Markers + reference

Mazus

9 species · Mazaceae · Lamiales

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Species 9
Genome length 153–154 kb
Candidate markers 271
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 719 0.0268 1.00 70.1 yes View details
rps16-trnQ-UUG LSC 1113 0.0167 1.00 56.8 yes View details
trnT-GGU-psbD LSC 923 0.0135 1.00 50.2 yes View details
psaA-ycf3 LSC 721 0.0176 1.00 57.7 yes View details
petA-psbJ LSC 979 0.0158 1.00 50.2 yes View details
psbE-petL LSC 876 0.0180 0.99 54.9 yes View details
rpl20-rps12 LSC 826 0.0164 1.00 59.9 yes View details
ndhF SSC 2214 0.0124 1.00 42.5 yes View details
ndhF-rpl32 SSC 511 0.0188 1.00 62.6 yes View details
rps15-ycf1 SSC 423 0.0280 1.00 57.7 yes View details
ycf1 SSC 5622 0.0135 1.00 48.1 yes View details
trnH-GUG-psbA LSC 288 0.0339 0.99 74.1 yes View details
rpl2-trnH-GUG IRa 108 0.0116 1.00 67.6 no View details
trnG-GCC-trnfM-CAU LSC 165 0.0387 1.00 63.2 yes View details
ndhD-psaC SSC 113 0.0331 1.00 61.8 yes View details
trnS-GCU-trnG-UCC LSC 775 0.0176 1.00 60.1 yes View details
ndhC-trnV-UAC LSC 1186 0.0151 1.00 56.6 yes View details
rps2-rpoC2 LSC 167 0.0236 1.00 55.8 yes View details
trnT-UGU-trnL-UAA LSC 613 0.0175 1.00 55.6 yes View details
rpoB-trnC-GCA LSC 1232 0.0101 1.00 55.5 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 303–356 1.000 88.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 317–370 1.000 88.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 316–369 1.000 88.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 318–371 1.000 88.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 352–405 1.000 85.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT GGGTTTGTTGCTGCCATTTT 1544–1571 0.889 79.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT GGGTTTGTTGCTGCCATTTT 1545–1572 0.889 79.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAAGGGTTTGTTGCTGCC 1549–1576 0.889 79.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAAAGGGTTTGTTGCTGCC 1550–1577 0.889 79.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT GCCGTACGAGGAGAAAACTT 1132–1151 0.889 79.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GGTTCGAATCCTTCCGTCC 1153–1202 1.000 78.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GTTCGAATCCTTCCGTCCC 1152–1201 1.000 78.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTTCGAATCCTTCCGTCC 1136–1185 1.000 78.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTCCC 1135–1184 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GTTCGAATCCTTCCGTCCC 1153–1202 1.000 77.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGGGTTAATCGAACGAATCACA 834–876 1.000 70.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AGGGTTAATCGAACGAATCACA 833–875 1.000 70.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGTTAATCGAACGAATCACAC 833–875 1.000 69.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGGTTAATCGAACGAATCACAC 832–874 1.000 69.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AGGGTTAATCGAACGAATCACA 888–930 1.000 68.7
rps2-rpoC2_p1 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TGCATGATAGACTAGAACAATCA 260–322 1.000 44.1
rps2-rpoC2_p2 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TTGCATGATAGACTAGAACAATCA 261–323 1.000 44.1
rps2-rpoC2_p3 rps2-rpoC2 AAATGAACTCCTGCCTCCAG TGCATGATAGACTAGAACAATCA 273–335 1.000 43.9
rps2-rpoC2_p4 rps2-rpoC2 GCCAAAATGAACTCCTGCCT TGCATGATAGACTAGAACAATCA 277–339 1.000 43.9
rps2-rpoC2_p5 rps2-rpoC2 CCATGGCCAAAATGAACTCC TGCATGATAGACTAGAACAATCA 282–344 1.000 43.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTGCCCCATTTGCATCCA CCGGATTTGAACTGGGGAAA 1280–1320 1.000 77.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTGCCCCATTTGCATCCA TTGTTGATTAGGCGACACCC 1298–1338 1.000 76.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCATTTGCATCCACGAGCAT CCGGATTTGAACTGGGGAAA 1274–1314 1.000 75.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTGCCCCATTTGCATCCA AAAAGGATTTGCAGTCCCCC 1262–1302 1.000 75.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCATTTGCATCCACGAGCAT TTGTTGATTAGGCGACACCC 1292–1332 1.000 74.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Mazus caducifer NC_065393.1 152759 View on NCBI ↗
Mazus gracilis PP078680.1 152859 View on NCBI ↗
Mazus humilis NC_077631.1 152854 View on NCBI ↗
Mazus miquelii NC_056339.1 153124 View on NCBI ↗
Mazus omeiensis NC_058532.1 153353 View on NCBI ↗
Mazus pumilus NC_042444.1 153149 View on NCBI ↗
Mazus pumilus var. delavayi OQ628314.1 152847 View on NCBI ↗
Mazus surculosus NC_077632.1 154027 View on NCBI ↗
Mazus xiuningensis NC_056340.1 153127 View on NCBI ↗