Markers + reference

Gigantochloa

6 species · Poaceae · Poales

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Species 6
Genome length 139–140 kb
Candidate markers 263
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1056 0.0018 1.00 50.2 yes View details
psbZ-trnfM-CAU LSC 791 0.0019 1.00 44.6 yes View details
trnG-UCC-trnT-GGU LSC 2033 0.0042 1.00 52.3 yes View details
petN-trnC-GCA LSC 900 0.0021 1.00 44.9 yes View details
rpoC2 LSC 4527 0.0007 1.00 24.2 yes View details
rbcL-psaI LSC 1247 0.0021 1.00 40.4 yes View details
rpl16 LSC 1509 0.0018 1.00 44.6 yes View details
rpl32-trnL-UAG SSC 718 0.0023 1.00 34.5 yes View details
rps19-psbA LSC 140 0.0095 1.00 48.7 no View details
rps3 LSC 720 0.0009 1.00 47.0 yes View details
trnS-GCU-psbD LSC 982 0.0003 1.00 46.7 yes View details
rpoC1 LSC 2049 0.0007 1.00 45.6 yes View details
clpP-psbB LSC 520 0.0019 0.98 44.8 yes View details
matK-trnK-UUU LSC 692 0.0021 1.00 44.6 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0007 1.00 44.6 yes View details
cemA LSC 693 0.0021 1.00 44.6 yes View details
psbM-petN LSC 736 0.0017 1.00 44.4 yes View details
trnC-GCA-rpoB LSC 1170 0.0003 1.00 44.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2736 1.000 73.6
trnK-UUU_p2 trnK-UUU ACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2735 1.000 73.5
trnK-UUU_p3 trnK-UUU ATACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2737 1.000 69.5
trnK-UUU_p4 trnK-UUU TACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2736 1.000 67.0
trnK-UUU_p5 trnK-UUU CAATGTCAACCAAGCCAGC CGTGCGGTGTAATTCCATTG 2733 1.000 66.9
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 861 1.000 68.5
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 861 1.000 66.6
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 860 1.000 66.6
matK-trnK-UUU_p4 matK-trnK-UUU TGAAAGAGAAGTGGGTAGACG CGTGCGGTGTAATTCCATTG 856 1.000 63.4
matK-trnK-UUU_p5 matK-trnK-UUU AGAGAAGTGGGTAGACGAAG CGTGCGGTGTAATTCCATTG 852 1.000 63.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1130–1137 1.000 78.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1141–1148 1.000 78.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1134–1141 1.000 77.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1145–1152 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1136–1143 1.000 75.8
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1127–1144 1.000 78.5
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1114–1131 1.000 77.9
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1113–1130 1.000 75.5
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1106–1123 1.000 75.3
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1100–1117 1.000 74.9
psbZ-trnfM-CAU_p1 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG CGAGGCTCATAACCTTGAGG 948–955 1.000 76.8
psbZ-trnfM-CAU_p2 psbZ-trnfM-CAU GCTTCTCCTGATGGTTGGTC CGAGGCTCATAACCTTGAGG 946–953 1.000 76.4
psbZ-trnfM-CAU_p3 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG CAGTTTGGTAGCTCACGAGG 963–970 1.000 76.4
psbZ-trnfM-CAU_p4 psbZ-trnfM-CAU GCTTCTCCTGATGGTTGGTC CAGTTTGGTAGCTCACGAGG 961–968 1.000 76.0
psbZ-trnfM-CAU_p5 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG GAGCGGAGTAGAGCAGTTTG 976–983 1.000 75.8
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2169–2177 1.000 43.8
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 2182–2190 1.000 43.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 2183–2191 1.000 43.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 2172–2180 1.000 42.8
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2171–2179 1.000 42.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Gigantochloa albociliata NC_050765.1 139417 View on NCBI ↗
Gigantochloa atroviolacea NC_050777.1 139533 View on NCBI ↗
Gigantochloa glabrata MK679788.1 139417 View on NCBI ↗
Gigantochloa nigrociliata NC_050778.1 139462 View on NCBI ↗
Gigantochloa parviflora NC_050749.1 139417 View on NCBI ↗
Gigantochloa verticillata NC_050779.1 139488 View on NCBI ↗