Markers + reference

Temochloa

3 species · Poaceae · Poales

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Species 3
Genome length 139–140 kb
Candidate markers 259
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 399 0.0150 1.00 64.1 yes View details
trnG-UCC-trnT-GGU LSC 3410 0.0052 1.00 58.8 yes View details
rpoC2 LSC 4575 0.0044 0.98 59.2 yes View details
rbcL LSC 1434 0.0014 1.00 41.7 yes View details
rbcL-psaI LSC 1253 0.0064 0.99 62.5 yes View details
petA-psbJ LSC 984 0.0061 1.00 62.6 yes View details
trnP-GGG-psaJ LSC 390 0.0068 1.00 50.5 yes View details
infA LSC 342 0.0019 1.00 30.4 yes View details
ndhF-rpl32 SSC 769 0.0078 1.00 51.9 yes View details
infA-rps8 LSC 112 0.0417 1.00 80.1 yes View details
rpl14-rpl16 LSC 109 0.0306 1.00 72.0 yes View details
petG-trnW-CCA LSC 122 0.0492 1.00 70.5 yes View details
rps19-psbA LSC 228 0.0175 1.00 64.1 no View details
ndhH SSC 1182 0.0023 1.00 60.2 yes View details
matK LSC 1536 0.0022 1.00 60.1 yes View details
trnS-GCU-psbD LSC 983 0.0020 1.00 60.1 yes View details
petA LSC 963 0.0021 1.00 60.1 yes View details
petB LSC 1474 0.0018 1.00 60.1 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TCAGAATGGAAAACGTGAAAGT CAACACCCTGTTCTGACCAT 1699 1.000 49.9
matK_p2 matK TCAGAATGGAAAACGTGAAAGT AATGCAACACCCTGTTCTGA 1703 1.000 49.2
matK_p3 matK TCAGAATGGAAAACGTGAAAGT ATGCAACACCCTGTTCTGAC 1702 1.000 49.0
matK_p4 matK ACATTTCAGAATGGAAAACGTGA CAACACCCTGTTCTGACCAT 1704 1.000 47.9
matK_p5 matK AGGGAACATTTCAGAATGGA CAACACCCTGTTCTGACCAT 1709 1.000 47.6
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTTTTACTCCTCACGCCCAG 592 1.000 79.6
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCACGCCCAG 543 1.000 79.4
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCACGCCCAG 540 1.000 77.4
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTACTCCTCACGCCCAG 541 1.000 77.4
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTACTCCTCACGCCCAG 542 1.000 77.4
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1127–1128 1.000 78.6
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1114–1115 1.000 78.0
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1113–1114 1.000 75.6
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1106–1107 1.000 75.4
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1100–1101 1.000 75.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU TGCCCCTTTGGTCTTTTGTT CGTGAAGAGAGTTGACACACT 248 0.667 57.0
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU TTGCCCCTTTGGTCTTTTGT CGTGAAGAGAGTTGACACACT 249 0.667 57.0
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU GCTCTTATTGCCCCTTTGGT CGTGAAGAGAGTTGACACACT 256 0.667 56.8
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AACAGAAAACCCATAGCCGG CGTGAAGAGAGTTGACACACT 831–852 0.667 56.8
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU TTTTTGTTGGGCAGGCAGTA CGTGAAGAGAGTTGACACACT 778–799 0.667 56.3
rpoC2_p1 rpoC2 CTGGTCGAATTAGGGGAAGC TCGATTCAACAAGGTGCCAA 2124–2268 1.000 84.3
rpoC2_p2 rpoC2 CTGGTCGAATTAGGGGAAGC TTCGATTCAACAAGGTGCCA 2125–2269 1.000 84.3
rpoC2_p3 rpoC2 CAACCATTTCGAGCACAACC TCGATTCAACAAGGTGCCAA 2229–2373 1.000 84.3
rpoC2_p4 rpoC2 CAACCATTTCGAGCACAACC TTCGATTCAACAAGGTGCCA 2230–2374 1.000 84.3
rpoC2_p5 rpoC2 TACGCGAGGGACTTTCTTTG TCGATTCAACAAGGTGCCAA 2564–2708 1.000 84.0
rbcL_p1 rbcL AGTAGACCCTGTCGTTGTGA AGCCGAGTTTAATTGCAATCA 1608 1.000 60.1
rbcL_p2 rbcL ATCGAGTAGACCCTGTCGTT AGCCGAGTTTAATTGCAATCA 1612 1.000 59.2
rbcL_p3 rbcL TAGACCCTGTCGTTGTGAGA AGCCGAGTTTAATTGCAATCA 1606 1.000 58.0
rbcL_p4 rbcL AGTAGACCCTGTCGTTGTGA AGCCGAGTTTAATTGCAATCAA 1608 1.000 57.8
rbcL_p5 rbcL GTAGACCCTGTCGTTGTGAG AGCCGAGTTTAATTGCAATCA 1607 1.000 57.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Temochloa elegans var. elegans OQ791222.1 139428 View on NCBI ↗
Temochloa elegans var. glabra OQ791223.1 139327 View on NCBI ↗
Temochloa liliana NC_085342.1 139510 View on NCBI ↗