Markers + reference

Hygrophila

2 species · Acanthaceae · Lamiales

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Species 2
Genome length 146–147 kb
Candidate markers 266
Primer pairs 90

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 469 0.0792 0.86 81.8 yes View details
rps16-trnQ-UUG LSC 1035 0.0544 0.96 80.8 yes View details
trnS-GCU-trnG-UCC LSC 805 0.0429 0.72 72.2 yes View details
accD-psaI LSC 747 0.0427 0.94 86.1 yes View details
clpP1 LSC 2104 0.0173 0.93 56.7 yes View details
ycf2 LSC 6669 0.0249 0.99 53.8 yes View details
ycf1 IRb 825 0.0049 0.99 54.7 no View details
ndhF-rpl32 SSC 547 0.0752 0.97 81.0 yes View details
ycf1 SSC 5406 0.0246 0.99 53.7 yes View details
ycf2 IRa 2685 0.0022 1.00 48.1 no View details
psbL-psbF LSC 24 0.0833 1.00 85.4 yes View details
trnG-GCC-trnfM-CAU LSC 169 0.0750 0.95 84.5 yes View details
trnE-UUC-trnT-GGU LSC 651 0.0442 0.94 79.7 yes View details
psaA-pafI LSC 659 0.0415 0.95 78.2 yes View details
trnL-UAG-ccsA SSC 94 0.0449 0.95 77.8 yes View details
psbI-trnS-GCU LSC 112 0.3056 0.96 77.1 yes View details
trnK-UUU-rps16 LSC 449 0.0550 0.93 75.7 yes View details
trnF-GAA-ndhJ LSC 695 0.0287 0.95 75.2 yes View details
ndhC-trnV-UAC LSC 1168 0.0416 0.95 75.2 yes View details
psaJ-rpl33 LSC 356 0.0538 0.99 74.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGTGCTAACCTTGGTATGGA 568–584 1.000 81.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 569–585 1.000 81.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCTAACCTTGGTATGGA 582–598 1.000 81.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGTGCTAACCTTGGTATGG 583–599 1.000 81.8
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCTAACCTTGGTATGGA 581–597 1.000 81.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 542–559 1.000 82.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GTGCTCAACCTACAGGAACT 541–558 1.000 76.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTACCGTTGAGTTAGCAACC GGTGCTCAACCTACAGGAAC 544–561 1.000 75.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 541–558 1.000 75.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC TCCTTGAGAAAGGTGCTCAAC 553–570 1.000 74.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1108–1117 1.000 85.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1112–1121 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1138–1147 1.000 80.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1100–1109 1.000 80.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1107–1116 1.000 79.4
psbI-trnS-GCU_p1 psbI-trnS-GCU TAGGGTCTCGCACAAAATCG TGGACTAAAGCGTCGGATTG 489–495 1.000 88.2
psbI-trnS-GCU_p2 psbI-trnS-GCU TAGGGTCTCGCACAAAATCG GTGGACTAAAGCGTCGGATT 490–496 1.000 88.2
psbI-trnS-GCU_p3 psbI-trnS-GCU ACCCGTTTCCAGTGAAAGAC TGGACTAAAGCGTCGGATTG 520 0.500 59.7
psbI-trnS-GCU_p4 psbI-trnS-GCU TGACCCGTTTCCAGTGAAAG TGGACTAAAGCGTCGGATTG 522 0.500 59.7
psbI-trnS-GCU_p5 psbI-trnS-GCU ACCCGTTTCCAGTGAAAGAC GTGGACTAAAGCGTCGGATT 521 0.500 59.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTACACCCGC 660–860 1.000 78.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTACACCCGC 659–859 1.000 78.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTACACCCGC 714–914 1.000 77.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTACACCCGC 661–861 1.000 76.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTACACCCGC 660–860 1.000 76.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 721–755 1.000 85.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 700–734 1.000 85.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 697–731 1.000 85.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 718–752 1.000 84.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TTGAACCGATGACTTACGCC 723–757 1.000 83.3

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
Hygrophila polysperma PV915200.1 146675 View on NCBI ↗
Hygrophila ringens PP056234.1 146119 View on NCBI ↗