Markers + reference

Artemisia

126 species · Asteraceae · Asterales

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Species 126
Genome length 151–151 kb
Candidate markers 270
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 382 0.0130 1.00 63.0 yes View details
petN-psbM LSC 533 0.0097 1.00 67.6 yes View details
trnR-UCU-trnG-UCC LSC 265 0.0375 0.78 59.6 yes View details
trnT-UGU-trnL-UAA LSC 521 0.0146 0.97 65.9 yes View details
ndhC-trnV-UAC LSC 1183 0.0082 0.97 59.3 yes View details
accD LSC 1503 0.0050 1.00 40.2 yes View details
rpl16 LSC 1434 0.0061 1.00 47.1 yes View details
ycf1 IRb 513 0.0038 1.00 49.2 no View details
ndhF-rpl32 SSC 1003 0.0084 0.99 71.4 yes View details
rpl32-trnL-UAG SSC 878 0.0108 1.00 74.2 yes View details
ycf1 SSC 5028 0.0067 1.00 53.2 yes View details
trnK-UUU-rps16 LSC 849 0.0081 0.99 70.2 yes View details
rps16-trnQ-UUG LSC 900 0.0079 1.00 66.1 yes View details
psaA-ycf3 LSC 716 0.0055 1.00 66.0 yes View details
atpI-atpH LSC 1127 0.0060 1.00 65.1 yes View details
trnE-UUC-rpoB LSC 870 0.0059 1.00 64.9 yes View details
psbE-petL LSC 1206 0.0052 1.00 63.3 yes View details
rpl22-rps19 LSC 92 0.0218 0.97 62.4 yes View details
ycf3-trnS-GGA LSC 840 0.0049 1.00 62.2 yes View details
ndhG-ndhI SSC 349 0.0101 1.00 61.7 yes View details
rpl16-rps3 LSC 159 0.0152 1.00 61.3 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 CCGTGCTAACCTTGGTATGG 492–583 1.000 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 506–597 1.000 88.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 505–596 1.000 88.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 507–598 1.000 88.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 493–584 1.000 87.8
trnK-UUU_p1 trnK-UUU GGGCGTGTCAACCAATATCT CGTTGGATTTGATACCCGGA 2854–2990 0.960 85.1
trnK-UUU_p2 trnK-UUU GGGCGTGTCAACCAATATCT TCGTTGGATTTGATACCCGG 2855–2991 0.960 85.1
trnK-UUU_p3 trnK-UUU TGGGCGTGTCAACCAATATC CGTTGGATTTGATACCCGGA 2855–2991 0.976 84.2
trnK-UUU_p4 trnK-UUU TGGGCGTGTCAACCAATATC TCGTTGGATTTGATACCCGG 2856–2992 0.976 84.2
trnK-UUU_p5 trnK-UUU ATGGGCGTGTCAACCAATAT CGTTGGATTTGATACCCGGA 2856–2992 0.976 82.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 844–981 0.976 87.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 843–980 0.976 87.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GGTGCTCAACCTACAGGAAC 905–1042 0.968 87.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGATGGTATGGACGAATCCC GGTGCTCAACCTACAGGAAC 904–1041 0.968 87.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC GGTGCTCAACCTACAGGAAC 929–1066 0.976 86.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 952–1002 1.000 87.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 963–1013 1.000 87.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACACCGGATCATGTCCTTC GAGGTTCGAATCCTTCCGTC 972–1022 1.000 86.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 970–1020 1.000 85.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1023–1073 0.976 84.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 664–712 1.000 70.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 664–712 1.000 68.6
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 665–713 1.000 64.4
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 656–704 1.000 64.3
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 650–698 0.992 63.1
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 641–1038 1.000 72.6
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 600–997 1.000 72.2
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 631–1028 1.000 71.8
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 636–1033 1.000 71.8
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 631–1028 1.000 71.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (126)

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

Species Accession Length (bp) Link
Artemisia absinthium var. calcigena MK188885.1 151193 View on NCBI ↗
Artemisia adamsii PP898105.1 151231 View on NCBI ↗
Artemisia anethifolia OP723187.1 151007 View on NCBI ↗
Artemisia anethoides OP723189.1 151094 View on NCBI ↗
Artemisia annua NC_034683.1 150952 View on NCBI ↗
Artemisia anomala OP723194.1 151367 View on NCBI ↗
Artemisia apiacea MG951483.1 151091 View on NCBI ↗
Artemisia bhutanica PP898085.1 151269 View on NCBI ↗
Artemisia blepharolepis PP898101.1 150908 View on NCBI ↗
Artemisia borotalensis NC_066237.1 151179 View on NCBI ↗
Artemisia brevifolia NC_079569.1 151145 View on NCBI ↗
Artemisia capillaris NC_031400.1 151056 View on NCBI ↗
Artemisia comaiensis PP898079.1 151298 View on NCBI ↗
Artemisia dalai-lamae OP723222.1 151103 View on NCBI ↗
Artemisia demissa OP723197.1 150826 View on NCBI ↗
Artemisia desertorum NC_063905.1 151094 View on NCBI ↗
Artemisia desertorum var. tongolensis PQ850019.1 151061 View on NCBI ↗
Artemisia deversa OP723198.1 151166 View on NCBI ↗
Artemisia dolosa OP723199.1 151097 View on NCBI ↗
Artemisia dubia PQ850012.1 151032 View on NCBI ↗
Artemisia eriopoda PQ850016.1 151105 View on NCBI ↗
Artemisia feddei MG951486.1 151112 View on NCBI ↗
Artemisia ferganensis NC_070196.1 150586 View on NCBI ↗
Artemisia finita NC_070197.1 151157 View on NCBI ↗
Artemisia forrestii OP723207.1 151125 View on NCBI ↗
Artemisia freyniana f. discolor NC_049570.1 151275 View on NCBI ↗
Artemisia frigida NC_020607.1 151076 View on NCBI ↗
Artemisia fukudo NC_044156.1 151021 View on NCBI ↗
Artemisia fulgens var. meiguensis PP898075.1 151201 View on NCBI ↗
Artemisia giraldii PQ850011.1 151045 View on NCBI ↗
Artemisia giraldii var. longipedunculata PQ850009.1 151009 View on NCBI ↗
Artemisia gmelinii NC_031399.1 151318 View on NCBI ↗
Artemisia gmelinii var. incana OP723213.1 151266 View on NCBI ↗
Artemisia gmelinii var. messerschmidiana OP723214.1 151272 View on NCBI ↗
Artemisia grenardii OP723215.1 151046 View on NCBI ↗
Artemisia gyitangensis PP898091.1 151199 View on NCBI ↗
Artemisia hallaisanensis NC_049571.1 151015 View on NCBI ↗
Artemisia halodendron OP723216.1 151096 View on NCBI ↗
Artemisia hedinii PP234576.1 151158 View on NCBI ↗
Artemisia imponens OP723219.1 151232 View on NCBI ↗
Artemisia indica ON381734.1 151161 View on NCBI ↗
Artemisia integrifolia PP898104.1 151117 View on NCBI ↗
Artemisia jacutica OP723221.1 150918 View on NCBI ↗
Artemisia japonica MG951491.1 151080 View on NCBI ↗
Artemisia jilongensis PP898086.1 151275 View on NCBI ↗
Artemisia juncea NC_070198.1 151004 View on NCBI ↗
Artemisia karatavica NC_070199.1 151114 View on NCBI ↗
Artemisia kaschgarica NC_069557.1 151091 View on NCBI ↗
Artemisia keiskeana MG951492.1 150858 View on NCBI ↗
Artemisia lactiflora NC_071925.1 151178 View on NCBI ↗
Artemisia lancea NC_071926.1 151132 View on NCBI ↗
Artemisia lavandulifolia OP723236.1 151233 View on NCBI ↗
Artemisia lercheana NC_070200.1 151089 View on NCBI ↗
Artemisia lessingiana NC_087977.1 151085 View on NCBI ↗
Artemisia leucotricha NC_070201.1 151056 View on NCBI ↗
Artemisia lingyeouruennii PP898096.1 151174 View on NCBI ↗
Artemisia littoricola PP493341.1 150985 View on NCBI ↗
Artemisia macrocephala PP234573.1 151035 View on NCBI ↗
Artemisia mairei PP898080.1 151045 View on NCBI ↗
Artemisia maritima NC_045093.1 151061 View on NCBI ↗
Artemisia marschalliana OP723226.1 150953 View on NCBI ↗
Artemisia mattfeldii OP723228.1 151183 View on NCBI ↗
Artemisia mattfeldii var. etomentosa PP898076.1 151087 View on NCBI ↗
Artemisia minchunensis NC_070202.1 151099 View on NCBI ↗
Artemisia minor PP898083.1 151083 View on NCBI ↗
Artemisia mongolica PP898103.1 151193 View on NCBI ↗
Artemisia mongolorum OP723230.1 151104 View on NCBI ↗
Artemisia montana NC_025910.1 151130 View on NCBI ↗
Artemisia myriantha OP723231.1 151128 View on NCBI ↗
Artemisia nakaii MG951494.1 151020 View on NCBI ↗
Artemisia nanschanica PQ850006.1 151031 View on NCBI ↗
Artemisia neosinensis PP898094.1 151172 View on NCBI ↗
Artemisia nortonii PP898084.1 151028 View on NCBI ↗
Artemisia obtusiloba OP723233.1 151052 View on NCBI ↗
Artemisia ordosica NC_046571.1 151209 View on NCBI ↗
Artemisia palustris OP723234.1 151038 View on NCBI ↗
Artemisia parviflora NC_086944.1 151047 View on NCBI ↗
Artemisia pewzowii OP723235.1 151013 View on NCBI ↗
Artemisia phaeolepis OP723237.1 151256 View on NCBI ↗
Artemisia phyllobotrys PP898077.1 151171 View on NCBI ↗
Artemisia prattii PQ850001.1 151052 View on NCBI ↗
Artemisia princeps NC_071927.1 151154 View on NCBI ↗
Artemisia pubescens OP723241.1 151045 View on NCBI ↗
Artemisia qingheensis NC_087976.1 151006 View on NCBI ↗
Artemisia qinlingensis PP898098.1 151181 View on NCBI ↗
Artemisia rubripes OP723242.1 151135 View on NCBI ↗
Artemisia santolina NC_070203.1 151112 View on NCBI ↗
Artemisia santonicum NC_070204.1 151256 View on NCBI ↗
Artemisia saposhnikovii OP723243.1 151077 View on NCBI ↗
Artemisia sawanensis NC_070205.1 151066 View on NCBI ↗
Artemisia schrenkiana NC_070206.1 151073 View on NCBI ↗
Artemisia scoparia NC_045286.1 151060 View on NCBI ↗
Artemisia scopiformis NC_070207.1 151017 View on NCBI ↗
Artemisia selengensis NC_039647.1 151215 View on NCBI ↗
Artemisia sericea PP898073.1 150870 View on NCBI ↗
Artemisia sichuanensis PP898074.1 151230 View on NCBI ↗
Artemisia sieversiana OP723251.1 150975 View on NCBI ↗
Artemisia smithii PP898097.1 151225 View on NCBI ↗
Artemisia sphaerocephala OP723255.1 151116 View on NCBI ↗
Artemisia stechmanniana NC_070112.1 151152 View on NCBI ↗
Artemisia stolonifera NC_049572.1 151144 View on NCBI ↗
Artemisia stricta PP898082.1 150770 View on NCBI ↗
Artemisia sublessingiana NC_070208.1 151065 View on NCBI ↗
Artemisia subulata OP723261.1 151156 View on NCBI ↗
Artemisia sylvatica PP898100.1 151200 View on NCBI ↗
Artemisia tafelii PP898088.1 151274 View on NCBI ↗
Artemisia tanacetifolia OP723263.1 151211 View on NCBI ↗
Artemisia tangutica PP898099.1 151191 View on NCBI ↗
Artemisia terrae-albae NC_070209.1 151107 View on NCBI ↗
Artemisia thellungiana OP723264.1 151221 View on NCBI ↗
Artemisia tournefortiana PP898072.1 151106 View on NCBI ↗
Artemisia transiliensis NC_070210.1 151122 View on NCBI ↗
Artemisia tridactyla PP898095.1 150654 View on NCBI ↗
Artemisia verlotiorum OP723266.1 151200 View on NCBI ↗
Artemisia vestita OP723192.1 150980 View on NCBI ↗
Artemisia viscida OP723265.1 151221 View on NCBI ↗
Artemisia viscidissima PP898078.1 151241 View on NCBI ↗
Artemisia vulgaris OP723269.1 151133 View on NCBI ↗
Artemisia waltonii PQ850004.1 151042 View on NCBI ↗
Artemisia waltonii var. waltonii PP898087.1 151038 View on NCBI ↗
Artemisia waltonii var. yushuensis PP898092.1 150636 View on NCBI ↗
Artemisia xerophytica OP723272.1 151046 View on NCBI ↗
Artemisia xigazeensis OP723273.1 151043 View on NCBI ↗
Artemisia yongii PP898089.1 151249 View on NCBI ↗
Artemisia younghusbandii PP234531.1 151042 View on NCBI ↗
Artemisia yunnanensis PP898090.1 151190 View on NCBI ↗