Markers + reference

Cochlearia

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 155–155 kb
Candidate markers 261
Primer pairs 85

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 6 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 1041 0.0016 1.00 44.8 no View details
ndhF SSC 2241 0.2837 0.91 80.9 yes View details
ndhF-rpl32 SSC 851 0.2424 0.88 81.6 yes View details
rpl32-trnL SSC 960 0.2498 0.90 82.2 yes View details
ccsA SSC 987 0.2481 0.74 68.2 yes View details
ndhD SSC 1524 0.2817 0.85 71.4 yes View details
ndhE SSC 306 0.2707 0.94 67.9 yes View details
ndhE-ndhG SSC 268 0.3022 0.95 68.0 yes View details
ndhA SSC 2191 0.2731 0.84 79.1 yes View details
ndhH SSC 1182 0.2530 0.80 69.9 yes View details
ycf1 SSC 5322 0.2011 0.86 75.7 yes View details
ndhG SSC 531 0.2640 0.89 80.7 yes View details
ndhD-psaC SSC 142 0.2500 0.83 73.7 yes View details
ndhI SSC 483 0.2664 0.83 68.4 yes View details
psaC-ndhE SSC 248 0.2507 0.90 66.5 yes View details
ndhG-ndhI SSC 361 0.2373 0.85 66.4 yes View details
accD-psaI LSC 641 0.0081 1.00 65.6 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
accD-psaI_p1 accD-psaI TGGATGCAATTGTACCACGT ATTGCAAGTGCCGGAAAAAC 810–880 1.000 79.0
accD-psaI_p2 accD-psaI TGGATGCAATTGTACCACGT CATTGCAAGTGCCGGAAAAA 811–881 1.000 79.0
accD-psaI_p3 accD-psaI TGGATGCAATTGTACCACGT AAAGAAGCCATTGCAAGTGC 819–889 1.000 78.8
accD-psaI_p4 accD-psaI TGGATGCAATTGTACCACGT TGCAAGTGCCGGAAAAACTA 808–878 1.000 77.5
accD-psaI_p5 accD-psaI TGGATGCAATTGTACCACGT GCAAGTGCCGGAAAAACTAG 807–877 1.000 77.4
ndhF_p1 ndhF GGATGATGAATTCCACGTTCG TGAAATCCACATGAGAGCCC 80–2984 0.750 65.9
ndhF_p2 ndhF GGATGATGAATTCCACGTTCG AAATCCACATGAGAGCCCTC 80–2982 0.750 63.5
ndhF_p3 ndhF GGATGATGAATTCCACGTTCG GAAATCCACATGAGAGCCCT 80–2983 0.750 63.5
ndhF_p4 ndhF GATGAATTCCACGTTCGAACA TGAAATCCACATGAGAGCCC 80–2980 0.750 62.0
ndhF_p5 ndhF TGATGAATTCCACGTTCGAAC TGAAATCCACATGAGAGCCC 80–2981 0.750 62.0
ndhF-rpl32_p1 ndhF-rpl32 TCCACATGCGTCGAAGATTT TTTTTCCCCGTTTGGTTCCT 80–1229 0.750 80.0
ndhF-rpl32_p2 ndhF-rpl32 GCAATAGGTCGTGTGAACCA TTTTTCCCCGTTTGGTTCCT 80–1620 0.750 79.1
ndhF-rpl32_p3 ndhF-rpl32 TGCAATAGGTCGTGTGAACC TTTTTCCCCGTTTGGTTCCT 80–1621 0.750 79.1
ndhF-rpl32_p4 ndhF-rpl32 GGTCGTGTGAACCAAAAACC TTTTTCCCCGTTTGGTTCCT 80–1614 0.750 79.1
ndhF-rpl32_p5 ndhF-rpl32 TGGTTGCTGTCGGAAAAAGT TTTTTCCCCGTTTGGTTCCT 80–1208 0.750 78.8
rpl32-trnL_p1 rpl32-trnL TCGCTCGATATGGAGTACGA TGCAGACTGAGGCATTTTGT 80–1793 0.750 80.6
rpl32-trnL_p2 rpl32-trnL TCGCTCGATATGGAGTACGA TCGAACCGAGATGCTTTAGC 80–1283 0.750 80.1
rpl32-trnL_p3 rpl32-trnL TCGCTCGATATGGAGTACGA TCCTAAGAGCAGCGTGTCTA 80–1257 0.750 79.7
rpl32-trnL_p4 rpl32-trnL TCGCTCGATATGGAGTACGA AGCAGCGTGTCTACCAATTT 80–1250 0.750 79.2
rpl32-trnL_p5 rpl32-trnL TCGCTCGATATGGAGTACGA CTAAGAGCAGCGTGTCTACC 80–1255 0.750 79.2
trnL_p1 trnL AGCGAAATCAATAGGTTCTTGA TGCAGACTGAGGCATTTTGT 80–1324 0.750 48.4
trnL_p2 trnL AGCGAAATCAATAGGTTCTTGA AAAGTAGGTCCGACTTTGCG 80–1464 0.750 46.8
trnL_p3 trnL AGCGAAATCAATAGGTTCTTGA GTAGGTCCGACTTTGCGAAA 80–1461 0.750 46.8
trnL_p4 trnL AAGCGAAATCAATAGGTTCTTGA TGCAGACTGAGGCATTTTGT 80–1325 0.750 46.1
trnL_p5 trnL AGCGAAATCAATAGGTTCTTGAA TGCAGACTGAGGCATTTTGT 80–1324 0.750 46.1
ccsA_p1 ccsA GCTAAAGCATCTCGGTTCGA TTATCGATGGCTTCCCTTGC 80–1717 0.750 81.1
ccsA_p2 ccsA GTTTTGAACAAGTTGCCGCT TTATCGATGGCTTCCCTTGC 80–1776 0.750 81.1
ccsA_p3 ccsA AAGTTGCCGCTATGGTGAAA TTATCGATGGCTTCCCTTGC 80–1767 0.750 81.0
ccsA_p4 ccsA TAGACACGCTGCTCTTAGGA TTATCGATGGCTTCCCTTGC 80–1743 0.750 80.7
ccsA_p5 ccsA AGTTGCCGCTATGGTGAAAT TTATCGATGGCTTCCCTTGC 80–1766 0.750 80.7

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
Cochlearia borzaeana LN866844.1 154599 View on NCBI ↗
Cochlearia islandica LN866845.1 154570 View on NCBI ↗
Cochlearia pyrenaica LN866846.1 154569 View on NCBI ↗
Cochlearia tridactylites NC_029332.1 154718 View on NCBI ↗