Markers + reference

Festuca

17 species · Poaceae · Poales

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Species 17
Genome length 133–135 kb
Candidate markers 261
Primer pairs 85

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 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 766 0.0163 0.97 61.4 yes View details
trnG-UCC-trnT-GGU LSC 661 0.0182 0.97 61.4 yes View details
psaA-ycf3 LSC 689 0.0141 0.94 59.4 yes View details
trnL-UAA-trnF-GAA LSC 341 0.0216 1.00 64.0 yes View details
trnF-GAA-ndhJ LSC 584 0.0138 0.98 66.7 yes View details
ndhC-trnV-UAC LSC 908 0.0127 0.94 64.6 yes View details
rbcL-psaI LSC 1177 0.0128 0.99 54.9 yes View details
petA-psbJ LSC 627 0.0176 0.97 57.3 yes View details
psbE-petL LSC 1168 0.0122 0.98 61.8 yes View details
trnP-UGG-psaJ LSC 337 0.0071 1.00 35.1 no View details
ndhF-rpl32 SSC 866 0.0174 0.99 68.3 yes View details
rpl32-trnL-UAG SSC 457 0.0321 0.97 69.2 yes View details
rpl22-rps19 LSC 78 0.0498 1.00 70.2 yes View details
rps19-psbA LSC 122 0.0545 1.00 69.2 no View details
trnT-UGU-trnL-UAA LSC 691 0.0137 0.99 65.1 yes View details
petG-trnW-CCA LSC 122 0.0482 1.00 65.0 no View details
trnC-GCA-rpoB LSC 1177 0.0104 0.99 64.0 yes View details
petN-trnC-GCA LSC 903 0.0132 1.00 62.5 yes View details
trnD-GUC-psbM LSC 697 0.0081 1.00 60.3 yes View details
psbK-psbI LSC 410 0.0153 0.98 60.1 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 85 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 705–859 1.000 87.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 716–870 1.000 86.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 709–863 1.000 86.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 720–874 1.000 85.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 711–865 1.000 84.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCCGTCCTGGGTCATTAGA 508–538 1.000 84.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GAATTTTTACTCCTCGCGCC 533–563 1.000 83.0
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGAATTTTTACTCCTCGCGC 534–564 1.000 83.0
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCCGTCCTGGGTCATTAGAT 507–537 1.000 83.0
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCCGTCCTGGGTCATTAGA 522–535 0.941 79.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 686–1250 1.000 49.0
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 682–1246 1.000 48.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 683–1247 1.000 48.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 689–1253 1.000 48.3
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 688–1252 1.000 48.3
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 591–818 1.000 65.5
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG AGAATGAACAGTGCAGTAGC 623–850 1.000 64.0
trnD-GUC-psbM_p3 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 592–819 1.000 61.3
trnD-GUC-psbM_p4 trnD-GUC-psbM CGCGGGGATTGTAGTTCAA AGAATGAACAGTGCAGTAGC 605–832 1.000 60.1
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 590–817 1.000 59.5
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TTTCTCGATTTTCGCTCGGA 1027–1047 1.000 80.9
petN-trnC-GCA_p2 petN-trnC-GCA CCACTCCTCCCCCATACTAC TTTCTCGATTTTCGCTCGGA 1083–1103 1.000 79.7
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TCTCGATTTTCGCTCGGATT 1025–1045 1.000 79.2
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TTCTCGATTTTCGCTCGGAT 1026–1046 1.000 79.1
petN-trnC-GCA_p5 petN-trnC-GCA TCCACTCCTCCCCCATACTA TTTCTCGATTTTCGCTCGGA 1084–1104 1.000 79.0
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG ATTCCCTCGTTTCCATTCCG 957–1266 1.000 86.5
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TGTGGACATTCCCTCGTTTC 964–1273 1.000 85.4
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 971–1280 1.000 84.3
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 972–1281 1.000 84.2
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG GGACATTCCCTCGTTTCCAT 961–1270 1.000 83.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Festuca alopecuros NC_059968.1 133855 View on NCBI ↗
Festuca alpestris PP335071.1 134200 View on NCBI ↗
Festuca brevipila MN309822.1 133331 View on NCBI ↗
Festuca halleri subsp. halleri PP335072.1 133624 View on NCBI ↗
Festuca heterophylla PP335073.1 133975 View on NCBI ↗
Festuca kryloviana PP864372.1 134020 View on NCBI ↗
Festuca norica PP335075.1 134010 View on NCBI ↗
Festuca pulchella var. jurana PP336770.1 135154 View on NCBI ↗
Festuca rubra PP335076.1 133347 View on NCBI ↗
Festuca rubra subsp. arctica PP864371.1 133791 View on NCBI ↗
Festuca rubra subsp. fallax MN309826.1 133841 View on NCBI ↗
Festuca rubra subsp. litoralis MN309823.1 133814 View on NCBI ↗
Festuca rubra subsp. rubra MN309825.1 133804 View on NCBI ↗
Festuca sinensis PP864374.1 134256 View on NCBI ↗
Festuca valesiaca PP335077.1 133341 View on NCBI ↗
Festuca varia PP335078.1 134435 View on NCBI ↗
Festuca violacea PP335074.1 134091 View on NCBI ↗