Markers + reference

Leontopodium

27 species · Asteraceae · Asterales

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Species 27
Genome length 151–151 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-UGA-psbZ LSC 337 0.0025 1.00 40.9 yes View details
rbcL LSC 1458 0.0021 1.00 47.1 yes View details
accD-psaI LSC 849 0.0010 1.00 48.8 yes View details
petA-psbJ LSC 764 0.0055 1.00 45.6 yes View details
ycf1 SSC 5118 0.0012 1.00 37.2 yes View details
ndhD SSC 1569 0.0014 1.00 42.3 yes View details
trnL-UAG-rpl32 SSC 547 0.0060 1.00 55.3 yes View details
rpl32-ndhF SSC 1017 0.0021 1.00 55.8 yes View details
ycf1 IRa 580 0.0012 1.00 42.8 no View details
ycf3 LSC 1940 0.0005 1.00 49.3 yes View details
trnG-UCC-psbD LSC 1633 0.0008 1.00 48.7 yes View details
atpI-atpH LSC 1108 0.0004 1.00 47.4 yes View details
psaA-ycf3 LSC 764 0.0010 1.00 47.3 yes View details
ndhC-trnV-UAC LSC 1189 0.0009 1.00 47.3 yes View details
rpl16 LSC 1382 0.0005 1.00 47.3 yes View details
trnT-UGU-trnL-UAA LSC 548 0.0016 1.00 47.0 yes View details
trnK-UUU-rps16 LSC 783 0.0010 1.00 46.9 yes View details
ycf4-cemA LSC 481 0.0009 1.00 46.9 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 978–984 1.000 77.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 977–983 1.000 77.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 917–923 1.000 77.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 916–922 1.000 77.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1002–1008 1.000 76.5
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1240–1252 0.963 77.6
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA TACCTTGACCAACTCCAGGT 1296–1308 0.963 76.9
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1256–1268 0.963 76.7
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1241–1253 0.963 76.4
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA GCAGTACCTTGACCAACTCC 1300–1312 0.963 76.3
trnG-UCC-psbD_p1 trnG-UCC-psbD AATCAAACCGAAAGACCCCT GAAACGGTCCCTACGTAACC 1769–1796 1.000 74.4
trnG-UCC-psbD_p2 trnG-UCC-psbD ATCAAACCGAAAGACCCCTT GAAACGGTCCCTACGTAACC 1768–1795 1.000 74.4
trnG-UCC-psbD_p3 trnG-UCC-psbD GAATCAAACCGAAAGACCCCT GAAACGGTCCCTACGTAACC 1770–1797 1.000 72.5
trnG-UCC-psbD_p4 trnG-UCC-psbD AATCAAACCGAAAGACCCCT ACAAAAACGAAACGGTCCCT 1777–1804 1.000 72.5
trnG-UCC-psbD_p5 trnG-UCC-psbD ATCAAACCGAAAGACCCCTT ACAAAAACGAAACGGTCCCT 1776–1803 1.000 72.5
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 455–459 1.000 79.4
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GACCAACCATCAGGAGAAGC 457–461 1.000 79.0
trnS-UGA-psbZ_p3 trnS-UGA-psbZ TCAACCACTCAGCCATCTCT CCAACCATCAGGAGAAGCAA 456–460 1.000 76.8
trnS-UGA-psbZ_p4 trnS-UGA-psbZ TCAACCACTCAGCCATCTCT GACCAACCATCAGGAGAAGC 458–462 1.000 76.4
trnS-UGA-psbZ_p5 trnS-UGA-psbZ TTCAACCACTCAGCCATCTC CCAACCATCAGGAGAAGCAA 457–461 1.000 75.7
psaA-ycf3_p1 psaA-ycf3 AGAAATGACCCGGTTTAGCC AGCCGCTGAGTATTGGAAAC 953–957 1.000 78.0
psaA-ycf3_p2 psaA-ycf3 AGAAATGACCCGGTTTAGCC CAAGCCGCTGAGTATTGGAA 955–959 1.000 78.0
psaA-ycf3_p3 psaA-ycf3 CCCATGCCTCGAATGAAGTT AGCCGCTGAGTATTGGAAAC 935–939 1.000 77.1
psaA-ycf3_p4 psaA-ycf3 CCCATGCCTCGAATGAAGTT CAAGCCGCTGAGTATTGGAA 937–941 1.000 77.1
psaA-ycf3_p5 psaA-ycf3 GTTTAGCCCATGCCTCGAAT AGCCGCTGAGTATTGGAAAC 941–945 1.000 76.5
ycf3_p1 ycf3 TGATGGGGCCAACAAACAAT TCCCGCGAGAAGTAATGAGA 2098–2106 1.000 76.5
ycf3_p2 ycf3 TGATGGGGCCAACAAACAAT GGATCATTTTCCCGCGAGAA 2107–2115 1.000 75.8
ycf3_p3 ycf3 TGATGGGGCCAACAAACAAT ATCATTTTCCCGCGAGAAGT 2105–2113 1.000 75.2
ycf3_p4 ycf3 TGATGGGGCCAACAAACAAT CCCGCGAGAAGTAATGAGAA 2097–2105 1.000 73.8
ycf3_p5 ycf3 TGATGGGGCCAACAAACAAT TTCCCGCGAGAAGTAATGAG 2099–2107 1.000 73.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (27)

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

Species Accession Length (bp) Link
Leontopodium andersonii NC_072078.1 151128 View on NCBI ↗
Leontopodium artemisiifolium NC_072079.1 151073 View on NCBI ↗
Leontopodium calocephalum NC_072080.1 151100 View on NCBI ↗
Leontopodium campestre NC_072081.1 151122 View on NCBI ↗
Leontopodium conglobatum NC_072082.1 151077 View on NCBI ↗
Leontopodium dedekensii NC_072083.1 151071 View on NCBI ↗
Leontopodium delavayanum NC_072084.1 151138 View on NCBI ↗
Leontopodium fangingense NC_072085.1 150754 View on NCBI ↗
Leontopodium forrestianum NC_072086.1 151143 View on NCBI ↗
Leontopodium franchetii NC_072087.1 151095 View on NCBI ↗
Leontopodium giraldii NC_072088.1 151093 View on NCBI ↗
Leontopodium himalayanum NC_072089.1 151107 View on NCBI ↗
Leontopodium jacotianum NC_072090.1 151074 View on NCBI ↗
Leontopodium japonicum NC_072091.1 151117 View on NCBI ↗
Leontopodium japonicum var. saxatile OP963982.1 151063 View on NCBI ↗
Leontopodium leiolepis NC_027835.1 151072 View on NCBI ↗
Leontopodium leontopodioides NC_072092.1 151138 View on NCBI ↗
Leontopodium longifolium NC_072093.1 151072 View on NCBI ↗
Leontopodium muscoides NC_072094.1 151135 View on NCBI ↗
Leontopodium nanum NC_072095.1 151132 View on NCBI ↗
Leontopodium ochroleucum NC_072096.1 151141 View on NCBI ↗
Leontopodium pusillum NC_072097.1 151130 View on NCBI ↗
Leontopodium sinense NC_072098.1 151072 View on NCBI ↗
Leontopodium smithianum NC_072099.1 151103 View on NCBI ↗
Leontopodium souliei NC_072100.1 151138 View on NCBI ↗
Leontopodium stracheyi NC_072101.1 151131 View on NCBI ↗
Leontopodium wilsonii NC_072102.1 151105 View on NCBI ↗