Markers + reference

Hippuris

2 species · Plantaginaceae · Lamiales

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Species 2
Genome length 152–153 kb
Candidate markers 273
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-trnV-UAC LSC 1109 0.0522 0.97 75.9 yes View details
trnV-UAC LSC 37 0.1622 1.00 72.5 yes View details
cemA LSC 690 0.0145 1.00 54.9 yes View details
ycf1 IRb 1221 0.0057 1.00 48.2 no View details
ndhF-rpl32 SSC 739 0.0353 1.00 68.1 yes View details
ccsA-ndhD SSC 246 0.0620 0.98 73.3 yes View details
ndhG-ndhI SSC 340 0.2260 0.86 76.1 yes View details
ndhA SSC 2186 0.0299 0.99 61.2 yes View details
ycf1 SSC 5766 0.0343 1.00 69.2 yes View details
trnL-UAG-ccsA SSC 106 0.0816 0.92 77.4 yes View details
cemA-petA LSC 214 0.1033 1.00 76.1 yes View details
rpl2-trnH-GUG IRa 76 0.1613 0.82 75.6 no View details
rps3-rpl22 LSC 25 0.0400 1.00 74.6 yes View details
ycf4-cemA LSC 475 0.0316 1.00 74.5 yes View details
trnM-CAU LSC 72 0.0694 1.00 73.6 yes View details
rps19-rpl2 IRb 54 0.0926 1.00 72.4 yes View details
trnK-UUU-rps16 LSC 901 0.0307 0.94 68.9 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 80 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 TTTCCTTGAAAGGGGTGCTC 1018–1038 1.000 84.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 1017–1037 1.000 84.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC TTTCCTTGAAAGGGGTGCTC 1004–1024 1.000 82.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC TTTCCTTGAAAGGGGTGCTC 1026–1046 1.000 79.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCCTTGAAAGGGGTGCT 1018–1038 1.000 79.1
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CTAGAAAGTTTCTCCGGCCC TGAATCAGAGCACATGGAGC 1472–1519 1.000 87.0
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CTAGAAAGTTTCTCCGGCCC TTGGTAGTGCTCCTGGATCA 1505–1552 1.000 86.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CTAGAAAGTTTCTCCGGCCC GACAAAAGGTTCGGTCCAGT 1777–1823 1.000 86.5
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CTAGAAAGTTTCTCCGGCCC CTGACAAAAGGTTCGGTCCA 1779–1825 1.000 86.5
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CTAGAAAGTTTCTCCGGCCC TGACAAAAGGTTCGGTCCAG 1778–1824 1.000 86.5
trnV-UAC_p1 trnV-UAC TTTTCAACAGGCTCGTGTCA TGAATCAGAGCACATGGAGC 550–590 1.000 90.4
trnV-UAC_p2 trnV-UAC TTTGTTGTGCTTCGCTAGGT TGAATCAGAGCACATGGAGC 713–753 1.000 88.8
trnV-UAC_p3 trnV-UAC TTTTCAACAGGCTCGTGTCA GACAAAAGGTTCGGTCCAGT 855–894 1.000 88.2
trnV-UAC_p4 trnV-UAC TTTTCAACAGGCTCGTGTCA CTGACAAAAGGTTCGGTCCA 857–896 1.000 88.2
trnV-UAC_p5 trnV-UAC TTTTCAACAGGCTCGTGTCA TGACAAAAGGTTCGGTCCAG 856–895 1.000 88.2
trnV-UAC_p1 trnV-UAC TTTTCAACAGGCTCGTGTCA AAACCAAATGGGACCCATCC 1134–1167 1.000 87.3
trnV-UAC_p2 trnV-UAC TTTTCAACAGGCTCGTGTCA CCCCTATTGCTACAGCTGTG 1704–1739 1.000 86.0
trnV-UAC_p3 trnV-UAC TTTTCAACAGGCTCGTGTCA CCCTATTGCTACAGCTGTGG 1703–1738 1.000 86.0
trnV-UAC_p4 trnV-UAC TTTGTTGTGCTTCGCTAGGT CCCCTATTGCTACAGCTGTG 1867–1902 1.000 85.4
trnV-UAC_p5 trnV-UAC TTTGTTGTGCTTCGCTAGGT CCCTATTGCTACAGCTGTGG 1866–1901 1.000 85.4
trnM-CAU_p1 trnM-CAU GGATGGGTCCCATTTGGTTT CCGTTGACTCCGGTATCTGA 136–138 1.000 75.3
trnM-CAU_p2 trnM-CAU GGATGGGTCCCATTTGGTTT CGTTGACTCCGGTATCTGAT 135–137 1.000 73.3
trnM-CAU_p3 trnM-CAU GGATGGGTCCCATTTGGTTT ACGCAGTTCAAAACGGAAAT 196–198 1.000 72.5
trnM-CAU_p4 trnM-CAU TGGGTCCCATTTGGTTTTCT CCGTTGACTCCGGTATCTGA 133–135 1.000 69.5
trnM-CAU_p5 trnM-CAU GGATGGGTCCCATTTGGTTT CCGTTGACTCCGGTATCTG 136–138 1.000 69.4
ycf4-cemA_p1 ycf4-cemA ATTCCCTTGACCCGTACTGA GAGAAATCCACCAGGGCAAA 649–650 1.000 80.9
ycf4-cemA_p2 ycf4-cemA TTCCCTTGACCCGTACTGAT GAGAAATCCACCAGGGCAAA 648–649 1.000 80.9
ycf4-cemA_p3 ycf4-cemA CTTGCGCGTACCAATTGAAG GAGAAATCCACCAGGGCAAA 575–576 1.000 80.7
ycf4-cemA_p4 ycf4-cemA GAACAAAAAGCCGCGGAATT GAGAAATCCACCAGGGCAAA 604–605 1.000 79.7
ycf4-cemA_p5 ycf4-cemA GCTATTCCCTTGACCCGTAC GAGAAATCCACCAGGGCAAA 652–653 1.000 79.5

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
Hippuris montana NC_072276.1 152375 View on NCBI ↗
Hippuris vulgaris NC_054196.1 152698 View on NCBI ↗