Markers + reference

Moquilea

2 species · Chrysobalanaceae · Malpighiales

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Species 2
Genome length 162–163 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 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 408 0.0425 0.98 71.6 yes View details
trnQ-UUG-psbK LSC 384 0.0156 1.00 58.1 yes View details
trnS-GCU-trnG-GCC LSC 943 0.0085 1.00 58.1 yes View details
rps2-rpoC2 LSC 251 0.0159 1.00 48.8 yes View details
rbcL-accD LSC 807 0.0124 1.00 62.3 yes View details
psbE-petL LSC 1476 0.0135 1.00 66.5 yes View details
psaJ-rpl33 LSC 506 0.0141 0.98 53.0 yes View details
psbH LSC 222 0.0045 1.00 40.3 yes View details
ycf1 IRb 1105 0.0036 1.00 48.6 no View details
ndhF SSC 2289 0.0062 0.99 47.3 yes View details
ycf1 SSC 5745 0.0056 1.00 45.4 yes View details
atpA-atpF LSC 64 0.0781 1.00 84.8 yes View details
rps19-trnH-GUG LSC 21 0.0476 1.00 79.9 no View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
psbT-psbN LSC 79 0.0759 1.00 71.9 yes View details
ndhG-ndhI SSC 460 0.0159 0.96 68.9 yes View details
trnfM-CAU-rps14 LSC 175 0.0229 1.00 65.6 yes View details
psbI-trnS-GCU LSC 134 0.0224 1.00 65.4 yes View details
ndhC-trnV-UAC LSC 1166 0.0079 0.98 65.1 yes View details
accD-psaI LSC 838 0.0049 0.97 64.9 yes View details
atpB-rbcL LSC 815 0.0063 0.98 64.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 534–552 1.000 79.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 535–553 1.000 79.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 535–553 1.000 79.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 536–554 1.000 79.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 527–545 1.000 78.4
trnK-UUU_p1 trnK-UUU TCGATCTTATCTAACTAGATTCAGCA TGGTTTGATTGTCTAGCGTGA 2756–2842 1.000 40.5
trnK-UUU_p2 trnK-UUU CGATCTTATCTAACTAGATTCAGCA TGGTTTGATTGTCTAGCGTGA 2755–2841 1.000 40.5
trnK-UUU_p3 trnK-UUU CGATCTTATCTAACTAGATTCAGCAG TGGTTTGATTGTCTAGCGTGA 2755–2841 1.000 40.5
trnK-UUU_p4 trnK-UUU TCGATCTTATCTAACTAGATTCAGC TGGTTTGATTGTCTAGCGTGA 2756–2842 1.000 40.5
trnK-UUU_p5 trnK-UUU TCGATCTTATCTAACTAGATTCAGCA TGGTTTGATTGTCTAGCGTG 2756–2842 1.000 40.5
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GTTGCCAAAGCCGGTAATTT TAGGCTTCGGGCAATTTTGT 591–606 1.000 76.6
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ATAGGTATACGCTGGGACGG TAGGCTTCGGGCAATTTTGT 556–570 1.000 76.5
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GTTGCCAAAGCCGGTAATTT GCTTCGGGCAATTTTGTGAA 588–603 1.000 76.0
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ATAGGTATACGCTGGGACGG GCTTCGGGCAATTTTGTGAA 553–567 1.000 76.0
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GTTGCCAAAGCCGGTAATTT GTAGGCTTCGGGCAATTTTG 592–607 1.000 75.0
psbI-trnS-GCU_p1 psbI-trnS-GCU TTTATCTAATGACCCGGGGC TGGACTAAAGCGTCGGATTG 250–256 1.000 73.4
psbI-trnS-GCU_p2 psbI-trnS-GCU TTTATCTAATGACCCGGGGC GTGGACTAAAGCGTCGGATT 251–257 1.000 73.4
psbI-trnS-GCU_p3 psbI-trnS-GCU TTTATCTAATGACCCGGGGC ATTGGGAGAGATGGCTGAGT 269–275 1.000 72.5
psbI-trnS-GCU_p4 psbI-trnS-GCU TTTATCTAATGACCCGGGGC CATTGGGAGAGATGGCTGAG 270–276 1.000 71.3
psbI-trnS-GCU_p5 psbI-trnS-GCU TTTTATCTAATGACCCGGGGC TGGACTAAAGCGTCGGATTG 251–257 1.000 71.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGGGATCCCTTAACTATTAGGCT 1043–1047 1.000 55.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AGGGATCCCTTAACTATTAGGCT 1042–1046 1.000 55.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATCAACGGAACCGGAAAGAG AGGGATCCCTTAACTATTAGGCT 1107–1111 1.000 55.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAATAGTTATTCCCCGAGGG 1059–1063 1.000 54.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAATAGTTATTCCCCGAGGG 1058–1062 1.000 54.3
atpA-atpF_p1 atpA-atpF TACTAATCTCGTCGGCTCGA TATTGGCATGTTTGGAGCGA 135 1.000 80.2
atpA-atpF_p2 atpA-atpF CCGTCGCCTACTTGAAGTAC TATTGGCATGTTTGGAGCGA 217 1.000 80.1
atpA-atpF_p3 atpA-atpF GTCGCCTACTTGAAGTACGG TATTGGCATGTTTGGAGCGA 215 1.000 80.1
atpA-atpF_p4 atpA-atpF TAATCTCGTCGGCTCGAATG TATTGGCATGTTTGGAGCGA 132 1.000 78.9
atpA-atpF_p5 atpA-atpF ACTTGAAGTACGGTACCGGT TATTGGCATGTTTGGAGCGA 208 1.000 77.9

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
Moquilea minutiflora NC_030573.1 162318 View on NCBI ↗
Moquilea tomentosa NC_030575.1 162547 View on NCBI ↗