Markers + reference

Loxostigma

2 species · Gesneriaceae · Lamiales

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Species 2
Genome length 154–154 kb
Candidate markers 277
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 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 323 0.1090 0.99 74.6 yes View details
rps16-trnQ-UUG LSC 1072 0.0282 0.99 75.8 yes View details
psbK-psbI LSC 454 0.0246 0.90 60.5 yes View details
trnS-GCU-trnG-UCC LSC 795 0.0281 0.98 66.2 yes View details
trnG-UCC-trnR-UCU LSC 224 0.0647 0.90 78.6 yes View details
trnC-GCA-petN LSC 807 0.0242 0.97 67.1 yes View details
petN-psbM LSC 1013 0.0290 0.99 73.5 yes View details
trnL-UAA-trnF-GAA LSC 336 0.0298 1.00 62.6 yes View details
ndhC-trnV-UAC LSC 1053 0.0285 1.00 63.7 yes View details
ycf1 IRb 837 0.0203 1.00 55.9 no View details
ndhF SSC 2232 0.0238 1.00 57.1 yes View details
ndhF-rpl32 SSC 761 0.0414 0.98 72.4 yes View details
ycf1 SSC 5445 0.0237 0.99 53.1 yes View details
rrn4.5-rrn5 IRb 263 0.0623 0.98 84.8 yes View details
rrn5-rrn4.5 IRa 263 0.0623 0.98 84.8 yes View details
petG-trnW-CCA LSC 122 0.0492 1.00 73.1 yes View details
trnD-GUC-trnY-GUA LSC 109 0.0550 1.00 72.6 yes View details
psbE-petL LSC 906 0.0198 0.95 71.2 yes View details
ndhD-psaC SSC 96 0.0729 1.00 70.9 yes View details
psbI-trnS-GCU LSC 116 0.0690 1.00 70.2 yes View details
trnK-UUU-rps16 LSC 819 0.0246 0.99 69.2 yes View details
psbM-trnD-GUC LSC 524 0.0289 0.99 69.0 yes View details
ycf4-cemA LSC 871 0.0279 0.99 67.7 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 TCAGTGCTATGCATGGTTCC 772–792 1.000 82.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 771–791 1.000 82.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 786–806 1.000 82.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 785–805 1.000 82.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 787–807 1.000 82.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT GGTGCTCAACCTACAGGAAC 1005–1010 1.000 80.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 923–928 1.000 79.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 922–927 1.000 79.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GGTGCTCAACCTACAGGAAC 937–942 1.000 78.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 932–937 1.000 78.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1162–1175 1.000 81.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1145–1158 1.000 81.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1163–1176 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1160–1173 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1159–1172 1.000 79.1
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGAAGAGTTTCAGAGTAAGCA 469–512 1.000 64.5
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTCAGAGTAAGCA 464–507 1.000 64.5
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAGAGTTTCAGAGTAAGCA 461–504 1.000 62.5
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAAGAGTTTCAGAGTAAGCA 462–505 1.000 62.5
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACGAAGAGTTTCAGAGTAAGCA 463–506 1.000 62.5
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCTGGACGTGAAGAATA TGGACTAAAGCGTCGGATTG 210 1.000 49.1
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCTGGACGTGAAGAATAA TGGACTAAAGCGTCGGATTG 209 1.000 49.1
psbI-trnS-GCU_p3 psbI-trnS-GCU AATCCTGGACGTGAAGAATA GTGGACTAAAGCGTCGGATT 211 1.000 49.1
psbI-trnS-GCU_p4 psbI-trnS-GCU ATCCTGGACGTGAAGAATAA GTGGACTAAAGCGTCGGATT 210 1.000 49.1
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCTGGACGTGAAGAATAA ATTGGGAGAGATGGCTGAGT 228 1.000 48.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 864–876 1.000 54.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 863–875 1.000 54.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 867–879 1.000 53.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 866–878 1.000 53.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 865–877 1.000 53.8

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
Loxostigma griffithii NC_082153.1 153711 View on NCBI ↗
Loxostigma kurzii NC_082151.1 153988 View on NCBI ↗