Markers + reference

Raphanus

3 species · Brassicaceae · Brassicales

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Species 3
Genome length 153–153 kb
Candidate markers 270
Primer pairs 110

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0013 1.00 36.6 yes View details
aptA LSC 1524 0.0004 1.00 38.4 yes View details
rpoC2 LSC 4143 0.0008 1.00 27.6 yes View details
trnC-GCA-petN LSC 612 0.0011 1.00 35.9 yes View details
trnT-UGU-trnL-UAA LSC 815 0.0041 1.00 49.1 yes View details
ndhC-trnV-UAC LSC 676 0.0059 1.00 50.2 yes View details
psaJ-rpl33 LSC 425 0.0047 1.00 45.9 yes View details
rpl20-rps12 LSC 762 0.0018 1.00 41.1 yes View details
psbH LSC 222 0.0000 1.00 21.7 yes View details
ycf1 IRb 1032 0.0000 1.00 39.2 no View details
rpl32-trnL-UAG SSC 659 0.0051 1.00 49.5 yes View details
rps15-ycf1 SSC 372 0.0072 1.00 46.1 yes View details
ycf1 SSC 5304 0.0015 1.00 30.4 yes View details
rps12-clpP LSC 181 0.0295 1.00 58.8 yes View details
trnH-GUG-psbA LSC 236 0.0198 1.00 52.6 yes View details
psbH-petB LSC 135 0.0198 1.00 52.6 yes View details
trnF-GAA-ndhJ LSC 595 0.0034 1.00 48.3 yes View details
ndhF-rpl32 SSC 810 0.0033 1.00 48.3 yes View details
matK-trnK-UUU LSC 673 0.0030 1.00 48.1 yes View details
accD LSC 1476 0.0023 1.00 47.7 yes View details
atpI LSC 750 0.0018 1.00 47.4 yes View details
psaA-ycf3 LSC 735 0.0009 1.00 47.1 yes View details
trnR-ACG-trnN-GUU IRb 613 0.0011 1.00 47.1 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GACCTAGCTGCTGTTGAGTC 303 1.000 80.7
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GACCTAGCTGCTGTTGAGTC 304 1.000 80.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 309 1.000 80.2
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 312 1.000 80.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 310 1.000 80.0
psbA_p1 psbA GAAGGCTTATATTGCTCGTT ATTTGTGTGCTTGGGAGTCC 1173 1.000 41.0
psbA_p2 psbA GAAGGCTTATATTGCTCGTTT ATTTGTGTGCTTGGGAGTCC 1173 1.000 40.1
psbA_p3 psbA GAAGGCTTATATTGCTCGTTTT ATTTGTGTGCTTGGGAGTCC 1173 1.000 40.1
psbA_p4 psbA AAGGCTTATATTGCTCGTTT ATTTGTGTGCTTGGGAGTCC 1172 1.000 40.1
psbA_p5 psbA AGGCTTATATTGCTCGTTTT ATTTGTGTGCTTGGGAGTCC 1171 1.000 40.1
matK-trnK-UUU_p1 matK-trnK-UUU GAGCCCCATCGAACTCTAAA ACGCACACATGACTGGATTT 892 1.000 71.7
matK-trnK-UUU_p2 matK-trnK-UUU GAGCCCCATCGAACTCTAAA AACGGTAGAGTACTCGGCTT 803–804 1.000 71.1
matK-trnK-UUU_p3 matK-trnK-UUU GAGCCCCATCGAACTCTAAA ACGGTAGAGTACTCGGCTTT 802–803 1.000 71.1
matK-trnK-UUU_p4 matK-trnK-UUU CGAGCCCCATCGAACTCTAA ACGCACACATGACTGGATTT 893 1.000 69.5
matK-trnK-UUU_p5 matK-trnK-UUU CGAGCCCCATCGAACTCTAA ACGGTAGAGTACTCGGCTTT 803–804 1.000 68.9
aptA_p1 aptA AGCCTTCCAAGCTAACGATG TCATGTTTGGTTCGGGAAGG 2538–2543 1.000 79.1
aptA_p2 aptA ACCCTTAGCCTTCCAAGCTA TCATGTTTGGTTCGGGAAGG 2544–2549 1.000 79.1
aptA_p3 aptA AGCCTTCCAAGCTAACGATG AATTAGAAAACGCCCGAGCT 2386–2391 1.000 79.0
aptA_p4 aptA ACCCTTAGCCTTCCAAGCTA AATTAGAAAACGCCCGAGCT 2392–2397 1.000 79.0
aptA_p5 aptA CGACGTCGACTAAAACCCTT TCATGTTTGGTTCGGGAAGG 2558–2563 1.000 78.9
atpI_p1 atpI ACCAACTATTCGATAATTGGGCT TCTTATTTCTGTCAGAGGGCA 820–821 1.000 40.3
atpI_p2 atpI ACCAACTATTCGATAATTGGGCT TCTTATTTCTGTCAGAGGGCAA 820–821 1.000 40.3
atpI_p3 atpI ACCAACTATTCGATAATTGGGCT TTCTTATTTCTGTCAGAGGGCA 821–822 1.000 40.3
atpI_p4 atpI ACCAACTATTCGATAATTGGGC TCTTATTTCTGTCAGAGGGCA 820–821 1.000 40.3
atpI_p5 atpI ACCAACTATTCGATAATTGGGCT AGTTCTTATTTCTGTCAGAGGGC 823–824 1.000 40.3
rpoC2_p1 rpoC2 AATTTGTTAACATGCCGCCG GATTGGTGCATTGTTCACGG 682 1.000 80.4
rpoC2_p2 rpoC2 AATTTGTTAACATGCCGCCG GGATTGGTGCATTGTTCACG 683 1.000 80.4
rpoC2_p3 rpoC2 AATTTGTTAACATGCCGCCG CAGGTGTTAGAAGTCCGCTC 1223 1.000 80.3
rpoC2_p4 rpoC2 ACGAGCCGAGCCATTATTTT CAGGTGTTAGAAGTCCGCTC 820 1.000 80.2
rpoC2_p5 rpoC2 AACATAATGACACCGAGCCC CAGGTGTTAGAAGTCCGCTC 1189 1.000 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Raphanus sativus NC_024469.1 153368 View on NCBI ↗
Raphanus sativus var. raphanistroides KX545461.1 153444 View on NCBI ↗
Raphanus sativus var. sativus KJ716483.1 153368 View on NCBI ↗