Markers + reference

Poa

8 species · Poaceae · Poales

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Species 8
Genome length 135–136 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

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1109 0.0123 0.98 48.9 yes View details
psbZ-trnG-GCC LSC 287 0.0319 1.00 57.0 yes View details
trnG-GCC-trnfM-CAU LSC 448 0.0209 0.98 58.8 yes View details
trnG-UCC-trnT-GGU LSC 1234 0.0122 0.75 45.2 yes View details
trnD-GUC-psbM LSC 695 0.0125 0.99 61.1 yes View details
petN-trnC-GCA LSC 887 0.0128 1.00 58.5 yes View details
trnC-GCA-rpoB LSC 1177 0.0164 0.99 60.1 yes View details
psbE-petL LSC 1276 0.0155 1.00 69.7 yes View details
ndhF SSC 2235 0.0067 0.99 48.0 yes View details
ndhF-rpl32 SSC 882 0.0158 0.99 59.6 yes View details
rpl32-trnL-UAG SSC 749 0.0206 1.00 63.5 yes View details
ndhA SSC 2139 0.0090 0.99 56.0 yes View details
petA-psbJ LSC 846 0.0165 0.98 65.3 yes View details
rpl22-rps19 IRb 69 0.0492 0.99 63.9 yes View details
ycf3-trnS-GGA LSC 616 0.0120 1.00 63.0 yes View details
rps8-rpl14 LSC 145 0.0129 0.97 62.9 yes View details
rps19-psbA LSC 118 0.0381 0.95 61.2 no View details
ndhC-trnV-UAC LSC 850 0.0113 0.97 56.0 yes View details
trnT-UGU-trnL-UAA LSC 832 0.0119 0.99 55.1 yes View details
trnS-GCU-psbD LSC 967 0.0065 1.00 54.6 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
rps16_p1 rps16 AGGAATACTAGTGATCTTCTCCT ACCACTTTGCAATGAAAAGAGG 1168–1191 1.000 43.5
rps16_p2 rps16 AGGAATACTAGTGATCTTCTCCT CCACTTTGCAATGAAAAGAGGA 1167–1190 1.000 43.5
rps16_p3 rps16 AGGAATACTAGTGATCTTCTCCTACT ACCACTTTGCAATGAAAAGAGG 1168–1191 1.000 43.5
rps16_p4 rps16 AGGAATACTAGTGATCTTCTCC ACCACTTTGCAATGAAAAGAGG 1168–1191 1.000 43.5
rps16_p5 rps16 GGAATACTAGTGATCTTCTCCT ACCACTTTGCAATGAAAAGAGG 1167–1190 1.000 43.5
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1106–1139 1.000 80.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1093–1126 1.000 79.6
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1077–1110 1.000 79.1
trnS-GCU-psbD_p4 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC GCCGGACCATCCTACAAAAA 1157–1190 1.000 78.5
trnS-GCU-psbD_p5 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC ACAAAAACGAAACGGTCCCT 1144–1177 1.000 78.0
psbZ-trnG-GCC_p1 psbZ-trnG-GCC AGTCTTTCTCGTAGCTATTCTGA TACCATTGAACTACGCTCGC 342–359 1.000 52.2
psbZ-trnG-GCC_p2 psbZ-trnG-GCC AGTCTTTCTCGTAGCTATTCTGAA TACCATTGAACTACGCTCGC 342–359 1.000 49.4
psbZ-trnG-GCC_p3 psbZ-trnG-GCC GTCTTTCTCGTAGCTATTCTGA TACCATTGAACTACGCTCGC 341–358 1.000 48.8
psbZ-trnG-GCC_p4 psbZ-trnG-GCC AGTCTTTCTCGTAGCTATTCTG TACCATTGAACTACGCTCGC 342–359 1.000 48.7
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TCGTAGCTATTCTGAATTCTCTCA TACCATTGAACTACGCTCGC 334–351 1.000 48.4
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA CGAGGCTCATAACCTTGAGG 373–538 1.000 81.8
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA CAGTTTGGTAGCTCACGAGG 388–553 1.000 81.3
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA GAGCGGAGTAGAGCAGTTTG 401–566 1.000 80.6
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA AGAGCGGAGTAGAGCAGTTT 402–567 1.000 79.9
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU TTGCCAAGGAGAAGATACGG CGAGGCTCATAACCTTGAGG 379–544 1.000 79.7
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1066–1332 1.000 47.0
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1062–1328 1.000 46.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1063–1329 1.000 46.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1069–1335 1.000 46.3
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1068–1334 1.000 46.3
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 797–819 1.000 61.3
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG AGAATGAACAGTGCAGTAGC 829–851 1.000 59.8
trnD-GUC-psbM_p3 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 798–820 1.000 57.2
trnD-GUC-psbM_p4 trnD-GUC-psbM CGCGGGGATTGTAGTTCAA AGAATGAACAGTGCAGTAGC 811–833 1.000 55.9
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 796–818 1.000 55.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Poa alsodes NC_050407.1 136070 View on NCBI ↗
Poa nemoralis NC_036974.1 135845 View on NCBI ↗
Poa palustris NC_027484.1 135446 View on NCBI ↗
Poa pratensis NC_057962.1 135649 View on NCBI ↗
Poa saltuensis NC_050408.1 136140 View on NCBI ↗
Poa saltuensis subsp. languida MT094326.1 136230 View on NCBI ↗
Poa trivialis NC_036975.1 135208 View on NCBI ↗
Poa wolfii NC_050409.1 135921 View on NCBI ↗