Markers + reference

Elytrophorus

2 species · Poaceae · Poales

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Species 2
Genome length 136–136 kb
Candidate markers 265
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 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 1067 0.0057 0.99 62.5 yes View details
trnG-GCC-trnfM-CAU LSC 365 0.0137 1.00 52.7 yes View details
trnG-UCC-trnT-GGU LSC 1997 0.0051 0.99 56.3 yes View details
trnD-GUC-psbM LSC 825 0.0097 1.00 64.6 yes View details
ycf3 LSC 1984 0.0035 1.00 59.8 yes View details
trnT-UGU-trnL-UAA LSC 700 0.0098 0.88 59.4 yes View details
trnF-GAA-ndhJ LSC 480 0.0042 1.00 58.6 yes View details
ndhC-trnV-UAC LSC 912 0.0077 1.00 63.2 yes View details
petA-psbJ LSC 932 0.0086 1.00 63.8 yes View details
psbE-petL LSC 1301 0.0054 1.00 56.9 yes View details
ndhF-rpl32 SSC 857 0.0070 1.00 49.4 yes View details
ndhA SSC 2114 0.0057 1.00 60.8 yes View details
psbL-psbF LSC 22 0.0455 1.00 77.9 yes View details
rpoB-rpoC1 LSC 37 0.0270 1.00 68.0 yes View details
rps3-rpl22 LSC 57 0.0175 1.00 62.6 yes View details
trnS-GCU-psbD LSC 983 0.0041 1.00 61.4 yes View details
psbB LSC 1527 0.0046 1.00 61.3 yes View details
trnV-UAC LSC 39 0.0256 1.00 60.9 yes View details
rbcL-psaI LSC 734 0.0027 0.99 60.9 yes View details
trnR-UCU-rps14 LSC 382 0.0105 0.99 60.8 yes View details
ycf3-trnS-GGA LSC 571 0.0035 1.00 60.3 yes View details
trnC-GCA-rpoB LSC 999 0.0020 1.00 59.9 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1141–1144 1.000 79.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1152–1155 1.000 78.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1145–1148 1.000 78.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1156–1159 1.000 77.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1147–1150 1.000 76.3
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1128 1.000 78.8
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1115 1.000 78.2
trnS-GCU-psbD_p3 trnS-GCU-psbD GTCCCAAATGATCCAAGGGG GCCGGACCATCCTACAAAAA 1197 1.000 77.3
trnS-GCU-psbD_p4 trnS-GCU-psbD GTCCCAAATGATCCAAGGGG ACAAAAACGAAACGGTCCCT 1184 1.000 76.7
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1114 1.000 75.9
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC CGAGGCTCATAACCTTGAGG 443–445 1.000 78.7
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 483–485 1.000 78.5
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC CAGTTTGGTAGCTCACGAGG 458–460 1.000 78.2
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CAGTTTGGTAGCTCACGAGG 498–500 1.000 78.0
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC TACAGAGCGGAGTAGAGCAG 475–477 1.000 77.8
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2091–2117 1.000 42.3
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2061–2087 1.000 42.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2057–2083 1.000 41.4
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 2058–2084 1.000 41.4
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2093–2119 1.000 41.4
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTT 990–996 1.000 66.6
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TCATTTTGGCTGGCTGTTTT 1022–1028 1.000 65.2
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AATCATTTTGGCTGGCTGTT 992–998 1.000 64.7
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATCATTTTGGCTGGCTGTTT 991–997 1.000 64.7
trnD-GUC-psbM_p5 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTTT 990–996 1.000 64.5
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1083 1.000 77.0
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1082 1.000 77.0
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TCAAGTTCTTCTGCCAAGCC 1149 1.000 76.4
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TCCCTCATTTCCATTCCGGA 1066 1.000 76.3
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CTTCTGCCAAGCCCTGATTA 1142 1.000 76.2

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
Elytrophorus globularis NC_035527.1 136403 View on NCBI ↗
Elytrophorus spicatus NC_025233.1 136346 View on NCBI ↗