Markers + reference

Pleuropogon

4 species · Poaceae · Poales

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Species 4
Genome length 134–135 kb
Candidate markers 201
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 201 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-psbD LSC 888 0.0216 0.95 64.8 yes View details
trnG-trnfM LSC 480 0.0297 0.97 71.2 yes View details
tRNA-Gly-trnT LSC 1571 0.0269 0.97 69.2 yes View details
psaA-ycf3 LSC 608 0.0285 1.00 70.6 yes View details
rbcL-petA LSC 2285 0.0181 0.99 57.9 yes View details
petA-psbJ LSC 826 0.0311 0.99 72.7 yes View details
psbE-petG LSC 1431 0.0233 0.94 69.9 yes View details
rpl16 LSC 1450 0.0156 0.98 46.8 yes View details
rps15-trnL SSC 4328 0.0238 0.98 63.6 yes View details
psbI-trnS LSC 120 0.0486 1.00 78.0 yes View details
ndhC-trnV LSC 808 0.0256 0.96 77.9 yes View details
psbZ-trnG LSC 259 0.0341 0.90 69.3 yes View details
psbM-trnC LSC 1642 0.0176 0.99 67.8 yes View details
trnT-tRNA-Leu LSC 763 0.0260 1.00 67.6 yes View details
rps11-rpl36 LSC 180 0.0361 0.96 67.5 yes View details
trnfM-tRNA-Gly LSC 95 0.0421 1.00 66.5 yes View details
trnT-trnE LSC 499 0.0190 0.94 65.2 yes View details
trnH-psbA IRa 572 0.0239 0.98 65.1 no View details
trnQ-psbI LSC 907 0.0186 1.00 64.5 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
trnQ-psbI_p1 trnQ-psbI GATCAAAACCCGCTGCCTTA ACGTCCTGGGTCATTGGATA 1035–1058 1.000 76.7
trnQ-psbI_p2 trnQ-psbI GATCAAAACCCGCTGCCTTA TACGTCCTGGGTCATTGGAT 1036–1059 1.000 76.7
trnQ-psbI_p3 trnQ-psbI GATCAAAACCCGCTGCCTTA TTTTTACTCCTCACGCCCAG 1059–1082 1.000 76.3
trnQ-psbI_p4 trnQ-psbI GATCAAAACCCGCTGCCTTA TTACGTCCTGGGTCATTGGA 1037–1060 1.000 74.9
trnQ-psbI_p5 trnQ-psbI ATCAAAACCCGCTGCCTTAC ACGTCCTGGGTCATTGGATA 1034–1057 1.000 74.4
psbI-trnS_p1 psbI-trnS ATCCAATGACCCAGGACGTA TAAAGCGGCGGATTGCTAAT 228–229 1.000 82.2
psbI-trnS_p2 psbI-trnS TATCCAATGACCCAGGACGT TAAAGCGGCGGATTGCTAAT 229–230 1.000 82.2
psbI-trnS_p3 psbI-trnS ATCCAATGACCCAGGACGTA CTTTCGATTTGGAACGGGGA 265–266 1.000 80.5
psbI-trnS_p4 psbI-trnS ATCCAATGACCCAGGACGTA TTTCGATTTGGAACGGGGAG 264–265 1.000 80.5
psbI-trnS_p5 psbI-trnS TATCCAATGACCCAGGACGT TTTCGATTTGGAACGGGGAG 265–266 1.000 80.5
trnS-psbD_p1 trnS-psbD ATTAGCAATCCGCCGCTTTA AGGAATTCTACCAAGGGCTA 955–1042 1.000 62.9
trnS-psbD_p2 trnS-psbD ATTAGCAATCCGCCGCTTTA TAGGAATTCTACCAAGGGCT 956–1043 1.000 62.9
trnS-psbD_p3 trnS-psbD ATTAGCAATCCGCCGCTTTA TTAGGAATTCTACCAAGGGCT 957–1044 1.000 61.6
trnS-psbD_p4 trnS-psbD GAGCGGAAAGAGAGGGATTC AGGAATTCTACCAAGGGCTA 1006–1093 1.000 61.1
trnS-psbD_p5 trnS-psbD GAGCGGAAAGAGAGGGATTC TAGGAATTCTACCAAGGGCT 1007–1094 1.000 61.1
psbZ-trnG_p1 psbZ-trnG TTGCTTCTCCTGATGGTTGG TCGAACCCGTATCTTCTCCT 291–427 1.000 81.6
psbZ-trnG_p2 psbZ-trnG GCTTCTCCTGATGGTTGGTC TCGAACCCGTATCTTCTCCT 289–425 1.000 81.2
psbZ-trnG_p3 psbZ-trnG TTGCTTCTCCTGATGGTTGG CCGTATCTTCTCCTTGGCAA 285–421 1.000 79.6
psbZ-trnG_p4 psbZ-trnG GCTTCTCCTGATGGTTGGTC CCGTATCTTCTCCTTGGCAA 283–419 1.000 79.2
psbZ-trnG_p5 psbZ-trnG TTGCTTCTCCTGATGGTTGG GGGAATCGAACCCGTATCTT 296–432 1.000 77.8
trnG-trnfM_p1 trnG-trnfM AGGAGAAGATACGGGTTCGA CGAGGCTCATAACCTTGAGG 547–581 1.000 81.1
trnG-trnfM_p2 trnG-trnfM AGGAGAAGATACGGGTTCGA CAGTTTGGTAGCTCACGAGG 562–596 1.000 80.5
trnG-trnfM_p3 trnG-trnfM AGGAGAAGATACGGGTTCGA GAGCGGAGTAGAGCAGTTTG 575–609 1.000 79.7
trnG-trnfM_p4 trnG-trnfM AGGAGAAGATACGGGTTCGA AGAGCGGAGTAGAGCAGTTT 576–610 1.000 79.1
trnG-trnfM_p5 trnG-trnfM TTGCCAAGGAGAAGATACGG CGAGGCTCATAACCTTGAGG 553–587 1.000 79.0
trnfM-tRNA-Gly_p1 trnfM-tRNA-Gly CCTCAAGGTTATGAGCCTCG AGCCTTCCAAGCTAACGATG 181–186 1.000 82.7
trnfM-tRNA-Gly_p2 trnfM-tRNA-Gly CCTCGTGAGCTACCAAACTG AGCCTTCCAAGCTAACGATG 166–171 1.000 82.7
trnfM-tRNA-Gly_p3 trnfM-tRNA-Gly CCTCAAGGTTATGAGCCTCG CCTAGCCTTCCAAGCTAACG 184–189 1.000 82.4
trnfM-tRNA-Gly_p4 trnfM-tRNA-Gly CCTCGTGAGCTACCAAACTG CCTAGCCTTCCAAGCTAACG 169–174 1.000 82.4
trnfM-tRNA-Gly_p5 trnfM-tRNA-Gly CCTCAAGGTTATGAGCCTCG CCAACGTCGACTATAACCCC 202–207 1.000 80.7

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
Pleuropogon californicus PZ098353.1 134231 View on NCBI ↗
Pleuropogon hooverianus NC_059983.1 135123 View on NCBI ↗
Pleuropogon refractus PZ098325.1 135199 View on NCBI ↗
Pleuropogon sabinei PZ098326.1 134388 View on NCBI ↗