Markers + reference

Cremolobus

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 155–155 kb
Candidate markers 260
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 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-trnG LSC 648 0.0237 0.98 61.4 yes View details
trnR-atpA LSC 295 0.0508 1.00 73.8 yes View details
atpH-atpI LSC 493 0.0329 0.99 68.7 yes View details
trnE-trnT LSC 821 0.0234 0.99 66.4 yes View details
trnT-trnL LSC 815 0.0233 1.00 66.3 yes View details
ycf1 IRb 1032 0.0048 1.00 48.6 no View details
rpl32-trnL SSC 875 0.0344 1.00 66.9 yes View details
ndhG-ndhI SSC 333 0.0370 0.97 62.3 yes View details
ycf1 SSC 5301 0.0249 1.00 56.7 yes View details
petD-rpoA LSC 199 0.0553 1.00 76.4 yes View details
trnH-psbA LSC 321 0.0381 0.98 72.4 yes View details
psbC-trnS LSC 181 0.0444 0.99 71.1 yes View details
rps16-trnQ LSC 439 0.0342 1.00 70.6 yes View details
psaJ-rpl33 LSC 426 0.0259 1.00 70.2 yes View details
atpF-atpH LSC 462 0.0238 1.00 69.6 yes View details
psbI-trnS LSC 91 0.0440 1.00 67.6 yes View details
rpl36-rps8 LSC 483 0.0231 0.99 67.5 yes View details
ndhJ-psbG LSC 103 0.0392 0.99 67.2 yes View details
rpoB-trnC LSC 1095 0.0239 0.99 66.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 378–379 1.000 82.3
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 393–394 1.000 82.1
trnH-psbA_p3 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 379–380 1.000 82.1
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 396–397 1.000 82.0
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 394–395 1.000 81.8
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 512–514 1.000 80.6
rps16-trnQ_p2 rps16-trnQ CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 522–524 1.000 79.8
rps16-trnQ_p3 rps16-trnQ CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 538–540 1.000 78.3
rps16-trnQ_p4 rps16-trnQ TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 539–541 1.000 78.2
rps16-trnQ_p5 rps16-trnQ ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 540–542 1.000 76.5
psbI-trnS_p1 psbI-trnS AATGATCCCGGACGTAATCC TTAATCGTACCGAGGGTTCG 163 1.000 68.5
psbI-trnS_p2 psbI-trnS AATGATCCCGGACGTAATCC GGGTTCGAATCCCTCTCTTT 150 1.000 66.8
psbI-trnS_p3 psbI-trnS AATGATCCCGGACGTAATCC GTTCGAATCCCTCTCTTTCCC 148 1.000 66.8
psbI-trnS_p4 psbI-trnS AATGATCCCGGACGTAATCC GGGTTCGAATCCCTCTCTTTC 150 1.000 66.7
psbI-trnS_p5 psbI-trnS AATGATCCCGGACGTAATCC GGTTCGAATCCCTCTCTTTCC 149 1.000 66.7
trnS-trnG_p1 trnS-trnG AGTCCACTCAGCCATCTCTC AATCAAACCGAGAGACCCTT 743–746 1.000 66.8
trnS-trnG_p2 trnS-trnG AGTCCACTCAGCCATCTCTC ATCAAACCGAGAGACCCTTT 742–745 1.000 66.8
trnS-trnG_p3 trnS-trnG AGTCCACTCAGCCATCTCTC AATCAAACCGAGAGACCCTTT 743–746 1.000 64.9
trnS-trnG_p4 trnS-trnG TAGTCCACTCAGCCATCTCT AATCAAACCGAGAGACCCTT 744–747 1.000 64.2
trnS-trnG_p5 trnS-trnG TAGTCCACTCAGCCATCTCT ATCAAACCGAGAGACCCTTT 743–746 1.000 64.2
trnR-atpA_p1 trnR-atpA GCGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 417–422 1.000 72.2
trnR-atpA_p2 trnR-atpA GCGAAAAGCGTCCATTGTC TTCAAGAGCAACTGGAACGT 418–423 1.000 72.2
trnR-atpA_p3 trnR-atpA GCGAAAAGCGTCCATTGTC ACATTAACCGCTGAAGCAGA 458–463 1.000 70.8
trnR-atpA_p4 trnR-atpA GCGAAAAGCGTCCATTGTC AGACATTAACCGCTGAAGCA 460–465 1.000 70.8
trnR-atpA_p5 trnR-atpA GCGAAAAGCGTCCATTGTCT TCAAGAGCAACTGGAACGTT 417–422 1.000 68.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 580–596 1.000 77.2
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 553–569 1.000 73.9
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 584–600 1.000 73.4
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 579–595 1.000 72.8
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 555–571 1.000 72.2

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
Cremolobus chilensis NC_065152.1 154552 View on NCBI ↗
Cremolobus peruvianus NC_049618.1 154690 View on NCBI ↗