Markers + reference

Aeluropus

3 species · Poaceae · Poales

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Species 3
Genome length 135–136 kb
Candidate markers 273
Primer pairs 110

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1256 0.0106 1.00 65.9 yes View details
psbK-psbI LSC 398 0.0084 1.00 53.6 yes View details
trnT-GGU-trnE-UUC LSC 475 0.0098 1.00 62.4 yes View details
trnY-GUA-trnD-GUC LSC 341 0.0078 1.00 51.0 yes View details
trnC-GCA-rpoB LSC 1037 0.0090 1.00 54.4 yes View details
trnT-UGU-trnL-UAA LSC 814 0.0090 1.00 61.3 yes View details
ycf4-cemA LSC 377 0.0125 0.99 54.2 yes View details
trnP-UGG-psaJ LSC 386 0.0104 1.00 51.0 yes View details
ndhF-rpl32 SSC 909 0.0066 1.00 51.4 yes View details
rpl32-trnL-UAG SSC 533 0.0175 1.00 63.3 yes View details
psaC-ndhE SSC 467 0.0121 1.00 49.9 yes View details
ndhA SSC 2140 0.0056 1.00 47.3 yes View details
ccsA-ndhD SSC 193 0.0259 1.00 68.7 yes View details
psbI-trnS-GCU LSC 119 0.0280 1.00 66.6 yes View details
rps3-rpl22 LSC 62 0.0109 0.98 64.6 yes View details
ndhC-trnV-UAC LSC 921 0.0087 1.00 64.3 yes View details
psbM-petN LSC 595 0.0045 1.00 64.0 yes View details
petA-psbJ LSC 924 0.0065 1.00 63.3 yes View details
petL-petG LSC 178 0.0075 1.00 62.4 yes View details
rps2 LSC 711 0.0038 1.00 61.1 yes View details
ycf3-trnS-GGA LSC 591 0.0068 1.00 61.0 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CCAAGCAAACCCCAAGGATT GCCGGTGTAATTCCATCGAT 2721–2728 1.000 74.6
trnK-UUU_p2 trnK-UUU CCAAGCAAACCCCAAGGAT GCCGGTGTAATTCCATCGAT 2721–2728 1.000 71.3
trnK-UUU_p3 trnK-UUU CCAAGCAAACCCCAAGGATT TTCAATGTTTTGCCAGGAGC 2742–2749 1.000 69.1
trnK-UUU_p4 trnK-UUU CCAAGCAAACCCCAAGGATTA GCCGGTGTAATTCCATCGAT 2721–2728 1.000 68.1
trnK-UUU_p5 trnK-UUU AACCAAGCAAACCCCAAGG GCCGGTGTAATTCCATCGAT 2723–2730 1.000 68.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1330–1339 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1341–1350 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGCATAAAACGAAATGGGGC 1392–1401 1.000 76.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GCATAAAACGAAATGGGGCG 1391–1400 1.000 76.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1334–1343 1.000 75.0
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTTACTCCTCACGTCCAGGA 589–590 1.000 78.1
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTACTCCTCACGTCCAGGA 540–541 1.000 77.9
psbK-psbI_p3 psbK-psbI ACCCGAAGCTTATGCCATTT TTTACTCCTCACGTCCAGGA 619–620 1.000 77.1
psbK-psbI_p4 psbK-psbI TTAGCGTTTGTTTGGCAAGC TTTACTCCTCACGTCCAGGA 549–550 1.000 77.1
psbK-psbI_p5 psbK-psbI AGCCAAATTACCCGAAGCTT TTTACTCCTCACGTCCAGGA 628–629 1.000 76.5
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCTGGACGTGAGGAGTA TAAAGCGGCGGATTGCTAAT 208 1.000 77.4
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCTGGACGTGAGGAGTAA TAAAGCGGCGGATTGCTAAT 207 1.000 77.4
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCTGGACGTGAGGAGT TAAAGCGGCGGATTGCTAAT 209 1.000 77.4
psbI-trnS-GCU_p4 psbI-trnS-GCU ATCCTGGACGTGAGGAGTAA CTTTCGATTTGGAACGGGGA 244 1.000 76.0
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCTGGACGTGAGGAGTAA TTTCGATTTGGAACGGGGAG 243 1.000 76.0
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GTGGTAGAGTAATGCCACGG GCTGCCTCCTTGAAAGAGAG 577–584 1.000 78.3
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GTGGTAGAGTAATGCCACGG TGTCCTGAACCACTAGACGA 556–563 1.000 78.2
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC GTGGTAGAGTAATGCCACGG AACCACTAGACGATAGGGGC 549–556 1.000 75.8
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GTGGTAGAGTAATGCCACGG TAATACTCCCTACCCCCAGG 612–619 1.000 71.5
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC CGGTAGAGTAATGCCATGGT GCTGCCTCCTTGAAAGAGAG 643–650 1.000 71.5
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GCGGTGCTCTAACCAATTGA 466 1.000 75.9
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GCGGTGCTCTAACCAATTGA 433 1.000 73.5
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT GCGGTGCTCTAACCAATTGA 432 1.000 73.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGCGGTGCTCTAACCAATT 467 1.000 71.3
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC GCGGTGCTCTAACCAATTGA 434 1.000 70.1

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
Aeluropus lagopoides NC_042858.1 135518 View on NCBI ↗
Aeluropus littoralis NC_053922.1 135498 View on NCBI ↗
Aeluropus sinensis MW194080.1 135563 View on NCBI ↗