Markers + reference

Rottboellia

2 species · Poaceae · Poales

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Species 2
Genome length 140–141 kb
Candidate markers 269
Primer pairs 85

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-trnfM-CAU LSC 490 0.0661 0.77 76.8 yes View details
trnG-UCC-trnM-CAU LSC 1949 0.0228 0.99 60.4 yes View details
trnY-GUA-trnD-GUC LSC 349 0.0201 1.00 58.3 yes View details
petN-trnC-GCA LSC 663 0.0217 0.90 62.5 yes View details
ycf3 LSC 2015 0.0163 0.98 59.7 yes View details
rpl32-trnL-UAG SSC 519 0.0312 0.99 62.4 yes View details
ndhA SSC 2108 0.0095 0.99 49.7 yes View details
ndhI-ndhA SSC 111 0.1308 0.96 87.0 yes View details
trnR-UCU-trnfM-CAU LSC 166 0.0482 1.00 76.5 yes View details
psbL-psbF LSC 22 0.0909 1.00 73.8 yes View details
trnT-GGU LSC 65 0.0615 1.00 73.2 yes View details
rpl22-rps19 LSC 92 0.0326 1.00 71.2 yes View details
trnV-UAC-trnM-CAU LSC 230 0.0227 0.96 69.7 yes View details
rpoA-rps11 LSC 72 0.0303 0.92 67.9 yes View details
rbcL-psaI LSC 866 0.0140 0.99 67.4 yes View details
rpl20-rps12 LSC 679 0.0177 1.00 67.3 yes View details
psbE-petL LSC 1262 0.0143 1.00 67.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA CGAGGCTCATAACCTTGAGG 460–572 1.000 82.6
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GTAGCGAGCGTAGTTCAGTG CGAGGCTCATAACCTTGAGG 499–611 1.000 82.0
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA CAGTTTGGTAGCTCACGAGG 475–587 1.000 82.0
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA CAGTTTTCGGCCCTACAGAG 505–617 1.000 81.9
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU ATGTAGCGAGCGTAGTTCAG CGAGGCTCATAACCTTGAGG 501–613 1.000 81.9
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2063–2076 1.000 43.4
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2033–2046 1.000 43.3
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GACTTCTGTCTTACCAAGGCA 2091–2104 1.000 43.0
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGACTTCTGTCTTACCAAGGC 2092–2105 1.000 43.0
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2029–2042 1.000 42.6
trnT-GGU_p1 trnT-GGU AGGCATAAGTCATCGGTTCA TCTCGCACTAAACTAAGTCA 185–187 1.000 41.7
trnT-GGU_p2 trnT-GGU TGGTAAGGCATAAGTCATCGG TCTCGCACTAAACTAAGTCA 190–192 1.000 41.7
trnT-GGU_p3 trnT-GGU GGTAAGGCATAAGTCATCGGT TCTCGCACTAAACTAAGTCA 189–191 1.000 41.7
trnT-GGU_p4 trnT-GGU GTGGTAGAGTAATGCCATGGT TCTCGCACTAAACTAAGTCA 207–209 1.000 41.5
trnT-GGU_p5 trnT-GGU AGCCCTTTTAACTCAGTGGT TCTCGCACTAAACTAAGTCA 222–224 1.000 41.4
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 473 1.000 77.0
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 440 1.000 74.6
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 439 1.000 74.5
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 472 1.000 72.9
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 441 1.000 71.3
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CTGCAAATCCTTTACCCCCA 731–940 1.000 82.2
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TGCAAATCCTTTACCCCCAG 730–939 1.000 82.2
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA ACTGCAAATCCTTTACCCCC 732–941 1.000 82.2
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA GCAAATCCTTTACCCCCAGT 729–938 1.000 82.2
petN-trnC-GCA_p5 petN-trnC-GCA GCCCAAGCGAGACTTACTAT TGCAAATCCTTTACCCCCAG 729–938 1.000 76.3
trnR-UCU-trnfM-CAU_p1 trnR-UCU-trnfM-CAU AGAAGACCTCTGTCCTATCCA TCCCCGCTAAGAAGGTAGAG 270–277 1.000 65.4
trnR-UCU-trnfM-CAU_p2 trnR-UCU-trnfM-CAU AGGTTTAGAAGACCTCTGTCCT TCCCCGCTAAGAAGGTAGAG 276–283 1.000 64.7
trnR-UCU-trnfM-CAU_p3 trnR-UCU-trnfM-CAU AGAAGACCTCTGTCCTATCCA CCAACCCCCTTTTATCCACC 293–300 1.000 64.6
trnR-UCU-trnfM-CAU_p4 trnR-UCU-trnfM-CAU AGGTTTAGAAGACCTCTGTCCT CCAACCCCCTTTTATCCACC 299–306 1.000 63.9
trnR-UCU-trnfM-CAU_p5 trnR-UCU-trnfM-CAU AGAAGACCTCTGTCCTATCCA ACCCCCTTTTATCCACCAGT 290–297 1.000 63.9

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
Rottboellia cochinchinensis NC_030615.1 140336 View on NCBI ↗
Rottboellia helferi NC_035036.1 140801 View on NCBI ↗