Markers + reference

Smilax

10 species · Smilacaceae · Liliales

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Species 10
Genome length 158–159 kb
Candidate markers 270
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-trnV-UAC LSC 1741 0.0303 0.90 70.2 yes View details
accD-psaI LSC 1044 0.0356 0.93 77.2 yes View details
petA-psbJ LSC 1287 0.0342 0.95 89.6 yes View details
psaJ-rpl33 LSC 456 0.0388 0.98 90.8 yes View details
rpl33-rps18 LSC 389 0.0384 0.94 74.8 yes View details
rpl22 LSC 375 0.0096 1.00 52.3 yes View details
ndhF SSC 2220 0.0077 1.00 50.2 yes View details
ndhF-rpl32 SSC 1143 0.0391 0.85 75.4 yes View details
psaC-ndhE SSC 509 0.0329 0.98 88.5 yes View details
rpl22-rps19 IRb 174 0.0672 0.82 87.5 yes View details
atpI-rps2 LSC 370 0.0360 0.92 85.4 yes View details
trnP-UGG-psaJ LSC 489 0.0303 0.93 81.3 yes View details
rps19-psbA IRa 293 0.0602 0.92 79.1 no View details
rps16-trnQ-UUG LSC 683 0.0218 0.98 76.1 yes View details
trnS-GCU-trnG-UCC LSC 912 0.0164 0.95 74.3 yes View details
rpl32-trnL-UAG SSC 765 0.0193 1.00 73.9 yes View details
trnG-UCC-trnR-UCU LSC 220 0.0309 0.86 73.6 yes View details
psbM-trnD-GUC LSC 1108 0.0113 0.98 72.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 721–767 1.000 87.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACAGTCGATCATGTCCT GAGGTTCGAATCCTTCCGTC 743–789 1.000 87.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 732–778 1.000 87.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 725–771 1.000 86.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGTCGATCATGTCCT CTCGGAGGTTCGAATCCTTC 747–793 1.000 86.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TGAAAAACCGAAAGACCCCT 1029–1157 1.000 82.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TGATGAGGGATAGCGGAGAG TGAAAAACCGAAAGACCCCT 1092–1220 1.000 81.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GAGGGATAGCGGAGAGAGAG TGAAAAACCGAAAGACCCCT 1088–1216 1.000 80.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AAGTGATGAGGGATAGCGGA TGAAAAACCGAAAGACCCCT 1095–1223 0.900 76.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAAGTGATGAGGGATAGCGG TGAAAAACCGAAAGACCCCT 1096–1224 0.900 76.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 250–300 1.000 72.7
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 253–303 1.000 72.4
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 256–306 1.000 71.9
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 259–309 1.000 71.6
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCAACGTCGACTATAACCCC AGAAGACCTCTGTCCTATCCA 271–321 1.000 70.8
atpI-rps2_p1 atpI-rps2 GTTGGCCTACTTCTACACCC ATTTCGATTCCAGCCAACGA 509–584 1.000 86.9
atpI-rps2_p2 atpI-rps2 GTTGGCCTACTTCTACACCC CAGCCAACGATGACGCTATA 499–574 1.000 86.8
atpI-rps2_p3 atpI-rps2 GTTGGCCTACTTCTACACCC ATTTGCGAGGGTCGTTCTAG 440–515 1.000 86.3
atpI-rps2_p4 atpI-rps2 GTTGGCCTACTTCTACACCC TTTCGATTCCAGCCAACGAT 508–583 0.900 82.3
atpI-rps2_p5 atpI-rps2 GGCCTACTTCTACACCCGAT TTTCGATTCCAGCCAACGAT 505–580 0.900 80.8
psbM-trnD-GUC_p1 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA GTACACTTCGCTGGGATTGT 1226–1276 1.000 68.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTACACTTCGCTGGGATTGT 1214–1264 1.000 67.3
psbM-trnD-GUC_p3 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA AGTTCAATCGGTCAGAGCAC 1217–1256 0.900 63.8
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 1205–1244 0.900 63.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AGCGGTAGGAACTAGAATGAAC AGTTCAATCGGTCAGAGCAC 1218–1257 0.900 61.6
trnL-UAA_p1 trnL-UAA AGCGGCATACACTTTTTAGA TGTTTGAACCGATGACGAAA 665–911 1.000 48.8
trnL-UAA_p2 trnL-UAA AGCGGCATACACTTTTTAGA TTGTTTGAACCGATGACGAA 666–912 1.000 48.8
trnL-UAA_p3 trnL-UAA AGCGGCATACACTTTTTAGA TTTGTTTGAACCGATGACGA 667–913 1.000 48.8
trnL-UAA_p4 trnL-UAA ACAACTAGATCCTGTCTCAAGG TGTTTGAACCGATGACGAAA 587–833 0.900 44.6
trnL-UAA_p5 trnL-UAA ACAACTAGATCCTGTCTCAAGG TTGTTTGAACCGATGACGAA 588–834 0.900 44.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Smilax cocculoides NC_070227.1 158418 View on NCBI ↗
Smilax gaudichaudiana NC_070229.1 157885 View on NCBI ↗
Smilax glycophylla NC_049023.1 158922 View on NCBI ↗
Smilax hypoglauca NC_070226.1 158118 View on NCBI ↗
Smilax lanceifolia var. opaca OP076941.1 158385 View on NCBI ↗
Smilax microphylla NC_056390.1 158246 View on NCBI ↗
Smilax nipponica NC_049024.1 158178 View on NCBI ↗
Smilax ocreata NC_070230.1 158223 View on NCBI ↗
Smilax retroflexa NC_070228.1 159007 View on NCBI ↗
Smilax weniae NC_067604.1 158204 View on NCBI ↗