Markers + reference

Ctenium

6 species · Poaceae · Poales

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Species 6
Genome length 134–135 kb
Candidate markers 269
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1095 0.0218 0.99 60.1 yes View details
trnG-UCC-trnE-UUC LSC 1571 0.0230 1.00 68.1 yes View details
trnD-GUC-psbM LSC 1006 0.0201 0.68 59.8 yes View details
psbM-petN LSC 702 0.0248 1.00 65.3 yes View details
petN-trnC-GCA LSC 735 0.0247 1.00 58.6 yes View details
trnR-UCU-rps14 LSC 381 0.0425 1.00 72.3 yes View details
trnF-GAA-ndhJ LSC 562 0.0280 1.00 66.6 yes View details
ndhC-trnV-UAC LSC 1136 0.0206 1.00 62.3 yes View details
rbcL-psaI LSC 839 0.0281 1.00 61.8 yes View details
petA-psbJ LSC 907 0.0228 1.00 56.7 yes View details
psbE-petL LSC 1198 0.0194 1.00 66.4 yes View details
rpl32-ndhF SSC 898 0.0340 1.00 76.3 yes View details
ndhF SSC 2220 0.0144 1.00 54.9 yes View details
psbC-trnS-UGA LSC 158 0.0253 0.99 70.7 yes View details
trnL-UAG-rpl32 SSC 530 0.0287 1.00 70.2 yes View details
ndhD-ccsA SSC 184 0.0412 0.99 68.9 yes View details
trnS-GGA-rps4 LSC 265 0.0229 1.00 68.2 yes View details
psaA-ycf3 LSC 452 0.0256 1.00 67.2 yes View details
atpI-atpH LSC 789 0.0203 1.00 66.4 yes View details
infA-rps8 LSC 79 0.0743 1.00 64.3 yes View details
trnC-GCA-rpoB LSC 1025 0.0198 0.98 63.3 yes View details
psaJ-rpl33 LSC 374 0.0310 1.00 63.2 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CAATGTCAACCAAGCAAGCC TGTTTTGCTAGGAGCGTCTG 2736–2760 0.833 72.4
trnK-UUU_p2 trnK-UUU CCAATGTCAACCAAGCAAGC TGTTTTGCTAGGAGCGTCTG 2737–2761 0.833 72.4
trnK-UUU_p3 trnK-UUU AACACCAAACCATCCGATGT TGTTTTGCTAGGAGCGTCTG 2953–2977 0.833 71.8
trnK-UUU_p4 trnK-UUU GCTTGTACTTTCGCGTCTCT TGTTTTGCTAGGAGCGTCTG 2884–2908 0.833 71.7
trnK-UUU_p5 trnK-UUU AGGACTCCCAAGCACACATA TGTTTTGCTAGGAGCGTCTG 2820–2844 0.833 71.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCTGTCTTCTCGAGCTCCA GAGGTTCGAATCCTTCCGTC 1324–1486 1.000 85.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTCTGTCTTCTCGAGCTCCA TGACAGGCATAACATCCACG 1848–2010 1.000 84.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGACAGGCATAACATCCACG 1691–1854 1.000 84.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTCTGTCTTCTCGAGCTCCA CTTACAGCAGCTTGCCAAAC 1897–2059 1.000 84.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCTGTCTTCTCGAGCTCCAT TGACAGGCATAACATCCACG 1847–2009 1.000 84.3
psbC-trnS-UGA_p1 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GAGAGATGGCTGAGTGGTTG 338–350 1.000 85.3
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCAGGCTTTGAAAAGGGAA GAGAGATGGCTGAGTGGTTG 303–315 1.000 85.3
psbC-trnS-UGA_p3 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG ATAGCCCCGGTCTTGAAAAC 318–330 1.000 84.9
psbC-trnS-UGA_p4 psbC-trnS-UGA ATTTGTGGCATGCAGGAAGA GAGAGATGGCTGAGTGGTTG 337–349 1.000 84.8
psbC-trnS-UGA_p5 psbC-trnS-UGA ATTTGTGGCATGCAGGAAGA ATAGCCCCGGTCTTGAAAAC 317–329 1.000 84.3
trnG-UCC-trnE-UUC_p1 trnG-UCC-trnE-UUC ACGAATCACACTTTTACCACT ACCACTAGACGATAGGGGC 1522–1639 1.000 51.4
trnG-UCC-trnE-UUC_p2 trnG-UCC-trnE-UUC AGAACGAATCACACTTTTACCAC ACCACTAGACGATAGGGGC 1525–1642 1.000 50.4
trnG-UCC-trnE-UUC_p3 trnG-UCC-trnE-UUC GAACGAATCACACTTTTACCACT ACCACTAGACGATAGGGGC 1524–1641 1.000 50.4
trnG-UCC-trnE-UUC_p4 trnG-UCC-trnE-UUC AACGAATCACACTTTTACCACT ACCACTAGACGATAGGGGC 1523–1640 1.000 49.5
trnG-UCC-trnE-UUC_p5 trnG-UCC-trnE-UUC TACCACTAAACTATACCCGC ACCACTAGACGATAGGGGC 1508–1625 1.000 48.8
trnD-GUC-psbM_p1 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC AGAATGAACAATGCAGTAGC 726–1116 1.000 52.0
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG AGAATGAACAATGCAGTAGC 759–1149 1.000 51.0
trnD-GUC-psbM_p3 trnD-GUC-psbM AATTGGTTAGAGCACCGCC AGAATGAACAATGCAGTAGC 724–1114 1.000 48.6
trnD-GUC-psbM_p4 trnD-GUC-psbM GTTCAATTGGTTAGAGCACCG AGAATGAACAATGCAGTAGC 728–1118 1.000 48.6
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TAGAATGAACAATGCAGTAGC 727–1117 1.000 48.6
psbM-petN_p1 psbM-petN ACAGCCAGCCAAAACGATTA AAACGAGGCTTTGTTTTGGC 1418–1547 0.833 76.5
psbM-petN_p2 psbM-petN ACAGCCAGCCAAAACGATTA AAGGGGGAACTACCAACAGA 1381–1510 0.833 76.1
psbM-petN_p3 psbM-petN ACAGCCAGCCAAAACGATTA AGTATGGGGGAGAAGTGGAC 748–883 0.833 75.9
psbM-petN_p4 psbM-petN ACAGCCAGCCAAAACGATTA GTATGGGGGAGAAGTGGACT 747–882 0.833 75.9
psbM-petN_p5 psbM-petN ACAGCCAGCCAAAACGATTA TAGTAAGTCTCGCTTGGGCT 806–941 0.833 75.4

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
Ctenium brachystachyum OR148038.1 134500 View on NCBI ↗
Ctenium chapadense NC_088434.1 134561 View on NCBI ↗
Ctenium concinnum NC_082100.1 133943 View on NCBI ↗
Ctenium concissum NC_085713.1 134558 View on NCBI ↗
Ctenium longiglume NC_088436.1 134178 View on NCBI ↗
Ctenium newtonii NC_085712.1 134044 View on NCBI ↗