on NCBI ↗
Acer pentaphyllum NC_049167.1 156269 View on NCBI ↗
Acer pictum subsp. mayrii NC_087599.1 156238 View on NCBI ↗
Acer pictum subsp. mono NC_049127.1 156985 View on NCBI ↗
Acer pictum subsp. okamotoanum PQ380007.1 156242 View on NCBI ↗
Acer pilosum MN864506.1 155586 View on NCBI ↗
Acer platanoides NC_051959.1 156385 View on NCBI ↗
Acer pseudoplatanus NC_087587.1 155816 View on NCBI ↗
Acer pseudosieboldianum NC_046487.1 157053 View on NCBI ↗
Acer pseudosieboldianum subsp. takesimense NC_046488.1 157023 View on NCBI ↗
Acer pseudosieboldianum var. microsieboldianum MW067067.1 156975 View on NCBI ↗
Acer pubinerve NC_087592.1 156869 View on NCBI ↗
Acer pycnanthum NC_056225.1 156172 View on NCBI ↗
Acer robustum NC_081008.1 156883 View on NCBI ↗
Acer rubescens NC_056226.1 156047 View on NCBI ↗
Acer rubrum MN864509.1 155683 View on NCBI ↗
Acer rufinerve NC_056227.1 156109 View on NCBI ↗
Acer saccharinum NC_056228.1 155684 View on NCBI ↗
Acer saccharum NC_051960.1 155684 View on NCBI ↗
Acer saccharum subsp. floridanum MW067072.1 156053 View on NCBI ↗
Acer saccharum subsp. leucoderme MW067073.1 156016 View on NCBI ↗
Acer saccharum subsp. nigrum MW067074.1 156017 View on NCBI ↗
Acer saccharum subsp. saccharum MW067075.1 156066 View on NCBI ↗
Acer saccharum subsp. skutchii MW067080.1 156016 View on NCBI ↗
Acer sempervirens NC_056229.1 155938 View on NCBI ↗
Acer serrulatum NC_056230.1 156891 View on NCBI ↗
Acer shenkanense NC_056231.1 156292 View on NCBI ↗
Acer sikkimense NC_056232.1 156553 View on NCBI ↗
Acer sinense NC_057529.1 156980 View on NCBI ↗
Acer sino-oblongum NC_040106.1 157121 View on NCBI ↗
Acer sinopurpurascens NC_087597.1 156059 View on NCBI ↗
Acer stachyophyllum NC_051961.1 155933 View on NCBI ↗
Acer stachyophyllum subsp. betulifolium OP219581.1 156118 View on NCBI ↗
Acer stachyophyllum subsp. stachyophyllum MW067081.1 155956 View on NCBI ↗
Acer sterculiaceum NC_050673.1 156158 View on NCBI ↗
Acer sterculiaceum subsp. franchetii OP219543.1 156032 View on NCBI ↗
Acer sterculiaceum subsp. sterculiaceum MN864510.1 156258 View on NCBI ↗
Acer sutchuenense subsp. tienchuanense NC_049166.1 156063 View on NCBI ↗
Acer sycopseoides NC_087589.1 156101 View on NCBI ↗
Acer tataricum NC_050674.1 155603 View on NCBI ↗
Acer tataricum subsp. aidzuense MW067085.1 155613 View on NCBI ↗
Acer tataricum subsp. ginnala OP219554.1 155595 View on NCBI ↗
Acer tataricum subsp. semenovii MW067086.1 155613 View on NCBI ↗
Acer tataricum subsp. tataricum MW067087.1 155584 View on NCBI ↗
Acer tataricum subsp. theiferum OP219564.1 155625 View on NCBI ↗
Acer tegmentosum NC_056233.1 156524 View on NCBI ↗
Acer tenuifolium NC_056234.1 157046 View on NCBI ↗
Acer tetramerum NC_081010.1 155988 View on NCBI ↗
Acer tonkinense NC_087594.1 156743 View on NCBI ↗
Acer triflorum NC_047296.1 156024 View on NCBI ↗
Acer truncatum NC_037211.1 156262 View on NCBI ↗
Acer tsinglingense MN393475.1 156039 View on NCBI ↗
Acer tutcheri NC_051542.1 156973 View on NCBI ↗
Acer velutinum NC_056236.1 155586 View on NCBI ↗
Acer wangchii NC_087604.1 155852 View on NCBI ↗
Acer wilsonii NC_040988.1 157067 View on NCBI ↗
Acer yangbiense NC_050351.1 155706 View on NCBI ↗
Acer yangjuechi NC_053258.1 157088 View on NCBI ↗