Markers + reference

Hydrocharis

3 species · Hydrocharitaceae · Alismatales

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Species 3
Genome length 154–160 kb
Candidate markers 268
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 2212 0.2770 0.94 80.4 yes View details
trnN-GUU-ycf1 IRb 329 0.4732 0.96 72.6 yes View details
ycf1 IRb 6420 0.3533 0.48 66.2 yes View details
ndhH IRb 1182 0.3596 0.10 61.4 yes View details
ndhH IRa 1182 0.0135 1.00 53.3 no View details
ycf1 IRa 6420 0.2101 0.88 74.0 no View details
trnC-GCA-petN LSC 688 0.0576 0.97 87.6 yes View details
ndhF-rpl32 SSC 988 0.0846 0.97 87.6 yes View details
atpH-atpI LSC 733 0.0627 0.97 85.7 yes View details
trnT-UGU-trnL-UAA LSC 868 0.0826 0.93 85.2 yes View details
trnS-GCU-trnG-UCC LSC 766 0.0865 0.96 85.0 yes View details
psbM-trnD-GUC LSC 819 0.0493 0.97 84.4 yes View details
psaA-ycf3 LSC 587 0.0757 0.98 83.9 yes View details
rps2-rpoC2 LSC 630 0.1697 0.97 83.7 yes View details
accD LSC 1698 0.0815 0.96 83.1 yes View details
trnD-GUC-trnY-GUA LSC 344 0.0645 0.98 82.9 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CAGGATCAGTCGTGGTCTTG GACAAGTCGGCCTAGATGTG 2457 0.333 52.7
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CAGGATCAGTCGTGGTCTTG TCTTGACAAGTCGGCCTAGA 2461 0.333 52.7
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG CCTTTCAGGATCAGTCGTGG GACAAGTCGGCCTAGATGTG 2462 0.333 52.6
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CCTTTCAGGATCAGTCGTGG TCTTGACAAGTCGGCCTAGA 2466 0.333 52.6
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG CAGGATCAGTCGTGGTCTTG TCAACGCCTCTTGACAAGTC 2469 0.333 52.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 821–952 1.000 59.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GAACGAATCACACTTTTACCACT 823–954 1.000 58.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AGAACGAATCACACTTTTACCAC 824–955 1.000 58.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AACGAATCACACTTTTACCACT 822–953 1.000 57.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT ACGAATCACACTTTTACCACT 822–953 1.000 57.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 820–1034 1.000 87.0
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 821–1035 1.000 85.8
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TTTTGCAACTTTAGCTGCGG 830–1044 1.000 85.1
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT ATCCATGGAGGGTCATCACT 787 0.333 51.4
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA ATCCATGGAGGGTCATCACT 788 0.333 50.2
rps2-rpoC2_p1 rps2-rpoC2 CATCATTGGCAGGAATCGGA TTATCGATCCCAGGGGGTAC 1742 0.333 52.9
rps2-rpoC2_p2 rps2-rpoC2 TCATCATTGGCAGGAATCGG TTATCGATCCCAGGGGGTAC 1743 0.333 52.9
rps2-rpoC2_p3 rps2-rpoC2 CTCCTGCTTTGATCATGCCT TTATCGATCCCAGGGGGTAC 1169 0.333 52.7
rps2-rpoC2_p4 rps2-rpoC2 TGACCAAAATGGACTCCTGC TTATCGATCCCAGGGGGTAC 1182 0.333 52.5
rps2-rpoC2_p5 rps2-rpoC2 ACCGTGACCAAAATGGACTC TTATCGATCCCAGGGGGTAC 1186 0.333 52.3
trnC-GCA-petN_p1 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC CTCCTCCCCCATACTACGAG 790–826 1.000 85.2
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGTTTTGGCGACATGGC CTCCTCCCCCATACTACGAG 848–884 1.000 85.0
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTTTTGGCGACATGGC AGCCCAAGCGAGACTTACTA 795–831 1.000 85.0
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTA CTCCTCCCCCATACTACGAG 815–851 1.000 84.6
trnC-GCA-petN_p5 trnC-GCA-petN GACATGGCCAAGTGGTAAGG CTCCTCCCCCATACTACGAG 836–872 1.000 84.2
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGAACTAGAATAAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 937–1066 1.000 47.3
psbM-trnD-GUC_p2 psbM-trnD-GUC AGTAAAAAGGCAGTAGGAACT TTCAATTGGTCAGAGCACCG 951–1080 1.000 47.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGTAAAAAGGCAGTAGGAACT TTCAATTGGTCAGAGCACCG 952–1081 1.000 47.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AAAAGGCAGTAGGAACTAGA TTCAATTGGTCAGAGCACCG 947–1076 1.000 47.2
psbM-trnD-GUC_p5 psbM-trnD-GUC AAAGGCAGTAGGAACTAGAA TTCAATTGGTCAGAGCACCG 946–1075 1.000 47.2

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
Hydrocharis chevalieri NC_061224.1 158066 View on NCBI ↗
Hydrocharis dubia NC_061221.1 159698 View on NCBI ↗
Hydrocharis morsus-ranae NC_061222.1 153881 View on NCBI ↗