Markers + reference

Chimonocalamus

10 species · Poaceae · Poales

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Species 10
Genome length 140–140 kb
Candidate markers 266
Primer pairs 90

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 32.0 yes View details
trnS-GCU-psbD LSC 981 0.0062 1.00 51.6 yes View details
trnG-UCC-trnT-GGU LSC 1970 0.0039 1.00 53.7 yes View details
atpF LSC 1422 0.0040 1.00 41.5 yes View details
trnT-UGU-trnL-UAA LSC 814 0.0043 1.00 59.6 yes View details
rbcL LSC 1434 0.0022 1.00 31.6 yes View details
ndhF-rpl32 SSC 907 0.0045 1.00 50.6 yes View details
rpl32-trnL-UAG SSC 702 0.0063 1.00 40.7 yes View details
ndhI SSC 543 0.0019 1.00 28.1 yes View details
rps19-psbA LSC 127 0.0460 1.00 71.5 no View details
rps16-trnQ-UUG LSC 1552 0.0026 1.00 57.4 yes View details
psaA-ycf3 LSC 651 0.0026 1.00 55.1 yes View details
trnD-GUC-psbM LSC 995 0.0013 1.00 53.9 yes View details
trnC-GCA-rpoB LSC 1086 0.0015 1.00 52.9 yes View details
ycf3 LSC 1980 0.0017 1.00 52.5 yes View details
psbE-petL LSC 1227 0.0029 1.00 51.8 yes View details
ycf3-trnS-GGA LSC 591 0.0010 1.00 48.6 yes View details
psaC-ndhE SSC 481 0.0049 1.00 48.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1160 1.000 68.7
psbA_p2 psbA TTTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1161 1.000 66.8
psbA_p3 psbA TCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1159 0.900 64.7
psbA_p4 psbA TCTGGCTTTCCTTCCTTCAAA AATACGTGTGCTTGGGAGTC 1159 0.900 62.7
psbA_p5 psbA TTCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1160 0.900 62.7
trnK-UUU_p1 trnK-UUU GACTCCCAAGCACACGTATT CGTGCGGTGTAATTCCATTG 2834–2845 1.000 78.5
trnK-UUU_p2 trnK-UUU AAAACACCGAACCATCCGAT CGTGCGGTGTAATTCCATTG 2971–2982 1.000 77.7
trnK-UUU_p3 trnK-UUU GCTTGTACTTTCGCGTCTCT CGTGCGGTGTAATTCCATTG 2900–2911 1.000 76.8
trnK-UUU_p4 trnK-UUU CACCGAACCATCCGATGTAA CGTGCGGTGTAATTCCATTG 2967–2978 1.000 76.8
trnK-UUU_p5 trnK-UUU TGCGGTCAATAAGGTAGGGA CGTGCGGTGTAATTCCATTG 2996–3000 0.900 74.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1607–1646 1.000 80.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1618–1657 1.000 79.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1611–1650 1.000 79.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1622–1661 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1667–1706 1.000 78.5
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1125–1129 1.000 79.7
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1112–1116 1.000 79.2
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1111–1115 1.000 76.8
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1104–1108 1.000 76.6
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1098–1102 1.000 76.2
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2101–2104 1.000 43.5
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 2114–2117 1.000 42.8
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 2115–2118 1.000 42.8
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 2104–2107 1.000 42.4
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2103–2106 1.000 42.4
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1070–1081 1.000 49.3
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1102–1113 1.000 47.8
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1071–1082 1.000 46.2
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1070–1081 1.000 46.2
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1071–1082 1.000 45.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Chimonocalamus cibarius NC_081916.1 139665 View on NCBI ↗
Chimonocalamus delicatus NC_081917.1 139583 View on NCBI ↗
Chimonocalamus dumosus NC_081918.1 139688 View on NCBI ↗
Chimonocalamus fimbriatus NC_081919.1 139665 View on NCBI ↗
Chimonocalamus griffithianus NC_081920.1 139753 View on NCBI ↗
Chimonocalamus longiligulatus NC_081921.1 139686 View on NCBI ↗
Chimonocalamus longiusculus NC_024714.1 139821 View on NCBI ↗
Chimonocalamus makuanensis NC_081924.1 139615 View on NCBI ↗
Chimonocalamus montanus NC_081922.1 139656 View on NCBI ↗
Chimonocalamus pallens NC_081923.1 139740 View on NCBI ↗