Markers + reference

Eriochloa

3 species · Poaceae · Poales

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Species 3
Genome length 140–140 kb
Candidate markers 265
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1275 0.0188 1.00 62.8 yes View details
trnG-GCC-trnfM-CAU LSC 260 0.0256 1.00 64.7 yes View details
trnG-UCC-trnE-UUC LSC 2347 0.0184 1.00 61.2 yes View details
petN-trnC-GCA LSC 907 0.0235 1.00 71.0 yes View details
rbcL-psaI LSC 854 0.0230 1.00 60.8 yes View details
ndhF SSC 2217 0.0090 1.00 48.4 yes View details
ndhF-rpl32 SSC 838 0.0175 1.00 57.1 yes View details
rpl32-trnL-UAG SSC 551 0.0279 1.00 67.8 yes View details
ccsA SSC 975 0.0164 1.00 59.6 yes View details
petA-psbJ LSC 906 0.0119 0.99 69.4 yes View details
psaC-ndhE SSC 486 0.0194 0.99 69.4 yes View details
trnfM-CAU-trnG-UCC LSC 92 0.1014 1.00 68.5 yes View details
trnY-GUA-trnD-GUC LSC 364 0.0211 1.00 66.8 yes View details
trnS-GCU-psbD LSC 1007 0.0133 1.00 65.2 yes View details
petL-petG LSC 179 0.0187 0.99 64.6 yes View details
trnT-UGU-trnL-UAA LSC 748 0.0143 1.00 64.3 yes View details
rpl20-rps12 LSC 706 0.0080 1.00 63.9 yes View details
psbM-petN LSC 766 0.0110 0.99 63.7 yes View details
rpl36-infA LSC 100 0.0267 1.00 63.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1349–1398 1.000 81.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1360–1409 1.000 80.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1353–1402 1.000 80.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1364–1413 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1355–1404 1.000 78.3
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1132–1152 1.000 81.1
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1119–1139 1.000 80.6
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1118–1138 1.000 78.2
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1111–1131 1.000 78.0
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1105–1125 1.000 77.6
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA CGAGGCTCATAACCTTGAGG 392–509 1.000 83.2
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA CAGTTTGGTAGCTCACGAGG 407–524 1.000 82.7
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA GAGCGGAGTAGAGCAGTTTG 420–537 1.000 82.0
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA TAGAGCGGAGTAGAGCAGTT 422–539 1.000 81.5
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA AGAGCGGAGTAGAGCAGTTT 421–538 1.000 81.3
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG AGCCTTCCAAGCTAACGATG 168–176 1.000 84.0
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG AGCCTTCCAAGCTAACGATG 183–191 1.000 83.9
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG CCTAGCCTTCCAAGCTAACG 171–179 1.000 83.7
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCTAGCCTTCCAAGCTAACG 186–194 1.000 83.6
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCAACGTCGACTATAACCCC 204–212 1.000 81.9
trnG-UCC-trnE-UUC_p1 trnG-UCC-trnE-UUC ACGAATCACACTTTTACCACT GCTGCCTCCTTGAAAGAGAG 2428–2509 1.000 52.0
trnG-UCC-trnE-UUC_p2 trnG-UCC-trnE-UUC ACGAATCACACTTTTACCACT TGTCCTGAACCACTAGACGA 2407–2488 1.000 51.9
trnG-UCC-trnE-UUC_p3 trnG-UCC-trnE-UUC AGAACGAATCACACTTTTACCAC GCTGCCTCCTTGAAAGAGAG 2431–2512 1.000 50.9
trnG-UCC-trnE-UUC_p4 trnG-UCC-trnE-UUC GAACGAATCACACTTTTACCACT GCTGCCTCCTTGAAAGAGAG 2430–2511 1.000 50.9
trnG-UCC-trnE-UUC_p5 trnG-UCC-trnE-UUC GAACGAATCACACTTTTACCACT TGTCCTGAACCACTAGACGA 2409–2490 1.000 50.8
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 470–490 1.000 80.6
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 437–457 1.000 78.5
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 436–456 1.000 78.4
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 469–489 1.000 76.5
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 438–458 1.000 75.1

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
Eriochloa meyeriana NC_030624.1 139890 View on NCBI ↗
Eriochloa punctata MT083942.1 139718 View on NCBI ↗
Eriochloa villosa PQ238362.1 139777 View on NCBI ↗