Markers + reference

Mentzelia

2 species · Loasaceae · Cornales

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Species 2
Genome length 159–159 kb
Candidate markers 270
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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 870 0.0506 1.00 75.1 yes View details
rps16-trnQ-UUG LSC 1664 0.0457 0.97 76.8 yes View details
trnC-GCA-petN LSC 849 0.0535 0.97 82.8 yes View details
trnT-UGU-trnL-UAA LSC 933 0.0412 0.96 79.7 yes View details
trnF-GAA-ndhJ LSC 702 0.0486 1.00 80.2 yes View details
ndhC-trnV-UAC LSC 1189 0.0474 0.90 78.2 yes View details
petA-psbJ LSC 1027 0.0647 0.99 78.7 yes View details
ycf1 IRb 971 0.0051 1.00 46.7 no View details
ndhF SSC 2223 0.0328 1.00 61.2 yes View details
ndhF-rpl32 SSC 1168 0.0578 0.96 84.6 yes View details
rpl32-trnL-UAG SSC 973 0.0526 0.98 81.4 yes View details
rps15-ycf1 SSC 401 0.0551 1.00 70.3 yes View details
ycf1 SSC 5706 0.0375 0.99 60.1 yes View details
trnW-CCA-trnP-UGG LSC 178 0.1067 1.00 79.8 yes View details
trnS-GCU-trnG-UCC LSC 771 0.0374 0.94 77.7 yes View details
trnR-UCU-atpA LSC 146 0.0703 0.88 77.4 yes View details
trnL-UAG-ccsA SSC 101 0.0700 0.99 75.8 yes View details
trnH-GUG-psbA LSC 351 0.0748 0.95 75.6 yes View details
ycf1-ndhF IRb 162 0.1119 0.88 75.4 yes View details
atpH-atpI LSC 1158 0.0352 0.96 75.1 yes View details
psaJ-rpl33 LSC 442 0.0468 0.97 75.1 yes View details
petD-rpoA LSC 201 0.0500 0.90 74.9 yes View details
psaB-psaA LSC 25 0.0400 1.00 73.7 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 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 GAGCTTAGTTTCCGTCTGGG 1042–1051 1.000 82.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 1048–1057 1.000 82.2
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGAGCTTAGTTTCCGTCTGG 1043–1052 1.000 82.2
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAGCTTAGTTTCCGTCTG 1044–1053 1.000 82.2
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 1056–1065 1.000 82.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ACTTCGGTCTAATCAAATAAAAATCA 935–962 1.000 43.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACTTCGGTCTAATCAAATAAAAATCA 934–961 1.000 43.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC ACTTCGGTCTAATCAAATAAAAATCA 996–1023 1.000 43.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGATGGTATGGACGAATCCC ACTTCGGTCTAATCAAATAAAAATCA 995–1022 1.000 43.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGGTATGGACGAATCCCTCA ACTTCGGTCTAATCAAATAAAAATCA 992–1019 1.000 43.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1737–1757 1.000 83.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1751–1771 1.000 81.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1741–1761 1.000 78.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1767–1787 1.000 78.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAGAAATCGAAATGGGGCGT 1797–1817 1.000 78.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCCAAACCGAAAGACCCC 869–884 1.000 85.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCCAAACCGAAAGACCCC 868–883 1.000 85.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCATCAACGGAAAGAGAGGG AATCCAAACCGAAAGACCCC 929–944 1.000 85.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AATCCAAACCGAAAGACCCC 923–938 1.000 84.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC AATCCAAACCGAAAGACCCC 871–886 1.000 82.9
trnR-UCU-atpA_p1 trnR-UCU-atpA ATCGGAATGAAAAGCGTCCA GAGGAAGCAGAAGCCCTTTT 288–306 1.000 84.9
trnR-UCU-atpA_p2 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT GAGGAAGCAGAAGCCCTTTT 287–305 1.000 84.9
trnR-UCU-atpA_p3 trnR-UCU-atpA ATCGGAATGAAAAGCGTCCA CATTCACCGAGGAAGCAGAA 296–314 1.000 84.7
trnR-UCU-atpA_p4 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT CATTCACCGAGGAAGCAGAA 295–313 1.000 84.7
trnR-UCU-atpA_p5 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT AAGACATTCACCGAGGAAGC 299–317 1.000 84.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CAAGCGGTATCCAAGCTCTT 1254–1267 1.000 85.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CAAGCGGTATCCAAGCTCTT 1310–1323 1.000 84.3
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA CAAGCGGTATCCAAGCTCTT 1255–1268 1.000 83.9
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC CAAGCGGTATCCAAGCTCTT 1314–1327 1.000 83.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC CAAGCGGTATCCAAGCTCTT 1269–1282 1.000 83.6

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
Mentzelia albicaulis NC_044830.1 159226 View on NCBI ↗
Mentzelia aspera NC_044838.1 159456 View on NCBI ↗