Markers + reference

Homalomena

2 species · Araceae · Alismatales

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Species 2
Genome length 165–170 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 803 0.0160 0.93 72.2 yes View details
trnS-GCU-trnG-UCC LSC 2633 0.0023 0.99 52.1 yes View details
rpoC2 LSC 4125 0.0010 1.00 54.4 yes View details
psbZ-trnG-GCC LSC 590 0.0102 0.99 65.1 yes View details
petA-psbJ LSC 1180 0.0136 0.99 67.1 yes View details
rpl32-trnL-UAG SSC 640 0.0047 1.00 61.4 yes View details
ndhG-ndhI SSC 694 0.0044 0.97 63.9 yes View details
rps15-ycf1 SSC 959 0.0099 0.95 69.2 yes View details
rpl2-trnH-GUG IRa 46 0.0000 1.00 64.2 no View details
psaC-ndhE SSC 635 0.0000 0.95 63.5 yes View details
trnT-UGU-trnL-UAA LSC 1279 0.0008 0.96 62.7 yes View details
trnF-GAA-ndhJ LSC 980 0.0010 0.97 61.8 yes View details
accD-psaI LSC 1362 0.0007 0.98 61.0 yes View details
ycf4-cemA LSC 1000 0.0030 1.00 60.6 yes View details
psbT-psbN LSC 74 0.0135 1.00 60.3 yes View details
atpF LSC 1391 0.0007 0.99 60.1 yes View details
psbM-trnD-GUC LSC 606 0.0017 1.00 60.0 yes View details
ycf3-trnS-GGA LSC 898 0.0011 0.99 60.0 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 85 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 CCTCTAGACCTAGCTGCTGT 830–869 1.000 83.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 844–883 1.000 83.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 843–882 1.000 83.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 845–884 1.000 83.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 833–872 1.000 83.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CATCGTTAGCTTGGAAGGCT 2783–2946 1.000 80.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GTGGAGAGAGAGGGATTCGA CATCGTTAGCTTGGAAGGCT 2832–2995 1.000 80.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGTTAGCTTGGAAGGCTAGG 2780–2943 1.000 80.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTGGAGAGAGAGGGATTCG CATCGTTAGCTTGGAAGGCT 2833–2996 1.000 80.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GTGGAGAGAGAGGGATTCGA CGTTAGCTTGGAAGGCTAGG 2829–2992 1.000 80.3
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA ATCAACCAAAAAGGGGAGGG 1565–1576 1.000 73.2
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA GGAGGGCGAAGTGATACAAA 1551–1562 1.000 72.6
atpF_p3 atpF AATTTCGTCGGCTCGAATGG ATCAACCAAAAAGGGGAGGG 1562–1573 1.000 70.4
atpF_p4 atpF AATTTCGTCGGCTCGAATGG GGAGGGCGAAGTGATACAAA 1548–1559 1.000 69.8
atpF_p5 atpF ACTAATTTCGTCGGCTCGAAT ATCAACCAAAAAGGGGAGGG 1565–1576 1.000 69.0
rpoC2_p1 rpoC2 GTTCCGCTCTCAACAATCCT ACGCAAGGTCTTCCAAAAGT 340 1.000 79.2
rpoC2_p2 rpoC2 CTCGTTCCGCTCTCAACAAT ACGCAAGGTCTTCCAAAAGT 343 1.000 77.8
rpoC2_p3 rpoC2 TCGTTCCGCTCTCAACAATC ACGCAAGGTCTTCCAAAAGT 342 1.000 77.7
rpoC2_p4 rpoC2 GTTCCGCTCTCAACAATCCT CGCAAGGTCTTCCAAAAGTG 339 1.000 76.4
rpoC2_p5 rpoC2 CTCGTTCCGCTCTCAACAAT CGCAAGGTCTTCCAAAAGTG 342 1.000 74.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 717–719 1.000 61.8
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCGCTGGGATTGTAGTTCAA 730–732 1.000 61.6
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC ATGTATGCTGTACATCCCGC 746–748 1.000 61.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA AGTTCAATCGGTCAGAGCAC 724–726 1.000 58.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTATGCTGTACATCCCGCTG 744–746 1.000 58.5
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTTCCGATGGATGG AATCGAACCCGCATCTTCTC 755–758 1.000 80.2
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTTCCGATGGATGG GAATCGAACCCGCATCTTCT 756–759 1.000 80.2
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTTCCGATGGATGG TACTTCACCATGGGCGGATA 780–783 1.000 79.1
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TTGCTTCTTCCGATGGATGG ACATTACTTCACCATGGGCG 784–787 1.000 78.7
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GCTTCTTCCGATGGATGGTC AATCGAACCCGCATCTTCTC 753–756 1.000 77.3

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
Homalomena occulta NC_054336.1 165398 View on NCBI ↗
Homalomena perplexa PX569150.1 169893 View on NCBI ↗