Markers + reference

Indocalamus

9 species · Poaceae · Poales

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Species 9
Genome length 140–140 kb
Candidate markers 268
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
infA LSC 342 0.0021 0.95 31.2 yes View details
psbJ-petA LSC 984 0.0032 1.00 44.7 yes View details
psaI-rbcL LSC 1308 0.0038 0.98 38.7 yes View details
ndhJ-trnF-GAA LSC 585 0.0032 0.99 48.1 yes View details
trnT-GGU-trnfM-CAU LSC 2809 0.0021 1.00 47.5 yes View details
trnQ-UUG-rps16 LSC 1546 0.0020 0.99 34.2 yes View details
rps16-trnK-UUU LSC 556 0.0035 1.00 50.8 yes View details
ndhF SSC 2220 0.0011 1.00 35.9 yes View details
rpl32-trnL-UAG SSC 702 0.0048 1.00 35.6 yes View details
atpH-atpI LSC 832 0.0017 0.98 51.7 yes View details
petN-psbM LSC 754 0.0017 1.00 50.9 yes View details
ycf3 LSC 1987 0.0001 1.00 50.0 yes View details
trnfM-CAU-trnG-UCC LSC 448 0.0029 0.98 50.0 yes View details
trnL-UAA-trnT-UGU LSC 816 0.0008 1.00 49.0 yes View details
rps19-rpl22 IRa 66 0.0177 0.98 48.4 no View details
psbB-clpP LSC 495 0.0013 1.00 46.8 yes View details
rps12-rpl20 LSC 696 0.0006 1.00 44.8 yes View details
cemA LSC 693 0.0006 1.00 44.8 yes View details
psbM-trnD-GUC LSC 982 0.0018 1.00 44.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
infA_p1 infA TTAAAGCGTATCAGCCGACC ATACGCACTCTCCTACGTGA 1051–1070 1.000 81.5
infA_p2 infA TTAAAGCGTATCAGCCGACC TCCACTACCAGCACCCTTTA 1322–1341 1.000 81.0
infA_p3 infA TTAAAGCGTATCAGCCGACC TTGCAAACCCACTGTACGAA 1286–1305 1.000 81.0
infA_p4 infA TTAAAGCGTATCAGCCGACC GTAATGCGGCATCTCTTCCA 1338–1357 1.000 80.9
infA_p5 infA TTAAAGCGTATCAGCCGACC TAATGCGGCATCTCTTCCAC 1337–1356 1.000 80.9
psbB-clpP_p1 psbB-clpP TATGCACCGAAAGCAATCGA ACCCAAGTCGCTTCTTCATC 625–627 1.000 79.7
psbB-clpP_p2 psbB-clpP TATGCACCGAAAGCAATCGA TCAACCCAAGTCGCTTCTTC 628–630 1.000 79.5
psbB-clpP_p3 psbB-clpP TATGCACCGAAAGCAATCGA CTTTTGGAACACCAATGGGC 585–587 1.000 79.2
psbB-clpP_p4 psbB-clpP TATGCACCGAAAGCAATCGA TTTGGAACACCAATGGGCAT 583–585 1.000 78.4
psbB-clpP_p5 psbB-clpP TATGCACCGAAAGCAATCGA AAGTCGCTTCTTCATCTCCG 621–623 1.000 78.2
rps12-rpl20_p1 rps12-rpl20 GAGGAACATGTGCTAGGGTG ACGCATTTTTGTTCGTCGTC 773 1.000 79.9
rps12-rpl20_p2 rps12-rpl20 CGACATGCCAACGGTTAAAC ACGCATTTTTGTTCGTCGTC 868 1.000 79.7
rps12-rpl20_p3 rps12-rpl20 GTCGAGGAACATGTGCTAGG ACGCATTTTTGTTCGTCGTC 776 1.000 79.5
rps12-rpl20_p4 rps12-rpl20 GAGGAACATGTGCTAGGGTG GTTTGAGGCAAATGAACGCA 788 1.000 78.9
rps12-rpl20_p5 rps12-rpl20 CGACATGCCAACGGTTAAAC GTTTGAGGCAAATGAACGCA 883 1.000 78.8
psbJ-petA_p1 psbJ-petA TCCTCTTTGGCTGATAGGTACT GGCCTTTTGTTCTTCTTCGC 1186 1.000 64.2
psbJ-petA_p2 psbJ-petA CCTCTTTGGCTGATAGGTACTG GGCCTTTTGTTCTTCTTCGC 1185 1.000 63.7
psbJ-petA_p3 psbJ-petA TTCCTCTTTGGCTGATAGGT GGCCTTTTGTTCTTCTTCGC 1187 1.000 62.8
psbJ-petA_p4 psbJ-petA ACGGTTCATATTCTGGATTGGG GGCCTTTTGTTCTTCTTCGC 1121 1.000 62.8
psbJ-petA_p5 psbJ-petA CGGTTCATATTCTGGATTGGGT GGCCTTTTGTTCTTCTTCGC 1120 1.000 62.8
cemA_p1 cemA TGCTAAAATGGAAAAGGGCT GAGTCAGCGAATGAAGCAGA 819 1.000 60.1
cemA_p2 cemA TGCTAAAATGGAAAAGGGCT AGAGTCAGCGAATGAAGCAG 820 1.000 60.0
cemA_p3 cemA TGCTAAAATGGAAAAGGGCTT GAGTCAGCGAATGAAGCAGA 819 1.000 58.5
cemA_p4 cemA TTGCTAAAATGGAAAAGGGCT GAGTCAGCGAATGAAGCAGA 820 1.000 58.5
cemA_p5 cemA TGCTAAAATGGAAAAGGGCTT AGAGTCAGCGAATGAAGCAG 820 1.000 58.5
psaI-rbcL_p1 psaI-rbcL CCATTGCAATTGCCGGAAAT GGCTTCAGGGGGTATTCATG 1660–1682 1.000 81.6
psaI-rbcL_p2 psaI-rbcL CCATTGCAATTGCCGGAAAT CGCCGGTACAGTAGTAGGTA 1810–1832 1.000 81.3
psaI-rbcL_p3 psaI-rbcL CCATTGCAATTGCCGGAAAT GTTATACCGGTGGCTTCAGG 1671–1693 1.000 81.3
psaI-rbcL_p4 psaI-rbcL CCATTGCAATTGCCGGAAAT CTTAACTGGGGGATTCACCG 1984–2006 1.000 81.2
psaI-rbcL_p5 psaI-rbcL CCAAGATAACTGGAAGCCCC GGCTTCAGGGGGTATTCATG 2198–2220 1.000 81.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Indocalamus amplexicaulis MW595311.1 139601 View on NCBI ↗
Indocalamus cordatus MW595300.1 139648 View on NCBI ↗
Indocalamus decorus MW533430.1 139598 View on NCBI ↗
Indocalamus hirsutissimus var. glabrifolius MW595297.1 139591 View on NCBI ↗
Indocalamus hispidus f. levis MW595292.1 139584 View on NCBI ↗
Indocalamus lacunosus MW595305.1 139630 View on NCBI ↗
Indocalamus longiauritus var. hengshanensis MW595302.1 139580 View on NCBI ↗
Indocalamus victorialis MW533431.1 139650 View on NCBI ↗
Indocalamus youxiuensis MW595291.1 139593 View on NCBI ↗