Markers + reference

Eremophila

192 species · Scrophulariaceae · Lamiales

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Species 192
Genome length 142–156 kb
Candidate markers 264
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petD LSC 1227 0.0102 1.00 62.8 yes View details
ycf1 IRb 792 0.0031 1.00 40.6 no View details
ndhF SSC 2232 0.0069 1.00 51.1 yes View details
rpl32-trnL-UAG SSC 877 0.0178 0.99 68.2 yes View details
ycf1 SSC 5379 0.0102 1.00 57.5 yes View details
ndhC-trnV-UAC LSC 1183 0.0080 0.99 72.7 yes View details
petN-psbM LSC 984 0.0088 1.00 68.7 yes View details
trnF-GAA-ndhJ LSC 639 0.0072 1.00 67.5 yes View details
psbE-petL LSC 922 0.0053 1.00 66.8 yes View details
rps2-rpoC2 LSC 229 0.0212 0.94 66.3 yes View details
atpB-rbcL LSC 779 0.0051 0.99 65.3 yes View details
atpH-atpI LSC 1025 0.0067 1.00 64.7 yes View details
ycf3-trnS-GGA LSC 854 0.0046 1.00 64.3 yes View details
trnC-GCA-petN LSC 842 0.0085 0.99 64.2 yes View details
trnK-UUU-rps16 LSC 989 0.0112 0.98 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 97–1997 0.984 76.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 97–1997 0.984 76.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GTGCTCAACCCACAGGAAC 896–1996 0.995 76.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCCACAGGAACT 100–1996 0.984 75.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGGAACT 100–1996 0.984 75.9
atpH-atpI_p1 atpH-atpI TACCCTCTACAGCTTGACCC TTTTTGCAACTTTAGCCGCG 1002–1306 1.000 86.8
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 917–1221 0.995 86.8
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 935–1239 0.995 86.5
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 934–1238 0.995 85.9
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG TTTTTGCAACTTTAGCCGCG 929–1233 1.000 85.8
rps2-rpoC2_p1 rps2-rpoC2 TGCAGAGATATAGGGTGCCA TCGATGATACATCAGAACAATCA 106–2120 0.958 50.3
rps2-rpoC2_p2 rps2-rpoC2 TGCAGAGATATAGGGTGCCA TTCGATGATACATCAGAACAATCA 107–2121 0.958 50.3
rps2-rpoC2_p3 rps2-rpoC2 TGCAGAGATATAGGGTGCCA CGATGATACATCAGAACAATCA 103–768 0.958 50.3
rps2-rpoC2_p4 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TCGATGATACATCAGAACAATCA 80–2122 0.948 49.9
rps2-rpoC2_p5 rps2-rpoC2 AAATGAACTCCTGCCTCCAG TCGATGATACATCAGAACAATCA 80–2119 0.906 48.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 80–993 1.000 91.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 80–991 1.000 91.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 80–994 1.000 90.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTAGAGCCCACTTCTTCCC 80–1003 0.995 90.1
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 80–939 0.995 89.9
petN-psbM_p1 petN-psbM TCGTAGTGTGGGGAAGAAGT TGCTACTGCGCTATTCATTCT 80–1123 1.000 80.3
petN-psbM_p2 petN-psbM ACTCGTAGTGTGGGGAAGAA TGCTACTGCGCTATTCATTCT 80–1125 0.995 80.1
petN-psbM_p3 petN-psbM CGTAGTGTGGGGAAGAAGTG TGCTACTGCGCTATTCATTCT 80–1122 1.000 79.7
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGCTATTCATTCT 80–1177 1.000 79.1
petN-psbM_p5 petN-psbM GTAGTGTGGGGAAGAAGTGG TGCTACTGCGCTATTCATTCT 80–1121 1.000 76.5
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG CCCTCGGTAAACAAAAGCCT 80–1070 0.995 84.1
ycf3-trnS-GGA_p2 ycf3-trnS-GGA GCCTCCTTTTCTCCTGAAGT CCCTCGGTAAACAAAAGCCT 80–1069 0.995 84.1
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG ACGGAAAGAGAGGGATTCGA 80–1091 1.000 83.8
ycf3-trnS-GGA_p4 ycf3-trnS-GGA GCCTCCTTTTCTCCTGAAGT ACGGAAAGAGAGGGATTCGA 80–1090 1.000 83.8
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG TTCCAATGCTACGCCTTGAA 80–1041 0.995 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (192)

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

Species Accession Length (bp) Link
Eremophila abietina NC_077291.1 151959 View on NCBI ↗
Eremophila accrescens NC_077446.1 151755 View on NCBI ↗
Eremophila acrida NC_077355.1 151726 View on NCBI ↗
Eremophila adenotricha NC_077455.1 151713 View on NCBI ↗
Eremophila aff. anomala RMF-2022 NC_077410.1 151530 View on NCBI ↗
Eremophila aff. clarkei RMF-2022 NC_077429.1 151758 View on NCBI ↗
Eremophila aff. compacta RMF-2022 NC_077346.1 151595 View on NCBI ↗
Eremophila alatisepala NC_077447.1 151713 View on NCBI ↗
Eremophila alternifolia NC_077332.1 151620 View on NCBI ↗
Eremophila annosocaulis NC_077456.1 151667 View on NCBI ↗
Eremophila anomala NC_077424.1 151561 View on NCBI ↗
Eremophila appressa NC_077412.1 151827 View on NCBI ↗
Eremophila arachnoides NC_077368.1 151743 View on NCBI ↗
Eremophila arenaria NC_077454.1 151782 View on NCBI ↗
Eremophila arguta NC_077443.1 151601 View on NCBI ↗
Eremophila attenuata NC_077441.1 151645 View on NCBI ↗
Eremophila aureivisca NC_077292.1 151782 View on NCBI ↗
Eremophila ballythunnensis NC_077430.1 147124 View on NCBI ↗
Eremophila barbata NC_077450.1 151400 View on NCBI ↗
Eremophila battii NC_077354.1 151752 View on NCBI ↗
Eremophila behriana NC_077400.1 151675 View on NCBI ↗
Eremophila bignoniiflora NC_077396.1 151504 View on NCBI ↗
Eremophila bowmanii NC_077372.1 151178 View on NCBI ↗
Eremophila brevifolia NC_077378.1 151534 View on NCBI ↗
Eremophila buirchellii NC_077451.1 151587 View on NCBI ↗
Eremophila caerulea NC_077448.1 151810 View on NCBI ↗
Eremophila calcicola NC_077362.1 151553 View on NCBI ↗
Eremophila calorhabdos NC_077436.1 151574 View on NCBI ↗
Eremophila campanulata NC_077335.1 151553 View on NCBI ↗
Eremophila canaliculata NC_077297.1 151684 View on NCBI ↗
Eremophila caperata NC_077299.1 151778 View on NCBI ↗
Eremophila capricornica NC_071842.1 151564 View on NCBI ↗
Eremophila christophori NC_077437.1 151678 View on NCBI ↗
Eremophila ciliata NC_077288.1 151773 View on NCBI ↗
Eremophila clavata NC_077386.1 151765 View on NCBI ↗
Eremophila complanata NC_077364.1 151640 View on NCBI ↗
Eremophila compressa NC_077392.1 151737 View on NCBI ↗
Eremophila conferta NC_077294.1 151533 View on NCBI ↗
Eremophila congesta NC_077358.1 151668 View on NCBI ↗
Eremophila conglomerata NC_077360.1 151682 View on NCBI ↗
Eremophila cordatisepala NC_077422.1 151193 View on NCBI ↗
Eremophila crassifolia NC_077276.1 151722 View on NCBI ↗
Eremophila cryptothrix NC_077305.1 151948 View on NCBI ↗
Eremophila cuneifolia NC_068053.1 151927 View on NCBI ↗
Eremophila debilis NC_077405.1 148273 View on NCBI ↗
Eremophila decipiens NC_077385.1 151561 View on NCBI ↗
Eremophila decussata NC_077371.1 151819 View on NCBI ↗
Eremophila delisseri NC_077369.1 151850 View on NCBI ↗
Eremophila dempsteri NC_077387.1 151765 View on NCBI ↗
Eremophila dendritica NC_077370.1 151719 View on NCBI ↗
Eremophila denticulata NC_077281.1 151529 View on NCBI ↗
Eremophila deserti NC_077391.1 151667 View on NCBI ↗
Eremophila dichroantha NC_077453.1 151767 View on NCBI ↗
Eremophila divaricata NC_077394.1 151722 View on NCBI ↗
Eremophila duttonii NC_077345.1 147427 View on NCBI ↗
Eremophila elderi NC_077381.1 151613 View on NCBI ↗
Eremophila enata NC_077327.1 151663 View on NCBI ↗
Eremophila eriocalyx NC_077295.1 151543 View on NCBI ↗
Eremophila falcata NC_077328.1 151706 View on NCBI ↗
Eremophila fallax NC_077397.1 151630 View on NCBI ↗
Eremophila fasciata NC_077298.1 151769 View on NCBI ↗
Eremophila flabellata NC_077324.1 151691 View on NCBI ↗
Eremophila flaccida NC_077374.1 151823 View on NCBI ↗
Eremophila foliosissima NC_077313.1 155561 View on NCBI ↗
Eremophila forrestii NC_077442.1 151542 View on NCBI ↗
Eremophila forrestii subsp. forrestii OP169585.1 151588 View on NCBI ↗
Eremophila fraseri NC_077414.1 151872 View on NCBI ↗
Eremophila fraseri subsp. fraseri NC_085223.1 151776 View on NCBI ↗
Eremophila freelingii NC_077398.1 152053 View on NCBI ↗
Eremophila georgei NC_077314.1 151615 View on NCBI ↗
Eremophila gibbifolia NC_050954.1 148717 View on NCBI ↗
Eremophila gibbosa NC_077389.1 151553 View on NCBI ↗
Eremophila gibsonii NC_077351.1 147536 View on NCBI ↗
Eremophila gilesii NC_077329.1 151574 View on NCBI ↗
Eremophila glabra NC_077333.1 151549 View on NCBI ↗
Eremophila glandulifera NC_077340.1 151583 View on NCBI ↗
Eremophila goodwinii NC_077380.1 151669 View on NCBI ↗
Eremophila gracillima NC_077440.1 151700 View on NCBI ↗
Eremophila granitica NC_077342.1 151755 View on NCBI ↗
Eremophila hillii NC_077293.1 151526 View on NCBI ↗
Eremophila hispida NC_077423.1 151605 View on NCBI ↗
Eremophila homoplastica NC_077306.1 151551 View on NCBI ↗
Eremophila hughesii NC_077280.1 151772 View on NCBI ↗
Eremophila humilis NC_077417.1 151558 View on NCBI ↗
Eremophila hygrophana NC_077339.1 151805 View on NCBI ↗
Eremophila incisa NC_077413.1 151511 View on NCBI ↗
Eremophila interstans NC_077365.1 151827 View on NCBI ↗
Eremophila ionantha NC_077343.1 151628 View on NCBI ↗
Eremophila jucunda NC_077317.1 151563 View on NCBI ↗
Eremophila koobabbiensis NC_077283.1 151586 View on NCBI ↗
Eremophila laanii NC_077349.1 151845 View on NCBI ↗
Eremophila lachnocalyx NC_077318.1 151934 View on NCBI ↗
Eremophila lactea NC_077425.1 151454 View on NCBI ↗
Eremophila lanata NC_077439.1 151601 View on NCBI ↗
Eremophila lanceolata NC_068054.1 151565 View on NCBI ↗
Eremophila latrobei NC_077322.1 151581 View on NCBI ↗
Eremophila latrobei subsp. filiformis OL977700.1 151550 View on NCBI ↗
Eremophila latrobei subsp. glabra OP169576.1 151574 View on NCBI ↗
Eremophila latrobei subsp. latrobei NC_085224.1 151601 View on NCBI ↗
Eremophila lehmanniana NC_077382.1 151543 View on NCBI ↗
Eremophila linearis NC_077321.1 147415 View on NCBI ↗
Eremophila longifolia NC_068055.1 151629 View on NCBI ↗
Eremophila lucida NC_077406.1 147492 View on NCBI ↗
Eremophila macdonnellii NC_077402.1 151325 View on NCBI ↗
Eremophila macgillivrayi NC_077444.1 151753 View on NCBI ↗
Eremophila mackinlayi NC_077373.1 151767 View on NCBI ↗
Eremophila macmillaniana NC_077315.1 151920 View on NCBI ↗
Eremophila maculata NC_077344.1 151693 View on NCBI ↗
Eremophila maculata subsp. brevifolia OL977702.1 142336 View on NCBI ↗
Eremophila magnifica NC_077309.1 151943 View on NCBI ↗
Eremophila magnifica subsp. magnifica OR726994.1 151766 View on NCBI ↗
Eremophila magnifica subsp. velutina OR726992.1 151742 View on NCBI ↗
Eremophila maitlandii NC_077308.1 151531 View on NCBI ↗
Eremophila malacoides NC_077325.1 151623 View on NCBI ↗
Eremophila margarethae NC_077326.1 151534 View on NCBI ↗
Eremophila micrantha NC_077457.1 151081 View on NCBI ↗
Eremophila microtheca NC_077359.1 151488 View on NCBI ↗
Eremophila miniata NC_077303.1 147535 View on NCBI ↗
Eremophila muelleriana NC_077296.1 151520 View on NCBI ↗
Eremophila naaykensii NC_084440.1 151683 View on NCBI ↗
Eremophila neglecta NC_077357.1 147643 View on NCBI ↗
Eremophila obliquisepala NC_077418.1 151668 View on NCBI ↗
Eremophila obovata NC_077356.1 151499 View on NCBI ↗
Eremophila occidens NC_077304.1 151707 View on NCBI ↗
Eremophila oldfieldii NC_077338.1 147491 View on NCBI ↗
Eremophila oppositifolia NC_050958.1 151715 View on NCBI ↗
Eremophila ovata NC_077352.1 151769 View on NCBI ↗
Eremophila paisleyi NC_077366.1 151761 View on NCBI ↗
Eremophila pallida NC_077300.1 151687 View on NCBI ↗
Eremophila parvifolia NC_077390.1 151561 View on NCBI ↗
Eremophila pentaptera NC_077353.1 151687 View on NCBI ↗
Eremophila perglandulosa NC_077307.1 151632 View on NCBI ↗
Eremophila petrophila NC_077347.1 151790 View on NCBI ↗
Eremophila phillipsii NC_077383.1 151677 View on NCBI ↗
Eremophila phyllopoda NC_077319.1 151839 View on NCBI ↗
Eremophila phyllopoda subsp. obliqua NC_085222.1 151756 View on NCBI ↗
Eremophila physocalyx NC_077363.1 151551 View on NCBI ↗
Eremophila pilosa NC_068056.1 151541 View on NCBI ↗
Eremophila platycalyx NC_077310.1 151939 View on NCBI ↗
Eremophila platycalyx subsp. pardalota OL977706.1 151947 View on NCBI ↗
Eremophila platythamnos NC_077330.1 147559 View on NCBI ↗
Eremophila polyclada NC_077266.1 151614 View on NCBI ↗
Eremophila praecox NC_077399.1 151148 View on NCBI ↗
Eremophila psilocalyx NC_077274.1 151692 View on NCBI ↗
Eremophila punctata NC_077334.1 151601 View on NCBI ↗
Eremophila pungens NC_077331.1 151677 View on NCBI ↗
Eremophila punicea NC_077312.1 151561 View on NCBI ↗
Eremophila pusilliflora NC_068057.1 151725 View on NCBI ↗
Eremophila pustulata NC_077341.1 151720 View on NCBI ↗
Eremophila racemosa NC_077384.1 151704 View on NCBI ↗
Eremophila recurva NC_077421.1 151562 View on NCBI ↗
Eremophila retropila NC_077320.1 151847 View on NCBI ↗
Eremophila revoluta NC_077279.1 151552 View on NCBI ↗
Eremophila rhegos NC_077420.1 151556 View on NCBI ↗
Eremophila rigens NC_077361.1 151387 View on NCBI ↗
Eremophila rigida NC_077302.1 151797 View on NCBI ↗
Eremophila rostrata NC_077282.1 151562 View on NCBI ↗
Eremophila rugosa NC_077377.1 151560 View on NCBI ↗
Eremophila saligna NC_077438.1 151634 View on NCBI ↗
Eremophila santalina NC_077403.1 151598 View on NCBI ↗
Eremophila scaberula NC_077289.1 151578 View on NCBI ↗
Eremophila scoparia NC_077388.1 151691 View on NCBI ↗
Eremophila serpens NC_077427.1 151563 View on NCBI ↗
Eremophila serrulata NC_077311.1 151588 View on NCBI ↗
Eremophila shonae NC_077336.1 151685 View on NCBI ↗
Eremophila simulans NC_077337.1 151661 View on NCBI ↗
Eremophila spathulata NC_077316.1 151904 View on NCBI ↗
Eremophila spectabilis NC_077411.1 151648 View on NCBI ↗
Eremophila splendens NC_077375.1 151555 View on NCBI ↗
Eremophila spongiocarpa NC_068058.1 151678 View on NCBI ↗
Eremophila spuria NC_077323.1 151721 View on NCBI ↗
Eremophila stenophylla NC_077350.1 151757 View on NCBI ↗
Eremophila strongylophylla NC_077348.1 151764 View on NCBI ↗
Eremophila sturtii NC_077395.1 147638 View on NCBI ↗
Eremophila subfloccosa NC_077278.1 151553 View on NCBI ↗
Eremophila subteretifolia NC_077284.1 151555 View on NCBI ↗
Eremophila succinea NC_077393.1 151669 View on NCBI ↗
Eremophila tenella NC_077376.1 151479 View on NCBI ↗
Eremophila ternifolia NC_077285.1 151605 View on NCBI ↗
Eremophila tetraptera NC_077379.1 151652 View on NCBI ↗
Eremophila tietkensii NC_077416.1 152000 View on NCBI ↗
Eremophila undulata NC_077367.1 151634 View on NCBI ↗
Eremophila veneta NC_077277.1 151557 View on NCBI ↗
Eremophila verrucosa NC_077428.1 151745 View on NCBI ↗
Eremophila verticillata NC_077290.1 151603 View on NCBI ↗
Eremophila virens NC_077286.1 151555 View on NCBI ↗
Eremophila viscida NC_077287.1 147471 View on NCBI ↗
Eremophila viscimarginata NC_077426.1 151680 View on NCBI ↗
Eremophila weldii NC_077270.1 151744 View on NCBI ↗
Eremophila willsii NC_077267.1 151723 View on NCBI ↗
Eremophila yinnetharrensis NC_077419.1 151554 View on NCBI ↗
Eremophila youngii NC_077415.1 151468 View on NCBI ↗