Markers + reference

Wallichia

2 species · Arecaceae · Arecales

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Species 2
Genome length 160–160 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 48.1 yes View details
psbC LSC 1422 0.0000 1.00 25.0 yes View details
trnT-UGU-trnL-UAA LSC 1123 0.0074 0.96 59.4 yes View details
petA-psbJ LSC 1025 0.0226 0.99 72.4 yes View details
rpl16 LSC 1687 0.0084 0.99 64.1 yes View details
ycf1 IRb 1347 0.0000 1.00 58.7 no View details
ndhF-rpl32 SSC 493 0.0153 0.93 69.5 yes View details
ycf1 SSC 5634 0.0028 1.00 49.6 yes View details
rps19-psbA LSC 224 0.0650 0.89 85.5 no View details
psbC-trnS-UGA LSC 141 0.0567 1.00 82.1 yes View details
psaC-ndhE SSC 642 0.0081 0.96 67.3 yes View details
psaJ-rpl33 LSC 584 0.0036 0.96 64.8 yes View details
ndhH-rps15 SSC 120 0.0171 0.97 64.7 yes View details
accD-psaI LSC 903 0.0023 0.96 63.8 yes View details
ndhC-trnV-UAC LSC 2099 0.0035 0.96 63.5 yes View details
rpl32-trnL-UAG SSC 772 0.0000 0.96 62.4 yes View details
rbcL-accD LSC 804 0.0013 0.97 62.1 yes View details
atpH-atpI LSC 683 0.0000 0.97 62.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTGCTCCATTCCTTCAACGA GTGTGCTTGGGAGTTCTTGA 1151 1.000 75.3
psbA_p2 psbA TTGCTCCATTCCTTCAACGA ATACGTGTGCTTGGGAGTTC 1155 1.000 74.8
psbA_p3 psbA TGCTCCATTCCTTCAACGAT GTGTGCTTGGGAGTTCTTGA 1150 1.000 73.5
psbA_p4 psbA TGCTCCATTCCTTCAACGAT ATACGTGTGCTTGGGAGTTC 1154 1.000 73.0
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGTGCTTGGGAGTTCTTGA 1150 1.000 71.2
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA TTGACCGTATTTACATATATCCT 2884–2888 1.000 40.5
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCTCA TTTGACCGTATTTACATATATCCT 2885–2889 1.000 40.5
trnK-UUU_p3 trnK-UUU TGCCAATGTCAACCAATCTCA TTTTGACCGTATTTACATATATCCT 2886–2890 1.000 40.5
trnK-UUU_p4 trnK-UUU GCCAATGTCAACCAATCTCA TTGACCGTATTTACATATATCCT 2883–2887 1.000 40.5
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTC TTGACCGTATTTACATATATCCT 2884–2888 1.000 40.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 742–744 1.000 77.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 770–772 1.000 77.4
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT TAGGTGAATCCATGGAGGGT 825–827 1.000 77.2
atpH-atpI_p4 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACGTTAGCCGC 853–855 1.000 77.1
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACGTTAGCCGC 826–828 1.000 76.6
psbC_p1 psbC TTTCCCAAGAAATCCGTGCA TAGCCGAGCCAGAACAGAAA 1585 1.000 71.7
psbC_p2 psbC TTTCCCAAGAAATCCGTGCA GCCGAGCCAGAACAGAAAAA 1583 1.000 71.6
psbC_p3 psbC TTTCCCAAGAAATCCGTGCA TAGCCGAGCCAGAACAGAA 1585 1.000 69.3
psbC_p4 psbC GCAGCGGAAGATCCTGAATT TAGCCGAGCCAGAACAGAAA 1568 1.000 69.2
psbC_p5 psbC AGGTATTCGTGCTTGGATGG TAGCCGAGCCAGAACAGAAA 1512 1.000 69.2
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 248 1.000 80.8
psbC-trnS-UGA_p2 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GGTTGATAGCTCCGGTCTTG 247 1.000 80.8
psbC-trnS-UGA_p3 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GGTTGATAGCTCCGGTCTTG 287 1.000 80.7
psbC-trnS-UGA_p4 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GATGGCCGAGTGGTTGATAG 258 1.000 80.2
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GATGGCCGAGTGGTTGATAG 298 1.000 80.1
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1173–1190 1.000 82.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACAATCAAGTCCGTAGCGTC 1194–1211 1.000 82.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1181–1198 1.000 81.6
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1205–1222 1.000 81.2
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACAATCAAGTCCGTAGCGTC 1226–1243 1.000 81.1

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
Wallichia densiflora NC_029949.1 159717 View on NCBI ↗
Wallichia gracilis NC_079761.1 159700 View on NCBI ↗