Markers + reference

Holcus

2 species · Poaceae · Poales

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Species 2
Genome length 136–136 kb
Candidate markers 267
Primer pairs 80

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 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-UGA-psbZ LSC 352 0.0000 1.00 34.8 yes View details
psbZ-trnG-GCC LSC 286 0.0035 1.00 54.5 yes View details
petN-trnC-GCA LSC 909 0.0011 1.00 59.5 yes View details
trnC-GCA-rpoB LSC 1178 0.0017 1.00 59.8 yes View details
rpoC2 LSC 4422 0.0002 1.00 53.5 yes View details
rbcL-psaI LSC 1408 0.0021 1.00 60.0 yes View details
clpP LSC 651 0.0015 1.00 59.6 yes View details
rpl32-trnL-UAG SSC 618 0.0016 1.00 59.7 yes View details
matK-trnK-UUU LSC 669 0.0000 1.00 58.9 yes View details
atpI-atpH LSC 578 0.0000 1.00 58.5 yes View details
ycf4-cemA LSC 450 0.0000 1.00 55.8 yes View details
rps8-rpl14 LSC 143 0.0000 0.99 53.2 yes View details
rpl16-rps3 LSC 144 0.0000 0.99 53.2 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
rps16 LSC 1092 0.0000 1.00 40.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACCCAATATCTTGCTAGAACAAG TACGTATGCTTGGGAGTCCT 1192 1.000 41.4
psbA_p2 psbA ACCCAATATCTTGCTAGAACA TACGTATGCTTGGGAGTCCT 1192 1.000 41.3
psbA_p3 psbA TGCTAGAACAAGATATTGGGT TACGTATGCTTGGGAGTCCT 1181 1.000 41.3
psbA_p4 psbA ACCCAATATCTTGCTAGAACAA TACGTATGCTTGGGAGTCCT 1192 1.000 40.0
psbA_p5 psbA TTGCTAGAACAAGATATTGGGT TACGTATGCTTGGGAGTCCT 1182 1.000 40.0
trnK-UUU_p1 trnK-UUU TGTCAACCAAATCAGCTCAA AATGTTTTGACAGAAGCGCG 2743–2744 1.000 59.6
trnK-UUU_p2 trnK-UUU TGTCAACCAAATCAGCTCAAAG AATGTTTTGACAGAAGCGCG 2743–2744 1.000 59.2
trnK-UUU_p3 trnK-UUU TGTCAACCAAATCAGCTCAA CGCGCAGTGTAATTCCATTG 2727–2728 1.000 58.4
trnK-UUU_p4 trnK-UUU TGTCAACCAAATCAGCTCAAAG CGCGCAGTGTAATTCCATTG 2727–2728 1.000 58.0
trnK-UUU_p5 trnK-UUU TGTCAACCAAATCAGCTCAAA AATGTTTTGACAGAAGCGCG 2743–2744 1.000 57.9
matK-trnK-UUU_p1 matK-trnK-UUU CCACAATCATGGGCAAATGC AATGTTTTGACAGAAGCGCG 889–890 1.000 77.1
matK-trnK-UUU_p2 matK-trnK-UUU CACAATCATGGGCAAATGCA AATGTTTTGACAGAAGCGCG 888–889 1.000 76.7
matK-trnK-UUU_p3 matK-trnK-UUU CCACAATCATGGGCAAATGC CGCGCAGTGTAATTCCATTG 873–874 1.000 75.9
matK-trnK-UUU_p4 matK-trnK-UUU CACAATCATGGGCAAATGCA CGCGCAGTGTAATTCCATTG 872–873 1.000 75.5
matK-trnK-UUU_p5 matK-trnK-UUU CACAATCATGGGCAAATGCAT AATGTTTTGACAGAAGCGCG 888–889 1.000 71.1
rps16_p1 rps16 GGATTGGCACGACATAAATCC TGCTCCATAGACAGCAAGTT 1327 1.000 57.7
rps16_p2 rps16 GATTGGCACGACATAAATCCA TGCTCCATAGACAGCAAGTT 1326 1.000 52.1
rps16_p3 rps16 TGGCACGACATAAATCCAAA TGCTCCATAGACAGCAAGTT 1323 1.000 51.9
rps16_p4 rps16 TTGGCACGACATAAATCCAA TGCTCCATAGACAGCAAGTT 1324 1.000 51.9
rps16_p5 rps16 TTGGCACGACATAAATCCAAA TGCTCCATAGACAGCAAGTT 1324 1.000 50.2
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GGCTGAGGAAGTCGCAATTA 427 1.000 79.6
trnS-UGA-psbZ_p2 trnS-UGA-psbZ GAGCTATCAACCACTCAGCC GGCTGAGGAAGTCGCAATTA 434 1.000 79.4
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GGAGCTATCAACCACTCAGC GGCTGAGGAAGTCGCAATTA 435 1.000 79.4
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC GGCTGAGGAAGTCGCAATTA 442 1.000 79.3
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 472 1.000 78.2
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TACCATTGAACTACGCTCGC 416 1.000 77.9
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TACCATTGAACTACGCTCGC 414 1.000 77.5
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TAAATTAAGTGGGCGAGCGG 478 1.000 75.8
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TAAATTAAGTGGGCGAGCGG 476 1.000 75.4
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TCGAACCCGTATCTTCTCCT 452 1.000 75.1

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
Holcus lanatus NC_036689.1 135668 View on NCBI ↗
Holcus lanatus subsp. lanatus PP336764.1 135678 View on NCBI ↗