Markers + reference

Archidasyphyllum

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 269
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 826 0.0024 1.00 60.1 yes View details
atpH-atpI LSC 1052 0.0010 0.99 59.9 yes View details
trnT-UGU-trnL-UAA LSC 580 0.0034 1.00 60.3 yes View details
rpl20-rps12 LSC 744 0.0000 0.96 59.7 yes View details
clpP LSC 2036 0.0005 0.99 59.2 yes View details
psbB LSC 1527 0.0000 1.00 34.5 yes View details
rrn23 IRb 2810 0.0007 1.00 56.4 yes View details
trnR-ACG-trnN-GUU IRb 470 0.0000 0.99 55.5 yes View details
ndhD SSC 1503 0.0000 1.00 28.6 yes View details
rrn23 IRa 2810 0.0007 1.00 56.4 no View details
ndhD-psaC SSC 119 0.0252 1.00 67.0 yes View details
psbT-psbN LSC 73 0.0274 1.00 64.8 yes View details
rpoA LSC 825 0.0000 0.96 62.4 yes View details
trnD-GUC LSC 74 0.0135 1.00 60.3 yes View details
accD-psaI LSC 671 0.0015 1.00 59.6 yes View details
petA-psbJ LSC 768 0.0013 1.00 59.5 yes View details
rps11 LSC 411 0.0000 0.94 59.4 yes View details
rpl32-trnL-UAG SSC 867 0.0000 0.99 59.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG TTCCTTGAAAAAGGCGCTCA 1006 1.000 77.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1023 1.000 77.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1022 1.000 77.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 962 1.000 76.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 961 1.000 76.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 1183–1188 1.000 78.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TCCCTGTCATGTTCCTTGGA 1239–1244 1.000 77.5
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1199–1204 1.000 77.2
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TCCCTGTCATGTTCCTTGGA 1184–1189 1.000 76.9
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TCCCTGTCATGTTCCTTGGA 1243–1248 1.000 76.9
trnD-GUC_p1 trnD-GUC CACAGAAAATGGAGAGGCGA TGGCCAATCTACCATCAGATG 219 1.000 67.6
trnD-GUC_p2 trnD-GUC TCACAGAAAATGGAGAGGCG TGGCCAATCTACCATCAGATG 220 1.000 67.6
trnD-GUC_p3 trnD-GUC CACAGAAAATGGAGAGGCGA CCAACAATTGGCCAATCTACC 227 1.000 67.4
trnD-GUC_p4 trnD-GUC TCACAGAAAATGGAGAGGCG CCAACAATTGGCCAATCTACC 228 1.000 67.4
trnD-GUC_p5 trnD-GUC TCCCTGTCCCTTCTTTCACA TGGCCAATCTACCATCAGATG 235 1.000 66.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 630 1.000 79.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 638 1.000 78.6
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 662 1.000 78.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 670 1.000 77.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 644 1.000 77.3
accD-psaI_p1 accD-psaI TCCAGAAGGGCTTATTCGATC AAAGAAGCCATTGCGATTGC 852 1.000 66.1
accD-psaI_p2 accD-psaI CCAGAAGGGCTTATTCGATCT AAAGAAGCCATTGCGATTGC 851 1.000 66.0
accD-psaI_p3 accD-psaI TTCCAGAAGGGCTTATTCGA AAAGAAGCCATTGCGATTGC 853 1.000 66.0
accD-psaI_p4 accD-psaI TCCAGAAGGGCTTATTCGAT AAAGAAGCCATTGCGATTGC 852 1.000 64.1
accD-psaI_p5 accD-psaI TCCAGAAGGGCTTATTCGATC TTGCGATTGCCGGAAATACT 842 1.000 64.0
petA-psbJ_p1 petA-psbJ ACGTGTACAAGGCCTTTTGT GGTTCATATTCCGGGTTGGG 913–914 1.000 77.2
petA-psbJ_p2 petA-psbJ GGCCTTTTGTTCTTCTTCGC GGTTCATATTCCGGGTTGGG 903–904 1.000 77.2
petA-psbJ_p3 petA-psbJ ACGTGTACAAGGCCTTTTGT CATATTCCGGGTTGGGTTCA 909–910 1.000 76.3
petA-psbJ_p4 petA-psbJ ACGTGTACAAGGCCTTTTGT TGGTTCATATTCCGGGTTGG 914–915 1.000 76.3
petA-psbJ_p5 petA-psbJ ACGTGTACAAGGCCTTTTGT GTTCATATTCCGGGTTGGGT 912–913 1.000 76.3

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
Archidasyphyllum diacanthoides NC_086794.1 152278 View on NCBI ↗
Archidasyphyllum excelsum MH899017.1 151880 View on NCBI ↗