Markers + reference

Lobularia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 153–153 kb
Candidate markers 268
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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1638 0.0295 0.99 74.3 yes View details
trnL-UAA-trnF-GAA LSC 360 0.0227 0.98 54.7 yes View details
ndhC-trnV-UAC LSC 704 0.0229 0.99 65.8 yes View details
petA-psbJ LSC 952 0.0222 0.99 67.5 yes View details
psbE-petL LSC 1238 0.0154 1.00 67.5 yes View details
petD LSC 1184 0.0101 1.00 50.0 yes View details
rpl16 LSC 1423 0.0178 0.99 58.7 yes View details
ycf1 SSC 1029 0.0010 1.00 55.1 no View details
ycf1 SSC 5325 0.0116 1.00 50.3 yes View details
psbI-trnS-GCU LSC 91 0.0471 0.93 79.2 yes View details
trnR-UCU-atpA LSC 74 0.0441 0.92 74.8 yes View details
trnW-CCA-trnP-UGG LSC 190 0.0316 1.00 70.7 yes View details
petN-psbM LSC 549 0.0150 0.97 68.5 yes View details
trnH-GUG-psbA LSC 290 0.0208 0.99 65.1 yes View details
ycf3-trnS-GGA LSC 240 0.0208 1.00 64.5 yes View details
trnS-GCU-trnG LSC 652 0.0154 0.99 64.3 yes View details
trnT-GGU-psbD LSC 1028 0.0059 0.98 63.7 yes View details
trnF-GAA LSC 73 0.0411 1.00 63.0 yes View details
ndhE-ndhG SSC 272 0.0193 0.95 63.0 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-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGTTGAGGCTCCATCTACCA 344–346 1.000 80.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 346–348 1.000 80.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 361–363 1.000 80.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGTTGAGGCTCCATCTACCA 345–347 1.000 80.2
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 364–366 1.000 80.1
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AACTCTACCGCAGATCTGGA GAGGTTCGAATCCTTCCGTC 1764–1785 1.000 80.9
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1696–1717 1.000 80.9
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1695–1716 1.000 80.9
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 1682–1703 1.000 78.5
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 1707–1728 1.000 77.6
psbI-trnS-GCU_p1 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT TAGGAGAGATGGCTGAGTGG 219–225 1.000 59.0
psbI-trnS-GCU_p2 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT TGAGTGGACTAAAGCGTTGG 206–212 1.000 58.5
psbI-trnS-GCU_p3 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT GCTGAGTGGACTAAAGCGTT 208–214 1.000 58.2
psbI-trnS-GCU_p4 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 169–175 1.000 57.5
psbI-trnS-GCU_p5 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT ATGGCTGAGTGGACTAAAGC 211–217 1.000 56.5
trnS-GCU-trnG_p1 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA AGGGGTTAAAGGAACGAATCA 727–730 1.000 63.6
trnS-GCU-trnG_p2 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA GGGGTTAAAGGAACGAATCAC 726–729 1.000 63.3
trnS-GCU-trnG_p3 trnS-GCU-trnG AACGCTTTAGTCCACTCAGC AGGGGTTAAAGGAACGAATCA 725–728 1.000 63.3
trnS-GCU-trnG_p4 trnS-GCU-trnG AACGCTTTAGTCCACTCAGC GGGGTTAAAGGAACGAATCAC 724–727 1.000 63.0
trnS-GCU-trnG_p5 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA AACCGAGAGACCCTTTAACT 752–755 1.000 62.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC TAACCCCTGAAGCAGAAAGC 227–233 1.000 73.5
trnR-UCU-atpA_p2 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC AAGAGCAACTGGAGCGTTTT 188–194 1.000 73.2
trnR-UCU-atpA_p3 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC AGCAACTGGAGCGTTTTCTA 185–191 1.000 71.5
trnR-UCU-atpA_p4 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC ATTCAAGAGCAACTGGAGCG 192–198 1.000 71.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC GCAACTGGAGCGTTTTCTAC 184–190 1.000 71.1
petN-psbM_p1 petN-psbM TCGTAGTGTGGGGAAGAAGT GCACTCTTCATTCTCGTTCCT 633–650 1.000 74.8
petN-psbM_p2 petN-psbM CGTAGTGTGGGGAAGAAGTG GCACTCTTCATTCTCGTTCCT 632–649 1.000 74.2
petN-psbM_p3 petN-psbM TCGTAGTGTGGGGAAGAAGT ACTGCACTCTTCATTCTCGT 636–653 1.000 74.1
petN-psbM_p4 petN-psbM CGTAGTGTGGGGAAGAAGTG ACTGCACTCTTCATTCTCGT 635–652 1.000 73.5
petN-psbM_p5 petN-psbM CTCTCGTAGTGTGGGGAAGA GCACTCTTCATTCTCGTTCCT 636–653 1.000 73.5

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
Lobularia libyca NC_035513.1 152542 View on NCBI ↗
Lobularia maritima NC_009274.1 152659 View on NCBI ↗