Markers + reference

Prinsepia

3 species · Rosaceae · Rosales

Back to catalogue

Species 3
Genome length 156–159 kb
Candidate markers 263
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnR-UCU LSC 269 0.0484 0.90 67.8 yes View details
trnC-GCA-petN LSC 955 0.0290 1.00 68.7 yes View details
psbZ-trnG-GCC LSC 388 0.0560 0.97 78.8 yes View details
trnT-UGU-trnL-UAA LSC 1172 0.0328 0.99 73.7 yes View details
trnF-GAA-ndhJ LSC 655 0.0422 0.99 82.6 yes View details
accD-psaI LSC 781 0.0290 1.00 67.6 yes View details
rpl2 IRb 1489 0.0018 1.00 45.6 no View details
ndhF SSC 2253 0.0169 1.00 54.9 yes View details
ndhF-rpl32 SSC 904 0.0453 0.99 77.5 yes View details
rpl32-trnL-UAG SSC 1534 0.0293 1.00 67.3 yes View details
rps15-ycf1 SSC 407 0.0411 1.00 73.0 yes View details
rpl2 IRa 1489 0.0018 1.00 45.6 yes View details
rpl2-trnH-GUG IRa 265 0.0893 1.00 86.6 no View details
rps19-rpl2 IRb 70 0.0429 1.00 75.8 yes View details
trnR-UCU-atpA LSC 118 0.0508 1.00 72.9 yes View details
ndhC-trnV-UAC LSC 485 0.0363 0.96 72.6 yes View details
atpA-atpF LSC 57 0.0247 0.95 72.5 yes View details
psaJ-rpl33 LSC 464 0.0327 0.99 72.2 yes View details
trnK-UUU-rps16 LSC 1101 0.0242 0.99 70.3 yes View details
psbA-trnK-UUU LSC 359 0.0481 0.87 70.1 yes View details
psbI-trnS-GCU LSC 129 0.0362 1.00 69.2 yes View details
psbJ-psbL LSC 105 0.0381 1.00 68.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACTCCATCCGACTAGTTCCG 357–462 1.000 81.9
psbA-trnK-UUU_p2 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACTAGTTCCGGGTTCGAGTC 347–452 1.000 80.3
psbA-trnK-UUU_p3 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC GACTAGTTCCGGGTTCGAGT 348–453 1.000 80.3
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 377–482 1.000 80.0
psbA-trnK-UUU_p5 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ATCCGACTAGTTCCGGGTTC 352–457 1.000 79.7
trnK-UUU_p1 trnK-UUU GGACTCCCAAGCACAAAAATT TGGTTTTGATTGCGTTGTGC 2860–2974 1.000 68.4
trnK-UUU_p2 trnK-UUU TCGAGGGCTTGTTATTCATCA TGGTTTTGATTGCGTTGTGC 2815–2920 1.000 67.0
trnK-UUU_p3 trnK-UUU GGGACTCCCAAGCACAAAAA TGGTTTTGATTGCGTTGTGC 2916–2975 0.667 60.5
trnK-UUU_p4 trnK-UUU GGGACTCCCAAGCACAAAA TGGTTTTGATTGCGTTGTGC 2916–2975 0.667 56.2
trnK-UUU_p5 trnK-UUU GGACTCCCAAGCACAAAAAT TGGTTTTGATTGCGTTGTGC 2915–2974 0.667 53.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC CGGGGGTTTTTACGGAACTT 1081–1272 1.000 82.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT CGGGGGTTTTTACGGAACTT 1080–1271 1.000 82.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC TTGAAAAAGGGGCTCAACCT 1132–1323 1.000 82.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TTGAAAAAGGGGCTCAACCT 1131–1322 1.000 82.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGGGGTTTTTACGGAACTT 997–1188 1.000 82.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 226–231 1.000 75.0
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 227–232 1.000 74.9
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA CAATTGGGAGGAGAGATGGC 250–255 1.000 74.6
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA AATTGGGAGGAGAGATGGCT 249–254 1.000 74.0
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 226–231 1.000 72.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGTCCTATCCATTAGACAATG 194–328 1.000 49.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGTCCTATCCATTAGACAATG 205–339 1.000 48.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGTCCTATCCATTAGACAATG 208–342 1.000 48.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGTCCTATCCATTAGACAATG 209–343 1.000 48.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT TGTCCTATCCATTAGACAATG 275–409 1.000 47.8
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTTACCGACGAAGCAGAAGC 221–358 1.000 64.6
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACATTTACCGACGAAGCAGA 224–361 1.000 63.2
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCA 226–363 1.000 63.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GACGAAGCAGAAGCCCTTTT 215–352 1.000 63.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGAAGCAGAAGCCCTTTTGA 213–350 1.000 63.1

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
Prinsepia sinensis NC_072921.1 159074 View on NCBI ↗
Prinsepia uniflora NC_063474.1 159179 View on NCBI ↗
Prinsepia utilis NC_021455.1 156328 View on NCBI ↗