Markers + reference

Atractylis

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 267
Primer pairs 105

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 469 0.0068 0.94 51.3 yes View details
trnK-UUU-rps16 LSC 826 0.0073 1.00 62.9 yes View details
rps16 LSC 1111 0.0036 1.00 51.6 yes View details
trnC-GCA-petN LSC 556 0.0072 1.00 58.4 yes View details
atpB-rbcL LSC 798 0.0050 1.00 56.9 yes View details
accD LSC 1614 0.0050 1.00 54.0 yes View details
petA-psbJ LSC 768 0.0052 1.00 61.9 yes View details
psbE-petL LSC 1303 0.0046 1.00 55.5 yes View details
trnP-UGG-psaJ LSC 313 0.0228 0.98 67.7 yes View details
ndhD SSC 1503 0.0040 1.00 48.4 yes View details
psaC-ndhD SSC 122 0.0583 0.98 78.1 yes View details
rps19-rpl2 IRb 59 0.0339 1.00 68.2 yes View details
rpl22-rps19 LSC 81 0.0130 0.95 64.7 yes View details
trnL-UAA LSC 50 0.0200 1.00 61.6 yes View details
trnL-UAG-rpl32 SSC 854 0.0047 1.00 61.4 yes View details
rpl32-ndhF SSC 1053 0.0038 1.00 61.4 yes View details
psbM-trnD-GUC LSC 654 0.0031 1.00 60.7 yes View details
rpl20-rps12 LSC 748 0.0027 1.00 60.3 yes View details
trnS-GCU-trnC-GCA LSC 768 0.0026 1.00 60.2 yes View details
trnY-GUA-trnE-UUC LSC 76 0.0132 1.00 60.1 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 CTGCCTTAATCCACTTGGCT TCGAAGCTCCATCTACAAATGG 493–523 1.000 65.8
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCGAAGCTCCATCTACAAATGG 494–524 1.000 65.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CGAAGCTCCATCTACAAATGG 492–522 1.000 65.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CGAAGCTCCATCTACAAATGG 493–523 1.000 65.3
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG TCGAAGCTCCATCTACAAATGG 486–516 1.000 64.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1023–1024 1.000 77.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1022–1023 1.000 77.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 962–963 1.000 76.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 961–962 1.000 76.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1047–1048 1.000 76.1
rps16_p1 rps16 AGAGCAAGAAAAGAAGGAAA ACCGACAGAACCAATGACTA 1279–1280 1.000 40.3
rps16_p2 rps16 AGAGCAAGAAAAGAAGGAAA GTACCGACAGAACCAATGACT 1281–1282 1.000 40.2
rps16_p3 rps16 AGAGCAAGAAAAGAAGGAAAT GTACCGACAGAACCAATGACT 1281–1282 1.000 40.2
rps16_p4 rps16 AGAGCAAGAAAAGAAGGAAA TACCGACAGAACCAATGACT 1280–1281 1.000 40.2
rps16_p5 rps16 AGAGCAAGAAAAGAAGGAAA GTACCGACAGAACCAATGAC 1281–1282 1.000 40.2
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 919 1.000 78.3
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 901 1.000 76.1
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 855 1.000 74.4
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 920 1.000 74.1
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 837 1.000 72.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 612 1.000 78.7
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 630 1.000 76.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 611 1.000 72.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 620 1.000 72.6
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 669 1.000 72.0
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TGCTGCTAGATCCCTTCTGA 807–808 1.000 51.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TGCTGCTAGATCCCTTCTGA 801–802 1.000 51.0
psbM-trnD-GUC_p3 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 770–771 1.000 50.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 764–765 1.000 50.3
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TGCTGCTAGATCCCTTCTGA 804–805 1.000 50.1

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
Atractylis echinata BK071825.1 153391 View on NCBI ↗
Atractylis humilis BK071826.1 153428 View on NCBI ↗