Markers + reference

Thymelaea

2 species · Thymelaeaceae · Malvales

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Species 2
Genome length 172–173 kb
Candidate markers 290
Primer pairs 105

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 290 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 343 0.0893 0.98 75.9 yes View details
rps16-trnQ-UUG LSC 1312 0.0420 0.98 75.4 yes View details
petN-psbM LSC 1085 0.0398 0.62 64.3 yes View details
trnT-GGU-psbD LSC 1243 0.0282 0.97 68.3 yes View details
ycf3-trnS-GGA LSC 870 0.0328 0.98 73.2 yes View details
trnF-GAA-ndhJ LSC 280 0.0993 0.97 82.9 yes View details
accD LSC 1617 0.0222 0.97 60.3 yes View details
rpl36-rps8 LSC 518 0.0465 1.00 71.7 yes View details
rpl16 LSC 1483 0.0333 0.99 63.8 yes View details
ndhF SSC 2253 0.0408 1.00 66.1 yes View details
ndhF-rpl32 SSC 395 0.0896 0.88 78.6 yes View details
psbF-psbE LSC 9 0.1111 1.00 76.9 yes View details
rpl16-rps3 LSC 151 0.0780 0.93 76.7 yes View details
rpoB-trnC-GCA LSC 1164 0.0309 0.97 73.8 yes View details
trnW-CCA-trnP-UGG LSC 185 0.0486 1.00 73.5 yes View details
trnE-UUC-trnT-GGU LSC 516 0.0369 1.00 72.7 yes View details
trnS-GCU-trnG-UCC LSC 733 0.0326 0.96 72.6 yes View details
ndhC-trnV-UAC LSC 594 0.0394 0.98 72.5 yes View details
psbE-petL LSC 1428 0.0284 0.96 72.4 yes View details
psbA-trnK-UUU LSC 283 0.0502 0.99 71.4 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 CTGCCTTAATCCACTTGGCT TGAAGCTCCATCTACAAATGG 397–403 1.000 59.6
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGAAGCTCCATCTACAAATGG 398–404 1.000 59.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TGAAGCTCCATCTACAAATGG 390–396 1.000 58.1
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTGAAGCTCCATCTACAAATGG 398–404 1.000 57.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTGAAGCTCCATCTACAAATGG 399–405 1.000 57.4
psbA-trnK-UUU_p1 psbA-trnK-UUU AACACACCAAACCATCCGAT ACTCCATCCGACTAGTTCCG 432–433 1.000 76.2
psbA-trnK-UUU_p2 psbA-trnK-UUU ACACACCAAACCATCCGATG ACTCCATCCGACTAGTTCCG 431–432 1.000 74.7
psbA-trnK-UUU_p3 psbA-trnK-UUU CACACCAAACCATCCGATGT ACTCCATCCGACTAGTTCCG 430–431 1.000 74.7
psbA-trnK-UUU_p4 psbA-trnK-UUU AACACACCAAACCATCCGAT ACTAGTTCCGGGTTCGAGTC 422–423 1.000 74.5
psbA-trnK-UUU_p5 psbA-trnK-UUU AACACACCAAACCATCCGAT GACTAGTTCCGGGTTCGAGT 423–424 1.000 74.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGCTATTCGAAG 1402–1423 1.000 83.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACATCGCTTCAAACGAAG TTTGGTCCCGCTATTCGAAG 1382–1403 1.000 82.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGCAAATCGACCATGTCCT TTTGGTCCCGCTATTCGAAG 1424–1445 1.000 82.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTTTGGTCCCGCTATTCGA 1404–1425 1.000 81.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACCACATCGCTTCAAACGAA TTTGGTCCCGCTATTCGAAG 1383–1404 1.000 81.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCCT 845–853 1.000 77.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCCTT 844–852 1.000 77.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCAAACCGAAAGACCCCT 844–852 1.000 77.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATCAAACCGAAAGACCCCTT 843–851 1.000 77.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGCACAACGGATTAGCAATC ATCAAACCGAAAGACCCCTT 859–867 1.000 76.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT CTGGGGTAAAGGGATTTGCA 1215–1235 1.000 80.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT TGGGGTAAAGGGATTTGCAG 1214–1234 1.000 80.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT ACTGGGGTAAAGGGATTTGC 1216–1236 1.000 80.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT GGGGTAAAGGGATTTGCAGT 1213–1233 1.000 80.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCCCATTTTCATCCCC TGGGGTAAAGGGATTTGCAG 1220–1240 1.000 78.6
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA AAACAGTCAGCCAAGGCAAT 780–1184 1.000 83.8
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA AACAGTCAGCCAAGGCAATT 779–1183 1.000 83.8
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG AAACAGTCAGCCAAGGCAAT 786–1190 1.000 82.3
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG AACAGTCAGCCAAGGCAATT 785–1189 1.000 82.3
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAACAGTCAGCCAAGGCAA 781–1185 1.000 82.0

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
Thymelaea dioica BK071451.1 172648 View on NCBI ↗
Thymelaea passerina BK071452.1 171885 View on NCBI ↗