Markers + reference

Trillium

4 species · Melanthiaceae · Liliales

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Species 4
Genome length 156–157 kb
Candidate markers 279
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 5 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-trnV-UAC LSC 883 0.0534 0.92 71.1 yes View details
atpE LSC 405 0.2947 0.88 58.8 yes View details
atpB LSC 1497 0.3051 0.93 64.2 yes View details
atpB-rbcL LSC 694 0.1177 0.96 74.0 yes View details
rbcL-accD LSC 823 0.1764 0.96 74.3 yes View details
accD LSC 1464 0.1087 0.99 70.6 yes View details
ycf1 IRb 174 0.0000 0.00 9.2 no View details
ycf1 SSC 5856 0.0795 0.89 76.3 yes View details
ycf1-trnN-GUU IRa 576 0.1088 0.99 84.6 yes View details
trnN-GUU-ycf1 IRb 576 0.0346 0.67 67.5 yes View details
ycf2-trnI-CAU IRa 160 0.1917 0.91 64.5 yes View details
trnF-GAA-ndhJ LSC 694 0.0065 0.97 64.0 yes View details
ndhF-rpl32 SSC 771 0.0220 0.95 61.4 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CCTGAAAGTTGGGTAGGCTG 776–792 1.000 81.3
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CTGAAAGTTGGGTAGGCTGG 775–791 1.000 81.3
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TTGATGCCTGAAAGTTGGGT 782–798 1.000 79.6
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ GGGATAGCTCAGTCGGTAGA CTGAAAGTTGGGTAGGCTGG 811–827 1.000 79.4
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGGATAGCTCAGTCGGTAGA CCTGAAAGTTGGGTAGGCTG 812–828 1.000 79.3
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCTCACTAAAGAAGGGGCCA CAAATAGAACCCGCCATCGA 2054–2270 0.500 59.3
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TCTCACTAAAGAAGGGGCCA TAGAACCCGCCATCGATTTG 2050–2266 0.500 59.3
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCTCACTAAAGAAGGGGCCA AGGTGCAAATTCAGATGCCA 2072–2288 0.500 59.1
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TGGTTCAGGCATTTGCTCAT CAAATAGAACCCGCCATCGA 2078–2294 0.500 59.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TGGTTCAGGCATTTGCTCAT TAGAACCCGCCATCGATTTG 2074–2290 0.500 59.0
trnV-UAC_p1 trnV-UAC ACAAAACTTTCTCGCTCGGT CTAGGACACGAGTAGAGGCA 1770–1986 0.500 59.3
trnV-UAC_p2 trnV-UAC ACAAAACTTTCTCGCTCGGT CCCTATTGCCACAGCTGTAG 2021–2237 0.500 59.3
trnV-UAC_p3 trnV-UAC TTCTATGGACCAAGCAACCG CTAGGACACGAGTAGAGGCA 1247 0.500 58.8
trnV-UAC_p4 trnV-UAC TTCTATGGACCAAGCAACCG CCCTATTGCCACAGCTGTAG 1498 0.500 58.8
trnV-UAC_p5 trnV-UAC ACAAAACTTTCTCGCTCGGT ACATTGATCCGCAAGAAGCT 1878–2094 0.500 58.7
atpE_p1 atpE CAAATCGATGGCGGGTTCTA TTGGTTTGACTGCCCTAACC 1801 0.500 59.5
atpE_p2 atpE TCGATGGCGGGTTCTATTTG TTGGTTTGACTGCCCTAACC 1797 0.500 59.5
atpE_p3 atpE CAAATCGATGGCGGGTTCTA GCAGTTTATGTACCTGCGGA 1571 0.500 59.4
atpE_p4 atpE TCGATGGCGGGTTCTATTTG GCAGTTTATGTACCTGCGGA 1567 0.500 59.4
atpE_p5 atpE TGGCATCTGAATTTGCACCT TTGGTTTGACTGCCCTAACC 1779 0.500 59.3
atpB_p1 atpB TGCCTCTACTCGTGTCCTAG TATATGGCGCAACCCAATCC 2380 0.500 58.9
atpB_p2 atpB CTACAGCTGTGGCAATAGGG TATATGGCGCAACCCAATCC 2129 0.500 58.9
atpB_p3 atpB TGCCTCTACTCGTGTCCTAG TGGCCGTTGAAACCGAAATA 2161 0.500 58.8
atpB_p4 atpB CTACAGCTGTGGCAATAGGG TGGCCGTTGAAACCGAAATA 1910 0.500 58.8
atpB_p5 atpB TGCCTCTACTCGTGTCCTAG GGTGACATAAGTCCCTCCCT 2579 0.500 58.8
atpB-rbcL_p1 atpB-rbcL GCCGACTGGAACACTTAGAG CGGTCTCTCCAACGCATAAA 1653 0.500 60.0
atpB-rbcL_p2 atpB-rbcL GCCGACTGGAACACTTAGAG AGATCCTCCAGACGTAGAGC 1416 0.500 59.9
atpB-rbcL_p3 atpB-rbcL GCCGACTGGAACACTTAGAG ATCCTCCAGACGTAGAGCTC 1414 0.500 59.9
atpB-rbcL_p4 atpB-rbcL GCCGACTGGAACACTTAGAG GATCCTCCAGACGTAGAGCT 1415 0.500 59.9
atpB-rbcL_p5 atpB-rbcL GCCGACTGGAACACTTAGAG TCTCGATCTGGTAGCATCGT 1268 0.500 59.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Trillium camschatcense NC_046451.1 156139 View on NCBI ↗
Trillium cuneatum NC_027185.1 156610 View on NCBI ↗
Trillium maculatum NC_027738.1 157359 View on NCBI ↗
Trillium tschonoskii NC_027739.1 156852 View on NCBI ↗