Markers + reference

Launaea

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–154 kb
Candidate markers 265
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 408 0.0637 1.00 85.2 yes View details
rps16-trnQ LSC 955 0.0168 1.00 60.6 yes View details
trnC-petN LSC 832 0.0263 0.96 62.8 yes View details
trnT-trnL LSC 581 0.0295 0.99 67.8 yes View details
ndhC-trnV LSC 1260 0.0202 0.94 63.8 yes View details
accD-psaI LSC 824 0.0205 0.89 64.2 yes View details
ycf4-cemA LSC 853 0.0197 0.95 60.4 yes View details
ycf1 SSC 4998 0.0204 1.00 52.5 yes View details
ndhG SSC 531 0.0188 1.00 58.8 yes View details
trnL-rpl32 SSC 927 0.0221 0.98 67.2 yes View details
petA-psbJ LSC 780 0.0181 0.99 69.9 yes View details
atpI-atpH LSC 1168 0.0115 0.97 68.6 yes View details
ndhA-ndhI SSC 78 0.0256 1.00 67.2 yes View details
trnR-trnT LSC 1259 0.0112 0.92 66.6 yes View details
rpl14-rpl16 LSC 125 0.0167 0.96 65.9 yes View details
trnT-psbD LSC 1377 0.0120 0.90 65.3 yes View details
trnW-trnP LSC 162 0.0370 1.00 65.1 yes View details
ycf1-rps15 SSC 403 0.0223 1.00 64.6 yes View details
petB-petD LSC 846 0.0095 1.00 64.2 yes View details
rrn5-trnR IRb 257 0.0195 1.00 63.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 526–537 1.000 80.2
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 540–551 1.000 80.1
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 539–550 1.000 80.1
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 541–552 1.000 80.0
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 527–538 1.000 79.7
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1028–1032 1.000 79.5
rps16-trnQ_p2 rps16-trnQ CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1043–1047 1.000 77.7
rps16-trnQ_p3 rps16-trnQ GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1042–1046 1.000 77.7
rps16-trnQ_p4 rps16-trnQ AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1032–1036 1.000 74.8
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1058–1062 1.000 74.7
trnC-petN_p1 trnC-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 874–889 1.000 83.3
trnC-petN_p2 trnC-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 892–907 1.000 81.0
trnC-petN_p3 trnC-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 873–888 1.000 77.4
trnC-petN_p4 trnC-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 882–897 1.000 77.3
trnC-petN_p5 trnC-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 931–946 1.000 76.4
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1266–1304 1.000 80.9
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA TACCTTGACCAACTCCAGGT 1322–1360 1.000 80.2
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1282–1320 1.000 80.0
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1267–1305 1.000 79.8
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA GCAGTACCTTGACCAACTCC 1326–1364 1.000 79.6
trnR-trnT_p1 trnR-trnT AGAAGACCTCTGTCCTATCCA ATTTGAACCGAGGGCTTACG 1258–1359 1.000 66.3
trnR-trnT_p2 trnR-trnT AGGTTTAGAAGACCTCTGTCCT ATTTGAACCGAGGGCTTACG 1264–1365 1.000 65.6
trnR-trnT_p3 trnR-trnT AGAAGACCTCTGTCCTATCCA GGATTTGAACCGAGGGCTTA 1260–1361 1.000 65.1
trnR-trnT_p4 trnR-trnT AGGTTTAGAAGACCTCTGTCCT GGATTTGAACCGAGGGCTTA 1266–1367 1.000 64.4
trnR-trnT_p5 trnR-trnT AGAAGACCTCTGTCCTATCCA ACGCCTTACCATGGGATTAC 1241–1342 1.000 63.3
trnT-psbD_p1 trnT-psbD CGTAAGCCCTCGGTTCAAAT GGACCAGCCTACAAAAACGA 1401–1512 1.000 81.8
trnT-psbD_p2 trnT-psbD TCCATGAACCAAGCCCTTTT GGACCAGCCTACAAAAACGA 1457–1568 1.000 80.7
trnT-psbD_p3 trnT-psbD TTCCATGAACCAAGCCCTTT GGACCAGCCTACAAAAACGA 1458–1569 1.000 80.7
trnT-psbD_p4 trnT-psbD CGTAAGCCCTCGGTTCAAAT ACAAAAACGAAACGGTCCCT 1391–1502 1.000 80.7
trnT-psbD_p5 trnT-psbD TAAGCCCTCGGTTCAAATCC GGACCAGCCTACAAAAACGA 1399–1510 1.000 80.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Launaea arborescens NC_060827.1 154086 View on NCBI ↗
Launaea nudicaulis NC_060828.1 153119 View on NCBI ↗