Markers + reference

Thamnocalamus

2 species · Poaceae · Poales

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Species 2
Genome length 140–140 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 556 0.0036 1.00 52.1 yes View details
psbM-petN LSC 768 0.0040 0.98 62.8 yes View details
trnC-GCA-rpoB LSC 1183 0.0060 0.98 52.1 yes View details
atpF LSC 1394 0.0043 1.00 56.1 yes View details
ycf3-trnS-GGA LSC 590 0.0068 1.00 62.4 yes View details
trnT-UGU-trnL-UAA LSC 813 0.0049 1.00 53.0 yes View details
petA-psbJ LSC 988 0.0051 1.00 61.4 yes View details
trnW-CAA-trnP-UGG LSC 130 0.0233 0.99 64.3 yes View details
trnP-UGG-psaJ LSC 393 0.0076 1.00 50.5 yes View details
rps12-clpP LSC 143 0.0210 1.00 64.6 yes View details
matK-trnK-UUU LSC 699 0.0058 0.99 63.2 yes View details
psbI-trnS-GCU LSC 120 0.0167 1.00 62.1 yes View details
ndhK LSC 741 0.0054 1.00 61.9 yes View details
ndhC-trnV-UAC LSC 769 0.0052 1.00 61.7 yes View details
trnE-UUC-trnY-GUA LSC 61 0.0164 1.00 60.7 yes View details
psaA-ycf3 LSC 620 0.0032 1.00 60.6 yes View details
rbcL-psaI LSC 1292 0.0023 0.99 60.6 yes View details
rps18 LSC 492 0.0000 0.96 60.6 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 TACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2755–2763 1.000 73.8
trnK-UUU_p2 trnK-UUU ACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2754–2762 1.000 73.7
trnK-UUU_p3 trnK-UUU ATACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2756–2764 1.000 69.7
trnK-UUU_p4 trnK-UUU TACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2755–2763 1.000 67.2
trnK-UUU_p5 trnK-UUU CAATGTCAACCAAGCCAGC CGTGCGGTGTAATTCCATTG 2752–2760 1.000 67.1
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 860–868 1.000 69.3
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 860–868 1.000 67.5
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 859–867 1.000 67.5
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 801–809 1.000 63.0
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA CGTGCGGTGTAATTCCATTG 860–868 1.000 62.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 690 1.000 66.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 691 1.000 65.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 688 1.000 65.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 687 1.000 65.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 689 1.000 64.4
psbI-trnS-GCU_p1 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG TAAAGCGGCGGATTGCTAAT 210 1.000 68.6
psbI-trnS-GCU_p2 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG CTTTCGATTTGGAACGGGGA 247 1.000 67.3
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG TTTCGATTTGGAACGGGGAG 246 1.000 67.3
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGGCGTGAGGA TAAAGCGGCGGATTGCTAAT 211 1.000 66.1
psbI-trnS-GCU_p5 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG ATGGCTGAGTGGACTAAAGC 224 1.000 65.6
trnE-UUC-trnY-GUA_p1 trnE-UUC-trnY-GUA CGTCTAGTGAAGTGATGCCC CTAGATTTTTGGGCCGAGCT 243 1.000 79.4
trnE-UUC-trnY-GUA_p2 trnE-UUC-trnY-GUA GTGAAGTGATGCCCCTATCG CTAGATTTTTGGGCCGAGCT 237 1.000 79.0
trnE-UUC-trnY-GUA_p3 trnE-UUC-trnY-GUA GAAGTGATGCCCCTATCGTC CTAGATTTTTGGGCCGAGCT 235 1.000 78.7
trnE-UUC-trnY-GUA_p4 trnE-UUC-trnY-GUA AAGTGATGCCCCTATCGTCT CTAGATTTTTGGGCCGAGCT 234 1.000 78.3
trnE-UUC-trnY-GUA_p5 trnE-UUC-trnY-GUA TCTAGTGAAGTGATGCCCCT CTAGATTTTTGGGCCGAGCT 241 1.000 77.9
psbM-petN_p1 psbM-petN TGGAAGTCAATATTCTCGCA TAGTAAGTCTCGCTTGGGCT 941–955 1.000 52.1
psbM-petN_p2 psbM-petN TGGAAGTCAATATTCTCGCA GTAGTATGGGGGAGGAGTGG 885–899 1.000 51.1
psbM-petN_p3 psbM-petN TGGAAGTCAATATTCTCGCA TAGTATGGGGGAGGAGTGGA 884–898 1.000 50.4
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT TAGTAAGTCTCGCTTGGGCT 916–930 1.000 50.2
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTTATTCT GTAGTATGGGGGAGGAGTGG 860–874 1.000 49.3

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
Thamnocalamus spathiflorus NC_024724.1 139778 View on NCBI ↗
Thamnocalamus unispiculatus NC_061040.1 139726 View on NCBI ↗