Markers + reference

Chimonobambusa

11 species · Poaceae · Poales

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Species 11
Genome length 139–140 kb
Candidate markers 271
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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psbD LSC 983 0.0035 1.00 51.9 yes View details
trnG-UCC-trnT-GGU LSC 1963 0.0023 1.00 65.0 yes View details
rbcL-psaI LSC 1286 0.0031 1.00 51.1 yes View details
rps18 LSC 513 0.0015 0.96 35.5 yes View details
rpl14 LSC 372 0.0029 1.00 30.7 yes View details
rps19 IRb 282 0.0000 1.00 33.8 no View details
ndhF SSC 2220 0.0002 1.00 36.1 yes View details
rpl32-trnL-UAG SSC 702 0.0038 1.00 50.1 yes View details
rps19 IRa 282 0.0000 1.00 21.5 yes View details
ndhH-ndhF SSC 108 0.0236 1.00 64.6 yes View details
rps16 LSC 1087 0.0012 1.00 51.7 yes View details
rpl14-rpl16 LSC 109 0.0047 1.00 51.1 yes View details
rps19-psbA LSC 130 0.0190 0.98 51.1 no View details
petB LSC 1466 0.0004 1.00 51.0 yes View details
rpoB LSC 3228 0.0005 1.00 50.7 yes View details
trnT-UGU-trnL-UAA LSC 819 0.0011 1.00 50.2 yes View details
ycf3 LSC 1995 0.0005 1.00 50.0 yes View details
rps16-trnQ-UUG LSC 1533 0.0004 1.00 49.7 yes View details
rpoC2 LSC 4554 0.0005 1.00 49.5 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
rps16_p1 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGA 1247–1248 1.000 51.4
rps16_p2 rps16 TGGCACGACATAAATCCAGT TCAATTCCCTATACCACTTTGCA 1252–1253 1.000 48.8
rps16_p3 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGAA 1247–1248 1.000 48.8
rps16_p4 rps16 TGGCACGACATAAATCCAGT TTCCCTATACCACTTTGCAATGA 1248–1249 1.000 48.8
rps16_p5 rps16 TGGCACGACATAAATCCAGT CCCTATACCACTTTGCAATGA 1246–1247 1.000 47.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1603–1609 1.000 78.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1614–1620 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1607–1613 1.000 77.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1618–1624 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1663–1669 1.000 77.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1126–1129 1.000 79.4
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1113–1116 1.000 78.8
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1112–1115 1.000 76.4
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1105–1108 1.000 76.2
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1099–1102 1.000 75.8
trnG-UCC_p1 trnG-UCC CAAACTGCTCTACTCCGCTC CTCGAATGGCTACCCTTGAC 906 1.000 76.7
trnG-UCC_p2 trnG-UCC CAAACTGCTCTACTCCGCTC CGAATGGCTACCCTTGACAA 904 1.000 76.3
trnG-UCC_p3 trnG-UCC TGGTGGACGAAAAAGGTTGA CTCGAATGGCTACCCTTGAC 871 1.000 76.2
trnG-UCC_p4 trnG-UCC AACTGGTGGACGAAAAAGGT CTCGAATGGCTACCCTTGAC 874 1.000 76.2
trnG-UCC_p5 trnG-UCC ACTGGTGGACGAAAAAGGTT CTCGAATGGCTACCCTTGAC 873 1.000 76.2
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 1475–2143 1.000 47.1
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 1488–2156 1.000 46.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 1489–2157 1.000 46.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 1478–2146 1.000 46.0
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 1477–2145 1.000 46.0
rpoB_p1 rpoB AGAAGGATTTGGTGTTGCTCA TTGTTGAGGGGAAACGAGTC 322 1.000 68.7
rpoB_p2 rpoB AATGCTACGATCTGGGGAAA TTGTTGAGGGGAAACGAGTC 240 1.000 67.5
rpoB_p3 rpoB AGAAGGATTTGGTGTTGCTCA GAGGGGAAACGAGTCCAATT 317 1.000 66.7
rpoB_p4 rpoB AATGCTACGATCTGGGGAAA GAGGGGAAACGAGTCCAATT 235 1.000 65.6
rpoB_p5 rpoB AGAAGGATTTGGTGTTGCTCA TGAGGGGAAACGAGTCCAAT 318 1.000 65.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Chimonobambusa angustifolia OK040768.1 139611 View on NCBI ↗
Chimonobambusa hejiangensis NC_053872.1 138908 View on NCBI ↗
Chimonobambusa hirtinoda OK046142.1 139561 View on NCBI ↗
Chimonobambusa montigena PQ459320.1 139597 View on NCBI ↗
Chimonobambusa paucispinosa PQ459324.1 139617 View on NCBI ↗
Chimonobambusa purpurea MW030500.1 139574 View on NCBI ↗
Chimonobambusa quadrangularis PP681661.1 139566 View on NCBI ↗
Chimonobambusa sangzhiensis NC_067555.1 139595 View on NCBI ↗
Chimonobambusa tuberculata PQ459322.1 139582 View on NCBI ↗
Chimonobambusa tumidissinoda NC_036814.1 139502 View on NCBI ↗
Chimonobambusa utilis PQ459325.1 139586 View on NCBI ↗