Markers + reference

Pellionia

5 species · Urticaceae · Rosales

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Species 5
Genome length 153–154 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 29.8 yes View details
trnK-UUU-rps16 LSC 781 0.0197 1.00 60.6 yes View details
rpoB-trnC-GCA LSC 1042 0.0154 1.00 56.6 yes View details
psbZ-trnG-GCC LSC 515 0.0167 1.00 53.5 yes View details
trnT-UGU-trnL-UAA LSC 612 0.0203 1.00 56.3 yes View details
ycf1 IRb 1148 0.0009 0.97 34.8 no View details
ndhF-rpl32 SSC 880 0.0198 0.97 64.3 yes View details
rpl32-trnL-UAG SSC 931 0.0230 0.98 70.7 yes View details
ccsA SSC 969 0.0068 1.00 43.7 yes View details
ccsA-ndhD SSC 273 0.0454 1.00 69.7 yes View details
rps15-ycf1 SSC 2040 0.0174 1.00 48.6 yes View details
ycf1 SSC 3600 0.0114 0.99 48.9 yes View details
trnH-GUG-psbA LSC 205 0.0546 1.00 73.4 yes View details
atpA-atpF LSC 63 0.0619 1.00 69.1 yes View details
accD-psaI LSC 668 0.0166 1.00 66.4 yes View details
trnG-GCC-trnfM-CAU LSC 166 0.0251 1.00 63.9 yes View details
rps4-trnT-UGU LSC 495 0.0133 0.81 61.0 yes View details
rps16-trnQ-UUG LSC 766 0.0160 0.98 60.1 yes View details
ndhH SSC 1182 0.0048 1.00 59.5 yes View details
psaI-ycf4 LSC 464 0.0112 1.00 57.8 yes View details
matK-trnK-UUU LSC 762 0.0129 1.00 57.1 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 CTGACGGTATGCCTCTAGGA 783–789 1.000 81.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCTGACGGTATGCCTCTAGG 784–790 1.000 81.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTGACGGTATGCCTCTAGGA 797–803 1.000 81.2
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCTGACGGTATGCCTCTAGG 798–804 1.000 81.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTGACGGTATGCCTCTAGGA 796–802 1.000 81.2
psbA_p1 psbA GATCCACTTGGCTACATCCG CCTGTCTACGAACGGAACTG 1734–1745 1.000 80.6
psbA_p2 psbA CAATCCACTGCCTTGATCCA CCTGTCTACGAACGGAACTG 1748–1759 1.000 80.6
psbA_p3 psbA AATCCACTGCCTTGATCCAC CCTGTCTACGAACGGAACTG 1747–1758 1.000 80.6
psbA_p4 psbA ACAATCCACTGCCTTGATCC CCTGTCTACGAACGGAACTG 1749–1760 1.000 80.6
psbA_p5 psbA GATCCACTTGGCTACATCCG ATGCAGCAAGGGTTCATCAA 1769–1780 1.000 80.2
matK-trnK-UUU_p1 matK-trnK-UUU AAGTGGGTATAGGAGGTCAT AACGGTAGAGTACTCGGCTT 851–872 1.000 53.0
matK-trnK-UUU_p2 matK-trnK-UUU AAGTGGGTATAGGAGGTCAT ACGGTAGAGTACTCGGCTTT 850–871 1.000 53.0
matK-trnK-UUU_p3 matK-trnK-UUU AAGTGGGTATAGGAGGTCAT GGGTTGCTAACTCAACGGTA 864–885 1.000 50.6
matK-trnK-UUU_p4 matK-trnK-UUU AAGTGGGTATAGGAGGTCAT TTCGGGTTGCTAACTCAACG 867–888 1.000 50.3
matK-trnK-UUU_p5 matK-trnK-UUU AAGTGGGTATAGGAGGTCAT CAACGGTAGAGTACTCGGCT 852–873 1.000 47.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC TGAACTTTCGCCTTAATCACT 915–951 1.000 55.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TGAACTTTCGCCTTAATCACT 914–950 1.000 55.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGAACTTTCGCCTTAATCACT 832–868 1.000 54.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGAACTTTCGCCTTAATCACT 831–867 1.000 54.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT TGAACTTTCGCCTTAATCACT 916–952 1.000 53.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 838–861 1.000 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 853–876 1.000 81.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 852–875 1.000 81.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGGTGTAAGAATCCACAGC GAGGTTCGAATCCTTCCGTC 872–895 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 859–882 1.000 80.0
atpA-atpF_p1 atpA-atpF TTTCATCGGCTCGAATGGTT TGGAACAATGAAAGAAATAACGGA 115–116 1.000 46.3
atpA-atpF_p2 atpA-atpF TCATCGGCTCGAATGGTTAC TGGAACAATGAAAGAAATAACGGA 113–114 1.000 46.3
atpA-atpF_p3 atpA-atpF TCATCGGCTCGAATGGTTAC TGGAACAATGAAAGAAATAACGG 113–114 1.000 46.3
atpA-atpF_p4 atpA-atpF ATTTCATCGGCTCGAATGGT TGGAACAATGAAAGAAATAACGGA 116–117 1.000 46.2
atpA-atpF_p5 atpA-atpF TTTCATCGGCTCGAATGGTT TGGAACAATGAAAGAAATAACGG 115–116 1.000 46.2

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
Pellionia pellucida PQ676436.1 154251 View on NCBI ↗
Pellionia retrohispida PQ287278.1 154313 View on NCBI ↗
Pellionia scabra NC_061695.1 153220 View on NCBI ↗
Pellionia viridis PQ676464.1 154249 View on NCBI ↗
Pellionia yunnanensis OR521109.1 153588 View on NCBI ↗