Markers + reference

Uvaria

2 species · Annonaceae · Magnoliales

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Species 2
Genome length 191–193 kb
Candidate markers 312
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 10 remaining regions by MarkerSeek score (out of 312 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1811 0.0269 0.86 66.3 yes View details
psbC-trnS-UGA LSC 422 0.0651 0.98 87.1 yes View details
infA-rps8 IRb 771 0.0834 0.99 79.0 yes View details
trnI-CAU-ycf2 IRb 493 0.0322 0.76 58.8 yes View details
trnN-GUU-ycf1 IRb 758 0.0536 0.96 77.5 yes View details
ndhF-rpl32 SSC 1239 0.0526 0.94 77.1 yes View details
ycf1-trnN-GUU IRa 758 0.0536 0.96 77.5 yes View details
ycf2-trnI-CAU IRa 460 0.0118 0.74 46.3 yes View details
rps8-infA IRa 771 0.0834 0.99 79.0 yes View details
rpoC1-rpoB LSC 26 0.0769 1.00 75.5 yes View details
atpF-atpH LSC 380 0.0289 1.00 70.8 yes View details
atpH-atpI LSC 1091 0.0165 1.00 68.2 yes View details
petN-psbM LSC 839 0.0179 1.00 67.5 yes View details
petD-trnH-GUG IRa 55 0.0000 0.99 67.1 no View details
trnT-UGU-trnL-UAA LSC 1173 0.0154 1.00 66.5 yes View details
rpl36 IRb 114 0.0263 1.00 65.7 yes View details
rpl36 IRa 114 0.0263 1.00 65.7 yes View details
trnS-GCU-trnG-UCC LSC 771 0.0091 1.00 64.0 yes View details
trnM-CAU-ycf4 LSC 974 0.0165 0.99 63.4 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GTTTGTCGGTCGGAATCTGA 907–908 1.000 79.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGTTTGTCGGTCGGAATCTG 908–909 1.000 79.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TTTCAAGCGATCAGAAGGGG GTTTGTCGGTCGGAATCTGA 975–976 1.000 79.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TTTCAAGCGATCAGAAGGGG AGTTTGTCGGTCGGAATCTG 976–977 1.000 79.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA GTTTGTCGGTCGGAATCTGA 955–956 1.000 77.4
atpF_p1 atpF CTCGAAGGGTTCCCATTAGC AAGGGGACGAGGTGATACAA 1722–1969 1.000 85.0
atpF_p2 atpF CTCGAAGGGTTCCCATTAGC AGGGGACGAGGTGATACAAA 1721–1968 1.000 85.0
atpF_p3 atpF GCTCGAAGGGTTCCCATTAG AAGGGGACGAGGTGATACAA 1723–1970 1.000 85.0
atpF_p4 atpF GCTCGAAGGGTTCCCATTAG AGGGGACGAGGTGATACAAA 1722–1969 1.000 85.0
atpF_p5 atpF CTCGAAGGGTTCCCATTAGC AAAAACAAGGGAAGGGGACG 1733–1980 1.000 83.0
atpF-atpH_p1 atpF-atpH TATTCAACCCGAAACTCCCG GTTGTGGCATTAGCGCTTTT 492–510 1.000 78.1
atpF-atpH_p2 atpF-atpH CCAGTAACCCAAGGAAACGA GTTGTGGCATTAGCGCTTTT 464–482 1.000 76.9
atpF-atpH_p3 atpF-atpH GGCCAGTAACCCAAGGAAAC GTTGTGGCATTAGCGCTTTT 466–484 1.000 75.4
atpF-atpH_p4 atpF-atpH TATTCAACCCGAAACTCCCG CCGGAAGCAGAGGGTAAAAT 570–588 1.000 75.0
atpF-atpH_p5 atpF-atpH TATTCAACCCGAAACTCCCG ATTTACGGACTGGTTGTGGC 504–522 1.000 74.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGCGAATCCATGGAAAGTC 1151 1.000 80.6
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT AGGCGAATCCATGGAAAGTC 1207 1.000 79.9
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA AGGCGAATCCATGGAAAGTC 1152 1.000 79.4
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC AGGCGAATCCATGGAAAGTC 1211 1.000 79.3
atpH-atpI_p5 atpH-atpI GGCAGTACCTTGACCAACTC AGGCGAATCCATGGAAAGTC 1212 1.000 79.3
rpoC1-rpoB_p1 rpoC1-rpoB TTTGGCCCAGGCACTAATTT GATCCTTGGCTCTGGAACTG 175 1.000 80.4
rpoC1-rpoB_p2 rpoC1-rpoB TTTTGGCCCAGGCACTAATT GATCCTTGGCTCTGGAACTG 176 1.000 80.4
rpoC1-rpoB_p3 rpoC1-rpoB TTTTTGGCCCAGGCACTAAT GATCCTTGGCTCTGGAACTG 177 1.000 80.4
rpoC1-rpoB_p4 rpoC1-rpoB TTTGGCCCAGGCACTAATTT TTGCTCGTTCGAGAACTACG 194 1.000 80.3
rpoC1-rpoB_p5 rpoC1-rpoB TTTTGGCCCAGGCACTAATT TTGCTCGTTCGAGAACTACG 195 1.000 80.3
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCGTTGTTCATTCT 940 1.000 68.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCGTTGTTCATTC 940 1.000 68.5
petN-psbM_p3 petN-psbM GGCTGCTTTGATGGTAGTCT TGCTACTGCGTTGTTCATTCT 985 1.000 68.1
petN-psbM_p4 petN-psbM GGCTGCTTTGATGGTAGTCT TGCTACTGCGTTGTTCATTC 985 1.000 67.9
petN-psbM_p5 petN-psbM GGGCTGCTTTGATGGTAGTC TGCTACTGCGTTGTTCATTCT 986 1.000 66.4

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
Uvaria dulcis NC_070221.1 190682 View on NCBI ↗
Uvaria macrophylla NC_041442.1 192782 View on NCBI ↗