Markers + reference

Tibetiodes

3 species · Asteraceae · Asterales

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Species 3
Genome length 153–153 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-rpoB LSC 1015 0.0173 0.99 62.7 yes View details
trnG-UCC-psbD LSC 1694 0.0335 0.97 81.5 yes View details
trnT-UGU-trnL-UAA LSC 716 0.0210 0.86 60.9 yes View details
rbcL-accD LSC 518 0.0248 0.98 47.2 yes View details
accD-psaI LSC 915 0.0189 0.95 61.6 yes View details
pafII-cemA LSC 880 0.0256 0.99 72.7 yes View details
petB LSC 1441 0.0111 1.00 53.4 yes View details
petA-psbJ LSC 718 0.0132 0.98 68.7 yes View details
psaA-pafI LSC 790 0.0095 0.98 67.6 yes View details
ndhI-ndhG SSC 147 0.0186 0.97 66.8 yes View details
petN-psbM LSC 513 0.0110 0.94 66.2 yes View details
trnL-UAG-rpl32 SSC 785 0.0184 0.99 64.5 yes View details
psbC-trnS-GCU LSC 227 0.0180 0.98 64.4 yes View details
trnK-UUU-rps16 LSC 811 0.0075 0.99 63.8 yes View details
trnH-GUG-psbA LSC 224 0.0137 0.87 62.6 yes View details
pafI-trnS-GGA LSC 860 0.0095 0.98 62.4 yes View details
atpB-rbcL LSC 689 0.0107 1.00 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 312–343 1.000 81.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 326–357 1.000 81.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 325–356 1.000 81.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 327–358 1.000 81.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 313–344 1.000 80.8
trnK-UUU_p1 trnK-UUU TCTATACACTATACAGACAATAGAA TCTGATTGTATCTACATACCCT 2639–2679 1.000 42.8
trnK-UUU_p2 trnK-UUU TTCTATACACTATACAGACAATAGA TCTGATTGTATCTACATACCCT 2640–2680 1.000 42.8
trnK-UUU_p3 trnK-UUU TCTATACACTATACAGACAATAGAA TCTGATTGTATCTACATACCCTT 2639–2679 1.000 42.8
trnK-UUU_p4 trnK-UUU TCTATACACTATACAGACAATAGAA TTCTGATTGTATCTACATACCCT 2640–2680 1.000 42.8
trnK-UUU_p5 trnK-UUU TTCTATACACTATACAGACAATAGA TCTGATTGTATCTACATACCCTT 2640–2680 1.000 42.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 962–965 1.000 76.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 956–959 1.000 76.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCGGTCTTCCAAACTTTA TTCCTTGAAAAAGGCGCTCA 1028–1031 1.000 74.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCGGTCTTCCAAACTTTAC TTCCTTGAAAAAGGCGCTCA 1027–1030 1.000 74.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TCCTTGAAAAAGGCGCTCAG 961–964 1.000 73.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 646–675 1.000 64.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 646–675 1.000 62.3
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 647–676 1.000 58.1
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 638–667 1.000 58.1
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 632–661 1.000 57.3
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 1147–1164 1.000 64.4
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG TCAAACCCTGATCAATGAACCT 1106–1123 1.000 63.8
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA TCAAACCCTGATCAATGAACCT 1137–1154 1.000 63.6
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG TCAAACCCTGATCAATGAACCT 1142–1159 1.000 63.6
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT ACCCTGATCAATGAACCTACA 1143–1160 1.000 62.2
trnG-UCC-psbD_p1 trnG-UCC-psbD AATGAAACCGAAAGACCCCT GAAACGGTCCCTACGTAACC 1855–2034 1.000 79.2
trnG-UCC-psbD_p2 trnG-UCC-psbD ATGAAACCGAAAGACCCCTT GAAACGGTCCCTACGTAACC 1854–2033 1.000 79.2
trnG-UCC-psbD_p3 trnG-UCC-psbD AATGAAACCGAAAGACCCCT GGACCAGCCTACAAAAACGA 1873–2052 1.000 78.3
trnG-UCC-psbD_p4 trnG-UCC-psbD ATGAAACCGAAAGACCCCTT GGACCAGCCTACAAAAACGA 1872–2051 1.000 78.3
trnG-UCC-psbD_p5 trnG-UCC-psbD GAATGAAACCGAAAGACCCCT GAAACGGTCCCTACGTAACC 1856–2035 1.000 77.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Tibetiodes diplostephioides NC_077584.1 152970 View on NCBI ↗
Tibetiodes farreri NC_077585.1 152774 View on NCBI ↗
Tibetiodes labrangensis OQ569735.1 153087 View on NCBI ↗