Markers + reference

Pentactina

2 species · Rosaceae · Rosales

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Species 2
Genome length 157–157 kb
Candidate markers 270
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 276 0.0388 0.93 70.1 yes View details
trnK-UUU-rps16 LSC 1009 0.0164 0.90 58.0 yes View details
rps16 LSC 1141 0.0105 1.00 50.5 yes View details
trnR-UCU-atpA LSC 598 0.0580 0.81 81.5 yes View details
petN-psbM LSC 598 0.0217 1.00 56.7 yes View details
psbM-trnD-GUC LSC 1225 0.0140 0.99 60.2 yes View details
trnS-UGA-psbZ LSC 370 0.0054 0.99 54.8 yes View details
psaI-ycf4 LSC 434 0.0189 0.98 59.8 yes View details
psbE-petL LSC 1364 0.0138 0.96 69.4 yes View details
rpl36-rps8 LSC 475 0.0197 0.96 66.8 yes View details
ycf1 IRb 1058 0.0019 0.98 61.5 no View details
rpl32-trnL-UAG SSC 1093 0.0112 0.98 66.8 yes View details
ycf1 SSC 5640 0.0064 0.99 47.0 yes View details
rps19-trnH-GUG LSC 44 0.1538 0.89 84.8 no View details
trnG-UCC-trnR-UCU LSC 157 0.0573 1.00 76.2 yes View details
rps11-rpl36 LSC 162 0.0679 1.00 70.7 yes View details
psbC-trnS-UGA LSC 258 0.0310 1.00 70.3 yes View details
trnS-GCU-trnG-UCC LSC 634 0.0119 0.93 69.7 yes View details
rpl22-rps19 LSC 67 0.0448 1.00 68.4 yes View details
trnG-GCC-trnfM-CAU LSC 185 0.0282 0.96 67.4 yes View details
rpl20-rps12 LSC 804 0.0139 0.99 66.2 yes View details
atpF-atpH LSC 470 0.0091 0.94 65.7 yes View details
ndhF-rpl32 SSC 1070 0.0122 0.99 65.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 392–401 1.000 84.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 406–415 1.000 84.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 405–414 1.000 84.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 407–416 1.000 84.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 331–340 1.000 83.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1191–1251 1.000 84.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 1285–1345 1.000 84.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACCGTAGTTAGGGCTCTACC AAAAAGGCGCTCAACCTACA 1357–1417 1.000 84.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAAGGCGCTCAACCTACA 1187–1247 1.000 84.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAAAGGCGCTCAACCTACA 1188–1248 1.000 84.3
rps16_p1 rps16 AGAGTTCCACCGAAAACCAC AACAACCCCAATCTTCACCC 1981–1988 1.000 81.6
rps16_p2 rps16 ACTTGTGTTGGATTGGCACT AACAACCCCAATCTTCACCC 2133–2144 1.000 81.4
rps16_p3 rps16 AGAGTTCCACCGAAAACCAC CCCCAATCTTCACCCTTTCC 1976–1983 1.000 80.5
rps16_p4 rps16 ACTTGTGTTGGATTGGCACT CCCCAATCTTCACCCTTTCC 2128–2139 1.000 80.3
rps16_p5 rps16 AGAGTTCCACCGAAAACCAC CAACCCCAATCTTCACCCTT 1979–1986 1.000 79.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACCGAAAGATCCCTTAACTCT 698–739 1.000 61.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACCGAAAGATCCCTTAACTCT 697–738 1.000 61.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACCGAAAGATCCCTTAACTCT 752–793 1.000 60.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGATCCCTTAACTCT 699–740 1.000 59.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGATCCCTTAACTCT 698–739 1.000 59.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 237–279 1.000 66.1
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 240–282 1.000 65.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 243–285 1.000 65.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 246–288 1.000 65.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 241–283 1.000 63.7
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG GAGGAAGCAGAAGCCCTTTT 672–756 1.000 73.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT GAGGAAGCAGAAGCCCTTTT 671–755 1.000 73.9
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG TTTACCGAGGAAGCAGAAGC 678–762 1.000 73.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT TTTACCGAGGAAGCAGAAGC 677–761 1.000 73.7
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 611–695 1.000 73.2

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
Pentactina rupicola NC_016921.1 156612 View on NCBI ↗
Pentactina schlothauerae PP189928.1 157043 View on NCBI ↗