Markers + reference

Asclepias

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 159–162 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 576 0.0460 0.91 75.9 yes View details
rps2-rpoC2 LSC 4968 0.0173 0.54 40.9 yes View details
ndhC-trnV-UAC LSC 1276 0.0204 0.92 63.4 yes View details
accD LSC 2319 0.0168 1.00 55.0 yes View details
ycf4 LSC 552 0.0697 0.99 77.9 yes View details
ycf4-cemA LSC 722 0.0160 0.61 47.5 yes View details
rpl16 LSC 1413 0.0135 1.00 52.8 yes View details
ycf1 IRb 1426 0.0039 0.90 56.7 no View details
ycf1-ndhF SSC 588 0.0310 0.93 72.3 yes View details
ccsA-ndhD SSC 251 0.0398 1.00 61.7 yes View details
ndhD SSC 1503 0.0060 1.00 49.6 yes View details
rps15-ycf1 SSC 378 0.0344 1.00 59.2 yes View details
ycf1 SSC 5793 0.0142 0.95 53.9 yes View details
trnH-GUG-psbA LSC 395 0.0371 0.95 80.0 yes View details
ndhD-psaC SSC 135 0.0821 0.99 75.8 yes View details
ndhF-rpl32 SSC 763 0.0198 0.99 69.1 yes View details
rpl32-trnL-UAG SSC 929 0.0227 0.95 67.5 yes View details
atpH-atpI LSC 1160 0.0147 1.00 67.4 yes View details
trnT-UGU-trnL-UAA LSC 815 0.0135 1.00 65.6 yes View details
trnP-UGG-psaJ LSC 458 0.0134 0.98 65.6 yes View details
rbcL-accD LSC 885 0.0132 0.94 65.1 yes View details
rpl20-rps12 LSC 915 0.0057 0.96 64.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 448–465 1.000 84.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 462–479 1.000 83.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 461–478 1.000 83.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 463–480 1.000 83.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 497–514 1.000 81.3
trnQ-UUG-psbK_p1 trnQ-UUG-psbK AAAACCCGTTGCCTTACCAC AAAAAGCGTAGGCCTCGG 653–707 1.000 60.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CAAAACCCGTTGCCTTACCA AAAAAGCGTAGGCCTCGG 654–708 1.000 60.7
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CCCAAAACCCGTTGCCTTA AAAAAGCGTAGGCCTCGG 656–710 1.000 58.3
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AAACCCGTTGCCTTACCAC AAAAAGCGTAGGCCTCGG 652–706 1.000 58.2
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AAAACCCGTTGCCTTACCA AAAAAGCGTAGGCCTCGG 653–707 1.000 56.3
atpH-atpI_p1 atpH-atpI CTCTACAGCTTGACCTGCAG CGCGGCTTATATCGGTGAAT 1311–1319 1.000 78.8
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGCGGCTTATATCGGTGAAT 1232–1240 1.000 78.6
atpH-atpI_p3 atpH-atpI CTCTACAGCTTGACCTGCAG CGGTGAATCCATGGAAGGTC 1299–1307 1.000 78.5
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT CGGTGAATCCATGGAAGGTC 1220–1228 1.000 78.3
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA CGCGGCTTATATCGGTGAAT 1233–1241 1.000 77.4
rps2-rpoC2_p1 rps2-rpoC2 TGAATTTTTGTGGTACTCTTGTCA ATCCCTCTGTCGAACACATA 170 1.000 47.1
rps2-rpoC2_p2 rps2-rpoC2 TGAATTTTTGTGGTACTCTTGTCA TCCCTCTGTCGAACACATAT 169 1.000 47.1
rps2-rpoC2_p3 rps2-rpoC2 TGAATTTTTGTGGTACTCTTGTCA ATATCCCTCTGTCGAACACA 172 1.000 47.0
rps2-rpoC2_p4 rps2-rpoC2 TGAATTTTTGTGGTACTCTTGTCA TATCCCTCTGTCGAACACAT 171 1.000 47.0
rps2-rpoC2_p5 rps2-rpoC2 TGAATTTTTGTGGTACTCTTGTCA AATATCCCTCTGTCGAACACA 173 1.000 46.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCCATTTC 876–896 1.000 78.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG CCGTAGCGTCTACCCATTTC 927–947 1.000 77.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCCATTTC 908–928 1.000 77.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAAGTCCGTAGCGTCTACCC 881–901 1.000 77.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG TAAGTCCGTAGCGTCTACCC 932–952 1.000 76.4
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GTCCTTTGTTAATCGGGGCT AGAAGGTCTACGGTTCGAGT 1321–1421 1.000 82.8
ndhC-trnV-UAC_p2 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT AGAAGGTCTACGGTTCGAGT 1307–1407 1.000 82.7
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GTCCTTTGTTAATCGGGGCT GAAGGTCTACGGTTCGAGTC 1320–1420 1.000 80.1
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT GAAGGTCTACGGTTCGAGTC 1306–1406 1.000 80.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TGGTCCTTTGTTAATCGGGG AGAAGGTCTACGGTTCGAGT 1323–1423 1.000 79.8

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
Asclepias nivea NC_022431.1 161592 View on NCBI ↗
Asclepias syriaca NC_022432.1 158719 View on NCBI ↗