Markers + reference

Syndiclis

4 species · Lauraceae · Laurales

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Species 4
Genome length 159–160 kb
Candidate markers 262
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 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpA LSC 1524 0.0007 1.00 36.5 yes View details
atpH-atpI LSC 921 0.0045 1.00 62.5 yes View details
psbM-trnD-GUC LSC 1134 0.0032 1.00 61.0 yes View details
petA-psbJ LSC 1148 0.0080 1.00 64.6 yes View details
psbE-petL LSC 1237 0.0047 1.00 62.2 yes View details
ycf1 SSC 1911 0.0014 1.00 48.6 no View details
rpl32-trnL-UAG SSC 1359 0.0037 1.00 60.1 yes View details
ccsA SSC 951 0.0014 1.00 45.3 yes View details
ycf1 SSC 5481 0.0029 0.76 43.5 yes View details
trnI-CAU-trnH-GUG LSC 2042 0.0024 1.00 59.5 no View details
atpA-atpF LSC 70 0.0643 0.99 79.5 yes View details
ycf4-cemA LSC 915 0.0035 1.00 62.2 yes View details
rps16-trnQ-UUG LSC 990 0.0030 1.00 61.6 yes View details
matK LSC 1524 0.0026 1.00 60.5 yes View details
trnE-UUC-trnT-GGU LSC 734 0.0020 1.00 60.3 yes View details
ndhF-rpl32 SSC 1196 0.0013 1.00 59.9 yes View details
trnC-GCA-petN LSC 1082 0.0014 1.00 59.8 yes View details
rpl16 LSC 1397 0.0011 1.00 59.8 yes View details
petD LSC 1212 0.0008 1.00 59.7 yes View details
ndhC-trnV-UAC LSC 1838 0.0022 1.00 59.6 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 AGATGGGGATTTATGCAATAACA GGATCGGGCAATCCAATCTC 2738–2753 1.000 40.4
trnK-UUU_p2 trnK-UUU TCTTTTCCGTATTGGTAATGGA GGATCGGGCAATCCAATCTC 2692 0.250 10.0
trnK-UUU_p3 trnK-UUU TCTTTTCCGTATTGGTAATGGA AATGTTTTGACGGGATCGGG 2704 0.250 10.0
trnK-UUU_p4 trnK-UUU TCTTTTCCGTATTGGTAATGGA GATCGGGCAATCCAATCTCT 2691 0.250 10.0
trnK-UUU_p5 trnK-UUU TCGTATTTTCTTTTCCGTATTGGT GGATCGGGCAATCCAATCTC 2700 0.250 10.0
matK_p1 matK CCACTACACTACTGCATGAGC CTTGTTCTGACCGTATCGCA 1715 1.000 68.7
matK_p2 matK CCACTACACTACTGCATGAGC TTGTTCTGACCGTATCGCAC 1714 1.000 66.4
matK_p3 matK TCAACCACTACACTACTGCA CTTGTTCTGACCGTATCGCA 1719 1.000 65.3
matK_p4 matK ACCACTACACTACTGCATGAG CTTGTTCTGACCGTATCGCA 1716 1.000 65.3
matK_p5 matK CACTACACTACTGCATGAGC CTTGTTCTGACCGTATCGCA 1714 1.000 64.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCAAGAATCCACAGCCGATA GAGGTTCGAATCCTTCCGTC 1091–1101 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1062–1072 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCAAGAATCCACAGCCGATA CTCGGAGGTTCGAATCCTTC 1095–1105 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1066–1076 1.000 78.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCCGATAATGTCCTT GAGGTTCGAATCCTTCCGTC 1083–1093 1.000 77.6
atpA_p1 atpA AGCCTTCCAAGCTAACGATG TTTTTGTCGGGTCGGAAGAG 2594–2596 1.000 79.2
atpA_p2 atpA AGCCTTCCAAGCTAACGATG AAGGAGCCCTAGGAACTCTG 2063–2065 1.000 79.2
atpA_p3 atpA AGCCTTCCAAGCTAACGATG CAAGGAGCCCTAGGAACTCT 2064–2066 1.000 79.2
atpA_p4 atpA AGCCTTCCAAGCTAACGATG CTGGGGGCCATGAAAGAAAT 1986–1988 1.000 79.2
atpA_p5 atpA AGCCTTCCAAGCTAACGATG GGAGCCCTAGGAACTCTGAA 2061–2063 1.000 79.2
atpA-atpF_p1 atpA-atpF CCCACTTGAAGGACTGTTCC CTGGGGGCCATGAAAGAAAT 206–207 1.000 82.0
atpA-atpF_p2 atpA-atpF CCCACTTGAAGGACTGTTCC AAGGAGCCCTAGGAACTCTG 283–284 1.000 81.0
atpA-atpF_p3 atpA-atpF CCCACTTGAAGGACTGTTCC CAAGGAGCCCTAGGAACTCT 284–285 1.000 81.0
atpA-atpF_p4 atpA-atpF CCCACTTGAAGGACTGTTCC GGAGCCCTAGGAACTCTGAA 281–282 1.000 81.0
atpA-atpF_p5 atpA-atpF CCCACTTGAAGGACTGTTCC TAATATTGGCATGCTGGGGG 219–220 1.000 80.4
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA CCCGTCATGTTCCTTGGATT 1053–1058 1.000 79.1
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCCGCAG 1006–1011 1.000 79.1
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT CCCGTCATGTTCCTTGGATT 1111–1116 1.000 79.0
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 1064–1069 1.000 79.0
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 1071–1076 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Syndiclis chinensis NC_068505.1 160286 View on NCBI ↗
Syndiclis fooningensis NC_051915.1 158576 View on NCBI ↗
Syndiclis kwangsiensis NC_051916.1 158654 View on NCBI ↗
Syndiclis marlipoensis MT621628.1 158636 View on NCBI ↗