Markers + reference

Ricotia

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 154–154 kb
Candidate markers 258
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 281 0.1009 0.94 78.4 yes View details
trnK-trnQ LSC 2190 0.0353 0.98 73.3 yes View details
trnS-trnT LSC 626 0.0456 0.99 80.5 yes View details
trnE-trnT LSC 662 0.0418 1.00 83.1 yes View details
ycf9-trnG LSC 505 0.0442 0.99 81.7 yes View details
psbE-ORF31 LSC 1375 0.0449 0.98 78.0 yes View details
trnP-psaJ LSC 334 0.0334 1.00 67.3 yes View details
psaJ-rpl33 LSC 423 0.0557 1.00 78.6 yes View details
ycf1 IRb 1032 0.0032 1.00 37.0 no View details
ndhF-rpl32 SSC 848 0.0427 0.96 79.7 yes View details
rpl32-trnL SSC 914 0.0491 0.97 81.3 yes View details
rps15-ycf1 SSC 378 0.0534 0.93 77.1 yes View details
ycf1 SSC 5391 0.0283 1.00 59.0 yes View details
trnL-ycf5 SSC 114 0.0556 0.99 83.4 yes View details
trnM-atpE LSC 147 0.0509 0.97 79.5 yes View details
psbG-ndhC LSC 64 0.0781 1.00 78.7 yes View details
petD-rpoA LSC 205 0.0504 1.00 76.9 yes View details
psbI-trnS LSC 90 0.0574 0.99 75.3 yes View details
ORF31-petG LSC 197 0.0372 0.95 73.3 yes View details
trnW-trnP LSC 187 0.0349 0.99 72.7 yes View details
trnD-trnY LSC 416 0.0317 1.00 72.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT TGAGGCTCCATCTACAAATGG 311–334 1.000 78.4
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC TGAGGCTCCATCTACAAATGG 312–335 1.000 78.2
trnH-psbA_p3 trnH-psbA AATCCACTTGGCTACATCCG TGAGGCTCCATCTACAAATGG 304–327 1.000 76.8
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTGAGGCTCCATCTACAAATGG 312–335 1.000 74.0
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC TTGAGGCTCCATCTACAAATGG 313–336 1.000 73.8
trnK-trnQ_p1 trnK-trnQ AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2201–2248 1.000 85.5
trnK-trnQ_p2 trnK-trnQ AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2200–2247 1.000 85.5
trnK-trnQ_p3 trnK-trnQ TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 2187–2234 1.000 83.2
trnK-trnQ_p4 trnK-trnQ AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 2212–2259 1.000 82.3
trnK-trnQ_p5 trnK-trnQ TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 2210–2257 1.000 81.0
psbI-trnS_p1 psbI-trnS AAATCTTGACGCATGGACGA TAGGAGAGATGGCTGAGTGG 504–654 1.000 86.5
psbI-trnS_p2 psbI-trnS AATCTTGACGCATGGACGAA TAGGAGAGATGGCTGAGTGG 503–653 1.000 86.5
psbI-trnS_p3 psbI-trnS AATCGTAGATGTGATGCCCG TAGGAGAGATGGCTGAGTGG 665–815 1.000 85.6
psbI-trnS_p4 psbI-trnS GTTTGGCAAGCAGCTGTAAG TAGGAGAGATGGCTGAGTGG 756–763 0.750 72.6
psbI-trnS_p5 psbI-trnS GTTTGGCAAGCAGCTGTAAG TGAGTGGACTAAAGCGTTGG 743–750 0.750 72.0
trnS-trnT_p1 trnS-trnT CCAACGCTTTAGTCCACTCA TACCACTAAACTATACCCGC 677–704 1.000 55.2
trnS-trnT_p2 trnS-trnT AACGCTTTAGTCCACTCAGC TACCACTAAACTATACCCGC 675–702 1.000 54.9
trnS-trnT_p3 trnS-trnT CCAACGCTTTAGTCCACTCA TTACCACTAAACTATACCCGC 678–705 1.000 54.1
trnS-trnT_p4 trnS-trnT AGAACGGGAAAGAGAGGGAT TACCACTAAACTATACCCGC 739–766 1.000 53.8
trnS-trnT_p5 trnS-trnT AACGCTTTAGTCCACTCAGC TTACCACTAAACTATACCCGC 676–703 1.000 53.8
trnD-trnY_p1 trnD-trnY CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 483–498 1.000 82.2
trnD-trnY_p2 trnD-trnY CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 482–497 1.000 82.2
trnD-trnY_p3 trnD-trnY CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 504–519 1.000 81.1
trnD-trnY_p4 trnD-trnY CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 503–518 1.000 80.9
trnD-trnY_p5 trnD-trnY CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 537–552 1.000 80.4
trnE-trnT_p1 trnE-trnT GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 767–861 1.000 86.5
trnE-trnT_p2 trnE-trnT TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 746–840 1.000 86.5
trnE-trnT_p3 trnE-trnT GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 746–840 1.000 86.2
trnE-trnT_p4 trnE-trnT TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 725–819 1.000 86.2
trnE-trnT_p5 trnE-trnT GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 743–837 1.000 86.0

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
Ricotia carnosula NC_039957.1 154328 View on NCBI ↗
Ricotia cretica NC_039958.1 154188 View on NCBI ↗
Ricotia davisiana NC_039959.1 154380 View on NCBI ↗
Ricotia lunaria NC_039961.1 154244 View on NCBI ↗