Markers + reference

Acanthus

3 species · Acanthaceae · Lamiales

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Species 3
Genome length 150–155 kb
Candidate markers 269
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 373 0.1153 1.00 78.0 yes View details
trnS-GCU-trnG-UCC LSC 715 0.0808 0.97 84.9 yes View details
atpH-atpI LSC 1011 0.0729 1.00 84.2 yes View details
rpoB-trnC-GCA LSC 1049 0.0569 1.00 81.2 yes View details
trnC-GCA-petN LSC 881 0.0687 0.98 84.4 yes View details
psaA-ycf3 LSC 650 0.0874 0.99 84.3 yes View details
rps4-trnT-UGU LSC 464 0.0772 0.94 84.4 yes View details
trnT-UGU-trnL-UAA LSC 801 0.1504 0.99 89.9 yes View details
ycf1 IRb 819 0.0317 0.99 68.2 no View details
ycf1-rpl32 SSC 2684 0.0437 0.98 73.3 yes View details
ycf1 SSC 5367 0.0524 1.00 71.2 yes View details
rpl2-psbA LSC 373 0.1629 0.94 78.4 no View details
rps16-trnQ-UUG LSC 1112 0.0566 0.97 84.4 yes View details
trnE-UUC-trnT-GGU LSC 604 0.0549 0.98 83.7 yes View details
trnD-GUC-trnY-GUA LSC 102 0.0654 1.00 82.6 yes View details
trnS-UGA-trnG-GCC LSC 787 0.0507 0.92 81.8 yes View details
accD-psaI LSC 728 0.0535 0.98 81.7 yes View details
trnG-GCC-trnfM-CAU LSC 171 0.0549 0.99 80.3 yes View details
atpA-atpF LSC 83 0.1044 1.00 80.0 yes View details
petA-psbJ LSC 779 0.0603 0.98 80.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1185–1272 1.000 88.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1189–1276 1.000 83.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1177–1264 1.000 83.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1184–1271 1.000 82.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1180–1267 1.000 80.8
psbK-psbI_p1 psbK-psbI CAAGCCGCTGTAAGTTTTCG ACGAAGAGTTTCAGAGTAAGCA 419–578 1.000 67.9
psbK-psbI_p2 psbK-psbI AGCCGCTGTAAGTTTTCGAT ACGAAGAGTTTCAGAGTAAGCA 417–576 1.000 67.6
psbK-psbI_p3 psbK-psbI AAGCCGCTGTAAGTTTTCGA ACGAAGAGTTTCAGAGTAAGCA 418–577 1.000 67.3
psbK-psbI_p4 psbK-psbI GCCGCTGTAAGTTTTCGATG ACGAAGAGTTTCAGAGTAAGCA 416–575 1.000 67.1
psbK-psbI_p5 psbK-psbI GCAAGCCGCTGTAAGTTTTC ACGAAGAGTTTCAGAGTAAGCA 420–579 1.000 65.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC TACCACTAAACTATACCCGC 753–927 1.000 51.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 767–941 1.000 51.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC AACGAATCACACTTTTACCACT 768–942 1.000 51.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC AAACGAATCACACTTTTACCACT 769–943 1.000 51.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCACTCAGCCATCTCTCC ACGAATCACACTTTTACCAC 767–941 1.000 51.7
atpA-atpF_p1 atpA-atpF AATTTCGTCGGCTCGAATGG GAGCAATGAAAGAAATAACTGA 132–171 1.000 48.7
atpA-atpF_p2 atpA-atpF ACTAATTTCGTCGGCTCGAA GAGCAATGAAAGAAATAACTGA 135–174 1.000 48.6
atpA-atpF_p3 atpA-atpF ACTAATTTCGTCGGCTCGAA GAGCAATGAAAGAAATAACTGAT 135–174 1.000 48.6
atpA-atpF_p4 atpA-atpF ACTAATTTCGTCGGCTCGAAT GAGCAATGAAAGAAATAACTGA 135–174 1.000 48.6
atpA-atpF_p5 atpA-atpF ACTAATTTCGTCGGCTCGAA GAGCAATGAAAGAAATAACTGATT 135–174 1.000 48.6
atpH-atpI_p1 atpH-atpI TGGCCCAAAGAAACGAAAGA TGCTTTGGCTTTACTCACGT 1994–2532 1.000 87.6
atpH-atpI_p2 atpH-atpI GATGCCCTCTACAGCTTGAC TGCTTTGGCTTTACTCACGT 1459–1987 1.000 86.7
atpH-atpI_p3 atpH-atpI GATGCCCTCTACAGCTTGAC GGCAAATAGGGGGTTTCCAA 1790–2318 1.000 85.7
atpH-atpI_p4 atpH-atpI GATGCCCTCTACAGCTTGAC CAAACCATTCCGACTAGGGG 1689 0.333 52.6
atpH-atpI_p5 atpH-atpI TGGCCCAAAGAAACGAAAGA CAAACCATTCCGACTAGGGG 2224 0.333 52.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT ACAAAGCATCAACGGTCTGT 1720–1817 0.667 71.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCTCTGTTCTGCTGCTACTG 1698–1844 0.667 69.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG CCTCTGTTCTGCTGCTACTG 1714–1860 0.667 69.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCCTACGCAAGCAAATTGTT CCTCTGTTCTGCTGCTACTG 1888–2034 0.667 69.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TCGCCGAACAGAGGATAGAT 1671 0.333 53.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Acanthus ebracteatus MT240944.1 150823 View on NCBI ↗
Acanthus leucostachyus NC_070388.1 154686 View on NCBI ↗
Acanthus mollis NC_070389.1 150339 View on NCBI ↗