Markers + reference

Muhlenbergia

3 species · Poaceae · Poales

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Species 3
Genome length 134–134 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1106 0.0018 1.00 51.4 yes View details
trnG-GCC-trnfM-CAU LSC 363 0.0037 1.00 53.8 yes View details
trnG-UCC-trnT-GGU LSC 986 0.0020 0.99 37.6 yes View details
rpoC2 LSC 4521 0.0007 1.00 41.2 yes View details
ndhC-trnV-UAC LSC 913 0.0030 0.99 62.1 yes View details
petA-psbJ LSC 936 0.0064 1.00 48.8 yes View details
rpl22 LSC 450 0.0030 1.00 31.3 yes View details
ndhF-rpl32 SSC 895 0.0037 1.00 48.6 yes View details
rpl32-trnL-UAG SSC 527 0.0164 1.00 55.2 yes View details
ccsA SSC 969 0.0014 1.00 33.8 yes View details
psbE-petL LSC 1295 0.0010 1.00 59.8 yes View details
ndhJ-ndhK LSC 114 0.0060 0.97 59.7 yes View details
trnS-GGA-rps4 LSC 261 0.0026 0.98 56.3 yes View details
trnS-UGA-psbZ LSC 353 0.0038 1.00 56.0 yes View details
trnT-UGU-trnL-UAA LSC 423 0.0000 1.00 55.8 yes View details
rps11-rpl36 LSC 175 0.0000 0.99 52.5 yes View details
psbM-petN LSC 732 0.0018 1.00 47.7 yes View details
rpl16 LSC 1412 0.0014 1.00 47.5 yes View details
atpB-rbcL LSC 802 0.0017 1.00 47.4 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_p1 trnK-UUU CAACGATTGGAAACGATTGGA CCTCCGGTGTAATTCCATCG 2719 1.000 64.6
trnK-UUU_p2 trnK-UUU CAACGATTGGAAACGATTGGA GCCTCCGGTGTAATTCCATC 2720 1.000 62.4
trnK-UUU_p3 trnK-UUU AACGATTGGAAACGATTGGA CCTCCGGTGTAATTCCATCG 2718 1.000 60.5
trnK-UUU_p4 trnK-UUU CAACGATTGGAAACGATTGG CCTCCGGTGTAATTCCATCG 2719 1.000 60.5
trnK-UUU_p5 trnK-UUU CAACGATTGGAAACGATTGGAT CCTCCGGTGTAATTCCATCG 2719 1.000 60.3
rps16_p1 rps16 AAGGGATATTAACGACCCCC TCTTGATACCACTTTGCAATGA 1199–1200 1.000 40.2
rps16_p2 rps16 AAGGGATATTAACGACCCCC ACCACTTTGCAATGAAATTAGAGG 1192–1193 1.000 40.2
rps16_p3 rps16 AAGGGATATTAACGACCCCC TCCACATTTCTCCATAGATAGCA 1281–1282 1.000 40.2
rps16_p4 rps16 AAGGGATATTAACGACCCCC TGCAATGAAATTAGAGGGATGT 1185–1186 1.000 40.2
rps16_p5 rps16 AAGGGATATTAACGACCCCC CACTTTGCAATGAAATTAGAGGGA 1190–1191 1.000 40.2
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 473 1.000 78.5
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GACCAACCATCAGGAGAAGC 475 1.000 78.1
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GTTTTCAAGACCGGGGCTAT CCAACCATCAGGAGAAGCAA 493 1.000 77.7
trnS-UGA-psbZ_p4 trnS-UGA-psbZ GTTTTCAAGACCGGGGCTAT GACCAACCATCAGGAGAAGC 495 1.000 77.3
trnS-UGA-psbZ_p5 trnS-UGA-psbZ GCTATCAACCACTCAGCCAT CCAACCATCAGGAGAAGCAA 478 1.000 76.0
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC ACCTGTTTTTGGCCCTACAG 488–491 1.000 79.7
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA ACCTGTTTTTGGCCCTACAG 528–531 1.000 79.6
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AATATATGCCGTAGCGAGCG ACCTGTTTTTGGCCCTACAG 541–544 1.000 79.5
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GACCCAGGCGGATATATCCT ACCTGTTTTTGGCCCTACAG 572–575 1.000 79.2
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT ACCTGTTTTTGGCCCTACAG 532–535 1.000 78.9
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TTGATCTTGCCGCGACATTA 1121–1130 1.000 52.4
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TTGCCGCGACATTACTCTAC 1115–1124 1.000 51.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TTGATCTTGCCGCGACATTA 1124–1133 1.000 51.4
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TTGATCTTGCCGCGACATTA 1123–1132 1.000 51.4
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGCGACATTACTCTACCAC 1112–1121 1.000 51.3
psbM-petN_p1 psbM-petN AAAACAGCCAGTCAAAACGA AGTATGGGGGAGAAGTGGAC 779–781 1.000 66.6
psbM-petN_p2 psbM-petN AAAACAGCCAGTCAAAACGA GTATGGGGGAGAAGTGGACT 778–780 1.000 66.6
psbM-petN_p3 psbM-petN AAAACAGCCAGTCAAAACGA TAGTAAGTCTCGCTTGGGCT 837–839 1.000 66.3
psbM-petN_p4 psbM-petN AAAACAGCCAGTCAAAACGA TATGGGGGAGAAGTGGACTC 777–779 1.000 66.2
psbM-petN_p5 psbM-petN AAAACAGCCAGTCAAAACGA GGGGGAGAAGTGGACTCTAG 774–776 1.000 65.8

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
Muhlenbergia huegelii NC_068117.1 134311 View on NCBI ↗
Muhlenbergia japonica NC_068118.1 134255 View on NCBI ↗
Muhlenbergia ramosa NC_068119.1 134265 View on NCBI ↗