Markers + reference

Tricyrtis

2 species · Liliaceae · Liliales

Back to catalogue

Species 2
Genome length 156–156 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1194 0.0207 0.97 65.0 yes View details
atpF LSC 1325 0.0143 1.00 57.7 yes View details
trnT-GGU-psbD LSC 1019 0.0090 0.98 51.5 yes View details
trnT-UGU-trnL-UAA LSC 964 0.0126 0.99 64.3 yes View details
ndhC-trnV-UAC LSC 544 0.0292 0.94 78.8 yes View details
accD-psaI LSC 882 0.0125 1.00 53.7 yes View details
psaI-ycf4 LSC 365 0.0192 1.00 50.6 yes View details
petA-psbJ LSC 851 0.0261 0.99 69.0 yes View details
petD-rpoA LSC 291 0.0597 0.92 72.7 yes View details
rps15-ycf1 SSC 1297 0.0170 1.00 63.6 yes View details
psbT-psbN LSC 69 0.0725 1.00 81.4 yes View details
rps3-rpl22 LSC 65 0.0357 0.86 70.3 yes View details
psaJ-rpl33 LSC 535 0.0150 1.00 66.0 yes View details
rps16-trnQ-UUG LSC 1477 0.0103 0.99 65.9 yes View details
trnE-UUC-trnT-GGU LSC 960 0.0075 0.97 65.2 yes View details
rbcL-accD LSC 821 0.0099 0.98 65.2 yes View details
atpH-atpI LSC 894 0.0080 0.98 64.9 yes View details
atpB-rbcL LSC 740 0.0095 0.99 64.9 yes View details
trnH-GUG-psbA IRa 431 0.0141 0.99 64.2 no View details
trnR-UCU-atpA LSC 101 0.0396 1.00 62.5 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1548–1551 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACAGTCGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1570–1573 1.000 79.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1559–1562 1.000 79.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1552–1555 1.000 78.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGTCGATCATGTCCT CTCGGAGGTTCGAATCCTTC 1574–1577 1.000 78.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1248–1268 1.000 55.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1251–1271 1.000 54.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1250–1270 1.000 54.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GAGGGATAGCGGAGAGAGAG ACGAATCACACTTTTACCACT 1307–1327 1.000 53.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATGAGGGATAGCGGAGAGAG ACGAATCACACTTTTACCACT 1309–1329 1.000 53.6
trnG-UCC_p1 trnG-UCC GACAAAGACTCCATTCATATACA AGGAAAATCCTCCAGGGAAT 863–865 1.000 40.8
trnG-UCC_p2 trnG-UCC GACAAAGACTCCATTCATATACAA AGGAAAATCCTCCAGGGAAT 863–865 1.000 40.8
trnG-UCC_p3 trnG-UCC ACAAAGACTCCATTCATATACA AGGAAAATCCTCCAGGGAAT 862–864 1.000 40.8
trnG-UCC_p4 trnG-UCC ACAAAGACTCCATTCATATACAA AGGAAAATCCTCCAGGGAAT 862–864 1.000 40.8
trnG-UCC_p5 trnG-UCC GACAAAGACTCCATTCATATACAAT AGGAAAATCCTCCAGGGAAT 863–865 1.000 40.8
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT GTTTCTACTTCAGGAACAAACA 205–217 1.000 42.3
trnR-UCU-atpA_p2 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT GAACTGTTTCTACTTCAGGAAC 210–222 1.000 42.2
trnR-UCU-atpA_p3 trnR-UCU-atpA AGGAATGAAAGGCGTCCATT GAACTGTTTCTACTTCAGGAAC 214 0.500 20.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAATGAAAGGCGTCCATTG GAACTGTTTCTACTTCAGGAAC 213 0.500 20.0
trnR-UCU-atpA_p5 trnR-UCU-atpA AGGAATGAAAGGCGTCCATT GTTTCTACTTCAGGAACAAACA 209 0.500 20.0
atpF_p1 atpF CTCGAAGGGTTGCCATTAGT GGCGAGTGAGGTGATACAAA 1487 1.000 74.8
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA GGCGAGTGAGGTGATACAAA 1501 1.000 72.8
atpF_p3 atpF GCTCGAAGGGTTGCCATTAG GGCGAGTGAGGTGATACAAA 1488 1.000 70.1
atpF_p4 atpF GCTCGAAGGGTTGCCATTA GGCGAGTGAGGTGATACAAA 1488 1.000 68.6
atpF_p5 atpF CTCGAAGGGTTGCCATTAGT GGCGAGTGAGGTGATACAAAA 1487 1.000 67.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 980–982 1.000 77.3
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 953–955 1.000 76.8
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1036–1038 1.000 76.7
atpH-atpI_p4 atpH-atpI AACGGAAGCGGCAGAAATAA TTTTTGCAACTTTAGCCGCG 978–980 1.000 76.2
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT TAGGTGAATCCATGGAGGGT 1009–1011 1.000 76.1

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
Tricyrtis macropoda NC_040223.1 155778 View on NCBI ↗
Tricyrtis xianjuensis NC_085731.1 155748 View on NCBI ↗