Markers + reference

Diheteropogon

5 species · Poaceae · Poales

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Species 5
Genome length 139–140 kb
Candidate markers 265
Primer pairs 95

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1545 0.0106 0.99 56.7 yes View details
trnG-UCC-trnT-GGU LSC 1780 0.0106 1.00 60.0 yes View details
trnT-GGU-trnE-UUC LSC 544 0.0187 1.00 60.5 yes View details
psbM-petN LSC 605 0.0160 1.00 70.5 yes View details
psaA-pafI LSC 608 0.0163 1.00 53.9 yes View details
rbcL-psaI LSC 954 0.0100 1.00 52.3 yes View details
petA-psbJ LSC 926 0.0143 1.00 65.2 yes View details
rpl16 LSC 1497 0.0089 1.00 47.0 yes View details
rpl32-trnL-UAG SSC 506 0.0318 1.00 68.9 yes View details
ndhH SSC 1182 0.0113 1.00 56.3 yes View details
trnY-GUA-trnD-GUC LSC 380 0.0123 1.00 59.4 yes View details
psbE-petL LSC 1257 0.0055 1.00 58.8 yes View details
ndhF-rpl32 SSC 880 0.0077 1.00 58.0 yes View details
rpoC2-rps2 LSC 320 0.0184 1.00 56.6 yes View details
trnS-GCU-psbD LSC 958 0.0052 1.00 56.1 yes View details
petN-trnC-GCA LSC 469 0.0111 1.00 56.1 yes View details
trnL-UAA-trnF-GAA LSC 376 0.0088 1.00 56.1 yes View details
atpI-atpH LSC 823 0.0029 1.00 54.6 yes View details
trnN-GUU-rps15 SSC 1595 0.0035 1.00 54.2 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1231–1618 1.000 84.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1242–1629 1.000 83.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1235–1622 1.000 82.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1246–1633 1.000 82.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1237–1624 1.000 81.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1088–1119 1.000 79.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1080–1111 1.000 76.6
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1074–1105 1.000 76.2
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CTTCGTAACCAGTCGTCCAT 1070–1101 1.000 76.0
trnS-GCU-psbD_p5 trnS-GCU-psbD AGTCCACTCAGCCATCTCTC ACAAAAACGAAACGGTCCCT 1069–1100 1.000 75.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1527–1895 1.000 43.4
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1529–1891 1.000 42.6
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1529–1892 1.000 42.6
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1530–1898 1.000 42.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1529–1897 1.000 42.6
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 80–666 1.000 74.3
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 80–645 1.000 74.3
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 80–629 1.000 74.3
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 80–608 1.000 74.3
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 80–634 1.000 73.5
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 80–504 1.000 81.8
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 80–471 1.000 79.4
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 80–470 1.000 79.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 80–503 1.000 77.6
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 80–472 1.000 76.1
psbM-petN_p1 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTAAGTCTCGCTTGGGCT 80–789 1.000 60.8
psbM-petN_p2 psbM-petN TGTTCATTCTAGTTCCTACTGCC GTAGTATGGGGGAGGAGTGG 80–733 1.000 59.9
psbM-petN_p3 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTATGGGGGAGGAGTGGA 80–732 1.000 59.2
psbM-petN_p4 psbM-petN GTTCATTCTAGTTCCTACTGCCT TAGTAAGTCTCGCTTGGGCT 80–788 1.000 58.7
psbM-petN_p5 psbM-petN TGTTCATTCTAGTTCCTACTGCC CGCTAGTAGTATGGGGGAGG 80–738 1.000 58.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Diheteropogon amplectens NC_087665.1 139705 View on NCBI ↗
Diheteropogon amplectens var. catangensis KU291497.1 139700 View on NCBI ↗
Diheteropogon filifolius NC_087699.1 139348 View on NCBI ↗
Diheteropogon grandiflorus NC_087700.1 138993 View on NCBI ↗
Diheteropogon hagerupii NC_087667.1 139647 View on NCBI ↗