Markers + reference

Halophila

2 species · Hydrocharitaceae · Alismatales

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Species 2
Genome length 167–169 kb
Candidate markers 272
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 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
rbcL-accD LSC 839 0.2330 0.70 78.8 yes View details
accD LSC 3429 0.1638 0.62 70.6 yes View details
clpP-psbB LSC 840 0.2340 0.74 78.1 yes View details
ycf2 IRb 6627 0.0955 0.95 75.9 no View details
rpl32-ycf1 IRb 874 0.2806 0.86 81.4 yes View details
ycf1 IRb 6744 0.1492 0.86 75.0 yes View details
psaC-ccsA SSC 1447 0.1512 0.37 65.3 yes View details
trnL-UAG-ycf1 SSC 671 0.2929 0.97 82.9 yes View details
ycf1 IRa 6744 0.1492 0.86 75.0 no View details
ycf1-rpl32 IRa 874 0.2759 0.85 81.1 yes View details
ycf2 IRa 6627 0.0955 0.95 75.9 yes View details
atpH-atpI LSC 937 0.0392 0.98 81.1 yes View details
ycf2-rps7 IRb 726 0.1700 0.83 80.4 yes View details
rps7-ycf2 IRa 726 0.1700 0.83 80.4 yes View details
clpP LSC 630 0.1365 1.00 78.9 yes View details
trnK-UUU-rps16 LSC 764 0.0476 0.94 77.0 yes View details
trnQ-UUG-psbK LSC 558 0.0558 0.96 76.7 yes View details
rps18 LSC 573 0.0890 0.82 76.6 yes View details
trnH-GUG-rpoA IRb 58 0.0877 0.98 76.6 yes View details
rpoA-trnH-GUG IRa 58 0.0877 0.98 76.6 yes View details
trnD-GUC-trnY-GUA LSC 458 0.0515 0.89 76.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GAGCAGTACATATGGTCTATTTGA 819–831 1.000 47.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGCAGTACATATGGTCTATTTGA 818–830 1.000 47.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC GAGCAGTACATATGGTCTATTTGA 824–836 1.000 47.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC AGCAGTACATATGGTCTATTTGA 823–835 1.000 47.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GAGCAGTACATATGGTCTATTTG 819–831 1.000 47.3
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CCCACCCCAATAACGAACTT CTTACAGCTGCTTGCCAAAC 1255–1301 1.000 84.8
trnQ-UUG-psbK_p2 trnQ-UUG-psbK AACAAATAGGCCCCAGTTCC CTTACAGCTGCTTGCCAAAC 1525–1585 1.000 84.8
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CAAGACCCCACCCCAATAAC CTTACAGCTGCTTGCCAAAC 1307 0.500 58.3
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG CTTACAGCTGCTTGCCAAAC 927 0.500 57.9
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CAAGACCCCACCCCAATAAC GGTAGAACAAGTCAAGGGGC 1500 0.500 57.4
atpH-atpI_p1 atpH-atpI TACCTTGTCCAACTCCAGGT TAGGTGAATCCTTGGAGGGT 1054–1055 1.000 77.9
atpH-atpI_p2 atpH-atpI GCAAGTCCTACGGCTAATCC TAGGTGAATCCTTGGAGGGT 1025–1026 1.000 77.9
atpH-atpI_p3 atpH-atpI AGAAGCAAGTCCTACGGCTA TAGGTGAATCCTTGGAGGGT 1029–1030 1.000 77.7
atpH-atpI_p4 atpH-atpI TAGAAGCAAGTCCTACGGCT TAGGTGAATCCTTGGAGGGT 1030–1031 1.000 77.7
atpH-atpI_p5 atpH-atpI TACCTTGTCCAACTCCAGGT AGGTGAATCCTTGGAGGGTC 1053–1054 1.000 77.5
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 488–528 1.000 81.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 487–527 1.000 81.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGAATCCTAGTTCGGGACTG TGGCAATATGTCTACGCTGG 544–584 1.000 81.1
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGAATCCTAGTTCGGGACTG GGCAATATGTCTACGCTGGT 543–583 1.000 81.1
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA ATCCTAGTTCGGGACTGACG TGGCAATATGTCTACGCTGG 541–581 1.000 80.2
rbcL-accD_p1 rbcL-accD CCTTGTCTCGTTATTGCCGA CCTTTTGCCCCTCTTTCACT 2096 0.500 60.0
rbcL-accD_p2 rbcL-accD CCTTGTCTCGTTATTGCCGA TCCTTTTGCCCCTCTTTCAC 2097 0.500 59.9
rbcL-accD_p3 rbcL-accD CAAATGGAGCGCTGAACTTG CCTTTTGCCCCTCTTTCACT 1585 0.500 59.8
rbcL-accD_p4 rbcL-accD CAAATGGAGCGCTGAACTTG TCCTTTTGCCCCTCTTTCAC 1586 0.500 59.7
rbcL-accD_p5 rbcL-accD GATTATCCGTGAAGCTGCCA CCTTTTGCCCCTCTTTCACT 1603 0.500 59.6
accD_p1 accD GACGGATCAGCTTGCCTTAA GGACCAAACGATCCGAATCA 530 0.500 59.7
accD_p2 accD GACGGATCAGCTTGCCTTAA ACCAAACGATCCGAATCAGG 528 0.500 59.6
accD_p3 accD AAAGGGGGCTTGAAAGATGG GGACCAAACGATCCGAATCA 783 0.500 59.4
accD_p4 accD AAAGGGGGCTTGAAAGATGG ACCAAACGATCCGAATCAGG 781 0.500 59.3
accD_p5 accD GGGCTTGAAAGATGGTTGGA GGACCAAACGATCCGAATCA 778 0.500 59.2

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
Halophila beccarii NC_051970.1 168585 View on NCBI ↗
Halophila ovalis NC_068806.1 167010 View on NCBI ↗