Markers + reference

Paris

39 species · Melanthiaceae · Liliales

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Species 39
Genome length 156–166 kb
Candidate markers 285
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 IRb 6906 0.0050 1.00 42.7 no View details
trnN_GUU-ycf1 IRb 334 0.0625 0.99 69.3 yes View details
ycf1 IRb 1337 0.0238 0.99 65.6 yes View details
ycf1 SSC 6162 0.0211 0.98 66.1 yes View details
ycf1-trnN_GUU IRa 334 0.0515 0.97 67.6 yes View details
ycf2 IRa 6906 0.0049 1.00 42.4 yes View details
ycf2-trnI_CAU IRa 196 0.0499 0.97 65.6 yes View details
trnK-UUU-rps16 LSC 757 0.0102 0.99 69.9 yes View details
rpl32-trnL_UAG SSC 835 0.0166 0.99 64.9 yes View details
trnI_CAU-ycf2 IRb 196 0.0450 1.00 63.6 yes View details
rps3-psbA LSC 80 0.0822 1.00 62.1 no View details
rpoB-trnC_GCA LSC 866 0.0153 0.98 60.5 yes View details
trnS_GCU-trnG_UCC LSC 1148 0.0094 0.97 60.3 yes View details
ndhF-rpl32 SSC 775 0.0134 1.00 59.8 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GCGCTCAACCTACAGTAACT 845–952 1.000 80.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GCGCTCAACCTACAGTAACT 846–953 1.000 79.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GCGCTCAACCTACAGTAACT 843–950 1.000 79.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GCGCTCAACCTACAGTAACT 842–949 1.000 79.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGCGCTCAACCTACAGTAAC 846–953 1.000 78.5
trnS_GCU-trnG_UCC_p1 trnS_GCU-trnG_UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCCTTAACT 787–1335 1.000 76.1
trnS_GCU-trnG_UCC_p2 trnS_GCU-trnG_UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 786–1334 1.000 76.1
trnS_GCU-trnG_UCC_p3 trnS_GCU-trnG_UCC GATAGAGCGGAGAGAGAGGG AACCGAAAGACCCCTTAACT 847–1395 1.000 74.5
trnS_GCU-trnG_UCC_p4 trnS_GCU-trnG_UCC CAATCCGACGCTTTAGTCCA AAACCGAAAGACCCCTTAACT 788–1336 1.000 74.2
trnS_GCU-trnG_UCC_p5 trnS_GCU-trnG_UCC AATCCGACGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 787–1335 1.000 74.2
rpoB-trnC_GCA_p1 rpoB-trnC_GCA CCAATTCTTCCGTCAAGCCT TAAAGGATTTGCAGTCCCCC 987–1144 1.000 83.5
rpoB-trnC_GCA_p2 rpoB-trnC_GCA TCCAATTCTTCCGTCAAGCC TAAAGGATTTGCAGTCCCCC 988–1145 1.000 83.4
rpoB-trnC_GCA_p3 rpoB-trnC_GCA CCAATTCTTCCGTCAAGCCT TTTGTTCATCAGGCGACACC 1024–1181 1.000 81.4
rpoB-trnC_GCA_p4 rpoB-trnC_GCA TCCAATTCTTCCGTCAAGCC TTTGTTCATCAGGCGACACC 1025–1182 1.000 81.3
rpoB-trnC_GCA_p5 rpoB-trnC_GCA CCAATTCTTCCGTCAAGCCT GACACCCGGATTTGAACTGG 1010–1167 1.000 80.9
trnI_CAU-ycf2_p1 trnI_CAU-ycf2 GTTGGGCGCTTTAACCATTC AGGATTTTAATTGATGTCGTTTCA 203–628 0.846 40.6
trnI_CAU-ycf2_p2 trnI_CAU-ycf2 AGTTGGGCGCTTTAACCATT AGGATTTTAATTGATGTCGTTTCA 204–629 0.846 40.6
trnI_CAU-ycf2_p3 trnI_CAU-ycf2 TTGGGCGCTTTAACCATTCA AGGATTTTAATTGATGTCGTTTCA 202–627 0.846 40.6
trnI_CAU-ycf2_p4 trnI_CAU-ycf2 GTTGGGCGCTTTAACCATTC GGATTTTAATTGATGTCGTTTCA 202–627 0.846 40.6
trnI_CAU-ycf2_p5 trnI_CAU-ycf2 ATTGAACATTGGCGTGCATC AGGATTTTAATTGATGTCGTTTCA 259–684 0.846 40.2
trnN_GUU-ycf1_p1 trnN_GUU-ycf1 TAGCATAGCAAAGACGCGTT GGAAGAGATAAGAGGGCCCT 823–1649 1.000 91.1
trnN_GUU-ycf1_p2 trnN_GUU-ycf1 TAGCATAGCAAAGACGCGTT CCTTCTTCCATAACCCGAGC 851–1677 0.974 90.6
trnN_GUU-ycf1_p3 trnN_GUU-ycf1 GGCAGAATAGCAGAGCAAGT CCTTCTTCCATAACCCGAGC 882–1708 0.974 90.3
trnN_GUU-ycf1_p4 trnN_GUU-ycf1 GAGCGAGCCCTTTAATTCCA CCTTCTTCCATAACCCGAGC 587–1413 0.974 90.3
trnN_GUU-ycf1_p5 trnN_GUU-ycf1 GTAACCCAGGCCAGAATCAG CCTTCTTCCATAACCCGAGC 999–1520 0.923 87.1
ycf1_p1 ycf1 TAGCATAGCAAAGACGCGTT CAAATGGAGTTGGGGTTGGA 1319–2600 0.769 82.7
ycf1_p2 ycf1 CCCGGAACTTCTTCGTAGTG CAAATGGAGTTGGGGTTGGA 853–2174 0.769 82.6
ycf1_p3 ycf1 CCGGAACTTCTTCGTAGTGG CAAATGGAGTTGGGGTTGGA 852–2173 0.769 82.6
ycf1_p4 ycf1 GAGCGAGCCCTTTAATTCCA CAAATGGAGTTGGGGTTGGA 1055–2336 0.769 82.4
ycf1_p5 ycf1 GAGCTACTGAGGAACAACGG CAAATGGAGTTGGGGTTGGA 939–2220 0.744 81.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (39)

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

Species Accession Length (bp) Link
Paris axialis NC_046459.1 156821 View on NCBI ↗
Paris bashanensis NC_046455.1 157320 View on NCBI ↗
Paris birmanica NC_046390.1 157857 View on NCBI ↗
Paris caobangensis NC_046460.1 158256 View on NCBI ↗
Paris caojianensis MZ147601.1 163853 View on NCBI ↗
Paris cronquistii NC_033511.1 156896 View on NCBI ↗
Paris daliensis NC_046454.1 158118 View on NCBI ↗
Paris delavayi NC_046456.1 158575 View on NCBI ↗
Paris dulongensis NC_046449.1 157342 View on NCBI ↗
Paris dunniana NC_033512.1 157174 View on NCBI ↗
Paris fargesii NC_033513.1 157518 View on NCBI ↗
Paris forrestii NC_046448.1 157198 View on NCBI ↗
Paris guizhouensis MW229085.1 156094 View on NCBI ↗
Paris incompleta NC_046452.1 157610 View on NCBI ↗
Paris japonica NC_044637.1 155957 View on NCBI ↗
Paris lancifolia NC_071786.1 158228 View on NCBI ↗
Paris lihengiana MW229107.1 156596 View on NCBI ↗
Paris liiana NC_052909.1 163860 View on NCBI ↗
Paris luquanensis NC_033514.1 157594 View on NCBI ↗
Paris mairei NC_033515.1 157079 View on NCBI ↗
Paris marmorata NC_033516.1 156755 View on NCBI ↗
Paris polyphylla NC_046458.1 158130 View on NCBI ↗
Paris polyphylla var. alba MW980523.1 163944 View on NCBI ↗
Paris polyphylla var. chinensis NC_033517.1 157847 View on NCBI ↗
Paris polyphylla var. emeiensis NC_050052.1 164854 View on NCBI ↗
Paris polyphylla var. stenophylla PQ838415.1 164767 View on NCBI ↗
Paris qiliangiana NC_046391.1 158354 View on NCBI ↗
Paris quadrifolia NC_033520.1 157907 View on NCBI ↗
Paris rugosa NC_038170.1 163200 View on NCBI ↗
Paris stigmatosa MN723866.1 165623 View on NCBI ↗
Paris tengchongensis NC_046393.1 157150 View on NCBI ↗
Paris thibetica NC_038161.1 162708 View on NCBI ↗
Paris undulata NC_046457.1 158286 View on NCBI ↗
Paris vaniotii NC_046450.1 156846 View on NCBI ↗
Paris variabilis MW229100.1 156697 View on NCBI ↗
Paris vietnamensis NC_033519.1 158224 View on NCBI ↗
Paris xichouensis NC_046394.1 158225 View on NCBI ↗
Paris xuefengshanensis ON059798.1 162116 View on NCBI ↗
Paris yanchii NC_046392.1 157918 View on NCBI ↗