Markers + reference

Panicum

7 species · Poaceae · Poales

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Species 7
Genome length 134–140 kb
Candidate markers 269
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1020 0.0630 0.98 85.0 yes View details
trnG-UCC-trnM-CAU LSC 1964 0.0283 1.00 74.1 yes View details
trnY-GUA-trnD-GUC LSC 323 0.0398 1.00 80.9 yes View details
trnD-GUC-psbM LSC 1043 0.0267 1.00 73.9 yes View details
trnC-GCA-rpoB LSC 1059 0.0221 0.98 67.0 yes View details
trnR-UCU-trnfM-CAU LSC 166 0.0663 1.00 74.9 yes View details
trnF-GAA-ndhJ LSC 607 0.0352 0.95 81.4 yes View details
rpl32-trnL-UAG SSC 516 0.0386 1.00 77.8 yes View details
rpl14-rpl16 LSC 109 0.0428 1.00 79.9 yes View details
trnV-UAC-trnM-CAU LSC 203 0.0377 1.00 75.0 yes View details
trnfM-CAU-trnG-UCC LSC 94 0.0350 1.00 73.3 yes View details
rpl16-rps3 LSC 147 0.0503 1.00 72.7 yes View details
petD-rpoA LSC 215 0.0313 1.00 71.4 yes View details
psaA-ycf3 LSC 634 0.0214 1.00 71.0 yes View details
ndhF-rpl32 SSC 854 0.0254 1.00 70.6 yes View details
ccsA-ndhD SSC 208 0.0332 1.00 70.5 yes View details
psbK-psbI LSC 385 0.0221 1.00 70.1 yes View details
psbI-trnS-GCU LSC 120 0.0258 1.00 68.5 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 90 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 865–1094 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 876–1105 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 869–1098 1.000 89.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 880–1109 1.000 88.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 871–1100 1.000 87.4
psbK-psbI_p1 psbK-psbI CAAGCCGCTGTAAGTTTTCG GGATTACGTCCTGGGTCATT 499–513 1.000 77.8
psbK-psbI_p2 psbK-psbI CGTGGATGTTATGCCTGTCA GGATTACGTCCTGGGTCATT 554–568 1.000 77.4
psbK-psbI_p3 psbK-psbI AGCCGCTGTAAGTTTTCGAT GGATTACGTCCTGGGTCATT 497–511 1.000 77.4
psbK-psbI_p4 psbK-psbI AAGCCGCTGTAAGTTTTCGA GGATTACGTCCTGGGTCATT 498–512 1.000 77.2
psbK-psbI_p5 psbK-psbI ACCCGAAGCTTATGCCATTT GGATTACGTCCTGGGTCATT 584–598 1.000 76.1
psbI-trnS-GCU_p1 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG TAAAGCGGCGGATTGCTAAT 210 1.000 71.6
psbI-trnS-GCU_p2 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG CTTTCGATTTGGAACGGGGA 247 1.000 69.9
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG TTTCGATTTGGAACGGGGAG 246 1.000 69.9
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGGCGTGAGGA TAAAGCGGCGGATTGCTAAT 211 1.000 69.2
psbI-trnS-GCU_p5 psbI-trnS-GCU TAATCCTGGGCGTGAGGAG ATGGCTGAGTGGACTAAAGC 224 1.000 68.4
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG AGCCTTCCAAGCTAACGATG 184–185 1.000 83.1
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG AGCCTTCCAAGCTAACGATG 169–170 1.000 83.1
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCTAGCCTTCCAAGCTAACG 187–188 1.000 82.8
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG CCTAGCCTTCCAAGCTAACG 172–173 1.000 82.8
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCAACGTCGACTATAACCCC 205–206 1.000 81.1
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1382–2048 1.000 51.2
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1378–2044 1.000 50.5
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1379–2045 1.000 50.5
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1385–2051 1.000 50.4
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1384–2050 1.000 50.4
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 447–479 1.000 86.0
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 414–446 1.000 84.2
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 413–445 1.000 84.1
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 446–478 1.000 81.9
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 415–447 1.000 80.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Panicum capillare NC_030493.1 134520 View on NCBI ↗
Panicum coloratum MT083944.1 139132 View on NCBI ↗
Panicum hallii MT083945.1 134169 View on NCBI ↗
Panicum incomtum NC_039619.1 139999 View on NCBI ↗
Panicum lycopodioides NC_036121.1 138954 View on NCBI ↗
Panicum sumatrense NC_032378.1 139384 View on NCBI ↗
Panicum virgatum NC_015990.1 139619 View on NCBI ↗