Markers + reference

Eulalia

2 species · Poaceae · Poales

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Species 2
Genome length 140–141 kb
Candidate markers 269
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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnM-CAU LSC 1754 0.0229 0.97 65.6 yes View details
trnT-GGU-trnE-UUC LSC 469 0.0527 0.97 74.3 yes View details
trnD-GUC-psbM LSC 1055 0.0156 0.79 60.8 yes View details
petN-trnC-GCA LSC 877 0.0222 0.97 64.6 yes View details
ndhC-trnV-UAC LSC 911 0.0144 0.99 58.9 yes View details
atpB-rbcL LSC 776 0.0184 0.98 65.4 yes View details
petL-petG LSC 167 0.0180 1.00 58.9 yes View details
ndhF-rpl32 SSC 848 0.0178 0.99 67.3 yes View details
rpl32-trnL-UAG SSC 521 0.0272 0.99 59.8 yes View details
ndhJ-ndhK LSC 98 0.0510 1.00 81.4 yes View details
petG-trnW-CCA LSC 116 0.0776 1.00 79.1 yes View details
ndhG-ndhI SSC 190 0.0273 0.96 71.7 yes View details
trnV-UAC-trnM-CAU LSC 224 0.0391 0.80 71.5 yes View details
rpl22-rps19 LSC 92 0.0326 1.00 69.4 yes View details
trnS-GCU-psbD LSC 1027 0.0144 0.95 68.6 yes View details
trnT-UGU-trnL LSC 787 0.0146 0.96 66.5 yes View details
trnK-UUU-rps16 LSC 549 0.0146 1.00 65.8 yes View details
trnF-GAA-ndhJ LSC 662 0.0122 0.87 64.7 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACA 681–688 1.000 69.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC GGTGCTCAACCTACAAGAACA 686–693 1.000 67.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAAC 681–688 1.000 65.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACA 680–687 1.000 65.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTACCAAGAGTCTGGACGA GGTGCTCAACCTACAAGAACA 737–744 1.000 64.6
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1126–1176 1.000 83.5
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1125–1175 1.000 83.2
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1122–1172 1.000 82.9
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1109–1159 1.000 82.4
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1112–1162 1.000 80.6
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 1868–2925 1.000 43.2
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1838–2925 1.000 43.0
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GACTTCTGTCTTACCAAGGCA 1896–2927 1.000 42.7
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1834–2927 1.000 42.3
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1835–2927 1.000 42.3
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AAAATGGAACTTCCGGGCTT TTGAACTACAATCCCTGCGG 1597–2927 1.000 82.2
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AAATGGAACTTCCGGGCTTT TTGAACTACAATCCCTGCGG 1596–2927 1.000 82.2
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AAAAATGGAACTTCCGGGCT GCATCGACCCAGGAAGAATT 1149–2926 1.000 82.1
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AAAATGGAACTTCCGGGCTT GCATCGACCCAGGAAGAATT 1148–2926 1.000 82.1
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC AAATGGAACTTCCGGGCTTT GCATCGACCCAGGAAGAATT 1147–2926 1.000 82.1
trnD-GUC-psbM_p1 trnD-GUC-psbM AATAGGCATGCCATACACCC GGCAGTAGGAACTAGAATGAACA 1213–2930 1.000 57.5
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG GGCAGTAGGAACTAGAATGAACA 1179–2928 1.000 56.0
trnD-GUC-psbM_p3 trnD-GUC-psbM AATAGGCATGCCATACACCC AGGCAGTAGGAACTAGAATGAAC 1214–2930 1.000 55.4
trnD-GUC-psbM_p4 trnD-GUC-psbM AATAGGCATGCCATACACCC AGGCAGTAGGAACTAGAATGA 1214–2928 1.000 54.1
trnD-GUC-psbM_p5 trnD-GUC-psbM AATAGGCATGCCATACACCC TGCGAGAATATTGACTTCCA 1174–2927 1.000 54.0
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CTGCAAATCCTTTACCCCCA 945–2927 1.000 78.7
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TGCAAATCCTTTACCCCCAG 944–2927 1.000 78.7
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA ACTGCAAATCCTTTACCCCC 946–2927 1.000 78.7
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA GCAAATCCTTTACCCCCAGT 943–2926 1.000 78.7
petN-trnC-GCA_p5 petN-trnC-GCA GCCCAAGCGAGACTTACTAT TGCAAATCCTTTACCCCCAG 943–2926 1.000 72.8

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
Eulalia aurea (in: monocots) NC_030503.1 140220 View on NCBI ↗
Eulalia siamensis NC_035031.1 140642 View on NCBI ↗