Markers + reference

Parietaria

5 species · Urticaceae · Rosales

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Species 5
Genome length 153–154 kb
Candidate markers 263
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 747 0.0404 0.99 59.7 yes View details
trnE-UUC-trnT-GGU LSC 648 0.0432 0.98 70.1 yes View details
rps4-trnT-UGU LSC 516 0.0348 0.99 67.8 yes View details
trnT-UGU-trnL-UAA LSC 994 0.0434 0.98 76.2 yes View details
accD-psaI LSC 701 0.0375 1.00 61.6 yes View details
clpP LSC 1995 0.0225 1.00 55.1 yes View details
trnN-GUU-rpl32 SSC 4675 0.0231 1.00 49.8 yes View details
rpl32-trnL-UAG SSC 839 0.0440 0.95 69.1 yes View details
ycf1 SSC 5694 0.0387 0.99 68.1 yes View details
trnH-GUG-psbA LSC 170 0.0780 1.00 71.4 yes View details
psbI-trnS-GCU LSC 96 0.0583 1.00 69.4 yes View details
rpoB-trnC-GCA LSC 1103 0.0302 0.99 68.0 yes View details
rps16-trnQ-UUG LSC 685 0.0409 1.00 67.1 yes View details
petG-trnW-CCA LSC 112 0.0625 1.00 66.7 yes View details
psbZ-trnG-GCC LSC 447 0.0394 0.99 66.3 yes View details
trnL-UAG-ccsA SSC 51 0.0680 0.98 66.0 yes View details
rps12-clpP LSC 162 0.0412 1.00 63.9 yes View details
petN-psbM LSC 689 0.0319 0.99 63.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA ATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 232–274 1.000 74.7
trnH-GUG-psbA_p2 trnH-GUG-psbA ATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 235–277 1.000 74.5
trnH-GUG-psbA_p3 trnH-GUG-psbA ATCCACTTGGCTACATCCGC CCTCTAGACCTAGCTGCTGT 232–274 1.000 74.0
trnH-GUG-psbA_p4 trnH-GUG-psbA CCACTTGGCTACATCCGC CCTCTAGACCTAGCTGCTGT 230–272 1.000 74.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ATCCACTTGGCTACATCCGC TTCCCTCTAGACCTAGCTGC 235–277 1.000 73.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGGTCTTCCAAACTCTACCG GCCGTACGAGGAGAAAACTT 1151–1184 1.000 84.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGGTCTTCCAAACTCTACCG TTTTCTTGAGCCGTACGAGG 1160–1193 1.000 84.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGACTCTCTGGCTTCCCTTT TTTTCTTGAGCCGTACGAGG 1728–1765 1.000 84.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG TTTTCTTGAGCCGTACGAGG 1202–1233 0.600 65.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG GCCGTACGAGGAGAAAACTT 1193–1224 0.600 65.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 758–794 1.000 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 762–798 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 750–786 1.000 78.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 757–793 1.000 78.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 753–789 1.000 76.5
psbI-trnS-GCU_p1 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG TTCGAATCCCTCTCTTTCCG 141–190 1.000 72.3
psbI-trnS-GCU_p2 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG GGGTTCGAATCCCTCTCTTT 144–193 1.000 71.3
psbI-trnS-GCU_p3 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG GGGTTCGAATCCCTCTCTTTC 144–193 1.000 71.2
psbI-trnS-GCU_p4 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG GGTTCGAATCCCTCTCTTTCC 143–192 1.000 71.2
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTCGAATCCCTCTCTTTCCG 140–189 1.000 70.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAACCCCGCGGATA TAGTGTAGTGGGGGCTATCG 1651–1660 0.400 58.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GATACCGGGGCTTTGCAATA TAGTGTAGTGGGGGCTATCG 1783–1792 0.400 58.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TAGTGTAGTGGGGGCTATCG 1899–1908 0.400 58.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG TAGTGTAGTGGGGGCTATCG 1779–1788 0.400 58.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TACCGGATCTCCACCTACAC TAGTGTAGTGGGGGCTATCG 2101–2110 0.400 57.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TCAGTCCCGATGGATCCAAA 1395–1402 1.000 81.9
petN-psbM_p2 petN-psbM ATCCCCTTTTGACTATGCGC TCAGTCCCGATGGATCCAAA 1492–1499 1.000 80.2
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT CAAGGAGGGTGCTGGTTTAT 1197–1201 0.600 62.0
petN-psbM_p4 petN-psbM TTCTGCTACTTCAAAGGCCG TCAGTCCCGATGGATCCAAA 1623–1628 0.600 61.8
petN-psbM_p5 petN-psbM TTCTGCTACTTCAAAGGCCG CAAGGAGGGTGCTGGTTTAT 1423–1427 0.600 61.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Parietaria debilis MN189966.1 152988 View on NCBI ↗
Parietaria floridana NC_062307.1 153538 View on NCBI ↗
Parietaria judaica NC_066035.1 152689 View on NCBI ↗
Parietaria mauritanica NC_066016.1 152689 View on NCBI ↗
Parietaria praetermissa NC_062411.1 153573 View on NCBI ↗