Markers + reference

Tripogon

2 species · Poaceae · Poales

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Species 2
Genome length 134–134 kb
Candidate markers 268
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 40.0 yes View details
atpA LSC 1524 0.0000 1.00 40.0 yes View details
trnR-UCU-rps14 LSC 379 0.0026 1.00 55.7 yes View details
trnP-UGG-psaJ LSC 369 0.0027 1.00 55.5 yes View details
rpl16 LSC 1498 0.0007 1.00 59.1 yes View details
ndhF SSC 2217 0.0005 1.00 57.5 yes View details
rpl32-trnL-UAG SSC 519 0.0019 1.00 58.2 yes View details
ndhF-rpl32 SSC 905 0.0000 1.00 58.9 yes View details
matK-trnK-UUU LSC 602 0.0000 1.00 40.0 yes View details
rps16 LSC 1002 0.0000 1.00 40.0 yes View details
rps16-trnQ-UUG LSC 753 0.0000 1.00 40.0 yes View details
trnS-GCU-psbD LSC 951 0.0000 1.00 40.0 yes View details
psbD LSC 1062 0.0000 1.00 40.0 yes View details
psbC LSC 1422 0.0000 1.00 40.0 yes View details
trnG-UCC-trnT-GGU LSC 1033 0.0000 1.00 40.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGGTATTTCTGGCTTTCCT GTATGCTTGGGAGTCCTTGC 1162 1.000 62.3
psbA_p2 psbA TGGGTATTTCTGGCTTTCCT TGGGAGTCCTTGCAATTTGA 1155 1.000 61.8
psbA_p3 psbA TGGGTATTTCTGGCTTTCCT GCTTGGGAGTCCTTGCAATT 1158 1.000 61.3
psbA_p4 psbA TGGGTATTTCTGGCTTTCCT TGTATGCTTGGGAGTCCTTG 1163 1.000 60.9
psbA_p5 psbA TGGGTATTTCTGGCTTTCCTT GTATGCTTGGGAGTCCTTGC 1162 1.000 60.5
matK-trnK-UUU_p1 matK-trnK-UUU ACCCTTTGAATTTTGCCATTTGT CCCGGTGTAATTCCATCGAT 775 1.000 50.0
matK-trnK-UUU_p2 matK-trnK-UUU ACCCTTTGAATTTTGCCATTTGT ATGTTTTCTCAGGAACCCCC 792 1.000 49.5
matK-trnK-UUU_p3 matK-trnK-UUU ACCCTTTGAATTTTGCCATTTG CCCGGTGTAATTCCATCGAT 775 1.000 48.0
matK-trnK-UUU_p4 matK-trnK-UUU CCCTTTGAATTTTGCCATTTGT CCCGGTGTAATTCCATCGAT 774 1.000 48.0
matK-trnK-UUU_p5 matK-trnK-UUU ACGAAGTATTGTTGACGAGA CCCGGTGTAATTCCATCGAT 812 1.000 47.6
rps16_p1 rps16 TTGTTGGATTGGCACCACAT TGGATCAATTCTCGATACCACT 1166–1167 1.000 51.3
rps16_p2 rps16 GCACCACATAAATGCAGCAA TGGATCAATTCTCGATACCACT 1155–1156 1.000 50.7
rps16_p3 rps16 TTTGTTGGATTGGCACCACA TGGATCAATTCTCGATACCACT 1167–1168 1.000 49.5
rps16_p4 rps16 TGTTGGATTGGCACCACATA TGGATCAATTCTCGATACCACT 1165–1166 1.000 48.9
rps16_p5 rps16 TTGTTGGATTGGCACCACAT TGGATCAATTCTCGATACCACTT 1166–1167 1.000 48.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCGCAGAAAACGAAATGGG 890 1.000 78.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 826 1.000 78.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GTCGCAGAAAACGAAATGGG 901 1.000 76.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 837 1.000 76.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 830 1.000 73.5
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1096 1.000 78.3
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1083 1.000 77.7
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1082 1.000 75.4
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1075 1.000 75.2
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1069 1.000 74.8
psbD_p1 psbD TGCTCGGAAATGGTTGAAGT GTCACGACCAGCTAAAACGA 1130 1.000 76.0
psbD_p2 psbD TGCTCGGAAATGGTTGAAGT TCACGACCAGCTAAAACGAA 1129 1.000 73.7
psbD_p3 psbD GTGCTCGGAAATGGTTGAAG GTCACGACCAGCTAAAACGA 1131 1.000 73.2
psbD_p4 psbD TATGAGGTGCTCGGAAATGG GTCACGACCAGCTAAAACGA 1137 1.000 73.2
psbD_p5 psbD GGTGCTCGGAAATGGTTGAA GTCACGACCAGCTAAAACGA 1132 1.000 72.1

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
Tripogon bromoides MW194093.1 133744 View on NCBI ↗
Tripogon chinensis MW194094.1 133744 View on NCBI ↗