Markers + reference

Blumea

8 species · Asteraceae · Asterales

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Species 8
Genome length 151–151 kb
Candidate markers 262
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 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 388 0.0325 0.91 69.5 yes View details
rps16-trnQ-UUG LSC 911 0.0198 1.00 61.7 yes View details
trnC-GCA-petN LSC 833 0.0184 1.00 63.1 yes View details
psbM-trnD-GUC LSC 671 0.0158 0.94 61.0 yes View details
ndhC-trnV-UAC LSC 338 0.0345 0.75 52.5 yes View details
ndhF SSC 2229 0.0097 1.00 45.3 yes View details
ndhF-rpl32 SSC 1055 0.0192 0.99 56.8 yes View details
rpl32-trnL-UAG SSC 859 0.0188 0.99 56.7 yes View details
ccsA-ndhD SSC 266 0.0367 0.98 63.8 yes View details
ndhD SSC 1503 0.0072 1.00 46.0 yes View details
ycf1 SSC 5109 0.0137 1.00 45.2 yes View details
trnS-GCU-trnC-GCA LSC 747 0.0137 1.00 63.9 yes View details
rpl20-rps12 LSC 735 0.0125 1.00 62.6 yes View details
trnE-UUC-rpoB LSC 893 0.0150 0.99 61.0 yes View details
rps15-ycf1 SSC 400 0.0209 0.97 60.2 yes View details
ycf2-trnL-CAA IRb 415 0.0203 1.00 59.8 yes View details
trnL-CAA-ycf2 IRa 415 0.0203 1.00 59.8 yes View details
ndhG-ndhI SSC 353 0.0230 0.97 58.7 yes View details
accD-psaI LSC 719 0.0143 1.00 56.8 yes View details
rps16 LSC 1134 0.0094 0.99 55.6 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 479–514 1.000 85.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 493–528 1.000 85.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 492–527 1.000 85.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 494–529 1.000 85.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 480–515 1.000 85.1
rps16_p1 rps16 TCCTACCCTTAGTTTTTCTTTCCT ACCGACTGAACCAATGACTA 1220–1240 0.875 39.4
rps16_p2 rps16 TCCTACCCTTAGTTTTTCTTTCCT TACCGACTGAACCAATGACT 1221–1241 0.875 39.4
rps16_p3 rps16 TCCTACCCTTAGTTTTTCTTTCC ACCGACTGAACCAATGACTA 1220–1240 0.875 39.4
rps16_p4 rps16 TCCTACCCTTAGTTTTTCTTTCC TACCGACTGAACCAATGACT 1221–1241 0.875 39.4
rps16_p5 rps16 TCCTACCCTTAGTTTTTCTTTCCTT ACCGACTGAACCAATGACTA 1220–1240 0.875 39.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 982–997 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 997–1012 1.000 80.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 996–1011 1.000 80.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 986–1001 1.000 78.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1012–1027 1.000 77.8
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 802–912 1.000 84.4
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 784–894 1.000 82.2
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 738–848 1.000 80.7
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 803–913 1.000 80.2
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 720–830 1.000 78.5
trnC-GCA-petN_p1 trnC-GCA-petN TGTATATCGTTTTGGCGGCA AGCCCAAGCGAGACTTACTA 928–949 1.000 83.8
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 873–894 1.000 83.6
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 891–912 1.000 81.3
trnC-GCA-petN_p4 trnC-GCA-petN TGTATATCGTTTTGGCGGCA GCCCAAGCGAGACTTACTAT 927–948 1.000 77.8
trnC-GCA-petN_p5 trnC-GCA-petN TGTATATCGTTTTGGCGGCA ATTAAAGCAGCCCAAGCGAG 936–957 1.000 77.7
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAGGCAGTAGGAACT TTCAATAGGCAAGAGCACCG 764–803 1.000 58.2
psbM-trnD-GUC_p2 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 749–788 1.000 57.0
psbM-trnD-GUC_p3 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 743–782 1.000 56.6
psbM-trnD-GUC_p4 psbM-trnD-GUC AAGTAGAAAGGCAGTAGGAACT TTCAATAGGCAAGAGCACCG 765–804 1.000 56.3
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 746–785 1.000 55.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Blumea aromatica NC_069835.1 151275 View on NCBI ↗
Blumea axillaris PX404823.1 151063 View on NCBI ↗
Blumea balsamifera NC_077558.1 151170 View on NCBI ↗
Blumea formosana PX404818.1 151281 View on NCBI ↗
Blumea martiniana PX404819.1 151168 View on NCBI ↗
Blumea megacephala PX404820.1 151042 View on NCBI ↗
Blumea repanda PX404821.1 151118 View on NCBI ↗
Blumea sinuata PX404822.1 150783 View on NCBI ↗