Markers + reference

Justicia

11 species · Acanthaceae · Lamiales

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Species 11
Genome length 148–152 kb
Candidate markers 272
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 462 0.0627 1.00 81.9 yes View details
rps16-trnQ (UUG) LSC 879 0.0620 0.95 82.3 yes View details
rpoB-trnC (GCA) LSC 1108 0.0530 0.94 89.4 yes View details
trnE (UUC)-trnT (GGU) LSC 629 0.0584 0.92 87.9 yes View details
trnS (UGA)-psbZ LSC 318 0.0444 0.96 70.8 yes View details
trnT (UGU)-trnL (UAA) LSC 703 0.0569 0.97 86.0 yes View details
rpl16 LSC 1479 0.0510 0.97 83.4 yes View details
rpl32-trnL (UAG) SSC 546 0.0607 0.93 77.7 yes View details
rps15-ycf1 SSC 403 0.0684 0.90 76.9 yes View details
ycf1 SSC 5238 0.0463 1.00 76.4 yes View details
trnS (GCU)-trnG (UCC) LSC 674 0.0572 0.99 90.5 yes View details
trnC (GCA)-petN LSC 700 0.0589 0.92 85.9 yes View details
atpF-atpH LSC 407 0.0436 0.97 84.6 yes View details
matK-trnK-UUU LSC 728 0.0542 0.97 83.7 yes View details
ndhC-trnV (UAC) LSC 965 0.0501 0.96 82.8 yes View details
petA-psbJ LSC 939 0.0522 0.94 82.4 yes View details
petN-psbM LSC 960 0.0527 1.00 82.3 yes View details
psbE-petL LSC 907 0.0375 0.98 82.1 yes View details
trnG (UCC)-trnR (UCU) LSC 164 0.0614 0.99 81.7 yes View details
accD-psaI LSC 627 0.0475 0.98 81.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ACTCCCAAGCACACGAATTT TTCTTCGGGTTGCTAACTCA 2626–2656 0.636 61.6
trnK-UUU_p2 trnK-UUU TGGGTAAAAGTGCAAACCGA TTCTTCGGGTTGCTAACTCA 2942–2972 0.636 60.9
trnK-UUU_p3 trnK-UUU TCTACTGGAGGAGCAGCAAT TTCTTCGGGTTGCTAACTCA 2833–2863 0.636 60.4
trnK-UUU_p4 trnK-UUU CTACTGGAGGAGCAGCAATG TTCTTCGGGTTGCTAACTCA 2832–2862 0.545 57.2
trnK-UUU_p5 trnK-UUU ACTCCCAAGCACACGAATTT AGCTCGTAGAATCTCCCTTCT 2750 0.091 33.0
matK-trnK-UUU_p1 matK-trnK-UUU ACCAAGATTTCCACGTGGAC AGCCGTCTATCGAATCGTTG 1854–1923 1.000 90.2
matK-trnK-UUU_p2 matK-trnK-UUU CCAAGATTTCCACGTGGACA AGCCGTCTATCGAATCGTTG 1853–1922 1.000 90.2
matK-trnK-UUU_p3 matK-trnK-UUU ACCAAGATTTCCACGTGGAC TCGATCCCGAAGAGAAGGAA 1824–1893 1.000 90.0
matK-trnK-UUU_p4 matK-trnK-UUU ACCAAGATTTCCACGTGGAC TCTATCCCAATGAGCCGTCT 1866–1935 0.818 83.2
matK-trnK-UUU_p5 matK-trnK-UUU CCAAGATTTCCACGTGGACA TCTATCCCAATGAGCCGTCT 1865–1934 0.818 83.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCCGTACGAGGAGAAAACTT 739–772 0.909 86.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 GGGAGAAGGTTTTTGGGGTT AGCCGTCTATCGAATCGTTG 1386–1422 0.545 68.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGGAGAAGGTTTTTGGGGTT TCGATCCCGAAGAGAAGGAA 1356–1392 0.545 68.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGGAGAAGGTTTTTGGGGTT GCCGTACGAGGAGAAAACTT 1459–1490 0.455 65.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGGAGAAGGTTTTTGGGGTT TCTATCCCAATGAGCCGTCT 1398–1434 0.364 60.7
rps16-trnQ (UUG)_p1 rps16-trnQ (UUG) GAGCACCCTCATCCCTAGAT AGCAGCTTGCCAAACAAAAG 1266–1593 0.909 87.7
rps16-trnQ (UUG)_p2 rps16-trnQ (UUG) GAGCACCCTCATCCCTAGAT CTTACAGCAGCTTGCCAAAC 1271–1598 0.909 87.7
rps16-trnQ (UUG)_p3 rps16-trnQ (UUG) GAGCACCCTCATCCCTAGAT GAGGTTCGAATCCTTCCGTC 691–1019 0.909 87.6
rps16-trnQ (UUG)_p4 rps16-trnQ (UUG) GAGCACCCTCATCCCTAGAT AAAAGCACAGGTACCACTGG 1562 0.091 43.3
rps16-trnQ (UUG)_p5 rps16-trnQ (UUG) ATTGAGCAATTCCAACCGGT AAAAGCACAGGTACCACTGG 1794 0.091 42.9
trnS (GCU)-trnG (UCC)_p1 trnS (GCU)-trnG (UCC) CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 628–771 1.000 63.7
trnS (GCU)-trnG (UCC)_p2 trnS (GCU)-trnG (UCC) AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 627–770 1.000 63.7
trnS (GCU)-trnG (UCC)_p3 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 682–825 1.000 62.5
trnS (GCU)-trnG (UCC)_p4 trnS (GCU)-trnG (UCC) CAATCCGACGCTTTAGTCCA GGAATATGACCGAAAGAACCT 670–813 0.909 59.4
trnS (GCU)-trnG (UCC)_p5 trnS (GCU)-trnG (UCC) AATCCGACGCTTTAGTCCAC GGAATATGACCGAAAGAACCT 669–812 0.909 59.4
trnG (UCC)-trnR (UCU)_p1 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 225–300 1.000 75.3
trnG (UCC)-trnR (UCU)_p2 trnG (UCC)-trnR (UCU) CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 228–303 1.000 75.1
trnG (UCC)-trnR (UCU)_p3 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 231–306 1.000 74.7
trnG (UCC)-trnR (UCU)_p4 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG CATTAGACAATGGACGCAGT 206–281 1.000 74.6
trnG (UCC)-trnR (UCU)_p5 trnG (UCC)-trnR (UCU) CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 234–309 1.000 74.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Justicia adhatoda NC_047476.1 149479 View on NCBI ↗
Justicia demissa NC_080242.1 150208 View on NCBI ↗
Justicia flava NC_044862.1 150888 View on NCBI ↗
Justicia gendarussa NC_080241.1 149735 View on NCBI ↗
Justicia latiflora NC_080236.1 148374 View on NCBI ↗
Justicia leptostachya NC_044668.1 149227 View on NCBI ↗
Justicia lianshanica NC_080243.1 148574 View on NCBI ↗
Justicia patentiflora NC_080238.1 149018 View on NCBI ↗
Justicia quadrifaria NC_080234.1 151739 View on NCBI ↗
Justicia vagabunda NC_080239.1 151247 View on NCBI ↗
Justicia ventricosa NC_059953.1 149700 View on NCBI ↗