Markers + reference

Dendrosenecio

11 species · Asteraceae · Asterales

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Species 11
Genome length 151–151 kb
Candidate markers 267
Primer pairs 110

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 420 0.0208 1.00 42.8 yes View details
psbK-psbI LSC 431 0.0032 1.00 36.7 yes View details
trnC-GCA-petN LSC 814 0.0021 1.00 47.0 yes View details
atpI-atpH LSC 1109 0.0016 1.00 43.0 yes View details
atpA LSC 1527 0.0007 1.00 42.2 yes View details
trnS-GGA-rps4 LSC 310 0.0034 1.00 32.9 yes View details
psbE-petL LSC 1233 0.0021 1.00 45.1 yes View details
psbB-psbT LSC 196 0.0000 1.00 32.4 yes View details
ycf1 SSC 5079 0.0009 1.00 49.9 yes View details
ndhI-ndhG SSC 361 0.0089 1.00 55.2 yes View details
rpl32-ndhF SSC 1060 0.0023 1.00 55.2 yes View details
psaA-ycf3 LSC 706 0.0003 0.99 48.0 yes View details
petD-rpoA LSC 200 0.0045 1.00 46.9 yes View details
clpP LSC 2030 0.0011 1.00 46.7 yes View details
ndhC-trnV-UAC LSC 774 0.0016 1.00 45.0 yes View details
rps16-trnQ-UUG LSC 958 0.0017 1.00 44.8 yes View details
trnF-GAA-ndhJ LSC 690 0.0014 1.00 44.6 yes View details
trnT-UGU-trnL-UAA LSC 578 0.0006 1.00 44.5 yes View details
ycf3-trnS-GGA LSC 855 0.0006 1.00 44.1 yes View details
petA-psbJ LSC 754 0.0005 1.00 44.0 yes View details
petD LSC 1199 0.0007 1.00 44.0 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 110 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 537–538 1.000 79.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 551–552 1.000 79.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 550–551 1.000 79.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 552–553 1.000 79.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 538–539 1.000 78.9
trnK-UUU_p1 trnK-UUU ACGTATATGCCCGTGTCAAC AGGGGATGGTCTAGCATTTT 2971–2995 1.000 65.5
trnK-UUU_p2 trnK-UUU ACATGACGTATATGCCCGTG AGGGGATGGTCTAGCATTTT 2976–3000 1.000 64.9
trnK-UUU_p3 trnK-UUU CATGACGTATATGCCCGTGT AGGGGATGGTCTAGCATTTT 2975–2999 1.000 64.9
trnK-UUU_p4 trnK-UUU GACGTATATGCCCGTGTCAA AGGGGATGGTCTAGCATTTT 2972–2996 1.000 64.4
trnK-UUU_p5 trnK-UUU ACGTATATGCCCGTGTCAAC AGGGGATGGTCTAGCATTTTT 2971–2995 1.000 63.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1031–1032 1.000 78.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AGAATAAGAATCCACGCCGG GAGGTTCGAATCCTTCCGTC 1063–1064 1.000 77.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1046–1047 1.000 76.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1045–1046 1.000 76.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1035–1036 1.000 73.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCTGGATTACG 566–568 1.000 72.9
psbK-psbI_p2 psbK-psbI TATGCCAGTCATACCCCTGT TCTTCACGTCCTGGATTACG 606–608 1.000 71.8
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCTGGATTACG 563–565 1.000 70.9
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCTGGATTACG 564–566 1.000 70.9
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCTGGATTACG 565–567 1.000 70.9
trnC-GCA-petN_p1 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 927 1.000 79.0
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 870 1.000 78.7
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 888 1.000 76.5
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 928 1.000 73.9
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 926 1.000 73.0
atpI-atpH_p1 atpI-atpH TTTTTGCAACTTTAGCCGCG ATAACGGAAGCGGCAGAAAT 1196–1198 1.000 75.9
atpI-atpH_p2 atpI-atpH TTTTTGCAACTTTAGCCGCG TACCTTGACCAACTCCAGGT 1252–1254 1.000 75.3
atpI-atpH_p3 atpI-atpH TTTTTGCAACTTTAGCCGCG AGCCAATCCAGCAGCAATAA 1212–1214 1.000 75.0
atpI-atpH_p4 atpI-atpH TCAGTGGTTCCTATCCCTGT ATAACGGAAGCGGCAGAAAT 1257–1259 1.000 74.9
atpI-atpH_p5 atpI-atpH TTTTTGCAACTTTAGCCGCG AATAACGGAAGCGGCAGAAA 1197–1199 1.000 74.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Dendrosenecio adnivalis subsp. friesiorum MK778419.1 150539 View on NCBI ↗
Dendrosenecio battiscombei NC_036833.1 150556 View on NCBI ↗
Dendrosenecio brassiciformis NC_037960.1 150551 View on NCBI ↗
Dendrosenecio cheranganiensis NC_037956.1 150606 View on NCBI ↗
Dendrosenecio erici-rosenii MK778420.1 150545 View on NCBI ↗
Dendrosenecio erici-rosenii subsp. alticola MK778421.1 150551 View on NCBI ↗
Dendrosenecio johnstonii NC_037959.1 150607 View on NCBI ↗
Dendrosenecio keniensis NC_036832.1 150548 View on NCBI ↗
Dendrosenecio keniodendron NC_036831.1 150555 View on NCBI ↗
Dendrosenecio kilimanjari NC_037957.1 150593 View on NCBI ↗
Dendrosenecio meruensis NC_037958.1 150587 View on NCBI ↗