Markers + reference

Sabia

9 species · Sabiaceae · Proteales

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Species 9
Genome length 162–162 kb
Candidate markers 271
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 379 0.0363 1.00 74.7 yes View details
rps16 LSC 1098 0.0114 1.00 53.4 yes View details
trnC-GCA-petN LSC 894 0.0114 1.00 54.0 yes View details
trnE-UUC-trnT-GGU LSC 797 0.0133 0.91 63.3 yes View details
ndhC-trnV-UAC LSC 2127 0.0108 0.99 58.4 yes View details
petA-psbJ LSC 1023 0.0121 1.00 60.4 yes View details
ndhF-rpl32 SSC 1027 0.0187 0.99 63.8 yes View details
rpl32-trnL-UAG SSC 1027 0.0119 0.98 61.0 yes View details
ccsA-ndhD SSC 272 0.0361 0.99 71.5 yes View details
ndhD SSC 1503 0.0027 1.00 41.5 yes View details
ndhA SSC 2209 0.0078 1.00 52.2 yes View details
trnL-UAG-ccsA SSC 113 0.0354 0.99 65.9 yes View details
trnT-UGU-trnL-UAA LSC 821 0.0100 1.00 65.2 yes View details
rps12-trnV-GAC IRb 1866 0.0012 1.00 60.6 yes View details
trnV-GAC-rps12 IRa 1866 0.0012 1.00 60.6 yes View details
trnK-UUU-rps16 LSC 824 0.0104 0.99 59.9 yes View details
psbC-trnS-UGA LSC 219 0.0188 0.99 59.8 yes View details
psbZ-trnG-GCC LSC 343 0.0088 1.00 59.8 yes View details
ycf3-trnS-GGA LSC 885 0.0089 1.00 59.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GTCGAAGCTCCATCCACAAA 343–439 1.000 87.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GTCGAAGCTCCATCCACAAA 357–453 1.000 87.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GTCGAAGCTCCATCCACAAA 356–452 1.000 87.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GTCGAAGCTCCATCCACAAA 358–454 1.000 87.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC GTCGAAGCTCCATCCACAAA 348–444 1.000 83.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGAGCTCAACCTACAGGAAC 936–957 1.000 79.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGAGCTCAACCTACAGGAAC 935–956 1.000 79.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GGAGCTCAACCTACAGGAAC 951–972 1.000 78.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGAGCTCAACCTACAGGAAC 945–966 1.000 78.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGAGCTCAACCTACAGGAAC 922–943 1.000 76.8
rps16_p1 rps16 TCAATCCCCTTTCTACCCGT AGCAATCCGTTGAAGATGCA 1520–1539 1.000 80.9
rps16_p2 rps16 TCAATCCCCTTTCTACCCGT GGCTTTTACGGGTGATTGGA 1663–1682 1.000 80.8
rps16_p3 rps16 TCAATCCCCTTTCTACCCGT GCAATCCGTTGAAGATGCAG 1519–1538 1.000 80.8
rps16_p4 rps16 ACCCGTCTCACGTCTCATAT GGCTTTTACGGGTGATTGGA 1649–1668 1.000 80.7
rps16_p5 rps16 TCAATCCCCTTTCTACCCGT TTCGGCTTTTACGGGTGATT 1666–1685 1.000 80.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AAACGACCCCCTCTTTGAAC 1450–1462 1.000 81.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AAACGACCCCCTCTTTGAAC 1394–1406 1.000 81.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC TTAAAGCAGCCCAAGCAAGA 1011–1013 0.444 59.0
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 955–957 0.444 58.8
trnC-GCA-petN_p5 trnC-GCA-petN AGGGGTTCAGTAATCCTCCC TTAAAGCAGCCCAAGCAAGA 1052–1054 0.444 58.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 834–907 1.000 84.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 813–886 1.000 84.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GGGGTTTTGTGGAAAAAGCC 867–940 1.000 84.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GGTTTTGTGGAAAAAGCCCC 865–938 1.000 84.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GGTTTTGTGGAAAAAGCCCC 844–917 1.000 83.9
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 323–326 1.000 81.0
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GATGGCCGAGTGGTTGATAG 334–337 1.000 80.3
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGGTTCGAATCCCTCTCTCT 269–272 1.000 80.2
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 366–369 1.000 78.9
psbC-trnS-UGA_p5 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGTTGATAGCTCCGGTCTTG 365–368 1.000 78.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Sabia campanulata subsp. ritchieae OP310790.1 162064 View on NCBI ↗
Sabia discolor PP733984.1 161581 View on NCBI ↗
Sabia fasciculata NC_069947.1 161602 View on NCBI ↗
Sabia japonica NC_069948.1 162209 View on NCBI ↗
Sabia limoniacea NC_069949.1 161621 View on NCBI ↗
Sabia parviflora NC_059863.1 162054 View on NCBI ↗
Sabia schumanniana NC_069950.1 162030 View on NCBI ↗
Sabia swinhoei NC_069951.1 161592 View on NCBI ↗
Sabia yunnanensis NC_029431.1 162080 View on NCBI ↗