Markers + reference

Elymandra

3 species · Poaceae · Poales

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Species 3
Genome length 140–140 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnT-GGU LSC 2011 0.0072 0.97 53.6 yes View details
trnT-GGU-trnE-UUC LSC 534 0.0361 0.99 81.2 yes View details
psbM-petN LSC 616 0.0101 0.96 54.2 yes View details
trnC-GCA-rpoB LSC 1206 0.0077 1.00 56.4 yes View details
rpoC2 LSC 4551 0.0031 1.00 42.8 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0133 0.99 63.2 yes View details
ndhC-trnV-UAC LSC 937 0.0114 1.00 66.6 yes View details
petA-psbJ LSC 899 0.0115 1.00 58.6 yes View details
psbE-petL LSC 1289 0.0042 0.99 58.4 yes View details
rpl33-rps18 LSC 291 0.0162 0.99 50.2 yes View details
rpl32-trnL-UAG SSC 561 0.0125 0.95 59.4 yes View details
ccsA SSC 966 0.0069 1.00 49.5 yes View details
petL-petG LSC 171 0.0390 1.00 79.4 yes View details
psbF-psbE LSC 10 0.0667 1.00 75.0 yes View details
rps3-rpl22 LSC 63 0.0212 1.00 71.4 yes View details
trnG-GCC-trnfM-CAU LSC 137 0.0292 1.00 70.9 yes View details
trnR-UCU-rps14 LSC 391 0.0170 1.00 66.7 yes View details
psaC-ndhE SSC 453 0.0118 1.00 63.2 yes View details
rpl20-rps12 LSC 689 0.0068 1.00 63.1 yes View details
trnS-GCU-psbD LSC 947 0.0050 0.99 62.8 yes View details
rpl22-rps19 LSC 87 0.0077 1.00 62.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1096–1148 1.000 80.0
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1095–1147 1.000 79.7
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1092–1144 1.000 79.4
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1079–1131 1.000 78.8
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1082–1134 1.000 77.0
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AATATAGGCCGTAGCAAGCG CGAGGCTCATAACCTTGAGG 287–350 1.000 79.0
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU AATATAGGCCGTAGCAAGCG CAGTTTTCGGCCCTACAGAG 332–395 1.000 78.5
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AATATAGGCCGTAGCAAGCG CAGTTTGGTAGCTCACGAGG 302–365 1.000 78.5
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AATATAGGCCGTAGCAAGCG CTACAGAGCGGAGTAGAGCA 320–383 1.000 78.1
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU AATATAGGCCGTAGCAAGCG TACAGAGCGGAGTAGAGCAG 319–382 1.000 78.1
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CTTCTGTCTTACCAAGGCCA 2111–2158 1.000 47.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACTTCTGTCTTACCAAGGCC 2112–2159 1.000 47.7
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CTTCTGTCTTACCAAGGCCA 2114–2161 1.000 46.6
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CTTCTGTCTTACCAAGGCCA 2113–2160 1.000 46.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACTTCTGTCTTACCAAGGCC 2114–2161 1.000 46.6
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 617–625 1.000 72.5
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 596–604 1.000 72.5
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 633–641 1.000 72.4
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 654–662 1.000 72.3
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 622–630 1.000 71.6
psbM-petN_p1 psbM-petN CTTTAGACCCCCAAAAGCGT GAAAGATAGAAAGCGGGGCA 1752–1790 1.000 81.2
psbM-petN_p2 psbM-petN CTTTAGACCCCCAAAAGCGT AAAGATAGAAAGCGGGGCAG 1751–1789 1.000 81.2
psbM-petN_p3 psbM-petN CTTTAGACCCCCAAAAGCGT TCTCTATTCCCGCGTCTTCT 1597–1635 1.000 81.2
psbM-petN_p4 psbM-petN CTTTAGACCCCCAAAAGCGT TCTCTCTATTCCCGCGTCTT 1599–1637 1.000 81.2
psbM-petN_p5 psbM-petN CTTTAGACCCCCAAAAGCGT GCAGCAGTAGGGTTTAGGTC 1752–1773 0.667 67.6
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1286–1309 1.000 78.6
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1285–1308 1.000 78.6
trnC-GCA-rpoB_p3 trnC-GCA-rpoB GATTTTTGATCAGGCGGCAC CCGGGTATTGTGGACATTCC 1325–1348 1.000 78.5
trnC-GCA-rpoB_p4 trnC-GCA-rpoB GATTTTTGATCAGGCGGCAC CGGGTATTGTGGACATTCCC 1324–1347 1.000 78.5
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TCCCTCATTTCCATTCCGGA 1269–1292 1.000 78.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Elymandra androphila MH181166.1 139731 View on NCBI ↗
Elymandra archaelymandra NC_087668.1 140048 View on NCBI ↗
Elymandra subulata MH181214.1 139800 View on NCBI ↗