Markers + reference

Schima

14 species · Theaceae · Ericales

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Species 14
Genome length 157–157 kb
Candidate markers 273
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1694 0.0032 1.00 55.1 yes View details
atpF-atpH LSC 389 0.0058 1.00 31.2 yes View details
petN-psbM LSC 1123 0.0036 1.00 56.8 yes View details
psbM-trnD-GUC LSC 1152 0.0029 0.99 36.0 yes View details
trnT-GGU-psbD LSC 1515 0.0026 1.00 40.9 yes View details
trnT-UGU-trnL-UAA LSC 994 0.0057 0.99 60.3 yes View details
petA-psbJ LSC 1038 0.0138 1.00 60.4 yes View details
rpl16 LSC 1407 0.0038 1.00 40.2 yes View details
ndhF-rpl32 SSC 828 0.0031 1.00 40.2 yes View details
rpl32-trnL-UAG SSC 908 0.0040 1.00 45.3 yes View details
ccsA SSC 963 0.0039 1.00 39.7 yes View details
rps15 SSC 273 0.0048 1.00 25.7 yes View details
ycf1 SSC 5652 0.0024 1.00 41.0 yes View details
atpH-atpI LSC 1153 0.0018 1.00 53.5 yes View details
ndhC-trnV-UAC LSC 410 0.0024 1.00 51.0 yes View details
psbE-petL LSC 1278 0.0028 1.00 50.6 yes View details
ndhF SSC 2247 0.0023 1.00 50.2 yes View details
trnK-UUU-rps16 LSC 815 0.0032 1.00 49.8 yes View details
trnF-GAA-ndhJ LSC 709 0.0026 1.00 49.8 yes View details
petD LSC 1245 0.0016 1.00 46.8 yes View details
trnC-GCA-petN LSC 727 0.0018 1.00 46.5 yes View details
trnS-GCU-trnG LSC 682 0.0012 1.00 45.3 yes View details
ycf4-cemA LSC 915 0.0025 0.99 44.9 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GGTGCTCAACCTACAGAAACT 981–990 1.000 72.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GGTGCTCAACCTACAGAAACT 982–991 1.000 72.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC GGTGCTCAACCTACAGAAACT 986–995 1.000 72.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT GGTGCTCAACCTACAGAAACT 984–993 1.000 72.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGAAACT 932–941 0.929 68.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1762–1774 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAACGAATCGTGTCC GAGGTTCGAATCCTTCCGTC 1785–1797 1.000 78.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAATTAAAATGGGGCGTGGC 1819–1831 1.000 77.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGAATCGTGTCCTT GAGGTTCGAATCCTTCCGTC 1783–1795 1.000 76.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1827–1839 1.000 76.8
trnS-GCU-trnG_p1 trnS-GCU-trnG ATTAGCAATCCGCCGCTTTA AACCGAGAGACCCCTTAACT 793–794 1.000 77.5
trnS-GCU-trnG_p2 trnS-GCU-trnG CTTTAGTCCACTCAGCCACC AACCGAGAGACCCCTTAACT 778–779 1.000 77.0
trnS-GCU-trnG_p3 trnS-GCU-trnG ACGGAAAGAGAGGGATTCGA AACCGAGAGACCCCTTAACT 842–843 1.000 76.6
trnS-GCU-trnG_p4 trnS-GCU-trnG TTTAGTCCACTCAGCCACCT AACCGAGAGACCCCTTAACT 777–778 1.000 75.7
trnS-GCU-trnG_p5 trnS-GCU-trnG GCTTTAGTCCACTCAGCCAC AACCGAGAGACCCCTTAACT 779–780 1.000 73.4
atpF-atpH_p1 atpF-atpH GAAAGAATCGGTTACATTTTTCA GGACTGGTTGTTGCATTAGC 459–473 1.000 41.2
atpF-atpH_p2 atpF-atpH GAAAGAATCGGTTACATTTTTCA CGGAGGGAAAAATACGAGGT 524–538 1.000 41.1
atpF-atpH_p3 atpF-atpH GAAAGAATCGGTTACATTTTTCA GAGGCGGAGGGAAAAATACG 528–542 1.000 41.1
atpF-atpH_p4 atpF-atpH GAAAGAATCGGTTACATTTTTCA GCGGAGGGAAAAATACGAGG 525–539 1.000 41.1
atpF-atpH_p5 atpF-atpH GAAAGAATCGGTTACATTTTTCA GGCGGAGGGAAAAATACGAG 526–540 1.000 41.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 1230–1240 1.000 79.8
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 1286–1296 1.000 79.2
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCCGCAG 1231–1241 1.000 78.6
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC TTTTGCAACTTTAGCCGCAG 1290–1300 1.000 78.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTGCAACTTTAGCCGCAG 1245–1255 1.000 78.4
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 806–811 1.000 76.9
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 781–786 1.000 76.0
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 867–872 1.000 75.3
trnC-GCA-petN_p4 trnC-GCA-petN TATCCTTTTGGCGACATGGC AGCCCAAGCGAGACTTACTA 839–844 1.000 74.8
trnC-GCA-petN_p5 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGAGTCCACTTCTTCCCCAT 842–847 1.000 74.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Schima argentea NC_035536.1 157245 View on NCBI ↗
Schima brevipedicellata NC_035537.1 157227 View on NCBI ↗
Schima crenata NC_035538.1 157288 View on NCBI ↗
Schima khasiana NC_035539.1 157252 View on NCBI ↗
Schima multibracteata NC_035540.1 157278 View on NCBI ↗
Schima noronhae NC_035541.1 157278 View on NCBI ↗
Schima parviflora NC_065157.1 157300 View on NCBI ↗
Schima remotiserrata NC_035542.1 157284 View on NCBI ↗
Schima sericans NC_035543.1 157302 View on NCBI ↗
Schima sericans var. paracrenata OL449826.1 157271 View on NCBI ↗
Schima sericans var. sericans OL449825.1 157245 View on NCBI ↗
Schima sinensis NC_035544.1 157297 View on NCBI ↗
Schima superba NC_035545.1 157254 View on NCBI ↗
Schima wallichii NC_035546.1 157240 View on NCBI ↗