Markers + reference

Hydrocotyle

18 species · Araliaceae · Apiales

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Species 18
Genome length 153–154 kb
Candidate markers 273
Primer pairs 100

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 849 0.0164 1.00 58.5 yes View details
rps16-trnQ-UUG LSC 1173 0.0154 1.00 63.5 yes View details
petN-psbM LSC 1096 0.0152 1.00 56.2 yes View details
ycf3-trnS-GGA LSC 865 0.0235 1.00 68.4 yes View details
petA-psbJ LSC 1058 0.0217 0.97 62.1 yes View details
rpl16 LSC 1398 0.0135 1.00 55.9 yes View details
rpl22 LSC 495 0.0096 1.00 46.3 yes View details
ycf1 IRb 789 0.0054 1.00 38.9 no View details
ndhF-rpl32 SSC 1217 0.0196 1.00 63.9 yes View details
rpl32-trnL-UAG SSC 784 0.0174 0.98 59.8 yes View details
ycf1 SSC 5499 0.0144 1.00 48.1 yes View details
rpl22-rps19 LSC 178 0.0653 1.00 72.0 yes View details
rpl16-rps3 LSC 147 0.0485 1.00 65.9 yes View details
rpoB-trnC-GCA LSC 1088 0.0156 1.00 62.3 yes View details
trnG-GCC-trnfM-CAU LSC 196 0.0179 0.99 60.1 yes View details
psbH-petB LSC 123 0.0388 1.00 59.3 yes View details
psbT-psbN LSC 83 0.0420 1.00 58.3 yes View details
psbM-trnD-GUC LSC 1179 0.0115 1.00 57.3 yes View details
psbK-psbI LSC 405 0.0165 1.00 55.9 yes View details
atpH-atpI LSC 1202 0.0134 0.97 55.8 yes View details
ndhC-trnV-UAC LSC 993 0.0153 0.97 55.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCAGCCTACAGCAACTGTTC 909–955 1.000 86.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAGCCTACAGCAACTGTTC 908–954 1.000 86.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTCAGCCTACAGCAACTGTT 910–956 1.000 86.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTCAGCCTACAGCAACTGTT 909–955 1.000 86.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TCAGCCTACAGCAACTGTTC 918–964 1.000 85.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1246–1415 1.000 87.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1261–1430 1.000 85.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1260–1429 1.000 85.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1267–1436 1.000 83.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1250–1419 1.000 82.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAAAGTTTGAGAGTAAGCA 452–479 1.000 56.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAAAGTTTGAGAGTAAGCA 449–476 1.000 54.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAAAAGTTTGAGAGTAAGCA 450–477 1.000 54.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACGAAAAGTTTGAGAGTAAGCA 451–478 1.000 54.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACGAAAAGTTTGAGAGTAAGCA 453–480 1.000 53.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGC 1202–1263 1.000 81.2
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TAGGTGAATCCATGGAGGGC 1258–1319 1.000 80.5
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TAGGTGAATCCATGGAGGGC 1203–1264 1.000 80.0
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC TAGGTGAATCCATGGAGGGC 1262–1323 1.000 79.8
atpH-atpI_p5 atpH-atpI GAAGCAAGTCCTACAGCCAA TAGGTGAATCCATGGAGGGC 1232–1293 0.944 77.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CTTACCACTCGGCCATATCG 1114–1151 1.000 85.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCGGATTTGAACTGGGGAAA 1154–1191 1.000 85.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA AAAAGGATTTGCAGTCCCCC 1136–1173 1.000 82.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCTTACCACTCGGCCATATC 1115–1152 1.000 82.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA TTTGTTGATCAGGCGACACC 1173–1210 1.000 79.4
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGCT 923–1197 1.000 71.9
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGCTT 923–1197 1.000 69.4
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGC 923–1197 1.000 67.5
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GTTCCTACTGCTTTTCTGCT 922–1196 1.000 67.5
petN-psbM_p5 petN-psbM TGGGGAAGAAGTGGACTCTA AGTTCCTACTGCTTTTCTGCT 922–1196 1.000 66.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (18)

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

Species Accession Length (bp) Link
Hydrocotyle calcicola NC_082575.1 153305 View on NCBI ↗
Hydrocotyle chiangdaoensis PV094900.1 153254 View on NCBI ↗
Hydrocotyle dielsiana NC_082576.1 153297 View on NCBI ↗
Hydrocotyle himalaica NC_082582.1 153299 View on NCBI ↗
Hydrocotyle hookeri NC_082583.1 153294 View on NCBI ↗
Hydrocotyle hookeri subsp. chinensis NC_082584.1 153289 View on NCBI ↗
Hydrocotyle hookeri subsp. handelii NC_082585.1 153306 View on NCBI ↗
Hydrocotyle leucocephala OR767309.1 153960 View on NCBI ↗
Hydrocotyle nepalensis MT561038.1 153353 View on NCBI ↗
Hydrocotyle peltiformis NC_082586.1 153311 View on NCBI ↗
Hydrocotyle pseudoconferta OK585058.1 153302 View on NCBI ↗
Hydrocotyle ranunculoides NC_082577.1 153669 View on NCBI ↗
Hydrocotyle salwinica NC_082587.1 153294 View on NCBI ↗
Hydrocotyle sibthorpioides NC_035502.1 152880 View on NCBI ↗
Hydrocotyle sibthorpioides var. batrachium NC_082588.1 152740 View on NCBI ↗
Hydrocotyle verticillata NC_015818.1 153207 View on NCBI ↗
Hydrocotyle vulgaris NC_085367.1 153165 View on NCBI ↗
Hydrocotyle wilfordii NC_082589.1 152950 View on NCBI ↗