Markers + reference

Megacarpaea

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

12 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
trnK-trnQ LSC 2325 0.0198 0.99 61.3 yes View details
trnS-trnT LSC 610 0.0286 1.00 68.1 yes View details
trnC-ycf6 LSC 620 0.0162 1.00 57.5 yes View details
psbM-trnD LSC 1056 0.0235 0.98 66.9 yes View details
trnD-trnY LSC 435 0.0324 1.00 64.1 yes View details
petA-psbJ LSC 1036 0.0242 0.94 65.5 yes View details
psbE-ORF31 LSC 955 0.0235 0.98 69.3 yes View details
rpl36-rps8 LSC 473 0.0352 1.00 68.1 yes View details
ycf1 IRb 1032 0.0062 1.00 48.7 no View details
ndhF-rpl32 SSC 810 0.0248 0.96 66.2 yes View details
rpl32-trnL SSC 907 0.0304 1.00 75.0 yes View details
ycf1 SSC 5337 0.0164 1.00 52.7 yes View details
trnH-psbA LSC 272 0.0392 1.00 78.1 yes View details
psbK-psbI LSC 293 0.0349 1.00 70.9 yes View details
trnT-trnR LSC 160 0.0270 0.99 69.1 yes View details
trnW-trnP LSC 186 0.0430 1.00 68.8 yes View details
trnR-atpA LSC 300 0.0282 0.98 67.9 yes View details
petD-rpoA LSC 219 0.0380 0.92 67.9 yes View details
rbcL-accD LSC 686 0.0215 0.99 66.8 yes View details
trnT-psbD LSC 1259 0.0174 0.96 66.4 yes View details
ndhE-ndhG SSC 261 0.0208 0.98 64.7 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 322–343 1.000 87.9
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 337–358 1.000 87.4
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 340–361 1.000 87.2
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT GCGCTAACCTTGGTATGGAA 387–408 1.000 86.5
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC GCGCTAACCTTGGTATGGAA 388–409 1.000 86.3
trnK-trnQ_p1 trnK-trnQ CCTTTCAGGATCAGTCGTGG GAGGTTCGAATCCTTCCGTC 2434–2478 1.000 85.3
trnK-trnQ_p2 trnK-trnQ TCAGGATCAGTCGTGGTCTT GAGGTTCGAATCCTTCCGTC 2430–2474 1.000 84.9
trnK-trnQ_p3 trnK-trnQ TTCAGGATCAGTCGTGGTCT GAGGTTCGAATCCTTCCGTC 2431–2475 1.000 84.9
trnK-trnQ_p4 trnK-trnQ AACTCTACCGCAGATCTGGA GAGGTTCGAATCCTTCCGTC 2407–2451 0.800 75.6
trnK-trnQ_p5 trnK-trnQ AAGCCGAGTACTCTACCGTT CTTACAGCTGCTTGCCAAAC 2902–2946 0.800 74.3
psbK-psbI_p1 psbK-psbI TGGCAAGCAGCTGTAAGTTT ACAAAAAGTTTGAGAGTAAGCA 338–346 1.000 47.0
psbK-psbI_p2 psbK-psbI TTGGCAAGCAGCTGTAAGTT ACAAAAAGTTTGAGAGTAAGCA 339–347 1.000 47.0
psbK-psbI_p3 psbK-psbI TTTGGCAAGCAGCTGTAAGT ACAAAAAGTTTGAGAGTAAGCA 340–348 1.000 47.0
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCA 341–349 1.000 46.9
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCAT 341–349 1.000 46.9
trnS-trnT_p1 trnS-trnT CCAACGCTTTAGTCCACTCA ACGAATCACACTTTTACCACT 675–763 1.000 55.1
trnS-trnT_p2 trnS-trnT AACGCTTTAGTCCACTCAGC ACGAATCACACTTTTACCACT 673–761 1.000 54.8
trnS-trnT_p3 trnS-trnT CCAACGCTTTAGTCCACTCA GAACGAATCACACTTTTACCACT 677–765 1.000 54.1
trnS-trnT_p4 trnS-trnT AACGCTTTAGTCCACTCAGC GAACGAATCACACTTTTACCACT 675–763 1.000 53.8
trnS-trnT_p5 trnS-trnT CCAACGCTTTAGTCCACTCA AACGAATCACACTTTTACCACT 676–764 1.000 53.2
trnT-trnR_p1 trnT-trnR AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 271–283 1.000 53.7
trnT-trnR_p2 trnT-trnR ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 277–289 1.000 53.6
trnT-trnR_p3 trnT-trnR AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 279–291 1.000 53.2
trnT-trnR_p4 trnT-trnR CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 291–303 1.000 53.1
trnT-trnR_p5 trnT-trnR AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 272–284 1.000 52.7
trnR-atpA_p1 trnR-atpA GGTTCAAATCCTATTGGACGC TCAAGAGCAACTGGAACGTT 349–365 1.000 71.7
trnR-atpA_p2 trnR-atpA GGTTCAAATCCTATTGGACGC TTCAAGAGCAACTGGAACGT 350–366 1.000 71.6
trnR-atpA_p3 trnR-atpA CGAAAAGCGTCCATTGTCTA TCAAGAGCAACTGGAACGTT 405–421 1.000 70.1
trnR-atpA_p4 trnR-atpA CGAAAAGCGTCCATTGTCTA TTCAAGAGCAACTGGAACGT 406–422 1.000 70.1
trnR-atpA_p5 trnR-atpA CGAAAAGCGTCCATTGTCTAA TCAAGAGCAACTGGAACGTT 405–421 1.000 68.1

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
Megacarpaea delavayi NC_034360.1 154401 View on NCBI ↗
Megacarpaea gigantea PX512475.1 154793 View on NCBI ↗
Megacarpaea megalocarpa NC_086849.1 154877 View on NCBI ↗
Megacarpaea orbiculata PX512477.1 154680 View on NCBI ↗
Megacarpaea polyandra NC_049678.1 154949 View on NCBI ↗