Markers + reference

Eremochloa

3 species · Poaceae · Poales

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Species 3
Genome length 139–139 kb
Candidate markers 265
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 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
trnK-UUU-rps16 LSC 547 0.0171 1.00 41.3 yes View details
rps16-trnQ-UUG LSC 980 0.0068 0.99 54.6 yes View details
trnG-UCC-trnT-GGU LSC 1996 0.0063 1.00 56.9 yes View details
rpoC2 LSC 4530 0.0032 1.00 42.2 yes View details
atpF LSC 1381 0.0043 1.00 51.6 yes View details
atpA LSC 1524 0.0018 1.00 46.5 yes View details
trnF-GAA-ndhJ LSC 601 0.0147 0.98 69.6 yes View details
rbcL-psaI LSC 962 0.0076 1.00 58.8 yes View details
psaI-ycf4 LSC 360 0.0074 1.00 52.7 yes View details
psaC-ndhE SSC 531 0.0118 0.96 69.0 yes View details
ndhA SSC 2119 0.0028 1.00 56.3 yes View details
trnS-GCU-psbD LSC 1024 0.0020 0.99 65.2 yes View details
psbE-petL LSC 1269 0.0063 1.00 63.2 yes View details
rpl20-rps12 LSC 694 0.0058 0.99 63.1 yes View details
rpoA LSC 1020 0.0033 1.00 60.8 yes View details
rps14-psaB LSC 142 0.0047 1.00 60.3 yes View details
ndhC-trnV-UAC LSC 943 0.0049 1.00 60.3 yes View details
ndhH SSC 1182 0.0023 1.00 60.2 yes View details
trnN-GUU-rps15 IRb 1152 0.0012 1.00 59.5 yes View details
rps15-trnN-GUU IRa 1152 0.0012 1.00 59.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TCGAGCCGTATGAGGAGAAA 967–996 1.000 78.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TTTCTCGAGCCGTATGAGGA 971–1000 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AACCTTTCCCTGCATTAGGC TCGAGCCGTATGAGGAGAAA 1192–1220 1.000 78.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AACCTTTCCCTGCATTAGGC TTTCTCGAGCCGTATGAGGA 1196–1224 1.000 77.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGGATCAGTCGTGGTCTTCT TCGAGCCGTATGAGGAGAAA 965–994 1.000 77.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1050–1057 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1061–1068 1.000 78.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1054–1061 1.000 78.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1065–1072 1.000 77.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1056–1063 1.000 76.6
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1126–1173 1.000 82.5
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1125–1172 1.000 82.2
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1122–1169 1.000 81.9
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1109–1156 1.000 81.3
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1112–1159 1.000 79.5
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2084–2116 1.000 43.1
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2054–2086 1.000 42.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2050–2082 1.000 42.2
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 2051–2083 1.000 42.2
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2086–2118 1.000 42.2
rpoC2_p1 rpoC2 GTTGGCGAAAAAGCGAAGAA CTGCCTCTTCGGGAAAATGA 881–914 1.000 79.1
rpoC2_p2 rpoC2 GTTGGCGAAAAAGCGAAGAA TCTGCCTCTTCGGGAAAATG 882–915 1.000 79.1
rpoC2_p3 rpoC2 TAACGCCAGATCGAATCGTG CTGCCTCTTCGGGAAAATGA 957–990 1.000 78.6
rpoC2_p4 rpoC2 GAGGAAGAATATCGGACCCG AGGCTCCCATATTCTTCCTCT 239 1.000 65.3
rpoC2_p5 rpoC2 GAGGAAGAATATCGGACCCG GGCTCCCATATTCTTCCTCTG 238 1.000 64.9
atpF_p1 atpF ACGAGCGAAGTAAGTGATCG AGCAAGGGAAAAATAATGCCT 1509–1510 1.000 55.7
atpF_p2 atpF ACGAGCGAAGTAAGTGATCG GAAGCAAGGGAAAAATAATGCCT 1511–1512 1.000 54.4
atpF_p3 atpF AAGGACGAGCGAAGTAAGTG AGCAAGGGAAAAATAATGCCT 1513–1514 1.000 54.3
atpF_p4 atpF ACGAGCGAAGTAAGTGATCG AAGCAAGGGAAAAATAATGCCT 1510–1511 1.000 53.6
atpF_p5 atpF CGAGCGAAGTAAGTGATCGA AGCAAGGGAAAAATAATGCCT 1508–1509 1.000 53.5

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
Eremochloa ciliaris NC_035028.1 138970 View on NCBI ↗
Eremochloa eriopoda NC_035023.1 138995 View on NCBI ↗
Eremochloa ophiuroides NC_036716.1 139061 View on NCBI ↗