Markers + reference

Calamagrostis

4 species · Poaceae · Poales

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Species 4
Genome length 137–137 kb
Candidate markers 267
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 11 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 402 0.0050 1.00 39.0 yes View details
trnT-GGU-trnE-UUC LSC 535 0.0044 1.00 50.9 yes View details
rpoC2 LSC 4443 0.0020 0.99 38.0 yes View details
atpA LSC 1524 0.0003 1.00 35.8 yes View details
rbcL-psaI LSC 1586 0.0039 1.00 37.6 yes View details
psbE-petL LSC 1311 0.0041 1.00 38.9 yes View details
trnW-CCA-trnP-UGG LSC 144 0.0046 1.00 33.3 yes View details
rpl33-rps18 LSC 282 0.0047 1.00 34.2 yes View details
infA LSC 324 0.0036 1.00 36.9 yes View details
rps3 LSC 720 0.0007 1.00 43.3 yes View details
ndhA SSC 2113 0.0038 1.00 50.6 yes View details
rps19-psbA LSC 122 0.0232 1.00 60.7 no View details
ndhH SSC 1182 0.0018 1.00 57.6 yes View details
petG-trnW-CCA LSC 122 0.0492 1.00 56.9 yes View details
psaJ-rpl33 LSC 431 0.0012 1.00 54.5 yes View details
trnfM-CAU-trnG-UCC LSC 104 0.0112 0.97 53.4 yes View details
ndhC-trnV-UAC LSC 914 0.0026 0.98 53.1 yes View details
rpl32-trnL-UAG SSC 638 0.0034 0.99 52.8 yes View details
rps11-rpl36 LSC 179 0.0140 1.00 52.2 yes View details
ndhF-rpl32 SSC 902 0.0030 0.99 52.1 yes View details
psaA-ycf3 LSC 646 0.0023 1.00 51.2 yes View details
ndhH IRb 198 0.0034 1.00 35.9 no 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
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTCCGTCCTGGGTCATTAGA 573–574 1.000 78.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCCGTCCTGGGTCATTAGA 524–525 1.000 78.1
psbK-psbI_p3 psbK-psbI CGTGGATGTTATGCCTGTCA GAATTTTTACTCCTCGCGCC 598–599 1.000 76.6
psbK-psbI_p4 psbK-psbI CGTGGATGTTATGCCTGTCA GGAATTTTTACTCCTCGCGC 599–600 1.000 76.6
psbK-psbI_p5 psbK-psbI CGTGGATGTTATGCCTGTCA TCCGTCCTGGGTCATTAGAT 572–573 1.000 76.5
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG AGCCTTCCAAGCTAACGATG 192–195 1.000 80.0
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCTAGCCTTCCAAGCTAACG 195–198 1.000 79.7
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG AGCCTTCCAAGCTAACGATG 177–180 1.000 79.7
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG CCTAGCCTTCCAAGCTAACG 180–183 1.000 79.5
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCAACGTCGACTATAACCCC 213–216 1.000 78.3
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT AAATACTCCCTACCCCCAGG 691 1.000 68.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA AAATACTCCCTACCCCCAGG 654 1.000 67.9
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 656 1.000 67.6
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 635 1.000 67.5
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 619 1.000 67.4
rpoC2_p1 rpoC2 CCCTTAGGCGTTATTGTACCT TGTCCAAGGTGAATTATTGCC 272 1.000 46.4
rpoC2_p2 rpoC2 CCCTTAGGCGTTATTGTACCT TTGTCCAAGGTGAATTATTGCC 273 1.000 44.1
rpoC2_p3 rpoC2 TCAAGAAATTTTTGGGCCCT TGTCCAAGGTGAATTATTGCC 288 1.000 42.5
rpoC2_p4 rpoC2 CCCTTAGGCGTTATTGTACC TGTCCAAGGTGAATTATTGCC 272 1.000 42.1
rpoC2_p5 rpoC2 TCAAGAAATTTTTGGGCCCTT TGTCCAAGGTGAATTATTGCC 288 1.000 41.1
atpA_p1 atpA TTCCCCTTGCTTCCGAAAAA TCTTTCTCAACGATTCCTCTTCT 1610 1.000 49.6
atpA_p2 atpA TTTCCCCTTGCTTCCGAAAA TCTTTCTCAACGATTCCTCTTCT 1611 1.000 49.6
atpA_p3 atpA TTTTCCCCTTGCTTCCGAAA TCTTTCTCAACGATTCCTCTTCT 1612 1.000 49.6
atpA_p4 atpA TTTTTCCCCTTGCTTCCGAA TCTTTCTCAACGATTCCTCTTCT 1613 1.000 49.6
atpA_p5 atpA TTCCCCTTGCTTCCGAAAAA TCTCAACGATTCCTCTTCTACT 1606 1.000 47.9
psaA-ycf3_p1 psaA-ycf3 GGTCTGGCCCATTCTTCAAA TATAGCGCTTACTCCGGGAA 807–815 1.000 79.7
psaA-ycf3_p2 psaA-ycf3 GGTCTGGCCCATTCTTCAAA GCGCTTACTCCGGGAAATTA 803–811 1.000 79.3
psaA-ycf3_p3 psaA-ycf3 GGTCTGGCCCATTCTTCAAA TGGTTTGATCAAGCTGCTGA 842–850 1.000 77.6
psaA-ycf3_p4 psaA-ycf3 TGTTCTTGAGAAATGGCCGG TATAGCGCTTACTCCGGGAA 826–834 1.000 76.5
psaA-ycf3_p5 psaA-ycf3 TTTTACTTCTGGTTCCGGCG TATAGCGCTTACTCCGGGAA 754–762 1.000 76.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Calamagrostis breviligulata NC_027465.1 136726 View on NCBI ↗
Calamagrostis epigejos NC_067046.1 136782 View on NCBI ↗
Calamagrostis epigejos subsp. epigejos PP328788.1 136771 View on NCBI ↗
Calamagrostis pickeringii NC_050417.1 136682 View on NCBI ↗