Markers + reference

Capsella

4 species · Brassicaceae · Brassicales

Back to catalogue

Species 4
Genome length 154–155 kb
Candidate markers 258
Primer pairs 110

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 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 290 0.0224 1.00 67.3 yes View details
trnK-rps16 LSC 675 0.0126 0.99 53.5 yes View details
rps16-trnQ LSC 395 0.0152 1.00 34.1 yes View details
trnT-psbD LSC 1257 0.0091 1.00 52.0 yes View details
trnL-trnF LSC 687 0.0116 1.00 52.1 yes View details
ndhC-trnV LSC 839 0.0114 1.00 53.3 yes View details
rbcL-accD LSC 712 0.0103 0.96 54.9 yes View details
psaJ-rpl33 LSC 429 0.0179 1.00 57.2 yes View details
clpP LSC 2037 0.0029 0.99 36.1 yes View details
ycf1 IRb 1026 0.0026 1.00 27.0 no View details
ndhF-rpl32 SSC 824 0.0103 1.00 64.1 yes View details
rpl32-trnL SSC 728 0.0098 1.00 60.2 yes View details
ycf1 SSC 5370 0.0061 1.00 51.1 yes View details
trnE-trnT LSC 830 0.0086 0.98 66.3 yes View details
rpl20-rps12 LSC 767 0.0048 1.00 62.2 yes View details
trnG-trnR LSC 157 0.0244 0.99 59.9 yes View details
accD LSC 1455 0.0015 1.00 54.6 yes View details
petA-psbJ LSC 978 0.0080 1.00 54.5 yes View details
atpB-rbcL LSC 799 0.0054 1.00 53.1 yes View details
rpoB-trnC LSC 1098 0.0053 1.00 52.9 yes View details
ycf3-trnS LSC 1077 0.0029 1.00 52.3 yes View details
rps12-clpP LSC 180 0.0296 0.99 51.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 363–365 1.000 80.8
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 366–368 1.000 80.7
trnH-psbA_p3 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 364–366 1.000 80.6
trnH-psbA_p4 trnH-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 367–369 1.000 80.5
trnH-psbA_p5 trnH-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 356–358 1.000 79.3
trnK_p1 trnK TCCCAAGCGCACAAATTCT TTGATCCCTGACGTACACAC 2949–2961 1.000 66.7
trnK_p2 trnK CCCAAGCGCACAAATTCTCT TTGATCCCTGACGTACACAC 2948–2960 1.000 66.1
trnK_p3 trnK CCCAAGCGCACAAATTCTCT TGCCAACATTGTATGGACCA 2999–3000 0.500 46.5
trnK_p4 trnK TCCCAAGCGCACAAATTCT TGCCAACATTGTATGGACCA 3000 0.250 37.0
trnK_p5 trnK TCCCAAGCGCACAAATTCTC TGCCAACATTGTATGGACCA 3000 0.250 36.3
trnK-rps16_p1 trnK-rps16 CTACCGCAGATTTGGACGAA AAAGGAGCTCACCCAACAAG 860–866 1.000 82.0
trnK-rps16_p2 trnK-rps16 CTACCGCAGATTTGGACGAA AAGGATTCTCCGGCGAGATA 1255–1260 1.000 81.5
trnK-rps16_p3 trnK-rps16 CTACCGCAGATTTGGACGAA TAAGGATTCTCCGGCGAGAT 1256–1261 1.000 81.5
trnK-rps16_p4 trnK-rps16 CCTTTCAGGATCAGTCGTGG AAGGATTCTCCGGCGAGATA 1286–1291 1.000 81.4
trnK-rps16_p5 trnK-rps16 CCTTTCAGGATCAGTCGTGG TAAGGATTCTCCGGCGAGAT 1287–1292 1.000 81.4
rps16-trnQ_p1 rps16-trnQ CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 460–470 1.000 74.8
rps16-trnQ_p2 rps16-trnQ GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 463–473 1.000 72.6
rps16-trnQ_p3 rps16-trnQ CGTTGCTTTCTACCACATCG ATAAAAAGCGAAATGGGGCG 521–531 1.000 70.6
rps16-trnQ_p4 rps16-trnQ CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 464–474 1.000 70.1
rps16-trnQ_p5 rps16-trnQ CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 490–500 1.000 69.9
trnG-trnR_p1 trnG-trnR AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTATGTCCT 241–243 1.000 47.4
trnG-trnR_p2 trnG-trnR ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTATGTCCT 247–249 1.000 47.3
trnG-trnR_p3 trnG-trnR AGCCTTCCAAGCTAACGATG AGAAGACCTATGTCCTATCCA 235–237 1.000 47.2
trnG-trnR_p4 trnG-trnR ACCCTTAGCCTTCCAAGCTA AGAAGACCTATGTCCTATCCA 241–243 1.000 47.1
trnG-trnR_p5 trnG-trnR CGACGTCGACTAAAACCCTT AGGTTTAGAAGACCTATGTCCT 261–263 1.000 47.0
rpoB-trnC_p1 rpoB-trnC CCGGGTATTGTAGATGTTCCC CCGGATTTGAACTGGGGAAA 1200–1201 1.000 71.0
rpoB-trnC_p2 rpoB-trnC GTTCCCTCTTTTTCATCCCCA CCGGATTTGAACTGGGGAAA 1185–1186 1.000 70.7
rpoB-trnC_p3 rpoB-trnC TGTTCCCTCTTTTTCATCCCC CCGGATTTGAACTGGGGAAA 1186–1187 1.000 70.7
rpoB-trnC_p4 rpoB-trnC CCGGGTATTGTAGATGTTCCC TAAGTCTGTTGTTGAGGCGG 1223–1224 1.000 70.4
rpoB-trnC_p5 rpoB-trnC GTTCCCTCTTTTTCATCCCCA TAAGTCTGTTGTTGAGGCGG 1208–1209 1.000 70.0

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
Capsella bursa-pastoris NC_009270.1 154490 View on NCBI ↗
Capsella grandiflora NC_028517.1 154638 View on NCBI ↗
Capsella orientalis NC_081111.1 154549 View on NCBI ↗
Capsella rubella NC_027693.1 154601 View on NCBI ↗