Markers + reference

Pachycladon

5 species · Brassicaceae · Brassicales

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Species 5
Genome length 154–155 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

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 274 0.0418 1.00 85.9 yes View details
trnK-rps16 LSC 666 0.0214 0.97 67.0 yes View details
rps16 LSC 1154 0.0116 1.00 57.6 yes View details
rps16-trnQ LSC 420 0.0228 1.00 67.8 yes View details
rpoB-trnC LSC 1119 0.0134 0.99 58.3 yes View details
psbM-trnD LSC 998 0.0132 0.99 62.0 yes View details
trnT-trnL LSC 764 0.0178 1.00 66.9 yes View details
atpB-rbcL LSC 801 0.0145 1.00 61.9 yes View details
psbE-petL LSC 1278 0.0153 1.00 66.2 yes View details
rpl32-trnL SSC 792 0.0235 0.99 63.0 yes View details
ycf1 SSC 5376 0.0107 1.00 45.6 yes View details
ndhK-ndhC LSC 66 0.0626 1.00 73.2 yes View details
atpH-atpI LSC 504 0.0175 1.00 69.2 yes View details
psbZ-trnG LSC 481 0.0188 1.00 66.8 yes View details
trnG-trnR LSC 153 0.0227 0.98 63.8 yes View details
clpP-psbB LSC 487 0.0103 1.00 62.0 yes View details
psbC-trnS LSC 175 0.0143 1.00 61.6 yes View details
rpl33-rps18 LSC 241 0.0111 0.96 60.6 yes View details
trnE-trnT LSC 817 0.0121 1.00 59.8 yes View details
trnT-psbD LSC 1138 0.0093 1.00 58.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 330–396 1.000 86.0
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 331–397 1.000 85.8
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 345–411 1.000 85.6
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 348–414 1.000 85.5
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 346–412 1.000 85.4
trnK-rps16_p1 trnK-rps16 TACCGTTGAGTTAGCAACCC ACGGAATTAAGTCTTAATAAAACGA 688–790 0.800 37.5
trnK-rps16_p2 trnK-rps16 AAAGCCGAGTACTCTACCGT ACGGAATTAAGTCTTAATAAAACGA 702–804 0.800 37.4
trnK-rps16_p3 trnK-rps16 AAGCCGAGTACTCTACCGTT ACGGAATTAAGTCTTAATAAAACGA 701–803 0.800 37.4
trnK-rps16_p4 trnK-rps16 AAAGCCGAGTACTCTACCGT ACGGAATTAAGTCTTAATAAAACGAA 702–804 0.800 37.4
trnK-rps16_p5 trnK-rps16 AAGCCGAGTACTCTACCGTT ACGGAATTAAGTCTTAATAAAACGAA 701–803 0.800 37.4
rps16_p1 rps16 ACGAGTCTTTCACATCCTCT TCAATTACACAAACTAGAGGAATGT 1213–1235 1.000 42.9
rps16_p2 rps16 ACGAGTCTTTCACATCCTCTT TCAATTACACAAACTAGAGGAATGT 1213–1235 1.000 42.9
rps16_p3 rps16 ACGAGTCTTTCACATCCTCT TGAATCAATTACACAAACTAGAGGA 1217–1239 1.000 42.9
rps16_p4 rps16 ACGAGTCTTTCACATCCTCT CAATTACACAAACTAGAGGAATGT 1212–1234 1.000 42.9
rps16_p5 rps16 ACGAGTCTTTCACATCCTCT TACACAAACTAGAGGAATGTT 1208–1230 1.000 42.9
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 440–523 1.000 85.2
rps16-trnQ_p2 rps16-trnQ CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 450–533 1.000 84.4
rps16-trnQ_p3 rps16-trnQ CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 466–549 1.000 82.9
rps16-trnQ_p4 rps16-trnQ TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 467–550 1.000 82.8
rps16-trnQ_p5 rps16-trnQ ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 468–551 1.000 81.1
trnG-trnR_p1 trnG-trnR AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 275–295 1.000 50.8
trnG-trnR_p2 trnG-trnR ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 281–301 1.000 50.7
trnG-trnR_p3 trnG-trnR CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 295–315 1.000 50.3
trnG-trnR_p4 trnG-trnR AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 283–303 1.000 50.3
trnG-trnR_p5 trnG-trnR AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 276–296 1.000 49.8
atpH-atpI_p1 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 668–676 1.000 81.2
atpH-atpI_p2 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 650–658 1.000 81.1
atpH-atpI_p3 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 672–680 1.000 80.5
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCCACTTTAGCTGCG 645–653 1.000 80.4
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTTGCCACTTTAGCTGCG 627–635 1.000 80.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Pachycladon cheesemanii NC_021102.1 154498 View on NCBI ↗
Pachycladon enysii NC_018565.1 154896 View on NCBI ↗
Pachycladon exile NC_069358.1 154578 View on NCBI ↗
Pachycladon fastigiatum KU170142.1 154492 View on NCBI ↗
Pachycladon radicatum NC_069342.1 154670 View on NCBI ↗