Markers + reference

Senecio

12 species · Asteraceae · Asterales

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Species 12
Genome length 150–151 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1102 0.0116 1.00 58.5 yes View details
rps16-trnQ-UUG LSC 973 0.0174 0.99 62.5 yes View details
trnS-GCU-trnC-GCA LSC 745 0.0145 1.00 66.9 yes View details
trnC-GCA-petN LSC 798 0.0227 1.00 73.1 yes View details
trnT-GGU-psbD LSC 1204 0.0134 1.00 60.3 yes View details
psbZ-trnG-UCC LSC 293 0.0105 0.99 40.4 yes View details
trnT-UGU-trnL-UAA LSC 575 0.0193 0.98 72.7 yes View details
trnF-GAA-ndhJ LSC 693 0.0130 1.00 63.5 yes View details
rbcL LSC 1458 0.0077 1.00 49.3 yes View details
ycf1 SSC 5067 0.0108 1.00 52.4 yes View details
trnL-UAG-rpl32 SSC 838 0.0186 1.00 63.7 yes View details
rpl32-ndhF SSC 1026 0.0134 1.00 56.6 yes View details
ycf1 IRa 567 0.0017 1.00 26.3 no View details
trnH-GUG-psbA LSC 254 0.0225 1.00 71.6 yes View details
atpF-atpA LSC 77 0.0533 0.99 71.4 yes View details
atpI-atpH LSC 1099 0.0113 1.00 70.5 yes View details
psbC-trnS-UGA LSC 233 0.0209 0.99 70.5 yes View details
ycf3-trnS-GGA LSC 911 0.0132 0.99 67.3 yes View details
ndhD-ccsA SSC 273 0.0169 1.00 66.9 yes View details
ndhC-trnV-UAC LSC 750 0.0166 1.00 66.5 yes View details
petA-psbJ LSC 758 0.0117 1.00 66.5 yes View details
rps18-rpl20 LSC 276 0.0201 1.00 66.2 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 373–543 1.000 83.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 387–557 1.000 83.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 386–556 1.000 83.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 388–558 1.000 83.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 374–544 1.000 83.1
rps16_p1 rps16 AGAAATCACTATCCTACCCTTAGT CCGAGCGAACCAATGACTAT 1218–1244 1.000 45.0
rps16_p2 rps16 AGAAATCACTATCCTACCCTTAGT GTCTATGTACCGAGCGAACC 1227–1253 1.000 44.9
rps16_p3 rps16 AGAAATCACTATCCTACCCT GTCTATGTACCGAGCGAACC 1227–1253 1.000 44.9
rps16_p4 rps16 AGAAATCACTATCCTACCCTT GTCTATGTACCGAGCGAACC 1227–1253 1.000 44.9
rps16_p5 rps16 AGAAATCACTATCCTACCCTTAGT TCTATGTACCGAGCGAACCA 1226–1252 1.000 44.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1030–1046 1.000 85.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1045–1061 1.000 83.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1044–1060 1.000 83.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1034–1050 1.000 80.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGAATAAGAATCCACGGCGG GAGGTTCGAATCCTTCCGTC 1062–1078 0.833 75.7
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 592–915 1.000 86.5
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 574–897 1.000 84.4
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 528–851 1.000 82.9
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 593–916 1.000 82.3
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 510–833 1.000 80.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 836–874 1.000 88.4
trnC-GCA-petN_p2 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 893–931 1.000 88.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 854–892 1.000 86.0
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 894–932 1.000 83.2
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 892–930 1.000 82.4
atpI-atpH_p1 atpI-atpH TTTTTGCAACTTTAGCCGCG ATAACGGAAGCGGCAGAAAT 1177–1211 1.000 82.5
atpI-atpH_p2 atpI-atpH TTTTTGCAACTTTAGCCGCG TACCTTGACCAACTCCAGGT 1233–1267 1.000 81.6
atpI-atpH_p3 atpI-atpH TTTTTGCAACTTTAGCCGCG AGCCAATCCAGCAGCAATAA 1193–1227 1.000 81.5
atpI-atpH_p4 atpI-atpH TTTTTGCAACTTTAGCCGCG AATAACGGAAGCGGCAGAAA 1178–1212 1.000 81.3
atpI-atpH_p5 atpI-atpH TCAGTGGTTCCTATCCCTGT ATAACGGAAGCGGCAGAAAT 1238–1272 1.000 81.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Senecio drukensis PP525151.1 150968 View on NCBI ↗
Senecio graciliflorus PP525152.1 151210 View on NCBI ↗
Senecio keniophytum MH483946.1 151413 View on NCBI ↗
Senecio moorei MH483949.1 151204 View on NCBI ↗
Senecio nemorensis NC_084102.1 151220 View on NCBI ↗
Senecio petrophyus NC_085200.1 151247 View on NCBI ↗
Senecio purtschelleri MH483947.1 151191 View on NCBI ↗
Senecio roseiflorus MH483948.1 151228 View on NCBI ↗
Senecio scandens NC_073505.1 150439 View on NCBI ↗
Senecio schweinfurthii MH483950.1 151260 View on NCBI ↗
Senecio thianschanicus PP525154.1 150907 View on NCBI ↗
Senecio vulgaris NC_046693.1 150806 View on NCBI ↗