Markers + reference

Distichlis

2 species · Poaceae · Poales

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Species 2
Genome length 135–139 kb
Candidate markers 265
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 4530 0.0151 1.00 48.6 yes View details
petD-rps11 LSC 1504 0.0621 0.93 79.8 yes View details
rpl16 LSC 3372 0.2017 0.86 77.4 yes View details
petG-trnW-CCA LSC 126 0.0806 0.98 82.8 yes View details
rpl14-rpl16 LSC 109 0.1193 1.00 78.1 yes View details
psaC-ndhE SSC 491 0.0172 0.95 71.0 yes View details
petA-psbJ LSC 904 0.0156 0.99 68.2 yes View details
rps18-rpl20 LSC 232 0.0308 0.98 67.2 yes View details
atpF-atpA LSC 94 0.0319 1.00 67.0 yes View details
trnF-GAA-ndhJ LSC 555 0.0145 0.99 67.0 yes View details
ndhF-rpl32 SSC 955 0.0253 0.95 66.7 yes View details
rpl22 LSC 450 0.0178 1.00 65.8 yes View details
atpA-trnR-UCU LSC 181 0.0316 0.87 65.5 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoC2_p1 rpoC2 CATCCTTTTCGCTGCACAAG AACTCGGACCAATCCACCTA 1037–1049 1.000 84.0
rpoC2_p2 rpoC2 CATCCTTTTCGCTGCACAAG TGGTGGTATCAAACTAGCGC 1136–1148 1.000 83.9
rpoC2_p3 rpoC2 ATAGCATCCTTTTCGCTGCA TGGTGGTATCAAACTAGCGC 1140–1152 1.000 83.8
rpoC2_p4 rpoC2 CATCCTTTTCGCTGCACAAG TGCAGGTCGAACTGAAACAA 1250–1262 1.000 83.4
rpoC2_p5 rpoC2 ATAGCATCCTTTTCGCTGCA TGCAGGTCGAACTGAAACAA 1254–1266 1.000 83.3
atpF-atpA_p1 atpF-atpA CCGTACAAGGAGCTCTAGGA CATCCCCCACTTGAACTACG 316 1.000 80.1
atpF-atpA_p2 atpF-atpA AAGCCGTACAAGGAGCTCTA CATCCCCCACTTGAACTACG 319 1.000 79.3
atpF-atpA_p3 atpF-atpA CCGTACAAGGAGCTCTAGGA TTGTTCAATACGTTCGCGGA 261 1.000 78.7
atpF-atpA_p4 atpF-atpA ATTTCCGTACGATTCGTGCT CATCCCCCACTTGAACTACG 265 1.000 78.4
atpF-atpA_p5 atpF-atpA AAGCCGTACAAGGAGCTCTA TTGTTCAATACGTTCGCGGA 264 1.000 77.9
atpA-trnR-UCU_p1 atpA-trnR-UCU TGAACGGTTTTCCCTTCAGG GGTTCAAATCCTATTGGACGC 219–234 1.000 72.0
atpA-trnR-UCU_p2 atpA-trnR-UCU TAGCAAGACATTCACCGAGC GGTTCAAATCCTATTGGACGC 279–294 1.000 71.8
atpA-trnR-UCU_p3 atpA-trnR-UCU AGGAACAGCTTGAACGGTTT GGTTCAAATCCTATTGGACGC 229–244 1.000 71.7
atpA-trnR-UCU_p4 atpA-trnR-UCU AGCTTGAACGGTTTTCCCTT GGTTCAAATCCTATTGGACGC 223–238 1.000 71.7
atpA-trnR-UCU_p5 atpA-trnR-UCU GAACGGTTTTCCCTTCAGGA GGTTCAAATCCTATTGGACGC 218–233 1.000 70.1
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGCTGGC 665–792 1.000 80.0
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ ATGCACAAGAAAGGGTCAGG TGAAAGTTGGATAGGCTGGC 718–845 1.000 79.6
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATAGGCTGGCCCTTACGTAA 655–782 1.000 79.4
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ ATGCACAAGAAAGGGTCAGG ATAGGCTGGCCCTTACGTAA 708–835 1.000 79.0
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GCACAAGAAAGGGTCAGGAT TGAAAGTTGGATAGGCTGGC 716–843 1.000 78.7
petA-psbJ_p1 petA-psbJ CGTCCAAGGCCTTTTGTTCT ACGGTTCGTATTCTGGATTGG 1048–1076 1.000 67.2
petA-psbJ_p2 petA-psbJ GATCCATTACGCGTCCAAGG ACGGTTCGTATTCTGGATTGG 1059–1087 1.000 66.4
petA-psbJ_p3 petA-psbJ CGTCCAAGGCCTTTTGTTCT GGTTCGTATTCTGGATTGGGT 1046–1074 1.000 65.8
petA-psbJ_p4 petA-psbJ CGTCCAAGGCCTTTTGTTCT GCTGATAGGTACTGTAACCGG 1104–1132 1.000 65.0
petA-psbJ_p5 petA-psbJ CGTCCAAGGCCTTTTGTTCT GGCTGATAGGTACTGTAACCG 1105–1133 1.000 65.0
petG-trnW-CCA_p1 petG-trnW-CCA GGGATTATTCGTGACTGCGT CAAAACCCGATGTCGTAGGT 221–223 1.000 83.1
petG-trnW-CCA_p2 petG-trnW-CCA GCGTATTTGCAATACAGGCG CAAAACCCGATGTCGTAGGT 205–207 1.000 81.9
petG-trnW-CCA_p3 petG-trnW-CCA AGCGGGATTATTCGTGACTG CAAAACCCGATGTCGTAGGT 224–226 1.000 81.8
petG-trnW-CCA_p4 petG-trnW-CCA GGGATTATTCGTGACTGCGT CCCGATGTCGTAGGTTCAAA 216–218 1.000 80.9
petG-trnW-CCA_p5 petG-trnW-CCA GGGATTATTCGTGACTGCGT TCCAAAACCCGATGTCGTAG 223–225 1.000 80.8

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
Distichlis bajaensis NC_029894.1 135452 View on NCBI ↗
Distichlis spicata NC_029895.1 138504 View on NCBI ↗