Markers + reference

Lobelia

45 species · Campanulaceae · Asterales

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Species 45
Genome length 162–167 kb
Candidate markers 283
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ORF198 LSC 597 0.1572 0.98 80.3 yes View details
ORF304 LSC 915 0.1228 1.00 82.6 yes View details
ORF304-trnC (GCA) LSC 466 0.0848 0.98 75.7 yes View details
ndhC-ORF227 LSC 453 0.0654 1.00 75.9 yes View details
ORF227 LSC 684 0.0955 1.00 79.5 yes View details
trnL (UAG)-rpl32 SSC 716 0.0512 1.00 81.0 yes View details
rpl32-ndhF SSC 1075 0.0433 1.00 80.5 yes View details
psbA-rbcL LSC 1032 0.0314 1.00 87.4 yes View details
trnH (GUG)-psbA LSC 341 0.0432 1.00 83.5 yes View details
rbcL-atpB LSC 817 0.0272 1.00 80.8 yes View details
rpl16-rps3 LSC 165 0.0519 1.00 78.8 yes View details
psbE-petL LSC 932 0.0191 1.00 76.5 yes View details
psbM-trnD (GUC) LSC 1013 0.0234 1.00 75.9 yes View details
atpH-atpI LSC 795 0.0302 1.00 75.8 yes View details
trnK (UUU)-rps16 LSC 487 0.0398 1.00 75.7 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
trnH (GUG)-psbA_p1 trnH (GUG)-psbA CAATCCACTGCCTTCATCCA CCGTGCTAACCTTGGTATGG 313–525 1.000 88.2
trnH (GUG)-psbA_p2 trnH (GUG)-psbA AATCCACTGCCTTCATCCAC CCGTGCTAACCTTGGTATGG 312–524 1.000 88.2
trnH (GUG)-psbA_p3 trnH (GUG)-psbA CAATCCACTGCCTTCATCCA ACCGTGCTAACCTTGGTATG 314–526 1.000 87.8
trnH (GUG)-psbA_p4 trnH (GUG)-psbA AATCCACTGCCTTCATCCAC ACCGTGCTAACCTTGGTATG 313–525 1.000 87.7
trnH (GUG)-psbA_p5 trnH (GUG)-psbA ACAATCCACTGCCTTCATCC CCGTGCTAACCTTGGTATGG 314–526 0.978 87.3
psbA-rbcL_p1 psbA-rbcL TACAGAAGCGACCCCATAGG ATTTGAGTTTGCCGCAATGG 862–1177 1.000 86.6
psbA-rbcL_p2 psbA-rbcL TACAGAAGCGACCCCATAGG GCTGCTTGTGAGGTATGGAA 891–1206 1.000 86.4
psbA-rbcL_p3 psbA-rbcL TACAGAAGCGACCCCATAGG TGAGTTTGCCGCAATGGATA 859–1174 1.000 86.3
psbA-rbcL_p4 psbA-rbcL TACAGAAGCGACCCCATAGG AGTTTGCCGCAATGGATACT 857–1172 1.000 86.2
psbA-rbcL_p5 psbA-rbcL ATCCAGTTACAGAAGCGACC ATTTGAGTTTGCCGCAATGG 869–1184 1.000 85.9
rbcL-atpB_p1 rbcL-atpB ACACCAGCTTTGAATCCAACA CAATGATTTGGCCGATACGC 860–956 1.000 81.0
rbcL-atpB_p2 rbcL-atpB AGTCTCTGTTTGTGGTGACA CAATGATTTGGCCGATACGC 831–927 1.000 80.7
rbcL-atpB_p3 rbcL-atpB ACACCAGCTTTGAATCCAACA CCCCAGAACCAGAAGGAGTA 812–908 0.978 80.1
rbcL-atpB_p4 rbcL-atpB ACACCAGCTTTGAATCCAACA AGCTACATCTAGGACCGGAC 880–976 0.911 77.6
rbcL-atpB_p5 rbcL-atpB AGTCTCTGTTTGTGGTGACA AGCTACATCTAGGACCGGAC 851–947 0.911 77.3
trnK (UUU)-rps16_p1 trnK (UUU)-rps16 AAAGCCGAGTACTCTACCGT AACGAACTTTGCCCCAATCA 548–672 0.867 82.9
trnK (UUU)-rps16_p2 trnK (UUU)-rps16 AAAGCCGAGTACTCTACCGT ACGAACTTTGCCCCAATCAA 547–671 0.867 82.9
trnK (UUU)-rps16_p3 trnK (UUU)-rps16 AAGCCGAGTACTCTACCGTT AACGAACTTTGCCCCAATCA 547–671 0.867 82.9
trnK (UUU)-rps16_p4 trnK (UUU)-rps16 AAGCCGAGTACTCTACCGTT ACGAACTTTGCCCCAATCAA 546–670 0.867 82.9
trnK (UUU)-rps16_p5 trnK (UUU)-rps16 TCAGTCGTGGTCTTCCAAAC ACGAACTTTGCCCCAATCAA 632–780 0.867 82.4
ORF198_p1 ORF198 TATCAAAGCGCATCCAACGA TTGTCGCTAGAGATTTGGGC 1664–2387 0.533 73.0
ORF198_p2 ORF198 AGCGAACATCAATTGCAACG TTGTCGCTAGAGATTTGGGC 1177–1821 0.511 72.0
ORF198_p3 ORF198 CGCATCCAACGAACTCCTTA TTGTCGCTAGAGATTTGGGC 1656–2379 0.489 71.3
ORF198_p4 ORF198 CGCATCCAACGAACTCCTTA TGACACGGGCAGTTGTAAAA 1572–1622 0.244 54.7
ORF198_p5 ORF198 TATCAAAGCGCATCCAACGA TGACACGGGCAGTTGTAAAA 1580–1630 0.244 54.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 918–959 1.000 89.6
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 934–975 1.000 88.7
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TCCCTGTCATGTTCCTTGGA 919–960 1.000 88.5
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 933–974 1.000 88.2
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 928–969 1.000 87.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (45)

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

Species Accession Length (bp) Link
Lobelia aberdarica NC_035365.1 163902 View on NCBI ↗
Lobelia acrochila NC_035366.1 164047 View on NCBI ↗
Lobelia bambuseti NC_035368.1 164051 View on NCBI ↗
Lobelia boninensis NC_033367.1 162436 View on NCBI ↗
Lobelia burttii subsp. burttii MF061183.1 163847 View on NCBI ↗
Lobelia burttii subsp. meruensis MF061184.1 163874 View on NCBI ↗
Lobelia burttii subsp. telmaticola MF061185.1 163808 View on NCBI ↗
Lobelia chinensis NC_035370.1 164396 View on NCBI ↗
Lobelia clavata NC_079627.1 165295 View on NCBI ↗
Lobelia colorata NC_079628.1 166173 View on NCBI ↗
Lobelia davidii NC_035372.1 166287 View on NCBI ↗
Lobelia deckenii subsp. deckenii MF061190.1 164120 View on NCBI ↗
Lobelia deckenii subsp. incipiens MF061191.1 164178 View on NCBI ↗
Lobelia doniana NC_035373.1 165003 View on NCBI ↗
Lobelia erectiuscula NC_079629.1 165119 View on NCBI ↗
Lobelia fenshamii MF061211.1 163860 View on NCBI ↗
Lobelia giberroa NC_035374.1 164477 View on NCBI ↗
Lobelia gregoriana subsp. elgonensis MF061194.1 164305 View on NCBI ↗
Lobelia gregoriana subsp. gregoriana MF061195.1 164389 View on NCBI ↗
Lobelia gregoriana subsp. sattimae KY354218.1 164349 View on NCBI ↗
Lobelia iteophylla NC_079631.1 165228 View on NCBI ↗
Lobelia jasionoides NC_033369.1 165612 View on NCBI ↗
Lobelia kauaensis NC_035375.1 165063 View on NCBI ↗
Lobelia laxiflora NC_033370.1 167217 View on NCBI ↗
Lobelia longisepala NC_033371.1 163840 View on NCBI ↗
Lobelia lukwangulensis NC_035376.1 163845 View on NCBI ↗
Lobelia melliana NC_035377.1 165413 View on NCBI ↗
Lobelia montana NC_079632.1 166239 View on NCBI ↗
Lobelia morogoroensis NC_033372.1 162826 View on NCBI ↗
Lobelia muscoides NC_035379.1 164719 View on NCBI ↗
Lobelia organensis NC_035382.1 163974 View on NCBI ↗
Lobelia pleotricha NC_079633.1 164966 View on NCBI ↗
Lobelia polyphylla NC_033373.1 167088 View on NCBI ↗
Lobelia pyramidalis NC_079634.1 165024 View on NCBI ↗
Lobelia rhynchopetalum NC_035384.1 164254 View on NCBI ↗
Lobelia ritabeaniana NC_035385.1 163440 View on NCBI ↗
Lobelia seguinii NC_035387.1 166534 View on NCBI ↗
Lobelia sessilifolia NC_035388.1 165656 View on NCBI ↗
Lobelia stricklandiae NC_033374.1 163930 View on NCBI ↗
Lobelia taliensis NC_079635.1 164928 View on NCBI ↗
Lobelia telekii NC_035390.1 164360 View on NCBI ↗
Lobelia thuliniana NC_033375.1 163459 View on NCBI ↗
Lobelia udzungwensis NC_035392.1 163628 View on NCBI ↗
Lobelia urens NC_035393.1 165407 View on NCBI ↗
Lobelia wollastonii NC_035394.1 164711 View on NCBI ↗