Markers + reference

Boechera

6 species · Brassicaceae · Brassicales

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Species 6
Genome length 155–155 kb
Candidate markers 270
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 304 0.0300 0.96 65.3 yes View details
trnK-AAA-rps16 LSC 684 0.0186 0.97 62.7 yes View details
rpoB-trnC-UGC LSC 1100 0.0105 1.00 55.3 yes View details
psbM-trnD-GAC LSC 1016 0.0118 0.99 59.2 yes View details
ndhC-trnV-GUA LSC 843 0.0142 0.99 70.3 yes View details
rbcL-accD LSC 680 0.0163 0.99 50.2 yes View details
accD-psaI LSC 672 0.0151 0.99 70.6 yes View details
trnP-CCA-psaJ LSC 373 0.0145 0.99 57.5 yes View details
psaJ-rpl33 LSC 423 0.0214 1.00 52.1 yes View details
ycf1 IRb 1032 0.0006 1.00 33.1 no View details
rpl32-trnL-CUA SSC 786 0.0188 1.00 71.7 yes View details
rps15-ycf1 SSC 3444 0.0102 1.00 52.1 yes View details
ycf1 SSC 2247 0.0073 1.00 59.4 yes View details
trnT-ACA-trnL-UUA LSC 764 0.0140 1.00 68.4 yes View details
psbZ-trnG-GGC LSC 477 0.0091 0.99 64.4 yes View details
trnE-GAA-trnT-ACC LSC 807 0.0116 1.00 62.6 yes View details
atpH-atpI LSC 498 0.0102 1.00 61.6 yes View details
psbE-petL LSC 1375 0.0078 1.00 59.8 yes View details
trnR-AGA-atpA LSC 281 0.0135 1.00 58.9 yes View details
trnT-ACC-psbD LSC 1233 0.0079 1.00 57.9 yes View details
atpF-atpH LSC 465 0.0123 1.00 57.8 yes View details
rps16-trnQ-CAA LSC 429 0.0092 0.99 56.7 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-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 366–391 1.000 87.1
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 369–394 1.000 87.0
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GGTGTAGCTGGTGTATTCGG 783–808 1.000 82.7
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CTGCGACTGCTGTTTTCTTG 926–951 1.000 82.3
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CTGCGACTGCTGTTTTCTTG 927–952 1.000 82.1
trnK-AAA-rps16_p1 trnK-AAA-rps16 CTACCGCAGATTTGGACGAA CCCAATGAGCCGTTTATCGA 976–1036 1.000 85.1
trnK-AAA-rps16_p2 trnK-AAA-rps16 CTACCGCAGATTTGGACGAA TCCCAATGAGCCGTTTATCG 977–1037 1.000 85.1
trnK-AAA-rps16_p3 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1007–1067 1.000 84.9
trnK-AAA-rps16_p4 trnK-AAA-rps16 CTACCGCAGATTTGGACGAA GGTTTGTTGCTGCCCTTTTT 1463–1514 1.000 84.1
trnK-AAA-rps16_p5 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG GGTTTGTTGCTGCCCTTTTT 1494–1545 1.000 83.9
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 492–520 1.000 81.8
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 502–530 1.000 81.0
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 518–546 1.000 79.4
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 519–547 1.000 79.3
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 520–548 1.000 77.6
trnR-AGA-atpA_p1 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC TCATAGCCTCGACCAAGACA 461–470 1.000 72.3
trnR-AGA-atpA_p2 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC CGACCAAGACATTAACCGCT 452–461 1.000 71.3
trnR-AGA-atpA_p3 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC TCGACCAAGACATTAACCGC 453–462 1.000 71.3
trnR-AGA-atpA_p4 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 403–412 1.000 71.2
trnR-AGA-atpA_p5 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC TTCAAGAGCAACTGGAACGT 404–413 1.000 71.1
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 581–583 1.000 77.8
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 554–556 1.000 74.5
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 585–587 1.000 74.0
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 580–582 1.000 73.3
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 556–558 1.000 72.8
atpH-atpI_p1 atpH-atpI AACCGAAGCAGCAGAAATCA TACAAGCGGGATTCAAGCTC 602–609 1.000 81.3
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 660–667 1.000 81.1
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 642–649 1.000 81.0
atpH-atpI_p4 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 664–671 1.000 80.4
atpH-atpI_p5 atpH-atpI AACCGAAGCAGCAGAAATCA ACCTGTCATGTTCCTGGGAT 626–633 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Boechera breweri NC_049593.1 155147 View on NCBI ↗
Boechera davidsonii NC_049594.1 154935 View on NCBI ↗
Boechera puberula NC_049597.1 155011 View on NCBI ↗
Boechera pulchra NC_049598.1 155348 View on NCBI ↗
Boechera stricta NC_049599.1 155033 View on NCBI ↗
Boechera suffrutescens NC_049600.1 155114 View on NCBI ↗