Markers + reference

Crambe

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 154–154 kb
Candidate markers 266
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 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0019 1.00 46.6 yes View details
trnS-GCU-trnG-UCC LSC 714 0.0319 0.96 74.0 yes View details
psaI-ycf4 LSC 430 0.0272 0.94 75.2 yes View details
petA-psbJ LSC 1107 0.0235 0.96 72.3 yes View details
psbE-petL LSC 1355 0.0126 1.00 57.2 yes View details
psaJ-rpl33 LSC 431 0.0307 0.98 74.6 yes View details
rpl16 LSC 1484 0.0162 1.00 57.0 yes View details
ycf1 SSC 1029 0.0029 1.00 46.3 no View details
rpl32-trnL-UAG SSC 687 0.0270 0.97 63.3 yes View details
rps15 SSC 267 0.0037 1.00 40.0 yes View details
ycf1 SSC 5301 0.0102 1.00 49.7 yes View details
trnH-GUG-psbA LSC 186 0.0543 0.99 79.9 yes View details
psbT-psbN LSC 65 0.0615 1.00 75.1 yes View details
ccsA-ndhD SSC 214 0.0333 0.98 73.4 yes View details
psbC-trnS-UGA LSC 179 0.0391 1.00 72.4 yes View details
psbL-psbF LSC 21 0.0476 1.00 71.0 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0099 0.99 65.1 yes View details
psbA-trnK-UUU LSC 266 0.0263 1.00 64.1 yes View details
trnF-GAA-ndhJ LSC 605 0.0137 0.96 64.0 yes View details
psaA-ycf3 LSC 731 0.0069 0.99 63.4 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0339 1.00 63.1 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 105 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 CCTCTAGACCTAGCTGCTGT 259–260 1.000 82.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 262–263 1.000 82.0
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 260–261 1.000 81.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 263–264 1.000 81.8
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 252–253 1.000 80.6
psbA_p1 psbA AGGTCTAGACTAACGCTAAAGA ATTTGTGTGCTTGGGAGTCC 1135 1.000 43.4
psbA_p2 psbA AGGTCTAGACTAACGCTAAAGAA ATTTGTGTGCTTGGGAGTCC 1135 1.000 41.2
psbA_p3 psbA GGTCTAGACTAACGCTAAAGA ATTTGTGTGCTTGGGAGTCC 1134 1.000 40.1
psbA_p4 psbA AGGTCTAGACTAACGCTAAAG ATTTGTGTGCTTGGGAGTCC 1135 1.000 40.1
psbA_p5 psbA AGGTCTAGACTAACGCTAAAGA AGAATTTGTGTGCTTGGGAGT 1138 1.000 40.1
psbA-trnK-UUU_p1 psbA-trnK-UUU TACAGAAGCGACCCCATAGG AAAATGCAAGCACGGTTTGG 429–431 1.000 73.2
psbA-trnK-UUU_p2 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC AAAATGCAAGCACGGTTTGG 436–438 1.000 72.5
psbA-trnK-UUU_p3 psbA-trnK-UUU AGTTACAGAAGCGACCCCAT AAAATGCAAGCACGGTTTGG 432–434 1.000 72.2
psbA-trnK-UUU_p4 psbA-trnK-UUU TACAGAAGCGACCCCATAGG ACTCCATCCGACTAGTTCCG 364 1.000 71.9
psbA-trnK-UUU_p5 psbA-trnK-UUU TACAGAAGCGACCCCATAGG TGAAAAATGCAAGCACGGTT 432–434 1.000 71.8
trnK-UUU_p1 trnK-UUU GGACTCCCAAGCACACAAAT TATCACGCACACATGACTGG 2979–2987 1.000 78.1
trnK-UUU_p2 trnK-UUU GGACTCCCAAGCACACAAAT ACGCACACATGACTGGATTT 2975–2983 1.000 77.3
trnK-UUU_p3 trnK-UUU ACTCCCAAGCACACAAATTCT TATCACGCACACATGACTGG 2977–2985 1.000 72.7
trnK-UUU_p4 trnK-UUU GGACTCCCAAGCACACAAA TATCACGCACACATGACTGG 2979–2987 1.000 72.2
trnK-UUU_p5 trnK-UUU ACTCCCAAGCACACAAATTCT ACGCACACATGACTGGATTT 2973–2981 1.000 71.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC AATCAAACCGAGAGACCCTT 818–825 1.000 70.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC ATCAAACCGAGAGACCCTTT 817–824 1.000 70.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA AATCAAACCGAGAGACCCTT 817–824 1.000 70.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA ATCAAACCGAGAGACCCTTT 816–823 1.000 70.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AAAGCGGAAGGGAAAGAGAG ATCAAACCGAGAGACCCTTT 886–893 1.000 68.0
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CCAGCGTAGACATATTGCCA AAGTATGCCCCCATCGTCTA 202 1.000 78.1
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACCAGCGTAGACATATTGCC AAGTATGCCCCCATCGTCTA 203 1.000 78.1
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC AGACAGCGAATTATTGGGCC AAGTATGCCCCCATCGTCTA 236 1.000 77.3
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC AAGTATGCCCCCATCGTCTA 181 1.000 77.3
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC AAGTATGCCCCCATCGTCTA 182 1.000 77.1

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
Crambe hispanica subsp. abyssinica MZ153236.1 153754 View on NCBI ↗
Crambe kralikii NC_049611.1 153919 View on NCBI ↗