Markers + reference

Yamazakia

2 species · Linderniaceae · Lamiales

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Species 2
Genome length 154–154 kb
Candidate markers 271
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 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 947 0.0407 0.96 80.2 yes View details
rps16-trnQ-UUG LSC 1244 0.0449 0.95 88.6 yes View details
trnT-UGU-trnL-UAA LSC 718 0.0376 0.96 77.5 yes View details
ndhC-trnV-UAC LSC 1170 0.0351 0.98 70.8 yes View details
trnW-CCA-trnP-UGG LSC 211 0.1090 1.00 83.9 yes View details
trnP-UGG-psaJ LSC 424 0.0259 1.00 61.8 yes View details
psaJ-rpl33 LSC 496 0.0467 0.99 69.6 yes View details
rps15-ycf1 SSC 385 0.0443 1.00 69.5 yes View details
ycf1 SSC 5544 0.0195 1.00 48.8 yes View details
rpl16-rps3 LSC 168 0.0482 0.99 77.3 yes View details
rps11-rpl36 LSC 111 0.0891 0.91 74.5 yes View details
trnD-GUC-trnY-GUA LSC 101 0.0693 1.00 71.1 yes View details
trnH-GUG-psbA LSC 236 0.0730 0.99 70.7 yes View details
accD-psaI LSC 611 0.0177 0.93 70.4 yes View details
rps18-rpl20 LSC 231 0.0476 1.00 70.4 yes View details
psbI-trnS-GCU LSC 124 0.0541 0.90 70.2 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0508 1.00 70.1 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 85 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 TCAGTGCTATGCATGGTTCC 685–1016 1.000 80.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 684–1015 1.000 80.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 699–1030 1.000 80.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 698–1029 1.000 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 700–1031 1.000 80.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGGGCTCAACCT 1050–1066 1.000 80.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGGGCTCAACCT 1049–1065 1.000 80.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TTGAAAAAGGGGCTCAACCT 1064–1080 1.000 79.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTGAAAAAGGGGCTCAACCT 1059–1075 1.000 79.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGGGCTCAACCTACAG 1045–1061 1.000 79.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1338–1375 1.000 85.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1280–1317 1.000 85.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAAATTGAAATGGGGCGTGG 1352–1389 1.000 83.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1294–1331 1.000 83.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAAATTGAAATGGGGCGTGG 1330–1367 1.000 80.6
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 224–237 1.000 85.9
psbI-trnS-GCU_p2 psbI-trnS-GCU CTTTTGTTTGGCAAGCTGCT TGGACTAAAGCGTCGGATTG 726–739 1.000 82.5
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 721–734 1.000 82.5
psbI-trnS-GCU_p4 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 722–735 1.000 82.5
psbI-trnS-GCU_p5 psbI-trnS-GCU CTTTTGTTTGGCAAGCTGCT GTGGACTAAAGCGTCGGATT 727–740 1.000 82.4
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CTGGTTCAAATCCAGCTCGG 155 1.000 72.5
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TCTACGCTGGTTCAAATCCA 161 1.000 70.5
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGTTCAAATCCAGCTCGG 154 1.000 69.8
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GTCTACGCTGGTTCAAATCCA 162 1.000 69.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGTCTACGCTGGTTCAAATCC 163 1.000 69.2
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC CTCTCTTTCAAGGAGGCAGC 147 1.000 76.7
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC CTCTCTTTCAAGGAGGCAGC 148 1.000 76.5
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC GCCAACGAATTTACAGTCCG CTCTCTTTCAAGGAGGCAGC 152 1.000 75.3
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC GATAGTATGAGGGCGGTTGG 203 1.000 74.7
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC GATAGTATGAGGGCGGTTGG 204 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
Yamazakia pusilla NC_082134.1 153876 View on NCBI ↗
Yamazakia viscosa NC_082135.1 154402 View on NCBI ↗