Markers + reference

Yinshania

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 155–156 kb
Candidate markers 270
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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 29.3 yes View details
trnK-AAA-rps16 LSC 743 0.0039 0.98 63.2 yes View details
rps16-trnQ-CAA LSC 502 0.0075 0.93 51.5 yes View details
psbM-trnD-GAC LSC 1037 0.0016 1.00 51.4 yes View details
petA-psbJ LSC 999 0.0035 1.00 51.8 yes View details
ycf1 IRb 1041 0.0006 1.00 40.4 no View details
ndhF-rpl32 SSC 803 0.0039 1.00 65.1 yes View details
rpl32-trnL-CUA SSC 553 0.0049 0.99 52.6 yes View details
ycf1 SSC 5382 0.0020 1.00 44.6 yes View details
trnS-AGC-trnG-GGA LSC 680 0.0015 0.99 60.7 yes View details
rpl16 LSC 1477 0.0017 1.00 60.1 yes View details
rpoB-trnC-UGC LSC 1040 0.0005 1.00 59.8 yes View details
trnG-GGA-trnR-AGA LSC 153 0.0131 1.00 56.9 yes View details
trnE-GAA-trnT-ACC LSC 828 0.0018 0.99 55.6 yes View details
trnH-CAC-psbA LSC 249 0.0147 1.00 53.3 yes View details
ycf2 IRb 6876 0.0002 1.00 52.7 yes View details
ycf2 IRa 6876 0.0002 1.00 52.7 yes View details
rps16 LSC 1155 0.0023 1.00 51.0 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
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 307 1.000 80.3
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 308 1.000 80.1
trnH-CAC-psbA_p3 trnH-CAC-psbA AATCCACTTGGCTACATCCG GCTGTTGAGGCTCCATCTAC 300 1.000 78.8
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 374 1.000 77.7
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 375 1.000 77.5
psbA_p1 psbA AGAAGGCTTATATTGCTCGT ATTTGTGTGCTTGGGAGTCC 1168 1.000 46.9
psbA_p2 psbA AAGAAGGCTTATATTGCTCGT ATTTGTGTGCTTGGGAGTCC 1169 1.000 45.7
psbA_p3 psbA AGAAGGCTTATATTGCTCGTT ATTTGTGTGCTTGGGAGTCC 1168 1.000 45.7
psbA_p4 psbA AAGAAGGCTTATATTGCTCGTT ATTTGTGTGCTTGGGAGTCC 1169 1.000 44.0
psbA_p5 psbA AGAAGGCTTATATTGCTCGTTT ATTTGTGTGCTTGGGAGTCC 1168 1.000 44.0
trnK-AAA-rps16_p1 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA CGCTCAACCAACAAGAACAG 918–933 1.000 77.5
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 850–865 1.000 77.4
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 849–864 1.000 77.4
trnK-AAA-rps16_p4 trnK-AAA-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 836–851 1.000 75.1
trnK-AAA-rps16_p5 trnK-AAA-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 861–876 1.000 74.2
rps16_p1 rps16 AAGCGAAAGAGGAGGAAAGA ACGCGTAAATTCACTATTCCA 1361–1362 1.000 41.8
rps16_p2 rps16 AGCGAAAGAGGAGGAAAGAA ACGCGTAAATTCACTATTCCA 1360–1361 1.000 41.8
rps16_p3 rps16 AAGCGAAAGAGGAGGAAAGAA ACGCGTAAATTCACTATTCCA 1361–1362 1.000 40.3
rps16_p4 rps16 AGCGAAAGAGGAGGAAAGAAA ACGCGTAAATTCACTATTCCA 1360–1361 1.000 40.3
rps16_p5 rps16 AGCGAAAGAGGAGGAAAGAA ACGCGTAAATTCACTATTCCAT 1360–1361 1.000 40.3
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 541–575 1.000 83.3
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 551–585 1.000 82.5
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 567–601 1.000 81.0
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 568–602 1.000 81.0
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 569–603 1.000 79.3
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 785–861 1.000 73.5
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 783–859 1.000 73.2
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 780–856 1.000 71.5
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 786–862 1.000 71.2
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 784–860 1.000 71.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Yinshania acutangula MK637817.1 155373 View on NCBI ↗
Yinshania furcatopilosa MK637818.1 155350 View on NCBI ↗
Yinshania henryi NC_061291.1 155553 View on NCBI ↗
Yinshania zayuensis NC_062044.1 155401 View on NCBI ↗