Markers + reference

Poikilospermum

2 species · Urticaceae · Rosales

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Species 2
Genome length 154–154 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 29.3 yes View details
petN-psbM LSC 562 0.0071 1.00 62.2 yes View details
psbZ-trnG-GCC LSC 449 0.0112 1.00 62.5 yes View details
clpP LSC 1998 0.0025 1.00 48.5 yes View details
trnR-ACG-trnN-GUU IRb 575 0.0070 1.00 62.2 yes View details
ndhF SSC 2235 0.0036 1.00 59.3 yes View details
rpl32-trnL-UAG SSC 857 0.0048 0.98 63.3 yes View details
ndhA SSC 2294 0.0026 1.00 58.6 yes View details
ycf1 SSC 5511 0.0024 1.00 39.1 yes View details
ycf1-trnN-GUU IRa 313 0.0000 1.00 25.8 yes View details
trnN-GUU-trnR-ACG IRa 575 0.0070 1.00 62.2 yes View details
trnH-GUG-psbA LSC 209 0.0478 1.00 68.1 yes View details
rps16-trnQ-UUG LSC 621 0.0017 0.95 64.2 yes View details
trnK-UUU-rps16 LSC 687 0.0044 1.00 61.4 yes View details
trnT-UGU-trnL-UAA LSC 820 0.0037 1.00 60.9 yes View details
ycf3-trnS-GGA LSC 901 0.0033 1.00 60.7 yes View details
trnE-UUC-trnT-GGU LSC 589 0.0034 1.00 60.5 yes View details
ycf4-cemA LSC 751 0.0027 1.00 60.3 yes View details
accD LSC 1494 0.0020 1.00 59.9 yes View details
psbE-petL LSC 1194 0.0017 1.00 59.9 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 ACCGCGCTAATCTTGGTATG 329 1.000 80.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ACCGCGCTAATCTTGGTATG 343 1.000 80.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ACCGCGCTAATCTTGGTATG 342 1.000 80.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC ACCGCGCTAATCTTGGTATG 344 1.000 80.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGCGCTAATCTTGGTATGGA 327 1.000 80.2
psbA_p1 psbA TGCTCCTTTATTTTCAAAAAGTCGT ATTCATGTGCTTGGGAGTCC 1160 1.000 40.0
psbA_p2 psbA TGCTCCTTTATTTTCAAAAAGTCG ATTCATGTGCTTGGGAGTCC 1160 1.000 40.0
psbA_p3 psbA GCTCCTTTATTTTCAAAAAGTCGT ATTCATGTGCTTGGGAGTCC 1159 1.000 40.0
psbA_p4 psbA TTGCTCCTTTATTTTCAAAAAGTCG ATTCATGTGCTTGGGAGTCC 1161 1.000 40.0
psbA_p5 psbA GCTCCTTTATTTTCAAAAAGTCG ATTCATGTGCTTGGGAGTCC 1159 1.000 40.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC TTCCTTGAAAAAGGCGCTCA 908–909 1.000 77.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TTCCTTGAAAAAGGCGCTCA 907–908 1.000 77.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 825–826 1.000 76.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 824–825 1.000 76.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT TTCCTTGAAAAAGGCGCTCA 909–910 1.000 76.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 669–694 1.000 81.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 683–708 1.000 79.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 690–715 1.000 78.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 673–698 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 699–724 1.000 76.8
petN-psbM_p1 petN-psbM TCGAGGACAAAACCCACATG TGCTACTGCACTGTTCATTCT 747–748 1.000 68.4
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 723–724 1.000 68.1
petN-psbM_p3 petN-psbM GATCGAGGACAAAACCCACA TGCTACTGCACTGTTCATTCT 749–750 1.000 67.8
petN-psbM_p4 petN-psbM GAGGACAAAACCCACATGGA TGCTACTGCACTGTTCATTCT 745–746 1.000 67.0
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 662–663 1.000 66.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 676–682 1.000 79.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 674–680 1.000 79.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 655–661 1.000 78.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 653–659 1.000 78.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 673–679 1.000 78.5

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
Poikilospermum cordifolium NC_064937.1 153801 View on NCBI ↗
Poikilospermum naucleiflorum NC_064978.1 153782 View on NCBI ↗