Markers + reference

Lophira

2 species · Ochnaceae · Malpighiales

Back to catalogue

Species 2
Genome length 160–160 kb
Candidate markers 260
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0019 1.00 47.8 yes View details
rps16 LSC 937 0.0021 1.00 60.1 yes View details
trnS-trnG LSC 1147 0.0028 0.93 64.7 yes View details
atpF LSC 1270 0.0000 1.00 27.3 yes View details
atpF-atpH LSC 459 0.0068 0.96 63.7 yes View details
trnE-trnT LSC 1081 0.0009 1.00 51.8 yes View details
trnG-trnM LSC 328 0.0091 1.00 58.3 yes View details
psaJ-rpl33 LSC 485 0.0041 1.00 54.1 yes View details
rps8 LSC 405 0.0000 1.00 22.0 yes View details
rps8-rpl14 LSC 235 0.0128 1.00 59.8 yes View details
ycf1 IRb 932 0.0000 1.00 40.0 no View details
ycf1 SSC 5541 0.0007 1.00 52.9 yes View details
rps19-rpl2 IRb 65 0.0154 1.00 61.3 yes View details
rpl2-rps19 IRa 65 0.0154 1.00 61.3 yes View details
trnR-trnN IRb 627 0.0000 0.98 60.4 yes View details
rpl32-trnL SSC 1055 0.0028 1.00 60.4 yes View details
trnN-trnR IRa 627 0.0000 0.98 60.4 yes View details
rbcL-accD LSC 894 0.0022 1.00 60.0 yes View details
ndhF-rpl32 SSC 880 0.0011 1.00 59.8 yes View details
ccsA-ndhD SSC 354 0.0030 0.94 59.8 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACTCATATACACTAAGACCAAAGTC ACTTGGGAGTCCCTGATGAT 1128 1.000 40.1
psbA_p2 psbA ACTCATATACACTAAGACCAAAGTC GTGTACTTGGGAGTCCCTGA 1132 1.000 40.1
psbA_p3 psbA ACTCATATACACTAAGACCAAAGT ACTTGGGAGTCCCTGATGAT 1128 1.000 40.1
psbA_p4 psbA ACTCATATACACTAAGACCAAAGT GTGTACTTGGGAGTCCCTGA 1132 1.000 40.1
psbA_p5 psbA ACTCATATACACTAAGACCAAAGTC TGTACTTGGGAGTCCCTGAT 1131 1.000 40.1
rps16_p1 rps16 ACAGTTCTTGTGGGTTGAGC ACCGGTTCAAAACTCAAGGA 1034–1035 1.000 71.9
rps16_p2 rps16 AGTTCTTGTGGGTTGAGCAC ACCGGTTCAAAACTCAAGGA 1032–1033 1.000 71.9
rps16_p3 rps16 GTTCTTGTGGGTTGAGCACT ACCGGTTCAAAACTCAAGGA 1031–1032 1.000 71.9
rps16_p4 rps16 CAGTTCTTGTGGGTTGAGCA ACCGGTTCAAAACTCAAGGA 1033–1034 1.000 71.9
rps16_p5 rps16 TCTTGTGGGTTGAGCACTTT ACCGGTTCAAAACTCAAGGA 1029–1030 1.000 71.0
trnS-trnG_p1 trnS-trnG CAATCCGACGCTTTAGTCCA GAATCTGAGTCAAGGGATCCC 1199–1254 1.000 72.3
trnS-trnG_p2 trnS-trnG CAATCCGACGCTTTAGTCCA GGAATCTGAGTCAAGGGATCC 1200–1255 1.000 72.3
trnS-trnG_p3 trnS-trnG AATCCGACGCTTTAGTCCAC GAATCTGAGTCAAGGGATCCC 1198–1253 1.000 72.3
trnS-trnG_p4 trnS-trnG AATCCGACGCTTTAGTCCAC GGAATCTGAGTCAAGGGATCC 1199–1254 1.000 72.3
trnS-trnG_p5 trnS-trnG ATCATCCATCAACGGAACCG GAATCTGAGTCAAGGGATCCC 1270–1325 1.000 71.9
atpF_p1 atpF GGGGGAAATAATGCCTACAGT ACAACAAATCGATAATTACTCTGTCT 1344–1349 1.000 40.0
atpF_p2 atpF GGGGGAAATAATGCCTACAGT ACAACAAATCGATAATTACTCTGTC 1344–1349 1.000 40.0
atpF_p3 atpF GGGGGAAATAATGCCTACAGT ACAACAAATCGATAATTACTCTGT 1344–1349 1.000 40.0
atpF_p4 atpF GGGGGAAATAATGCCTACAGT AACAACAAATCGATAATTACTCTGTCT 1345–1350 1.000 40.0
atpF_p5 atpF GGGGGAAATAATGCCTACAGT AGAACAACAAATCGATAATTACTCTGT 1347–1352 1.000 40.0
atpF-atpH_p1 atpF-atpH GCCCCAAGGAAAGGAAAGAA AGCGGAGGGAAAAATACGAG 592–611 1.000 80.4
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AGCGGAGGGAAAAATACGAG 624–643 1.000 79.3
atpF-atpH_p3 atpF-atpH GCCCCAAGGAAAGGAAAGAA CGGAGGGAAAAATACGAGGT 590–609 1.000 77.4
atpF-atpH_p4 atpF-atpH GCCCCAAGGAAAGGAAAGAA GCGGAGGGAAAAATACGAGG 591–610 1.000 77.2
atpF-atpH_p5 atpF-atpH GCCCCAAGGAAAGGAAAGAA AAGCGGAGGGAAAAATACGA 593–612 1.000 76.7
trnE-trnT_p1 trnE-trnT AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 1168–1171 1.000 78.9
trnE-trnT_p2 trnE-trnT AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 1166–1169 1.000 78.9
trnE-trnT_p3 trnE-trnT AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 1147–1150 1.000 78.4
trnE-trnT_p4 trnE-trnT AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 1145–1148 1.000 78.4
trnE-trnT_p5 trnE-trnT GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 1165–1168 1.000 78.3

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
Lophira alata MZ274135.1 159925 View on NCBI ↗
Lophira lanceolata MZ274136.1 159869 View on NCBI ↗