Markers + reference

Sinosasa

2 species · Poaceae · Poales

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Species 2
Genome length 140–140 kb
Candidate markers 266
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 31.9 yes View details
trnK-UUU LSC 33 0.0303 1.00 69.9 yes View details
rps16 LSC 1091 0.0000 1.00 27.2 yes View details
rps16-trnQ-UUG LSC 1556 0.0013 1.00 59.4 yes View details
psbK-psbI LSC 404 0.0025 1.00 52.1 yes View details
trnS-GCU-psbD LSC 1008 0.0010 0.99 58.3 yes View details
trnD-GUC-psbM LSC 1033 0.0029 1.00 60.7 yes View details
rbcL-psaI LSC 1299 0.0054 1.00 61.8 yes View details
rps19 IRb 282 0.0000 1.00 33.8 no View details
rpl32-trnL-UAG SSC 703 0.0028 1.00 60.4 yes View details
rps19 IRa 282 0.0000 1.00 21.2 yes View details
rps19-psbA LSC 135 0.0233 0.96 70.0 no View details
trnfM-CAU LSC 57 0.0175 1.00 62.6 yes View details
trnC-GCA-rpoB LSC 1216 0.0000 0.98 60.8 yes View details
rpl16 LSC 1539 0.0013 1.00 59.4 yes View details
petN-trnC-GCA LSC 909 0.0000 0.78 58.9 yes View details
atpI-atpH LSC 832 0.0000 1.00 58.9 yes View details
trnfM-CAU LSC 74 0.0000 1.00 33.8 no 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
psbA_p1 psbA TCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1159 1.000 68.5
psbA_p2 psbA TTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1160 1.000 68.5
psbA_p3 psbA TCTGGCTTTCCTTCCTTCAAA AATACGTGTGCTTGGGAGTC 1159 1.000 66.5
psbA_p4 psbA TTCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1160 1.000 66.5
psbA_p5 psbA TTTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1161 1.000 66.5
trnK-UUU_p1 trnK-UUU TACCAATGTCAACCAAGCCA AAATGCAAGCACGATTTGGG 230 1.000 74.4
trnK-UUU_p2 trnK-UUU ACCAATGTCAACCAAGCCAG AAATGCAAGCACGATTTGGG 229 1.000 74.3
trnK-UUU_p3 trnK-UUU TACCAATGTCAACCAAGCCA CATAGGGAAAGTCGTGTGCA 255 1.000 74.2
trnK-UUU_p4 trnK-UUU TACCAATGTCAACCAAGCCA ACATAGGGAAAGTCGTGTGC 256 1.000 74.2
trnK-UUU_p5 trnK-UUU ACCAATGTCAACCAAGCCAG CATAGGGAAAGTCGTGTGCA 254 1.000 74.2
rps16_p1 rps16 TGGCACGACATAAATCCAGT TGCAATGAAATTAGAGGAATGT 1238 1.000 40.0
rps16_p2 rps16 TGGCACGACATAAATCCAGT TGCAATGAAATTAGAGGAATGTTTG 1238 1.000 40.0
rps16_p3 rps16 TGGCACGACATAAATCCAGT GCAATGAAATTAGAGGAATGTTTGT 1237 1.000 40.0
rps16_p4 rps16 TGGCACGACATAAATCCAGT TGCAATGAAATTAGAGGAATGTT 1238 1.000 40.0
rps16_p5 rps16 TGGCACGACATAAATCCAGT TTGCAATGAAATTAGAGGAATGT 1239 1.000 40.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1630–1631 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1641–1642 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1634–1635 1.000 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1645–1646 1.000 76.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1690–1691 1.000 76.6
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCACGCCCAG 548 1.000 78.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCACGCCCAG 545 1.000 76.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTACTCCTCACGCCCAG 546 1.000 76.2
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTACTCCTCACGCCCAG 547 1.000 76.2
psbK-psbI_p5 psbK-psbI AAATTGCCCGAAGCTTATGC TTTTTACTCCTCACGCCCAG 632 1.000 74.0
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1142–1153 1.000 79.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1129–1140 1.000 78.6
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1128–1139 1.000 76.3
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1121–1132 1.000 76.1
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1115–1126 1.000 75.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Sinosasa longiligulata NC_036825.1 139928 View on NCBI ↗
Sinosasa mingyueshanensis PP681652.1 139697 View on NCBI ↗