Markers + reference

Heteropogon

5 species · Poaceae · Poales

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Species 5
Genome length 135–140 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 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 1070 0.0120 0.99 59.3 yes View details
trnG-UCC-trnT-GGU LSC 1657 0.0111 1.00 57.1 yes View details
trnT-GGU-trnE-UUC LSC 531 0.0181 0.99 58.5 yes View details
trnC-GCA-rpoB LSC 1207 0.0141 1.00 57.7 yes View details
rpoC2 LSC 4515 0.0053 1.00 43.8 yes View details
trnT-UGU-trnL-UAA LSC 719 0.0184 1.00 60.3 yes View details
rbcL-psaI LSC 906 0.0112 1.00 58.9 yes View details
petA-psbJ LSC 903 0.0158 1.00 63.5 yes View details
rpl16 LSC 1492 0.0102 1.00 56.2 yes View details
ndhF-rpl32 SSC 869 0.0151 0.98 62.0 yes View details
rpl32-trnL-UAG SSC 531 0.0298 1.00 65.0 yes View details
trnF-GAA-ndhJ LSC 593 0.0150 0.99 72.1 yes View details
atpF-atpA LSC 91 0.0220 0.99 67.2 yes View details
rpl16-rps3 LSC 144 0.0368 1.00 65.6 yes View details
ndhC-trnV-UAC LSC 909 0.0058 1.00 65.2 yes View details
ccsA-ndhD SSC 180 0.0267 1.00 65.1 yes View details
trnL-UAA-trnF-GAA LSC 374 0.0166 0.95 64.7 yes View details
psbM-petN LSC 623 0.0123 0.97 64.2 yes View details
trnD-GUC-psbM LSC 1065 0.0101 0.99 61.8 yes View details
CD878_pgr008-trnI-GAU IRb 303 0.0233 1.00 61.3 yes View details
trnI-GAU-CD878_pgr001 IRa 303 0.0233 1.00 61.3 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 105 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 1144–1618 1.000 81.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1148–1622 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1150–1624 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACTCGGAGGTTCGAATCCTT 1149–1623 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGTTACTC 1165–1639 1.000 78.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU TTTCCACCGAGCTGAAACAA TCACTAGACGATAGCACCGT 879–2990 1.000 85.4
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU TTTTGCTTCGCGACTACGTA TCACTAGACGATAGCACCGT 2514–2839 1.000 85.2
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU TTTTGCTTCGCGACTACGTA GCATCGACCCAGGAAGAATT 2659–2984 1.000 85.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU TTTCCACCGAGCTGAAACAA GCATCGACCCAGGAAGAATT 1024–2872 0.600 65.4
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT CACTCTGTGCTTCCTTCGTT 2667–2673 0.400 54.8
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 564–621 1.000 73.8
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 543–600 1.000 73.8
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 569–626 1.000 73.0
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GGTAAGGCATAAGTCATCGGT GCTGCCTCCTTGAAAGAGAG 568–625 1.000 73.0
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG TGTCCTGAACCACTAGACGA 548–605 1.000 73.0
trnD-GUC-psbM_p1 trnD-GUC-psbM AATAGGCATGCCATACACCC GGCAGTAGGAACTAGAATGAACA 1200–1232 1.000 56.2
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG GGCAGTAGGAACTAGAATGAACA 1166–1198 1.000 54.8
trnD-GUC-psbM_p3 trnD-GUC-psbM AATAGGCATGCCATACACCC AGGCAGTAGGAACTAGAATGAAC 1201–1233 1.000 54.1
trnD-GUC-psbM_p4 trnD-GUC-psbM AATAGGCATGCCATACACCC AGGCAGTAGGAACTAGAATGA 1201–1233 1.000 52.9
trnD-GUC-psbM_p5 trnD-GUC-psbM AATAGGCATGCCATACACCC TGCGAGAATATTGACTTCCA 1161–1193 1.000 52.8
psbM-petN_p1 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTAAGTCTCGCTTGGGCT 757–777 1.000 57.9
psbM-petN_p2 psbM-petN TGTTCATTCTAGTTCCTACTGCC GTAGTATGGGGGAGGAGTGG 701–721 1.000 57.1
psbM-petN_p3 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTATGGGGGAGGAGTGGA 700–720 1.000 56.4
psbM-petN_p4 psbM-petN GTTCATTCTAGTTCCTACTGCCT TAGTAAGTCTCGCTTGGGCT 756–776 1.000 55.8
psbM-petN_p5 psbM-petN TGTTCATTCTAGTTCCTACTGCC CGCTAGTAGTATGGGGGAGG 706–726 1.000 55.7
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCCTCATTTCCATTCCGGA 1266–1336 1.000 65.4
trnC-GCA-rpoB_p2 trnC-GCA-rpoB CTGGGGGTAAAGGATTTGCA CCCTCATTTCCATTCCGGA 1274–1344 1.000 64.1
trnC-GCA-rpoB_p3 trnC-GCA-rpoB TGGGGGTAAAGGATTTGCAG CCCTCATTTCCATTCCGGA 1273–1343 1.000 64.1
trnC-GCA-rpoB_p4 trnC-GCA-rpoB ACTGGGGGTAAAGGATTTGC CCCTCATTTCCATTCCGGA 1275–1345 1.000 64.1
trnC-GCA-rpoB_p5 trnC-GCA-rpoB GGGGGTAAAGGATTTGCAGT CCCTCATTTCCATTCCGGA 1272–1342 1.000 64.1

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
Heteropogon contortus NC_035027.1 134982 View on NCBI ↗
Heteropogon fischerianus NC_059828.1 135014 View on NCBI ↗
Heteropogon melanocarpus NC_059829.1 139830 View on NCBI ↗
Heteropogon ritchiei NC_059830.1 139424 View on NCBI ↗
Heteropogon triticeus NC_035025.1 140120 View on NCBI ↗