Markers + reference

Arabidella

7 species · Brassicaceae · Brassicales

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Species 7
Genome length 154–155 kb
Candidate markers 265
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 283 0.0563 0.96 75.0 yes View details
trnS-trnT LSC 659 0.0267 0.98 70.9 yes View details
trnR-atpA LSC 291 0.0386 0.92 64.3 yes View details
trnT-trnL LSC 787 0.0259 0.99 67.4 yes View details
trnL-trnF LSC 833 0.0951 0.74 72.6 yes View details
trnF-ndhJ LSC 592 0.0155 0.98 60.8 yes View details
petA-psbJ LSC 987 0.0235 0.98 63.4 yes View details
rpl16 LSC 1509 0.0145 0.97 61.4 yes View details
ycf1 IRb 1032 0.0025 1.00 37.8 no View details
ndhF-rpl32 SSC 835 0.0270 1.00 67.9 yes View details
rpl32-trnL SSC 784 0.0376 0.99 76.1 yes View details
ycf1 SSC 5379 0.0146 1.00 50.1 yes View details
psaA-ycf3 LSC 717 0.0119 0.95 70.1 yes View details
psaI-ycf4 LSC 402 0.0118 1.00 63.5 yes View details
rpoB-trnC LSC 1100 0.0149 1.00 63.4 yes View details
rps12-clpP LSC 181 0.0284 1.00 63.2 yes View details
rpl20-rps12 LSC 757 0.0143 1.00 63.1 yes View details
rps16-trnQ LSC 421 0.0249 0.98 62.3 yes View details
trnE-trnT LSC 820 0.0166 0.99 62.3 yes View details
trnT-psbD LSC 1132 0.0163 0.98 61.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 330–347 1.000 89.1
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 345–362 1.000 88.9
trnH-psbA_p3 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 331–348 1.000 88.9
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 348–365 1.000 88.8
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 346–363 1.000 88.7
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 488–494 1.000 85.3
rps16-trnQ_p2 rps16-trnQ CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 498–504 1.000 84.4
rps16-trnQ_p3 rps16-trnQ TCAATTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 495–501 1.000 81.0
rps16-trnQ_p4 rps16-trnQ AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 492–498 1.000 80.5
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 518–524 1.000 80.1
trnS-trnT_p1 trnS-trnT CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCA 720–748 1.000 60.4
trnS-trnT_p2 trnS-trnT AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCA 718–746 1.000 60.1
trnS-trnT_p3 trnS-trnT CCAACGCTTTAGTCCACTCA AGGGATTAAAGGAACGAATCACA 730–758 1.000 59.6
trnS-trnT_p4 trnS-trnT AACGCTTTAGTCCACTCAGC AGGGATTAAAGGAACGAATCACA 728–756 1.000 59.3
trnS-trnT_p5 trnS-trnT ACACACCGAGAAAGGGAAAG GGAACGAATCACACTTTTACCA 797 0.143 19.0
trnR-atpA_p1 trnR-atpA GGTTCAAATCCTATTGGACGC TCAAGAGCAACTGGAACGTT 323–359 1.000 74.4
trnR-atpA_p2 trnR-atpA GCGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 413–416 0.429 54.2
trnR-atpA_p3 trnR-atpA GCGAAAAGCGTCCATTGTC TTCAAGAGCAACTGGAACGT 414–417 0.429 54.2
trnR-atpA_p4 trnR-atpA GCGAAAAGCGTCCATTGTCT TCAAGAGCAACTGGAACGTT 413–416 0.429 50.4
trnR-atpA_p5 trnR-atpA GCGAAAAGCGTCCATTGTCT TTCAAGAGCAACTGGAACGT 414–417 0.429 50.4
rpoB-trnC_p1 rpoB-trnC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1188–1197 1.000 82.1
rpoB-trnC_p2 rpoB-trnC CCCTCTTTTCCATCCCCAAG CCGGATTTGAACTGGGGAAA 1185–1194 1.000 82.1
rpoB-trnC_p3 rpoB-trnC CTCTTTTCCATCCCCAAGCA CCGGATTTGAACTGGGGAAA 1183–1192 1.000 81.6
rpoB-trnC_p4 rpoB-trnC TCCCTCTTTTCCATCCCCAA CCGGATTTGAACTGGGGAAA 1186–1195 1.000 81.4
rpoB-trnC_p5 rpoB-trnC TTCCCTCTTTTCCATCCCCA CCGGATTTGAACTGGGGAAA 1187–1196 1.000 81.4
trnE-trnT_p1 trnE-trnT TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 889–906 1.000 82.4
trnE-trnT_p2 trnE-trnT TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 868–885 1.000 82.1
trnE-trnT_p3 trnE-trnT TGTCCTGAACCACTAGACGA TGGCGTTACTCTACCACTGA 865–882 1.000 81.9
trnE-trnT_p4 trnE-trnT TGTCCTGAACCACTAGACGA CCGATGACTTACGCCTTACC 886–903 1.000 81.3
trnE-trnT_p5 trnE-trnT TGTCCTGAACCACTAGACGA TTGAACCGATGACTTACGCC 891–908 1.000 80.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Arabidella chrysodema NC_069351.1 155337 View on NCBI ↗
Arabidella eremigena NC_069352.1 154701 View on NCBI ↗
Arabidella filifolia NC_069344.1 155076 View on NCBI ↗
Arabidella glaucescens NC_069345.1 154993 View on NCBI ↗
Arabidella nasturtium NC_069346.1 154986 View on NCBI ↗
Arabidella procumbens NC_069338.1 154421 View on NCBI ↗
Arabidella trisecta NC_049590.1 155067 View on NCBI ↗