Markers + reference

Clematis

160 species · Ranunculaceae · Ranunculales

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Species 160
Genome length 159–160 kb
Candidate markers 278
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps4-rps16 LSC 563 0.0137 1.00 73.0 yes View details
atpB-rbcL LSC 863 0.0097 1.00 64.2 yes View details
ycf1 IRb 1710 0.0044 1.00 41.6 no View details
ndhF SSC 2235 0.0087 1.00 56.2 yes View details
ndhF-rpl32 SSC 1041 0.0228 0.99 67.9 yes View details
rpl32-trnL-UAG SSC 784 0.0180 0.98 70.3 yes View details
ndhD SSC 1479 0.0039 1.00 44.8 yes View details
ndhE-ndhG SSC 277 0.0289 0.99 75.4 yes View details
ndhG SSC 534 0.0020 1.00 33.2 yes View details
ndhG-ndhI SSC 492 0.0162 0.97 71.6 yes View details
ycf1 SSC 5643 0.0074 1.00 69.9 yes View details
infA-rps4 IRa 23 0.0496 1.00 78.3 no View details
rps16-trnK-UUU LSC 649 0.0116 0.99 72.7 yes View details
psbE-petL LSC 1380 0.0089 1.00 72.1 yes View details
atpH-atpI LSC 1104 0.0055 1.00 68.7 yes View details
ycf4-cemA LSC 599 0.0103 1.00 67.1 yes View details
psbI-trnS-GCU LSC 86 0.0301 1.00 67.0 yes View details
trnS-GGA-trnV-UAC LSC 1112 0.0115 1.00 67.0 yes View details
petB LSC 1431 0.0052 1.00 66.9 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
rps4-rps16_p1 rps4-rps16 GTAAGTGGGTCGGTTTGGAA ATTCCTTCAAGTCGCACGTT 661–710 1.000 89.0
rps4-rps16_p2 rps4-rps16 GTAAGTGGGTCGGTTTGGAA AAGTCGCACGTTGCTTTCTA 653–702 1.000 88.8
rps4-rps16_p3 rps4-rps16 AAGTGGGTCGGTTTGGAAAT ATTCCTTCAAGTCGCACGTT 659–708 1.000 88.0
rps4-rps16_p4 rps4-rps16 AAGTGGGTCGGTTTGGAAAT AAGTCGCACGTTGCTTTCTA 651–700 1.000 87.9
rps4-rps16_p5 rps4-rps16 AGTAAGTGGGTCGGTTTGGA ATTCCTTCAAGTCGCACGTT 662–711 1.000 86.4
rps16-trnK-UUU_p1 rps16-trnK-UUU GCTCAACCTACGGAAACTGT TCTACCAACGGTATGGACGA 783–845 1.000 89.7
rps16-trnK-UUU_p2 rps16-trnK-UUU GCTCAACCTACGGAAACTGT AAAGCCGAGTACTCTACCGT 718–780 1.000 89.3
rps16-trnK-UUU_p3 rps16-trnK-UUU GCTCAACCTACGGAAACTGT AAGCCGAGTACTCTACCGTT 717–779 1.000 89.3
rps16-trnK-UUU_p4 rps16-trnK-UUU CCTTGAAAAAGGCGCTCAAC TCTACCAACGGTATGGACGA 796–858 1.000 89.1
rps16-trnK-UUU_p5 rps16-trnK-UUU CTTGAAAAAGGCGCTCAACC TCTACCAACGGTATGGACGA 795–857 1.000 89.1
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 174–184 1.000 81.7
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 175–185 1.000 81.7
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 193–203 1.000 80.8
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 174–184 1.000 79.4
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 175–185 1.000 79.4
atpH-atpI_p1 atpH-atpI TCCAGGTCCAATAGAAGCCA ATAGGGGAATCCATGGAGGG 902–1275 1.000 91.2
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 875–1248 1.000 90.3
atpH-atpI_p3 atpH-atpI GATACCTTCTACGGCTTGGC ATAGGGGAATCCATGGAGGG 944–1317 1.000 90.2
atpH-atpI_p4 atpH-atpI CGATACCTTCTACGGCTTGG ATAGGGGAATCCATGGAGGG 945–1318 1.000 90.2
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA ATAGGGGAATCCATGGAGGG 857–1193 0.981 89.8
trnS-GGA-trnV-UAC_p1 trnS-GGA-trnV-UAC AGGCTTTTGTTTACCGAGGG AGAAGGTCTACGGTTCGAGT 964–1214 1.000 89.7
trnS-GGA-trnV-UAC_p2 trnS-GGA-trnV-UAC TTTAGGAGAGATGGCCGAGT AGAAGGTCTACGGTTCGAGT 1015–1265 1.000 89.1
trnS-GGA-trnV-UAC_p3 trnS-GGA-trnV-UAC GGCTTTTGTTTACCGAGGGT AGAAGGTCTACGGTTCGAGT 963–1213 1.000 87.3
trnS-GGA-trnV-UAC_p4 trnS-GGA-trnV-UAC AGGCTTTTGTTTACCGAGGG GAAGGTCTACGGTTCGAGTC 963–1213 1.000 86.9
trnS-GGA-trnV-UAC_p5 trnS-GGA-trnV-UAC TCTTTAGGAGAGATGGCCGA AGAAGGTCTACGGTTCGAGT 1017–1267 1.000 86.8
atpB-rbcL_p1 atpB-rbcL CATCCAGTACCGGACCAATG AGCCAACACTCGCTTTAGTC 953–1037 0.975 89.0
atpB-rbcL_p2 atpB-rbcL CATCCAGTACCGGACCAATG GCCAACACTCGCTTTAGTCT 952–1036 0.975 89.0
atpB-rbcL_p3 atpB-rbcL CATCCAGTACCGGACCAATG TGAAGCCAACACTCGCTTTA 956–1040 0.975 88.6
atpB-rbcL_p4 atpB-rbcL CATCCAGTACCGGACCAATG AAGCCAACACTCGCTTTAGT 954–1038 0.975 88.6
atpB-rbcL_p5 atpB-rbcL TTCTTCAAGAGCGGAAACCC GCCAACACTCGCTTTAGTCT 906–990 0.975 88.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (160)

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

Species Accession Length (bp) Link
Clematis acerifolia NC_039844.1 159552 View on NCBI ↗
Clematis acerifolia var. elobata NC_065272.1 159690 View on NCBI ↗
Clematis aethusifolia OR801209.1 159682 View on NCBI ↗
Clematis akebioides OR801210.1 159600 View on NCBI ↗
Clematis akoensis PQ834329.1 159716 View on NCBI ↗
Clematis alpina PP328796.1 159577 View on NCBI ↗
Clematis alpina subsp. ochotensis MT876505.1 159631 View on NCBI ↗
Clematis alpina subsp. sibirica PQ874705.1 159701 View on NCBI ↗
Clematis alternata NC_039577.1 159476 View on NCBI ↗
Clematis apiifolia NC_081049.1 159682 View on NCBI ↗
Clematis apiifolia var. argentilucida PQ636498.1 159637 View on NCBI ↗
Clematis aristata PX223807.1 159524 View on NCBI ↗
Clematis armandi NC_069848.1 159353 View on NCBI ↗
Clematis armandi var. hefengensis PQ834331.1 159317 View on NCBI ↗
Clematis aureolata NC_069849.1 159548 View on NCBI ↗
Clematis barbellata var. obtusa PX223808.1 159597 View on NCBI ↗
Clematis brachiata NC_065250.1 159678 View on NCBI ↗
Clematis brachyura NC_042793.1 159532 View on NCBI ↗
Clematis brevicaudata NC_039579.1 159583 View on NCBI ↗
Clematis brevipes PQ834333.1 159670 View on NCBI ↗
Clematis buchananiana PQ834334.1 159737 View on NCBI ↗
Clematis cadmia NC_065251.1 159714 View on NCBI ↗
Clematis calcicola NC_066977.1 159658 View on NCBI ↗
Clematis campestris NC_065264.1 159671 View on NCBI ↗
Clematis canescens NC_065265.1 159752 View on NCBI ↗
Clematis chinensis NC_066718.1 159497 View on NCBI ↗
Clematis chingii PX223809.1 159651 View on NCBI ↗
Clematis chrysocoma NC_065266.1 159584 View on NCBI ↗
Clematis cirrhosa PQ834338.1 159480 View on NCBI ↗
Clematis clarkeana PQ834339.1 159709 View on NCBI ↗
Clematis connata NC_065267.1 159768 View on NCBI ↗
Clematis connata var. confusa PQ834340.1 159720 View on NCBI ↗
Clematis courtoisii PQ834343.1 159570 View on NCBI ↗
Clematis crassifolia NC_065268.1 159312 View on NCBI ↗
Clematis crassipes PX223810.1 159675 View on NCBI ↗
Clematis crispa NC_065269.1 159304 View on NCBI ↗
Clematis danxiacola PQ246280.1 159506 View on NCBI ↗
Clematis delavayi NC_065270.1 159659 View on NCBI ↗
Clematis dolichopoda PQ874706.1 159670 View on NCBI ↗
Clematis drummondii NC_065271.1 159729 View on NCBI ↗
Clematis fasciculiflora PQ874707.1 159665 View on NCBI ↗
Clematis finetiana PQ874708.1 159505 View on NCBI ↗
Clematis flammula PQ874709.1 159594 View on NCBI ↗
Clematis florida NC_058885.1 159606 View on NCBI ↗
Clematis fruticosa NC_065273.1 159796 View on NCBI ↗
Clematis fusca NC_060524.1 159624 View on NCBI ↗
Clematis fusca var. coreana KM652489.1 159609 View on NCBI ↗
Clematis glabrifolia PQ874712.1 159557 View on NCBI ↗
Clematis glaucophylla NC_065274.1 159302 View on NCBI ↗
Clematis gouriana NC_081050.1 159681 View on NCBI ↗
Clematis gracilifolia PQ874713.1 159717 View on NCBI ↗
Clematis grandidentata NC_081051.1 159634 View on NCBI ↗
Clematis grata PQ874714.1 159599 View on NCBI ↗
Clematis gratopsis NC_081052.1 159643 View on NCBI ↗
Clematis grewiiflora PQ874715.1 159816 View on NCBI ↗
Clematis guniuensis NC_050373.1 159682 View on NCBI ↗
Clematis hancockiana PQ874717.1 159592 View on NCBI ↗
Clematis henryi NC_070190.1 159707 View on NCBI ↗
Clematis henryi var. ternata MW380948.1 159675 View on NCBI ↗
Clematis heracleifolia NC_039845.1 159565 View on NCBI ↗
Clematis hexapetala NC_065276.1 159534 View on NCBI ↗
Clematis hexapetala var. tchefouensis PQ874719.1 159535 View on NCBI ↗
Clematis hirsuta PQ874720.1 159616 View on NCBI ↗
Clematis hirsutissima PQ874723.1 159613 View on NCBI ↗
Clematis hirsutissima var. scottii PQ874722.1 159321 View on NCBI ↗
Clematis huchouensis NC_065277.1 159590 View on NCBI ↗
Clematis insidiosa PQ874724.1 159777 View on NCBI ↗
Clematis integrifolia NC_081053.1 159630 View on NCBI ↗
Clematis intricata NC_065278.1 159593 View on NCBI ↗
Clematis japonica PQ874725.1 159758 View on NCBI ↗
Clematis javana PQ874726.1 159483 View on NCBI ↗
Clematis jingdungensis PQ874727.1 159699 View on NCBI ↗
Clematis kirilowii PQ874728.1 159509 View on NCBI ↗
Clematis kockiana PQ874729.1 159714 View on NCBI ↗
Clematis koreana PQ874730.1 159622 View on NCBI ↗
Clematis kweichowensis PQ874731.1 159746 View on NCBI ↗
Clematis lancifolia NC_065279.1 159447 View on NCBI ↗
Clematis lasiandra NC_065286.1 159688 View on NCBI ↗
Clematis lasiantha NC_065280.1 159334 View on NCBI ↗
Clematis leschenaultiana NC_065281.1 159622 View on NCBI ↗
Clematis liboensis PX223811.1 159670 View on NCBI ↗
Clematis ligusticifolia NC_065282.1 159600 View on NCBI ↗
Clematis linearifolia PQ874732.1 159581 View on NCBI ↗
Clematis loureiroana NC_039690.1 159624 View on NCBI ↗
Clematis macropetala NC_041477.1 159647 View on NCBI ↗
Clematis mae PQ874733.1 159546 View on NCBI ↗
Clematis mandshurica NC_079957.1 159564 View on NCBI ↗
Clematis mauritiana PQ874734.1 159846 View on NCBI ↗
Clematis metouensis PQ874736.1 159641 View on NCBI ↗
Clematis meyeniana PQ874737.1 159601 View on NCBI ↗
Clematis montana NC_057507.1 159523 View on NCBI ↗
Clematis montana var. glabrescens PQ874738.1 159623 View on NCBI ↗
Clematis nannophylla NC_065283.1 159814 View on NCBI ↗
Clematis napaulensis PQ874739.1 159733 View on NCBI ↗
Clematis obscura PQ874740.1 159639 View on NCBI ↗
Clematis occidentalis PQ874741.1 159536 View on NCBI ↗
Clematis orientalis NC_071961.1 159543 View on NCBI ↗
Clematis otophora NC_069850.1 159534 View on NCBI ↗
Clematis parviloba NC_081054.1 159664 View on NCBI ↗
Clematis pashanensis PQ874743.1 159520 View on NCBI ↗
Clematis patens NC_063559.1 159603 View on NCBI ↗
Clematis patens subsp. tientaiensis NC_085220.1 159644 View on NCBI ↗
Clematis peterae NC_081055.1 159676 View on NCBI ↗
Clematis petriei NC_065284.1 159425 View on NCBI ↗
Clematis pierotii PQ874744.1 159639 View on NCBI ↗
Clematis pinchuanensis PQ874745.1 159744 View on NCBI ↗
Clematis pinnata NC_065248.1 159652 View on NCBI ↗
Clematis pitcheri PQ874746.1 159295 View on NCBI ↗
Clematis pogonandra PQ874747.1 159660 View on NCBI ↗
Clematis potaninii NC_058760.1 159691 View on NCBI ↗
Clematis pseudoconnata PQ834341.1 159711 View on NCBI ↗
Clematis pseudootophora PQ874748.1 159553 View on NCBI ↗
Clematis pseudopogonandra PQ874749.1 159636 View on NCBI ↗
Clematis psilandra NC_081056.1 159622 View on NCBI ↗
Clematis pubescens NC_065285.1 159391 View on NCBI ↗
Clematis qingchengshanica PQ874750.1 159686 View on NCBI ↗
Clematis quinquefoliolata NC_065287.1 159724 View on NCBI ↗
Clematis ranunculoides NC_081994.1 159741 View on NCBI ↗
Clematis recta PP328797.1 159596 View on NCBI ↗
Clematis rehderiana NC_069851.1 159582 View on NCBI ↗
Clematis repens NC_039578.1 159507 View on NCBI ↗
Clematis reticulata NC_065288.1 159284 View on NCBI ↗
Clematis rubifolia PQ874753.1 159624 View on NCBI ↗
Clematis rutoides NC_065289.1 159678 View on NCBI ↗
Clematis serratifolia NC_060523.1 159648 View on NCBI ↗
Clematis shenlungchiaensis PQ874755.1 159657 View on NCBI ↗
Clematis shensiensis PQ874756.1 159553 View on NCBI ↗
Clematis siamensis PQ874757.1 159735 View on NCBI ↗
Clematis simensis PQ874758.1 159633 View on NCBI ↗
Clematis songarica PP998037.1 159584 View on NCBI ↗
Clematis songorica NC_065290.1 159822 View on NCBI ↗
Clematis speciosa NC_081062.1 159753 View on NCBI ↗
Clematis stans NC_081057.1 159671 View on NCBI ↗
Clematis stans var. austrojaponensis ON411443.1 159775 View on NCBI ↗
Clematis subumbellata NC_081058.1 159687 View on NCBI ↗
Clematis tamurae PQ874760.1 159623 View on NCBI ↗
Clematis tangutica NC_080984.1 159584 View on NCBI ↗
Clematis tashiroi PQ874761.1 159740 View on NCBI ↗
Clematis terniflora NC_028000.1 159528 View on NCBI ↗
Clematis texensis PQ874763.1 159294 View on NCBI ↗
Clematis tibetana NC_069852.1 159540 View on NCBI ↗
Clematis tomentella NC_065291.1 159818 View on NCBI ↗
Clematis tosaensis PQ874765.1 159783 View on NCBI ↗
Clematis tsaii PQ874766.1 159682 View on NCBI ↗
Clematis tsugetorum NC_081059.1 159611 View on NCBI ↗
Clematis tubulosa NC_065249.1 159653 View on NCBI ↗
Clematis tubulosa var. ichangensis ON411454.1 159654 View on NCBI ↗
Clematis uncinata NC_039846.1 159524 View on NCBI ↗
Clematis urophylla NC_065292.1 159696 View on NCBI ↗
Clematis urticifolia NC_081060.1 159720 View on NCBI ↗
Clematis villosa PV600631.1 159600 View on NCBI ↗
Clematis virginiana NC_065293.1 159561 View on NCBI ↗
Clematis viridis NC_065294.1 159847 View on NCBI ↗
Clematis vitalba NC_081061.1 159710 View on NCBI ↗
Clematis viticella PQ874767.1 159646 View on NCBI ↗
Clematis williamsii NC_065295.1 159645 View on NCBI ↗
Clematis xiangguiensis NC_065296.1 159575 View on NCBI ↗
Clematis yui PQ874768.1 159301 View on NCBI ↗
Clematis yunnanensis PQ874769.1 159699 View on NCBI ↗
Clematis zandaensis PQ874770.1 159543 View on NCBI ↗