Markers + reference

Sinalliaria

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 154–154 kb
Candidate markers 225
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 225 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 263 0.0732 0.94 78.5 yes View details
trnS-trnG LSC 475 0.0347 0.97 69.8 yes View details
trnR-atpA LSC 295 0.0556 0.92 77.2 yes View details
psbM-trnD LSC 989 0.0144 0.98 58.0 yes View details
trnE-trnT LSC 810 0.0247 1.00 63.9 yes View details
psbE-petL LSC 1369 0.0280 0.99 62.5 yes View details
petL-trnP LSC 691 0.0277 0.99 65.6 yes View details
trnP-psaJ LSC 336 0.0092 0.97 49.0 yes View details
psaJ-rpl33 LSC 445 0.0384 1.00 67.1 yes View details
rpl32-trnL SSC 657 0.0292 0.99 65.4 yes View details
ndhH-trnN SSC 6327 0.0141 1.00 48.5 yes View details
rps11-rpl36 LSC 111 0.0450 1.00 77.9 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
cemA-petA LSC 225 0.0356 1.00 69.1 yes View details
ycf4-cemA LSC 465 0.0194 1.00 67.1 yes View details
rpl14-rpl16 LSC 118 0.0254 1.00 67.1 yes View details
trnL-trnF LSC 343 0.0262 1.00 65.5 yes View details
rpl22-rps19 LSC 57 0.0179 0.98 64.4 yes View details
trnF-ndhJ LSC 587 0.0172 0.99 64.2 yes View details
trnT-psbD LSC 1091 0.0101 1.00 63.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 321–346 1.000 86.8
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 322–347 1.000 86.6
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 336–361 1.000 86.4
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 339–364 1.000 86.3
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 337–362 1.000 86.2
trnK_p1 trnK CTACTGGAGGAGCAGCAATG TTATCCCTGACGCACACATG 2890 0.500 59.4
trnK_p2 trnK CTGGAGGAGCAGCAATGAAT TTATCCCTGACGCACACATG 2887 0.500 59.4
trnK_p3 trnK CTACTGGAGGAGCAGCAATG CCATTTATCCCTGACGCACA 2894 0.500 59.3
trnK_p4 trnK CTGGAGGAGCAGCAATGAAT CCATTTATCCCTGACGCACA 2891 0.500 59.3
trnK_p5 trnK TGCAAACCAATAGCTGCAGA TTATCCCTGACGCACACATG 2990 0.500 59.1
trnS-trnG_p1 trnS-trnG ACGCTTTAATCCACTCAGCC AATCAAACCGAGAGACCCTT 580–587 1.000 69.6
trnS-trnG_p2 trnS-trnG ACGCTTTAATCCACTCAGCC ATCAAACCGAGAGACCCTTT 579–586 1.000 69.6
trnS-trnG_p3 trnS-trnG CGCTTTAATCCACTCAGCCA AATCAAACCGAGAGACCCTT 579–586 1.000 69.6
trnS-trnG_p4 trnS-trnG CGCTTTAATCCACTCAGCCA ATCAAACCGAGAGACCCTTT 578–585 1.000 69.6
trnS-trnG_p5 trnS-trnG CGGAAGGGAAAGAGAGGGAT ATCAAACCGAGAGACCCTTT 644–651 1.000 67.3
trnR-atpA_p1 trnR-atpA GCGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 399–417 1.000 76.3
trnR-atpA_p2 trnR-atpA GCGAAAAGCGTCCATTGTC TTCAAGAGCAACTGGAACGT 400–418 1.000 76.3
trnR-atpA_p3 trnR-atpA GCGAAAAGCGTCCATTGTC ACATTAACCGCTGAAGCAGA 440–458 1.000 74.9
trnR-atpA_p4 trnR-atpA GCGAAAAGCGTCCATTGTC AGACATTAACCGCTGAAGCA 442–460 1.000 74.9
trnR-atpA_p5 trnR-atpA GCGAAAAGCGTCCATTGTCT TCAAGAGCAACTGGAACGTT 399–417 1.000 72.5
rpoC1-rpoB_p1 rpoC1-rpoB TTTTAGTGGCCCAAGCACTT ACGATCTTTGGCTCTGGAAC 181 1.000 79.0
rpoC1-rpoB_p2 rpoC1-rpoB TTTTTAGTGGCCCAAGCACT ACGATCTTTGGCTCTGGAAC 182 1.000 79.0
rpoC1-rpoB_p3 rpoC1-rpoB AGTGGCCCAAGCACTTATTT ACGATCTTTGGCTCTGGAAC 177 1.000 77.2
rpoC1-rpoB_p4 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA ACGATCTTTGGCTCTGGAAC 222 1.000 76.7
rpoC1-rpoB_p5 rpoC1-rpoB GTGGCCCAAGCACTTATTTG ACGATCTTTGGCTCTGGAAC 176 1.000 76.7
psbM-trnD_p1 psbM-trnD AGGAACGAGAATGAAGAGTGC GTTCGAGCCCCGTCAGTC 1064–1082 1.000 42.5
psbM-trnD_p2 psbM-trnD ACGAGAATGAAGAGTGCAGT GTTCGAGCCCCGTCAGTC 1060–1078 1.000 42.5
psbM-trnD_p3 psbM-trnD GGAACGAGAATGAAGAGTGCA GTTCGAGCCCCGTCAGTC 1063–1081 1.000 42.5
psbM-trnD_p4 psbM-trnD AACGAGAATGAAGAGTGCAGT GTTCGAGCCCCGTCAGTC 1061–1079 1.000 42.5
psbM-trnD_p5 psbM-trnD GGAACGAGAATGAAGAGTGC GTTCGAGCCCCGTCAGTC 1063–1081 1.000 42.5

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
Sinalliaria limprichtiana NC_034287.1 153746 View on NCBI ↗
Sinalliaria limprichtiana var. grandifolia NC_034286.1 153964 View on NCBI ↗