Markers + reference

Sinosenecio

7 species · Asteraceae · Asterales

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Species 7
Genome length 150–152 kb
Candidate markers 272
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 834 0.0198 0.97 77.5 yes View details
rps16 LSC 1096 0.0134 1.00 55.1 yes View details
psbK-psbI LSC 450 0.0229 1.00 59.4 yes View details
trnC-GCA-petN LSC 796 0.0115 1.00 68.0 yes View details
atpA LSC 1527 0.0026 1.00 35.3 yes View details
trnT-UGU-trnL-UAA LSC 632 0.0218 0.98 68.4 yes View details
trnF-GAA-ndhJ LSC 773 0.0151 0.96 56.7 yes View details
accD-psaI LSC 656 0.0266 0.99 64.6 yes View details
ycf1 IRb 597 0.0089 1.00 39.3 no View details
ndhF-rpl32 SSC 1034 0.0196 1.00 58.2 yes View details
ycf1 SSC 5088 0.0125 1.00 50.6 yes View details
atpA-trnR-UCU LSC 116 0.0511 1.00 71.9 yes View details
psbI-trnS-GCU LSC 138 0.0348 1.00 67.8 yes View details
ndhC-trnV-UAC LSC 774 0.0143 0.98 67.0 yes View details
trnH-GUG-psbA LSC 409 0.0193 1.00 65.8 yes View details
psbE-petL LSC 1214 0.0097 1.00 65.8 yes View details
pafI-trnS-GGA LSC 889 0.0107 1.00 63.5 yes View details
trnS-GCU-trnC-GCA LSC 736 0.0114 1.00 63.4 yes View details
rpl14-rpl16 LSC 117 0.0288 0.98 63.2 yes View details
trnL-UAG-ccsA SSC 116 0.0183 1.00 63.1 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 100 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 520–542 1.000 81.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 534–556 1.000 81.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 533–555 1.000 81.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 535–557 1.000 81.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 521–543 1.000 80.8
trnK-UUU_p1 trnK-UUU ACTATGACAATGGGTTGCACA TCTGATTGTATCTACATATCCTTT 2673–2691 1.000 43.0
trnK-UUU_p2 trnK-UUU ACTATGACAATGGGTTGCACA TTCTGATTGTATCTACATATCCTT 2674–2692 1.000 43.0
trnK-UUU_p3 trnK-UUU ACTATGACAATGGGTTGCACA TCTGATTGTATCTACATATCCTTTT 2673–2691 1.000 43.0
trnK-UUU_p4 trnK-UUU ACTATGACAATGGGTTGCACA TTCTGATTGTATCTACATATCCTTT 2674–2692 1.000 43.0
trnK-UUU_p5 trnK-UUU ACTATGACAATGGGTTGCACA TCTGATTGTATCTACATATCCTTTTTC 2676–2691 0.714 30.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 943–980 1.000 82.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 942–979 1.000 82.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 958–995 1.000 81.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1028–1065 1.000 81.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 1027–1064 1.000 81.1
rps16_p1 rps16 ACTTGTGTTGGATTGGCACT GTCTATGTACCGAGCGAACC 1558–1591 1.000 82.9
rps16_p2 rps16 ACTTGTGTTGGATTGGCACT CCGAGCGAACCAATGACTAT 1549–1582 1.000 82.0
rps16_p3 rps16 ACTTGTGTTGGATTGGCACT TCTATGTACCGAGCGAACCA 1557–1590 1.000 81.8
rps16_p4 rps16 ACTTGTGTTGGATTGGCACT TTCGGGAAGTTGGAAATGGG 1829–1862 0.857 77.3
rps16_p5 rps16 TGTTGGATTGGCACTGCATA TTCGGGAAGTTGGAAATGGG 1824–1857 0.857 76.2
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ATTGGGAGAGATGGCTGAGT 789–822 1.000 86.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCGAATCCCTCTCTTTCCGT 716–749 1.000 86.2
psbK-psbI_p3 psbK-psbI TTCGTCAATTCCAGCCCAAA ATTGGGAGAGATGGCTGAGT 1241–1288 1.000 85.8
psbK-psbI_p4 psbK-psbI TTCGTCAATTCCAGCCCAAA TCGAATCCCTCTCTTTCCGT 1168–1215 1.000 85.6
psbK-psbI_p5 psbK-psbI TTCGTCAATTCCAGCCCAAA CCTCTCTTTCCGTTTCCGTT 1161–1208 1.000 85.5
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCAGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 249–256 1.000 78.0
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCAGGACGTGAAGA CGAGTTATTCGTACCGAGGG 197–204 1.000 77.3
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCAGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 249–256 1.000 75.6
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCCAATGATCCAGGACG ATTGGGAGAGATGGCTGAGT 268–275 1.000 74.4
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCAGGACGTGAAGA GATGGCTGAGTGGACGAAAG 240–247 1.000 74.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Sinosenecio albonervius NC_061767.1 151224 View on NCBI ↗
Sinosenecio baojingensis MZ325394.1 151315 View on NCBI ↗
Sinosenecio chienii PV748923.1 151993 View on NCBI ↗
Sinosenecio eriopodus PQ164523.1 151212 View on NCBI ↗
Sinosenecio jishouensis NC_057061.1 151257 View on NCBI ↗
Sinosenecio oldhamianus NC_057622.1 150926 View on NCBI ↗
Sinosenecio yaanensis PV748924.1 150344 View on NCBI ↗