Markers + reference

Pouzolzia

3 species · Urticaceae · Rosales

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Species 3
Genome length 153–159 kb
Candidate markers 273
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 865 0.0693 0.98 83.6 yes View details
trnC-GCA-petN LSC 883 0.0837 0.96 84.1 yes View details
trnF-GAA-ndhJ LSC 543 0.0781 1.00 87.8 yes View details
rpl36-rps8 IRb 826 0.2650 0.48 72.9 yes View details
ndhF-rpl32 SSC 1150 0.0601 0.97 85.3 yes View details
rpl32-trnL-UAG SSC 834 0.0777 0.98 85.0 yes View details
ycf1 SSC 5760 0.0628 0.99 73.1 yes View details
trnT-UGU-trnL-UAA LSC 1050 0.0622 0.96 87.6 yes View details
rps16-trnQ-UUG LSC 637 0.0634 0.97 85.8 yes View details
matK-trnK-UUU LSC 796 0.0687 0.97 85.3 yes View details
trnE-UUC-trnT-GGU LSC 663 0.0569 0.97 83.9 yes View details
rpoB-trnC-GCA LSC 1003 0.0650 0.99 82.4 yes View details
trnL-UAA-trnF-GAA LSC 386 0.0557 0.99 81.3 yes View details
trnG-GCC-trnfM-CAU LSC 189 0.0618 0.94 81.1 yes View details
psbE-petL LSC 1108 0.0531 1.00 80.7 yes View details
trnW-CCA-trnP-UGG LSC 150 0.0537 0.99 80.3 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GGACTCCCAAGCACATGAAT TTGGGATTCCGTTTGTGTCT 2917 0.333 47.1
trnK-UUU_p2 trnK-UUU CTCCATGTCAACCAGCTTCA TTGGGATTCCGTTTGTGTCT 2835 0.333 46.6
trnK-UUU_p3 trnK-UUU TCTCCATGTCAACCAGCTTC TTGGGATTCCGTTTGTGTCT 2836 0.333 44.3
trnK-UUU_p4 trnK-UUU GGACTCCCAAGCACATGAAT ATTGGGATTCCGTTTGTGTCT 2918 0.333 43.0
trnK-UUU_p5 trnK-UUU TCCATGTCAACCAGCTTCAA TTGGGATTCCGTTTGTGTCT 2834 0.333 42.9
matK-trnK-UUU_p1 matK-trnK-UUU AATATCCTTGAAACTCTTCCA AACGGTAGAGTACTCGGCTT 790–842 1.000 51.4
matK-trnK-UUU_p2 matK-trnK-UUU AATATCCTTGAAACTCTTCCA ACGGTAGAGTACTCGGCTTT 789–841 1.000 51.4
matK-trnK-UUU_p3 matK-trnK-UUU AAATATCCTTGAAACTCTTCCA AACGGTAGAGTACTCGGCTT 791–843 1.000 51.4
matK-trnK-UUU_p4 matK-trnK-UUU AAATATCCTTGAAACTCTTCCA ACGGTAGAGTACTCGGCTTT 790–842 1.000 51.4
matK-trnK-UUU_p5 matK-trnK-UUU AATATCCTTGAAACTCTTCCA GGGTTGCTAACTCAACGGTA 803–855 1.000 51.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 GACGACATGCTGCTTTTTCC TTTTCTTGAGCCGTACGAGG 1268–1297 1.000 89.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 GACGACATGCTGCTTTTTCC GCCGTACGAGGAGAAAACTT 1259–1288 1.000 89.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 GACGACATGCTGCTTTTTCC TTTGGTTGGGCAACGAAAAC 1429 0.333 53.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CTGTCCTCCCCCTTTTCAAC TTTGGTTGGGCAACGAAAAC 1942 0.333 52.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATTCAGACGACATGCTGCTT TTTGGTTGGGCAACGAAAAC 1434 0.333 52.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 692–719 1.000 88.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 707–734 1.000 86.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 706–733 1.000 86.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGGTGTAAGAATCCACAGC GAGGTTCGAATCCTTCCGTC 726–753 1.000 85.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 713–740 1.000 84.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1577–1763 1.000 88.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACTCCACAACGGCATTTTCT CCGGATTTGAACTGGGGAAA 1747–1933 1.000 87.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TACCGGATCTCCACCTACAC CCGGATTTGAACTGGGGAAA 1785–1971 1.000 87.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACTCCACAACGGCATTTTCT AATCTACGCTTGGCTTGCTT 1844 0.333 51.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AATCTACGCTTGGCTTGCTT 1674 0.333 51.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGACTTATT 651–950 1.000 91.1
trnC-GCA-petN_p2 trnC-GCA-petN GGGTGTCGCCTGATTAACAA CAGCCCAAGCGAGACTTATT 633–932 1.000 90.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCGAGACTTATT 669–968 1.000 88.9
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC CAGCCCAAGCGAGACTTATT 646–945 1.000 85.1
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 658–957 1.000 84.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Pouzolzia hirta NC_053931.1 159086 View on NCBI ↗
Pouzolzia sanguinea var. elegans MN189968.1 153715 View on NCBI ↗
Pouzolzia zeylanica PP056245.1 153430 View on NCBI ↗