Markers + reference

Strobilanthes

9 species · Acanthaceae · Lamiales

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Species 9
Genome length 144–145 kb
Candidate markers 264
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1126 0.0248 0.97 73.5 yes View details
psbK-psbI LSC 411 0.0366 0.97 75.8 yes View details
trnS-GCU-trnS-CGA LSC 907 0.0376 0.95 80.7 yes View details
trnC-GCA-petN LSC 829 0.0294 0.99 81.4 yes View details
trnE-UUC-trnT-GGU LSC 724 0.0467 0.90 82.9 yes View details
rps4-trnT-UGU LSC 522 0.0338 1.00 82.1 yes View details
psaJ-rpl33 LSC 341 0.0355 1.00 73.0 yes View details
ycf2 LSC 6093 0.0130 1.00 50.2 yes View details
ndhF-rpl32 SSC 587 0.0296 1.00 78.1 yes View details
rpl32-trnL-UAG SSC 504 0.0390 0.98 78.0 yes View details
trnP-TGG-psaJ LSC 295 0.0454 0.95 79.2 yes View details
ycf2-psbA LSC 124 0.0671 0.98 72.3 yes View details
atpF-atpH LSC 395 0.0305 1.00 71.1 yes View details
trnK-UUU-rps16 LSC 415 0.0282 1.00 68.8 yes View details
rpl33-rps18 LSC 197 0.0293 0.97 68.8 yes View details
petN-psbM LSC 886 0.0133 0.99 68.5 yes View details
trnG-GCC-trnM-CAU LSC 185 0.0288 1.00 67.9 yes View details
accD-psaI LSC 751 0.0157 0.97 67.7 yes View details
psaA-ycf3 LSC 680 0.0187 0.99 67.0 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
trnK-UUU_p1 trnK-UUU TACAGAAGCGACCCCATAGG TCGCCCCCTACCTTTATCAA 2915–3000 0.778 73.0
trnK-UUU_p2 trnK-UUU CCCAAGCACACGACTTTTCT TCGCCCCCTACCTTTATCAA 2826–2911 0.778 72.4
trnK-UUU_p3 trnK-UUU TACAGAAGCGACCCCATAGG TTCGCCCCCTACCTTTATCA 2916–2998 0.667 68.0
trnK-UUU_p4 trnK-UUU ATCCAGTTACAGAAGCGACC TCGCCCCCTACCTTTATCAA 2922–2988 0.556 61.9
trnK-UUU_p5 trnK-UUU ATCCAGTTACAGAAGCGACC TTCGCCCCCTACCTTTATCA 2923–2989 0.556 61.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AACCCAATCGCCCTTTTGAT TGCTGCCATTTTGAAGGGAT 1567–1655 1.000 87.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACCCAATCGCCCTTTTGATT TGCTGCCATTTTGAAGGGAT 1566–1654 1.000 87.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATAGAATCCCCTCGTCCTGG TGCTGCCATTTTGAAGGGAT 1515 0.111 43.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATAGAATCCCCTCGTCCTGG ATCAACAGGCCATGGGATTC 1566 0.111 43.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATAGAATCCCCTCGTCCTGG GAATCAACAGGCCATGGGAT 1568 0.111 43.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 995–1241 1.000 87.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTCTGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1006–1252 1.000 87.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TTCTGTCCTTCAAGTCGCAC TTCGGAGGTTCGAATCCTTC 1010–1256 1.000 83.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 999–1245 1.000 83.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCTGTCCTTCAAGTCGCAC TAAGGCAACGGGTTTTGGTC 1036–1282 1.000 82.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGAAGAGTTTCAGGGTAAGCA 448–467 1.000 81.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTCAGGGTAAGC 449–468 1.000 81.4
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT CGAAGAGTTTCAGGGTAAGCA 453–472 1.000 81.3
psbK-psbI_p4 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGAAGAGTTTCAGGGTAAGC 454–473 1.000 81.3
psbK-psbI_p5 psbK-psbI TTTTGTTTGGCAAGCTGCTG CGAAGAGTTTCAGGGTAAGCA 452–471 1.000 79.0
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACCACTAAACTACACCCGCT 820–1053 1.000 86.6
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACCACTAAACTACACCCGCT 819–1052 1.000 86.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC ACCACTAAACTACACCCGCT 822–1055 1.000 83.8
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA CGACGCTTTAGTCCACTCAG ACCACTAAACTACACCCGCT 815–1048 1.000 83.6
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA TACCACTAAACTACACCCGC 821–1054 1.000 83.6
atpF-atpH_p1 atpF-atpH AGAAAGAGTACCATGCTGCG TGATTTCTGCTGCTTCCGTT 987–1024 1.000 86.5
atpF-atpH_p2 atpF-atpH ACAGGTTGTCAATTCAGCGT TGATTTCTGCTGCTTCCGTT 1132–1189 1.000 86.1
atpF-atpH_p3 atpF-atpH AGAAAGAGTACCATGCTGCG CGGAACCAAGAAACGGAAGA 1262–1292 1.000 85.9
atpF-atpH_p4 atpF-atpH AGAAAGAGTACCATGCTGCG TCGGAACCAAGAAACGGAAG 1263–1293 1.000 85.9
atpF-atpH_p5 atpF-atpH AGAAAGAGTACCATGCTGCG AACCCTCGTATTCTTGTGGC 1343–1372 0.889 80.8

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
Strobilanthes bantonensis MT576695.1 144591 View on NCBI ↗
Strobilanthes biocullata MW044601.1 144012 View on NCBI ↗
Strobilanthes crispa MW599987.1 144987 View on NCBI ↗
Strobilanthes cusia NC_037485.1 144133 View on NCBI ↗
Strobilanthes dalzielii NC_084379.1 144580 View on NCBI ↗
Strobilanthes lupulina NC_066801.1 144647 View on NCBI ↗
Strobilanthes medahinnensis NC_058776.1 144893 View on NCBI ↗
Strobilanthes sarcorrhiza PQ631129.1 144713 View on NCBI ↗
Strobilanthes tonkinensis NC_059902.1 144765 View on NCBI ↗