Markers + reference

Themeda

13 species · Poaceae · Poales

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Species 13
Genome length 139–140 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

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 556 0.0139 0.99 53.7 yes View details
rps16-trnQ-UUG LSC 1067 0.0069 1.00 57.5 yes View details
psbZ-trnG-GCC LSC 284 0.0062 1.00 35.4 yes View details
trnG-UCC-trnM-CAU LSC 1299 0.0075 1.00 58.2 yes View details
trnT-GGU-trnE-UUC LSC 469 0.0325 0.97 75.5 yes View details
trnD-GUC-psbM LSC 1052 0.0072 0.97 58.1 yes View details
petN-rpoB LSC 1732 0.0072 1.00 57.7 yes View details
trnT-UGU-trnL-UAA LSC 797 0.0099 1.00 59.3 yes View details
trnF-GAA-ndhJ LSC 590 0.0095 1.00 52.0 yes View details
petA-psbJ LSC 905 0.0081 1.00 61.8 yes View details
ndhF-rpl32 SSC 857 0.0081 1.00 64.9 yes View details
rpl32-trnL-UAG SSC 531 0.0113 1.00 53.5 yes View details
atpI-atpH LSC 827 0.0064 0.99 66.7 yes View details
ndhC-trnV-UAC LSC 802 0.0078 1.00 63.2 yes View details
psaA-ycf3 LSC 615 0.0090 0.98 60.9 yes View details
trnS-GCU-psbD LSC 944 0.0039 1.00 56.8 yes View details
rpl14-rpl16 LSC 112 0.0137 1.00 55.3 yes View details
ccsA-ndhD SSC 180 0.0197 1.00 55.0 yes View details
psbE-petL LSC 1263 0.0076 1.00 54.6 yes View details
petB LSC 1406 0.0032 1.00 52.7 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
trnK-UUU_p1 trnK-UUU AACTCAGATTGCTCTTTTCT CAGGAGCGTTCGGTGTAATT 2646–2655 1.000 41.6
trnK-UUU_p2 trnK-UUU AAACTCAGATTGCTCTTTTCT CAGGAGCGTTCGGTGTAATT 2647–2656 1.000 41.6
trnK-UUU_p3 trnK-UUU AACTCAGATTGCTCTTTTCT AGGAGCGTTCGGTGTAATTT 2645–2654 1.000 41.6
trnK-UUU_p4 trnK-UUU AAACTCAGATTGCTCTTTTCT AGGAGCGTTCGGTGTAATTT 2646–2655 1.000 41.6
trnK-UUU_p5 trnK-UUU AACTCAGATTGCTCTTTTCT GGAGCGTTCGGTGTAATTTC 2644–2653 1.000 41.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TCGAGCCGTATGAGGAGAAA 965–978 1.000 81.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TTTCTCGAGCCGTATGAGGA 969–982 1.000 81.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AACCTTTCCCTGCATTAGGC TCGAGCCGTATGAGGAGAAA 1194–1210 1.000 81.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AACCTTTCCCTGCATTAGGC TTTCTCGAGCCGTATGAGGA 1198–1214 1.000 81.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACCCAGGAAAGAAAGGGAGT TCGAGCCGTATGAGGAGAAA 1460–1476 1.000 80.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1114–1171 1.000 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1125–1182 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1118–1175 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1129–1186 1.000 82.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1120–1177 1.000 80.9
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1091–1139 1.000 80.7
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1090–1138 1.000 80.5
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1087–1135 1.000 80.1
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1074–1122 1.000 79.6
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1077–1125 1.000 77.8
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TCGAACCCGTATCTTCTCCT 450–451 1.000 76.3
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TCGAACCCGTATCTTCTCCT 448–449 1.000 75.9
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TTACCACTGAACTACGCTCG 415–416 1.000 74.9
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TTACCACTGAACTACGCTCG 413–414 1.000 74.5
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CCGTATCTTCTCCTTGGCAA 444–445 1.000 74.3
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TCGAACCGATGACTTCTGTC 1415–2127 1.000 51.3
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CGAACCGATGACTTCTGTCT 1414–2126 1.000 51.2
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC TCGAACCGATGACTTCTGTC 1418–2130 1.000 50.2
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT TCGAACCGATGACTTCTGTC 1417–2129 1.000 50.2
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT CGAACCGATGACTTCTGTCT 1416–2128 1.000 50.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Themeda anathera NC_059838.1 138941 View on NCBI ↗
Themeda arguens NC_035019.1 138827 View on NCBI ↗
Themeda arundinacea NC_035014.1 139742 View on NCBI ↗
Themeda avenacea NC_066807.1 139339 View on NCBI ↗
Themeda cymbaria NC_059839.1 139036 View on NCBI ↗
Themeda huttonensis NC_059840.1 139655 View on NCBI ↗
Themeda minor NC_059841.1 139649 View on NCBI ↗
Themeda mooneyi NC_059842.1 139865 View on NCBI ↗
Themeda quadrivalvis NC_035492.1 138961 View on NCBI ↗
Themeda strigosa NC_059843.1 139085 View on NCBI ↗
Themeda tremula NC_059844.1 138665 View on NCBI ↗
Themeda triandra NC_035016.1 138865 View on NCBI ↗
Themeda villosa NC_035021.1 139589 View on NCBI ↗