Markers + reference

Trachycarpus

6 species · Arecaceae · Arecales

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Species 6
Genome length 159–159 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

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 33.7 yes View details
psbK-psbI LSC 399 0.0045 1.00 31.2 yes View details
trnD-GUC-trnY-GUA LSC 384 0.0064 1.00 35.1 yes View details
accD-psaI LSC 885 0.0081 1.00 59.5 yes View details
rpl32-trnL-UAG SSC 809 0.0043 1.00 40.3 yes View details
ndhD SSC 1512 0.0013 1.00 33.4 yes View details
psaC-ndhE SSC 764 0.0093 0.98 63.0 yes View details
ndhA SSC 2173 0.0017 1.00 41.9 yes View details
rps15-ycf1 SSC 390 0.0065 1.00 38.9 yes View details
ycf1 SSC 5628 0.0013 1.00 44.1 yes View details
rps19-psbA LSC 240 0.0603 0.93 82.4 no View details
trnH-GUG-rpl2 IRb 46 0.0246 1.00 53.4 yes View details
rpl2-trnH-GUG IRa 46 0.0246 1.00 53.4 yes View details
atpB-rbcL LSC 769 0.0016 1.00 50.8 yes View details
trnF-GAA-ndhJ LSC 711 0.0009 1.00 49.9 yes View details
rbcL-accD LSC 786 0.0013 1.00 49.8 yes View details
rpl22-rps19 IRb 59 0.0181 1.00 49.7 yes View details
trnT-UGU-trnL-UAA LSC 994 0.0016 1.00 48.2 yes View details
ndhC-trnM-CAU LSC 2728 0.0008 1.00 46.4 yes View details
psbE-petL LSC 1299 0.0003 1.00 45.5 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
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 73.4
psbA_p4 psbA TGCTCCATTCCTTCAACGAT ATACGTGTGCTTGGGAGTTC 1154 1.000 72.9
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGTGCTTGGGAGTTCTTGA 1150 1.000 71.2
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGCCCTGGATCAT 525 1.000 78.0
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGATTACGCCCTGGATCAT 522 1.000 76.0
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGATTACGCCCTGGATCAT 523 1.000 76.0
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGATTACGCCCTGGATCAT 524 1.000 76.0
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGCCCTGGATCATT 524 1.000 75.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 530 1.000 77.4
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT GGGGACGGACTGTAAATTCG 473 1.000 77.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGACGGACTGTAAATTCGT 529 1.000 77.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT GGGACGGACTGTAAATTCGT 472 1.000 77.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC GGGGACGGACTGTAAATTCG 533 1.000 74.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1042–1053 1.000 79.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1050–1061 1.000 79.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1074–1085 1.000 78.9
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1082–1093 1.000 78.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 1065–1076 1.000 78.0
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGCTGGC 806–825 1.000 80.4
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATAGGCTGGCCCTTACGTAA 796–815 1.000 79.8
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ GGAAATGGTCGGGATAGCTC TGAAAGTTGGATAGGCTGGC 852–871 1.000 79.4
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ AATGGTCGGGATAGCTCAGT TGAAAGTTGGATAGGCTGGC 849–868 1.000 79.1
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ ATGGTCGGGATAGCTCAGTT TGAAAGTTGGATAGGCTGGC 848–867 1.000 79.1
ndhC-trnM-CAU_p1 ndhC-trnM-CAU TCCTTCACTAACCGGTGCTA CCCGCCGTATGAAAGCAATA 2851–2883 1.000 77.7
ndhC-trnM-CAU_p2 ndhC-trnM-CAU TAACCGGTGCTAAAACTCCG CCCGCCGTATGAAAGCAATA 2843–2875 1.000 77.6
ndhC-trnM-CAU_p3 ndhC-trnM-CAU TCCTTCACTAACCGGTGCTA ATCACTCAATTGGCTTCGGT 2913–2945 1.000 76.9
ndhC-trnM-CAU_p4 ndhC-trnM-CAU TAACCGGTGCTAAAACTCCG ATCACTCAATTGGCTTCGGT 2905–2937 1.000 76.9
ndhC-trnM-CAU_p5 ndhC-trnM-CAU TCCTTCACTAACCGGTGCTA CCGCCGTATGAAAGCAATAC 2850–2882 1.000 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Trachycarpus fortunei NC_053365.1 158613 View on NCBI ↗
Trachycarpus geminisectus NC_079815.1 159018 View on NCBI ↗
Trachycarpus martianus NC_079755.1 158605 View on NCBI ↗
Trachycarpus nanus NC_057594.1 158713 View on NCBI ↗
Trachycarpus oreophilus NC_079756.1 159049 View on NCBI ↗
Trachycarpus princeps NC_079757.1 158708 View on NCBI ↗