Markers + reference

Taeniatherum

2 species · Poaceae · Poales

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Species 2
Genome length 137–137 kb
Candidate markers 267
Primer pairs 85

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 11 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-psaI LSC 1668 0.0012 1.00 59.1 yes View details
trnI-CAU-trnL-CAA IRb 2384 0.0004 1.00 57.4 yes View details
ndhB-rps7 IRb 299 0.0067 1.00 56.3 yes View details
rps7 IRb 471 0.0000 1.00 33.6 no View details
trnN-GUU-rps15 IRb 1531 0.0013 1.00 59.4 yes View details
rps15-trnN-GUU IRa 1531 0.0013 1.00 59.4 yes View details
rps7 IRa 471 0.0000 1.00 33.6 yes View details
trnL-CAA-trnI-CAU IRa 2384 0.0004 1.00 57.4 yes View details
infA-rps8 LSC 80 0.0125 1.00 59.7 yes View details
rpl32-trnL-UAG SSC 710 0.0014 1.00 59.7 yes View details
psaA-ycf3 LSC 675 0.0015 1.00 59.6 yes View details
rps16-trnQ-UUG LSC 749 0.0013 1.00 59.5 yes View details
psbD LSC 1062 0.0009 1.00 59.3 yes View details
petA-psbJ LSC 826 0.0000 0.99 59.3 yes View details
psbE-petL LSC 1172 0.0009 1.00 59.2 yes View details
ndhH SSC 1182 0.0008 1.00 59.2 yes View details
rrn16 IRb 1492 0.0007 1.00 59.1 yes View details
rrn16 IRa 1492 0.0007 1.00 59.1 yes View details
ndhH IRb 213 0.0000 1.00 33.8 no 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 822 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 833 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGTGTCGCATAAAACCCGAA 891 1.000 77.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 826 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC AGTGTCGCATAAAACCCGAA 902 1.000 77.1
psbD_p1 psbD AGTGATATGAGGTGCTCGGA GTCACGACCAGCTAAAACGA 1142 1.000 77.7
psbD_p2 psbD TGCTCGGAAATGGTTGAAGT GTCACGACCAGCTAAAACGA 1130 1.000 76.1
psbD_p3 psbD AGTGATATGAGGTGCTCGGA TCACGACCAGCTAAAACGAA 1141 1.000 75.4
psbD_p4 psbD TGCTCGGAAATGGTTGAAGT TCACGACCAGCTAAAACGAA 1129 1.000 73.8
psbD_p5 psbD GTGCTCGGAAATGGTTGAAG GTCACGACCAGCTAAAACGA 1131 1.000 73.3
psaA-ycf3_p1 psaA-ycf3 GTCTGGCCCATTCCTCAAAA TATAGCGCTTACTCCGGGAA 836 1.000 79.4
psaA-ycf3_p2 psaA-ycf3 GTCTGGCCCATTCCTCAAAA GCGCTTACTCCGGGAAATTA 832 1.000 79.0
psaA-ycf3_p3 psaA-ycf3 CTGGCCCATTCCTCAAAAGA TATAGCGCTTACTCCGGGAA 834 1.000 78.2
psaA-ycf3_p4 psaA-ycf3 TCTGGCCCATTCCTCAAAAG TATAGCGCTTACTCCGGGAA 835 1.000 78.2
psaA-ycf3_p5 psaA-ycf3 CTGGCCCATTCCTCAAAAGA GCGCTTACTCCGGGAAATTA 830 1.000 77.9
rbcL-psaI_p1 rbcL-psaI CGCAGCTTGTGAAGTATGGA GTCATTGCAATTGCCGGAAA 1803 1.000 77.3
rbcL-psaI_p2 rbcL-psaI AGTTCGAGCCGGTAGATACT GTCATTGCAATTGCCGGAAA 1768 1.000 76.7
rbcL-psaI_p3 rbcL-psaI GGCGATCAAATTCGAGTTCG GTCATTGCAATTGCCGGAAA 1782 1.000 76.6
rbcL-psaI_p4 rbcL-psaI TGGAAGGCGATCAAATTCGA GTCATTGCAATTGCCGGAAA 1787 1.000 76.3
rbcL-psaI_p5 rbcL-psaI AGCTTGCAAATGGAGTCCTG GTCATTGCAATTGCCGGAAA 1830 1.000 75.8
petA-psbJ_p1 petA-psbJ ATCCATTACGTGTCCAAGGC GCTGGTATTGCTGTGATTGG 1015–1020 1.000 73.2
petA-psbJ_p2 petA-psbJ GGCCTTTTGTTCTTCTTCGC GCTGGTATTGCTGTGATTGG 998–1003 1.000 73.1
petA-psbJ_p3 petA-psbJ CATTACGTGTCCAAGGCCTT GCTGGTATTGCTGTGATTGG 1012–1017 1.000 72.1
petA-psbJ_p4 petA-psbJ ATCCATTACGTGTCCAAGGC ACTGTAGCTGGTATTGCTGTG 1021–1026 1.000 71.9
petA-psbJ_p5 petA-psbJ GGCCTTTTGTTCTTCTTCGC ACTGTAGCTGGTATTGCTGTG 1004–1009 1.000 71.8
psbE-petL_p1 psbE-petL TGACAAATAACCAACCCGCA AGGCGTATCTTGTTCAAGCC 1376 1.000 77.8
psbE-petL_p2 psbE-petL CAACCCGCAATGAATAGGGA AGGCGTATCTTGTTCAAGCC 1365 1.000 77.6
psbE-petL_p3 psbE-petL ACCAACCCGCAATGAATAGG AGGCGTATCTTGTTCAAGCC 1367 1.000 76.1
psbE-petL_p4 psbE-petL TGACAAATAACCAACCCGCA GGCGTATCTTGTTCAAGCCA 1375 1.000 75.5
psbE-petL_p5 psbE-petL CAACCCGCAATGAATAGGGA GGCGTATCTTGTTCAAGCCA 1364 1.000 75.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Taeniatherum caput-medusae NC_037160.1 136827 View on NCBI ↗
Taeniatherum caput-medusae subsp. caput-medusae MH285856.1 136861 View on NCBI ↗