Markers + reference

Hemerocallis

3 species · Asphodelaceae · Asparagales

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Species 3
Genome length 156–156 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

9 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
psbK-psbI LSC 449 0.0015 1.00 42.0 yes View details
atpF LSC 1643 0.0008 1.00 59.0 yes View details
rpoB-trnC-GCA LSC 1076 0.0012 1.00 59.6 yes View details
psbM-trnD-GUC LSC 947 0.0014 1.00 57.1 yes View details
psaA-ycf3 LSC 845 0.0016 0.99 48.0 yes View details
psbE-petL LSC 1111 0.0018 1.00 55.2 yes View details
petL-petG LSC 194 0.0034 1.00 35.9 yes View details
trnL-UAG-rpl32 SSC 723 0.0129 1.00 67.0 yes View details
rpl32-ndhF SSC 1032 0.0042 1.00 61.5 yes View details
trnT-UGU-trnL-UAA LSC 986 0.0007 1.00 59.3 yes View details
accD LSC 1512 0.0009 1.00 59.3 yes View details
rps16-trnQ-UUG LSC 1752 0.0004 1.00 59.2 yes View details
clpP LSC 2087 0.0000 1.00 57.6 yes View details
rps14-psaB LSC 144 0.0000 0.99 53.9 yes View details
trnT-GGU-psbD LSC 840 0.0016 1.00 47.3 yes View details
rps3 LSC 657 0.0010 1.00 46.9 yes View details
ndhD-ccsA SSC 661 0.0000 1.00 46.9 yes View details
petA-psbJ LSC 837 0.0008 1.00 46.8 yes View details
matK LSC 1551 0.0009 1.00 46.7 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
matK_p1 matK CCACTACACTACTACATGTGCA CCCTGTTTTGACCATATCGC 1749 1.000 51.4
matK_p2 matK ACCACTACACTACTACATGTGC CCCTGTTTTGACCATATCGC 1750 1.000 51.4
matK_p3 matK CCACTACACTACTACATGTGCA CCTGTTTTGACCATATCGCAC 1748 1.000 49.2
matK_p4 matK ACCACTACACTACTACATGTGC CCTGTTTTGACCATATCGCAC 1749 1.000 49.2
matK_p5 matK CCACTACACTACTACATGTGCA ACCCTGTTTTGACCATATCGC 1750 1.000 47.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATCCACAGCGAGTCATGTC GAGGTTCGAATCCTTCCGTC 1837–1849 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GAATCCACAGCGAGTCATGT GAGGTTCGAATCCTTCCGTC 1838–1850 1.000 79.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGCGAGTCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1831–1843 1.000 79.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCATGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1826–1838 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCGAGTCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1829–1841 1.000 79.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGGCCGGGATCATTAGATA 569 1.000 79.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGGCCGGGATCATTAGAT 570 1.000 79.2
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGGCCGGGATCATTAGA 571 1.000 77.3
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGGCCGGGATCATTAGATA 566 1.000 77.1
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGGCCGGGATCATTAGAT 567 1.000 77.1
atpF_p1 atpF TCGAAGAGTTGCCATTAGTGT AGGGCGAGCCAAGTGATATA 1809–1810 1.000 64.4
atpF_p2 atpF TCGAAGAGTTGCCATTAGTGT GGGCGAGCCAAGTGATATAA 1808–1809 1.000 62.4
atpF_p3 atpF CGAAGAGTTGCCATTAGTGTC AGGGCGAGCCAAGTGATATA 1808–1809 1.000 61.9
atpF_p4 atpF CGAAGAGTTGCCATTAGTGT AGGGCGAGCCAAGTGATATA 1808–1809 1.000 60.1
atpF_p5 atpF CGAAGAGTTGCCATTAGTGTC GGGCGAGCCAAGTGATATAA 1807–1808 1.000 59.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGGTATGGTGGACATTCCCT TAAAGGATTTGCAGTCCCCC 1158–1161 1.000 73.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CAGGTATGGTGGACATTCCC TAAAGGATTTGCAGTCCCCC 1159–1162 1.000 73.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCAGGTATGGTGGACATTCC TAAAGGATTTGCAGTCCCCC 1160–1163 1.000 73.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGGTATGGTGGACATTCCCT TTTTTGAGAAGGCGACACCC 1194–1197 1.000 72.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CAGGTATGGTGGACATTCCC TTTTTGAGAAGGCGACACCC 1195–1198 1.000 71.9
psbM-trnD-GUC_p1 psbM-trnD-GUC TTGGCTGACTGTTTTTACGT AGTTCAATCGGTCAGAGCAC 1109 1.000 62.0
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 1060 1.000 61.6
psbM-trnD-GUC_p3 psbM-trnD-GUC TTGGCTGACTGTTTTTACGT TGCTATACACCTCGTTGGGA 1133 1.000 61.5
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TGCTATACACCTCGTTGGGA 1084 1.000 61.2
psbM-trnD-GUC_p5 psbM-trnD-GUC TGGCTGACTGTTTTTACGTAGA AGTTCAATCGGTCAGAGCAC 1108 1.000 60.9

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
Hemerocallis fulva NC_041649.1 155855 View on NCBI ↗
Hemerocallis hybrid cultivar NC_066650.1 156053 View on NCBI ↗
Hemerocallis minor NC_058266.1 156063 View on NCBI ↗