Markers + reference

Oldeania

4 species · Poaceae · Poales

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Species 4
Genome length 139–140 kb
Candidate markers 264
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psbD LSC 980 0.0073 1.00 64.5 yes View details
trnfM-CAU-trnT-GGU LSC 2804 0.0040 1.00 47.0 yes View details
ndhC-trnV-UAC LSC 752 0.0084 1.00 51.8 yes View details
rbcL-psaI LSC 1286 0.0074 1.00 64.4 yes View details
ycf4-cemA LSC 416 0.0149 0.97 67.8 yes View details
petA-psbJ LSC 991 0.0051 0.99 59.5 yes View details
rpl16 LSC 1502 0.0055 1.00 50.3 yes View details
rpl32-trnL-UAG SSC 710 0.0085 1.00 56.0 yes View details
ndhI SSC 543 0.0028 1.00 36.3 yes View details
psbM-petN LSC 794 0.0069 0.98 65.7 yes View details
psbT-psbN LSC 48 0.0521 1.00 63.8 yes View details
atpB-rbcL LSC 779 0.0051 1.00 62.2 yes View details
ndhF-rpl32 SSC 879 0.0034 1.00 61.3 yes View details
trnP-GGG-psaJ LSC 425 0.0086 0.94 60.8 yes View details
rps19-psbA LSC 127 0.0210 1.00 60.2 no View details
ndhA SSC 2115 0.0042 1.00 60.1 yes View details
rpl22-rps19 IRb 64 0.0234 1.00 59.5 yes View details
ycf3-trnS-GGA LSC 591 0.0042 1.00 58.6 yes View details
psaA LSC 2253 0.0011 1.00 58.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GACTCCCAAGCACACGTATT CGTGCGGTGTAATTCCATTG 2835–2892 1.000 78.4
trnK-UUU_p2 trnK-UUU GCTTGTACTTTCGCGTCTCT CGTGCGGTGTAATTCCATTG 2901–2958 1.000 76.8
trnK-UUU_p3 trnK-UUU CACCGAACCATCCGATGTAA CGTGCGGTGTAATTCCATTG 2968–2997 0.500 56.6
trnK-UUU_p4 trnK-UUU TGCGGTCAATAAGGTAGGGA CGTGCGGTGTAATTCCATTG 2997 0.250 47.6
trnK-UUU_p5 trnK-UUU AAAACACCGAACCATCCGAT CGTGCGGTGTAATTCCATTG 2972 0.250 47.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1125–1145 1.000 79.7
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1112–1132 1.000 79.2
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1111–1131 1.000 76.8
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1104–1124 1.000 76.6
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1098–1118 1.000 76.2
trnfM-CAU-trnT-GGU_p1 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG TCGAACCGATGACTTACGTC 2964–2976 0.750 66.4
trnfM-CAU-trnT-GGU_p2 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG CGAACCGATGACTTACGTCT 2963–2975 0.750 66.3
trnfM-CAU-trnT-GGU_p3 trnfM-CAU-trnT-GGU CCTCGTGAGCTACCAAACTG TCGAACCGATGACTTACGTC 2949–2961 0.750 66.0
trnfM-CAU-trnT-GGU_p4 trnfM-CAU-trnT-GGU CCTCGTGAGCTACCAAACTG CGAACCGATGACTTACGTCT 2948–2960 0.750 65.9
trnfM-CAU-trnT-GGU_p5 trnfM-CAU-trnT-GGU CAAGGTTATGAGCCTCGTGA TCGAACCGATGACTTACGTC 2961–2973 0.750 62.9
psbM-petN_p1 psbM-petN TGGAAGTCAATATTCTCGCA TAGTAAGTCTCGCTTGGGCT 963–981 1.000 52.9
psbM-petN_p2 psbM-petN TGGAAGTCAATATTCTCGCA GTAGTATGGGGGAGGAGTGG 907–925 1.000 52.0
psbM-petN_p3 psbM-petN TGGAAGTCAATATTCTCGCA TAGTATGGGGGAGGAGTGGA 906–924 1.000 51.3
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT TAGTAAGTCTCGCTTGGGCT 938–956 1.000 51.1
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTTATTCT GTAGTATGGGGGAGGAGTGG 882–900 1.000 50.2
psaA_p1 psaA AGCTAAGCCTTGGCTAAACC TTGGCGGGTCTCTTTGTATG 2362 1.000 78.3
psaA_p2 psaA GCTAAGCCTTGGCTAAACCT TTGGCGGGTCTCTTTGTATG 2361 1.000 78.3
psaA_p3 psaA AGCTAAGCCTTGGCTAAACC GTTGGCGGGTCTCTTTGTAT 2363 1.000 78.3
psaA_p4 psaA GCTAAGCCTTGGCTAAACCT GTTGGCGGGTCTCTTTGTAT 2362 1.000 78.3
psaA_p5 psaA AATACGACGAGTAGTGGGGT TTGGCGGGTCTCTTTGTATG 2386 1.000 78.2
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTTTTCCCCTGAGGTTGTCG ACGGAAAGAGAGGGATTCGA 778 1.000 79.1
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTTTCCCCTGAGGTTGTCG TTCCAATGCTACGCCTTGAA 728 1.000 78.8
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTTTTCCCCTGAGGTTGTCG AGTTCCAATGCTACGCCTTG 730 1.000 76.0
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTTTCCCCTGAGGTTGTCG CAGTTCCAATGCTACGCCTT 731 1.000 76.0
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTTTTCCCCTGAGGTTGTCG TCCAATGCTACGCCTTGAAC 727 1.000 75.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Oldeania alpina NC_036813.1 139599 View on NCBI ↗
Oldeania cf. madagascariensis PFM-2018 NC_036823.1 139649 View on NCBI ↗
Oldeania ibityensis NC_036818.1 139130 View on NCBI ↗
Oldeania itremoensis NC_036821.1 139751 View on NCBI ↗