Markers + reference

Ochna

2 species · Ochnaceae · Malpighiales

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Species 2
Genome length 157–158 kb
Candidate markers 268
Primer pairs 110

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 7 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 379 0.0185 1.00 64.8 yes View details
trnK-UUU-rps16 LSC 923 0.0088 0.98 57.6 yes View details
rps16 LSC 956 0.0084 1.00 50.7 yes View details
trnS-GCU-trnG-UCC LSC 885 0.0126 0.99 62.1 yes View details
atpF LSC 1258 0.0000 1.00 26.1 yes View details
atpF-atpH LSC 495 0.0121 1.00 63.5 yes View details
rpoB-trnC-GCA LSC 1203 0.0058 1.00 53.3 yes View details
psbC-trnS-UGA LSC 234 0.0342 1.00 64.5 yes View details
atpB-rbcL LSC 783 0.0090 0.99 62.6 yes View details
ycf4-cemA LSC 569 0.0088 1.00 53.2 yes View details
rpl22 LSC 432 0.0162 1.00 64.1 yes View details
ycf2-trnL-CAA IRb 947 0.0084 1.00 60.6 yes View details
trnL-CAA-ycf2 IRa 947 0.0084 1.00 60.6 yes View details
psbM-trnD-GUC LSC 1221 0.0066 1.00 62.7 yes View details
trnE-UUC-trnT-GGU LSC 962 0.0042 0.98 62.7 yes View details
petN-psbM LSC 1309 0.0039 0.99 62.3 yes View details
ccsA SSC 972 0.0051 1.00 61.7 yes View details
trnT-GGU-psbD LSC 1529 0.0039 1.00 61.0 yes View details
ndhC-trnV-UAC LSC 1074 0.0037 1.00 61.0 yes View details
rbcL-accD LSC 859 0.0035 1.00 60.9 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 110 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 AGCTGCTGTTGAAGTTCCAT 435–437 1.000 78.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 449–451 1.000 77.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 448–450 1.000 77.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 450–452 1.000 77.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 498–500 1.000 77.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 ATGGACGAAGCCCTTTCTTC TGAGTTGGTTTTCGCTGGAA 1084–1098 1.000 80.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 GGACGAAGCCCTTTCTTCAT TGAGTTGGTTTTCGCTGGAA 1082–1096 1.000 80.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAAGCCCTTTCTTC AGTTGGTTTTCGCTGGAACT 1082–1096 1.000 80.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAAGCCCTTTCTTCAT AGTTGGTTTTCGCTGGAACT 1080–1094 1.000 80.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGACGAAGCCCTTTCTTCAT ATGAGTTGGTTTTCGCTGGA 1083–1097 1.000 78.6
rps16_p1 rps16 TCGGGTTTATTTTATACAATCAA GCCGAGCCAATGACTATTCA 1056–1536 1.000 40.5
rps16_p2 rps16 TCGGGTTTATTTTATACAATCAA TACTATATACCGGCCGAGCC 1068–1548 1.000 40.5
rps16_p3 rps16 TCGGGTTTATTTTATACAATCAAT GCCGAGCCAATGACTATTCA 1056–1536 1.000 40.5
rps16_p4 rps16 TCGGGTTTATTTTATACAATCAAT TACTATATACCGGCCGAGCC 1068–1548 1.000 40.5
rps16_p5 rps16 TCGGGTTTATTTTATACAATCAA CGAGCCAATGACTATTCACGA 1054–1534 1.000 40.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGGAATCTAAGCCGAGGGAT 994–995 1.000 80.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGGAATCTAAGCCGAGGGAT 993–994 1.000 80.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTGGAATCTAAGCCGAGGGA 995–996 1.000 80.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTGGAATCTAAGCCGAGGGA 994–995 1.000 80.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATCATCCATCAACGGAACCG TGGAATCTAAGCCGAGGGAT 1065–1066 1.000 80.4
atpF_p1 atpF CCATTGCCCCTCTTTCTTGT CTCGCTTTCTTCCTTCCCTC 2308–2317 1.000 79.5
atpF_p2 atpF CCATTGCCCCTCTTTCTTGT CGGGAAGGACTGATTTGAGG 2348–2357 1.000 79.4
atpF_p3 atpF CACTCACCGGTATTTGAGCA CTCGCTTTCTTCCTTCCCTC 1954–1963 1.000 79.4
atpF_p4 atpF CCATTGCCCCTCTTTCTTGT ATTTCTGCCGCTTCCGTTAT 2692–2701 1.000 79.3
atpF_p5 atpF CCATTGCCCCTCTTTCTTGT GCTGTAGAAGGTATCGCGAG 2602–2611 1.000 79.3
atpF-atpH_p1 atpF-atpH GCCCCAAGGAAAGGAAAGAA AGCGGAGGGAAAAATACGAG 647–656 1.000 78.2
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AGCGGAGGGAAAAATACGAG 679–688 1.000 77.3
atpF-atpH_p3 atpF-atpH GCCCCAAGGAAAGGAAAGAA CGGAGGGAAAAATACGAGGT 645–654 1.000 75.2
atpF-atpH_p4 atpF-atpH GCCCCAAGGAAAGGAAAGAA GCGGAGGGAAAAATACGAGG 646–655 1.000 75.0
atpF-atpH_p5 atpF-atpH GCCCCAAGGAAAGGAAAGAA AAGCGGAGGGAAAAATACGA 648–657 1.000 74.5

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
Ochna integerrima NC_072724.1 157329 View on NCBI ↗
Ochna serrulata NC_072725.1 157835 View on NCBI ↗