Markers + reference

Hilaria

2 species · Poaceae · Poales

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Species 2
Genome length 135–135 kb
Candidate markers 271
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1133 0.0205 0.99 66.2 yes View details
trnM-CAU-trnE-UUC LSC 553 0.0201 0.99 57.2 yes View details
trnY-GUA-trnD-GUC LSC 321 0.0312 1.00 61.0 yes View details
psbM-petN LSC 635 0.0210 0.97 72.4 yes View details
petN-trnC-GCA LSC 941 0.0175 0.97 67.0 yes View details
trnT-UGU-trnL-UAA LSC 505 0.0270 0.95 66.4 yes View details
rbcL-psaI LSC 755 0.0212 1.00 56.8 yes View details
petG-trnW-CCA LSC 131 0.0846 0.99 77.1 yes View details
trnP-UGG-psaJ LSC 403 0.0126 0.99 55.9 yes View details
psaJ-rpl33 LSC 417 0.0240 1.00 55.8 yes View details
ndhF-rpl32 SSC 734 0.0193 0.99 58.6 yes View details
ccsA SSC 939 0.0096 1.00 50.3 yes View details
ccsA-ndhD SSC 187 0.0489 0.98 71.1 yes View details
atpA-trnR-UCU LSC 140 0.0301 0.95 68.5 yes View details
petA-psbJ LSC 908 0.0145 0.98 68.2 yes View details
rpl32-trnL-UAG SSC 508 0.0236 1.00 66.1 yes View details
atpI-atpH LSC 818 0.0135 1.00 63.9 yes View details
rpl22 LSC 450 0.0133 1.00 63.3 yes View details
atpH-atpF LSC 443 0.0137 0.99 63.2 yes View details
trnD-GUC-psbM LSC 1125 0.0149 0.95 63.1 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CAAGCAAGCCCCAATGATTG ATGTTTTGCCAGGAACCTCC 2741 0.500 56.9
trnK-UUU_p2 trnK-UUU TGCGGTCAATAAGGTAGGGA ATGTTTTGCCAGGAACCTCC 2995 0.500 56.0
trnK-UUU_p3 trnK-UUU CAATGTCAACCAAGCAAGCC ATGTTTTGCCAGGAACCTCC 2751 0.500 55.4
trnK-UUU_p4 trnK-UUU CCAATGTCAACCAAGCAAGC ATGTTTTGCCAGGAACCTCC 2752 0.500 55.4
trnK-UUU_p5 trnK-UUU AACACCAAACCATCCGATGT ATGTTTTGCCAGGAACCTCC 2968 0.500 54.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1205–1207 1.000 80.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1216–1218 1.000 78.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGCATAAAACGAAATGGGGC 1267–1269 1.000 77.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GCATAAAACGAAATGGGGCG 1266–1268 1.000 77.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1209–1211 1.000 75.9
trnM-CAU-trnE-UUC_p1 trnM-CAU-trnE-UUC TAAGTCATCGGTTCAAATCC TGTCCTGAACCACTAGACGA 604 1.000 42.3
trnM-CAU-trnE-UUC_p2 trnM-CAU-trnE-UUC TAAGTCATCGGTTCAAATCC AACCACTAGACGATAGGGGC 597 1.000 42.3
trnM-CAU-trnE-UUC_p3 trnM-CAU-trnE-UUC TAAGTCATCGGTTCAAATCC ACCACTAGACGATAGGGGC 596 1.000 42.3
trnM-CAU-trnE-UUC_p4 trnM-CAU-trnE-UUC TAAGTCATCGGTTCAAATCC GCTGCCTCCTTGAAAGAGAG 625 1.000 42.2
trnM-CAU-trnE-UUC_p5 trnM-CAU-trnE-UUC TAAGTCATCGGTTCAAATCC TAATACTCCCTACCCCCAGG 660 1.000 42.1
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GCGGTGCTCTAACCAATTGA 413 1.000 74.7
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT GCGGTGCTCTAACCAATTGA 412 1.000 74.5
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC GCGGTGCTCTAACCAATTGA 414 1.000 71.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC CTGGTTCAAATCCAGCTCGG GCGGTGCTCTAACCAATTGA 376 1.000 70.4
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GGCGGTGCTCTAACCAATT 414 1.000 70.1
trnD-GUC-psbM_p1 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TAATCGTTTTGGCTGGCTGT 1241–1292 1.000 79.2
trnD-GUC-psbM_p2 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC CGTTTTGGCTGGCTGTTTTT 1237–1288 1.000 77.2
trnD-GUC-psbM_p3 trnD-GUC-psbM AATTGGTTAGAGCACCGCC TAATCGTTTTGGCTGGCTGT 1239–1290 1.000 74.6
trnD-GUC-psbM_p4 trnD-GUC-psbM AATTGGTTAGAGCACCGCC CGTTTTGGCTGGCTGTTTTT 1235–1286 1.000 72.6
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC ATCGTTTTGGCTGGCTGTTT 1239–1290 1.000 72.3
psbM-petN_p1 psbM-petN ACAGCCAGCCAAAACGATTA AGTATGGGGGAGAAGTGGAC 681–843 1.000 81.3
psbM-petN_p2 psbM-petN ACAGCCAGCCAAAACGATTA GTATGGGGGAGAAGTGGACT 680–842 1.000 81.3
psbM-petN_p3 psbM-petN ACAGCCAGCCAAAACGATTA TAGTAAGTCTCGCTTGGGCT 739–901 1.000 80.9
psbM-petN_p4 psbM-petN ACAGCCAGCCAAAACGATTA TATGGGGGAGAAGTGGACTC 679–841 1.000 80.9
psbM-petN_p5 psbM-petN ACAGCCAGCCAAAACGATTA GGGGGAGAAGTGGACTCTAG 676–838 1.000 80.6

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
Hilaria cenchroides NC_029415.1 134824 View on NCBI ↗
Hilaria rigida NC_029896.1 135318 View on NCBI ↗