Markers + reference

Amana

10 species · Liliaceae · Liliales

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Species 10
Genome length 151–152 kb
Candidate markers 268
Primer pairs 95

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 323 0.0076 1.00 61.3 yes View details
psbK-psbI LSC 189 0.0401 0.88 69.0 yes View details
trnS-GCU-trnR-UCU LSC 1651 0.0064 1.00 63.4 yes View details
petA-psbJ LSC 652 0.0179 1.00 64.2 yes View details
psbE-petL LSC 1053 0.0103 1.00 59.2 yes View details
psaJ-rpl33 LSC 520 0.0159 1.00 72.5 yes View details
rpoA LSC 1068 0.0063 1.00 39.9 yes View details
rpl32-trnL-UAG SSC 728 0.0120 0.99 74.2 yes View details
rps15-ycf1 SSC 428 0.0157 0.98 53.1 yes View details
ndhF-rpl32 SSC 684 0.0106 0.99 66.9 yes View details
accD-psaI LSC 812 0.0080 1.00 66.7 yes View details
trnE-UUC-trnT-GGU LSC 929 0.0051 0.93 66.3 yes View details
ycf3-trnS-GGA LSC 578 0.0070 1.00 64.7 yes View details
rps16 LSC 1120 0.0037 1.00 62.5 yes View details
trnK-UUU-rps16 LSC 678 0.0043 0.98 62.1 yes View details
psaA-ycf3 LSC 602 0.0051 1.00 61.9 yes View details
ndhC-trnV-UAC LSC 974 0.0057 0.99 61.3 yes View details
rpoB-trnC-GCA LSC 864 0.0061 1.00 61.2 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_p1 trnK-UUU TTTCAAGGACTCCCAAGCAC GGCGGAATCCTGTATTGCAA 2944–2979 1.000 77.8
trnK-UUU_p2 trnK-UUU TTTCAAGGACTCCCAAGCAC TTGGCGGAATCCTGTATTGC 2946–2981 1.000 77.8
trnK-UUU_p3 trnK-UUU AGGACTCCCAAGCACACATA GGCGGAATCCTGTATTGCAA 2939–2974 1.000 75.3
trnK-UUU_p4 trnK-UUU AGGACTCCCAAGCACACATA TTGGCGGAATCCTGTATTGC 2941–2976 1.000 75.3
trnK-UUU_p5 trnK-UUU TTTCAAGGACTCCCAAGCAC GGCGGAATCCTGTATTGCA 2944–2979 1.000 74.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCCACAGTAACTGT 763–786 1.000 80.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCCACAGTAACTGT 762–785 1.000 80.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAATGGCGCTCAACC 775–798 1.000 79.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAATGGCGCTCAAC 775–798 1.000 79.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAATGGCGCTCAACC 774–797 1.000 79.7
rps16_p1 rps16 AGATGCTAGGACCCTCTCTT ACATATCAGTTGATCCAATGACT 1208–1292 1.000 45.2
rps16_p2 rps16 AGATGCTAGGACCCTCTCTT TCAGTTGATCCAATGACTATTCA 1203–1287 1.000 45.2
rps16_p3 rps16 AGATGCTAGGACCCTCTCTT TGAATCAATTCCATATCGGTTTTGA 1169–1253 1.000 45.2
rps16_p4 rps16 AGATGCTAGGACCCTCTCTT TCAATTCCATATCGGTTTTGA 1165–1249 1.000 45.2
rps16_p5 rps16 AGATGCTAGGACCCTCTCTT CAGTTGATCCAATGACTATTCATGA 1202–1286 1.000 45.2
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG AAAAAGCATAAGCCTCGGG 483–503 1.000 56.5
trnQ-UUG-psbK_p2 trnQ-UUG-psbK TTGATTCTGAGGGTCTGGGA AAAAAGCATAAGCCTCGGG 505–525 1.000 55.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK TGATTCTGAGGGTCTGGGAC AAAAAGCATAAGCCTCGGG 504–524 1.000 54.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AGGATTCGAACCTCCGAGTA AAAAAGCATAAGCCTCGGG 481–501 1.000 54.7
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AAGGATTCGAACCTCCGAGT AAAAAGCATAAGCCTCGGG 482–502 1.000 54.6
psbK-psbI_p1 psbK-psbI GCTGCTGTAAGTTTTCGATGA GGATTGCGTCCTGGATCATT 281–305 1.000 71.5
psbK-psbI_p2 psbK-psbI GCTGCTGTAAGTTTTCGATGA TTCTTCACGTCCAGGATTGC 294–318 1.000 70.0
psbK-psbI_p3 psbK-psbI GCTGCTGTAAGTTTTCGATG GGATTGCGTCCTGGATCATT 281–305 1.000 67.4
psbK-psbI_p4 psbK-psbI GCTGCTGTAAGTTTTCGATG TTCTTCACGTCCAGGATTGC 294–318 1.000 65.9
psbK-psbI_p5 psbK-psbI GCTGCTGTAAGTTTTCGATGA GGATTGCGTCCTGGATCATTA 281–305 1.000 62.8
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU TGATGAGGGATAGCGGAGAG AGAAGACCTCTGTCCTATCCA 1764–1821 1.000 66.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU TGATGAGGGATAGCGGAGAG AGGTTTAGAAGACCTCTGTCCT 1770–1827 1.000 65.8
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU GAGGGATAGCGGAGAGAGAG AGAAGACCTCTGTCCTATCCA 1760–1817 1.000 65.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU GATGAGGGATAGCGGAGAGA AGAAGACCTCTGTCCTATCCA 1763–1820 1.000 65.5
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ATGAGGGATAGCGGAGAGAG AGAAGACCTCTGTCCTATCCA 1762–1819 1.000 65.4

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
Amana anhuiensis NC_034706.1 150723 View on NCBI ↗
Amana baohuaensis NC_053609.1 150757 View on NCBI ↗
Amana edulis NC_034707.1 150810 View on NCBI ↗
Amana erythronioides OQ101212.1 150951 View on NCBI ↗
Amana hejiaqingii NC_068818.1 151571 View on NCBI ↗
Amana nanyueensis NC_064407.1 151234 View on NCBI ↗
Amana polymorpha OQ101213.1 151551 View on NCBI ↗
Amana tianmuensis NC_072908.1 151518 View on NCBI ↗
Amana wanzhensis NC_034705.1 150576 View on NCBI ↗
Amana yunmengensis ON764435.1 151502 View on NCBI ↗