Markers + reference

Gelidocalamus

17 species · Poaceae · Poales

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Species 17
Genome length 139–140 kb
Candidate markers 280
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 556 0.0072 1.00 56.7 yes View details
trnG-UCC-trnfM-CAU LSC 441 0.0050 1.00 42.4 yes View details
trnG-UCC-trnT-GGU LSC 1986 0.0054 0.99 60.4 yes View details
trnD-GUC-psbM LSC 990 0.0052 1.00 51.4 yes View details
trnF-GAA-ndhJ LSC 583 0.0057 1.00 51.8 yes View details
rbcL LSC 1434 0.0042 1.00 45.9 yes View details
rpoA LSC 1020 0.0022 1.00 36.5 yes View details
infA LSC 324 0.0023 1.00 26.9 yes View details
rpl22 LSC 450 0.0042 1.00 30.1 yes View details
ndhF-rpl32 SSC 889 0.0057 1.00 52.2 yes View details
rpl32-trnL-UAG SSC 702 0.0067 1.00 43.0 yes View details
rpl22-rps19 IRb 77 0.0637 1.00 65.8 yes View details
rps19-psbA LSC 128 0.0230 1.00 60.3 no View details
trnT-UGU-trnL-UAA LSC 817 0.0050 1.00 57.2 yes View details
ycf3 LSC 2000 0.0010 1.00 54.8 yes View details
petB LSC 1466 0.0015 1.00 54.2 yes View details
infA-rps8 LSC 111 0.0388 1.00 52.4 yes View details
ndhC-trnV-UAC LSC 756 0.0031 1.00 52.2 yes View details
ndhG-ndhI SSC 246 0.0115 1.00 51.5 yes View details
psbE-petL LSC 1228 0.0034 1.00 51.2 yes View details
rps16-trnQ-UUG LSC 1533 0.0028 1.00 50.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 690 1.000 68.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 691 1.000 66.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 688 1.000 66.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 687 1.000 66.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 689 1.000 65.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1603–1638 1.000 80.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1614–1649 1.000 79.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1607–1642 1.000 79.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1618–1653 1.000 78.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1663–1698 1.000 78.3
trnG-UCC-trnfM-CAU_p1 trnG-UCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 559–574 1.000 79.1
trnG-UCC-trnfM-CAU_p2 trnG-UCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CAGTTTGGTAGCTCACGAGG 574–589 1.000 78.6
trnG-UCC-trnfM-CAU_p3 trnG-UCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT CGAGGCTCATAACCTTGAGG 563–578 1.000 78.3
trnG-UCC-trnfM-CAU_p4 trnG-UCC-trnfM-CAU TAGCGAGCGTAGTTCAATGG CGAGGCTCATAACCTTGAGG 561–576 1.000 78.1
trnG-UCC-trnfM-CAU_p5 trnG-UCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA GAGCGGAGTAGAGCAGTTTG 587–602 1.000 77.9
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 1854–2144 1.000 48.0
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 1867–2157 1.000 47.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 1868–2158 1.000 47.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 1857–2147 1.000 46.9
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 1856–2146 1.000 46.9
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1073–1098 1.000 50.2
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1105–1130 1.000 48.8
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1074–1099 1.000 47.2
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1073–1098 1.000 47.2
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1074–1099 1.000 46.1
ycf3_p1 ycf3 ATCAACAACCAAACCACCCA AGAGCATATGGATCGATCGA 2127–2144 1.000 61.8
ycf3_p2 ycf3 TCAACAACCAAACCACCCAT AGAGCATATGGATCGATCGA 2126–2143 1.000 61.8
ycf3_p3 ycf3 ATCAACAACCAAACCACCCA AGAGCATATGGATCGATCGAT 2127–2144 1.000 58.3
ycf3_p4 ycf3 TCAACAACCAAACCACCCAT AGAGCATATGGATCGATCGAT 2126–2143 1.000 58.3
ycf3_p5 ycf3 GATCAACAACCAAACCACCC AGAGCATATGGATCGATCGA 2128–2145 1.000 56.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Gelidocalamus albozonatus PP999719.1 139615 View on NCBI ↗
Gelidocalamus annulatus PP999733.1 139650 View on NCBI ↗
Gelidocalamus dongdingensis PV849988.1 139412 View on NCBI ↗
Gelidocalamus fengkaiensis PP999722.1 139764 View on NCBI ↗
Gelidocalamus kunishii NC_062076.1 139535 View on NCBI ↗
Gelidocalamus latifolius PP999742.1 139575 View on NCBI ↗
Gelidocalamus longiinternodus PP999729.1 139587 View on NCBI ↗
Gelidocalamus monophyllus PP999724.1 139716 View on NCBI ↗
Gelidocalamus multifolius NC_072534.1 139745 View on NCBI ↗
Gelidocalamus rutilans PP999726.1 139688 View on NCBI ↗
Gelidocalamus solidus PP999736.1 139600 View on NCBI ↗
Gelidocalamus stellatus NC_072532.1 139576 View on NCBI ↗
Gelidocalamus stellatus var. wugongshanensis PP999734.1 139602 View on NCBI ↗
Gelidocalamus subsolidus PP999731.1 139742 View on NCBI ↗
Gelidocalamus tessellatus NC_024719.1 139712 View on NCBI ↗
Gelidocalamus xunwuensis PP999727.1 139704 View on NCBI ↗
Gelidocalamus zixingensis NC_072533.1 139500 View on NCBI ↗