Markers + reference

Leiospora

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 155–155 kb
Candidate markers 266
Primer pairs 110

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 347 0.0059 0.97 59.7 yes View details
trnK-AAA-rps16 LSC 692 0.0029 0.99 61.3 yes View details
trnS-AGC-trnG-GGA LSC 616 0.0033 0.99 61.3 yes View details
trnR-AGA-atpA LSC 308 0.0065 1.00 42.3 yes View details
rpoC2 LSC 4122 0.0012 1.00 49.1 yes View details
rpoB-trnC-UGC LSC 1106 0.0027 0.99 61.1 yes View details
atpB-rbcL LSC 793 0.0038 1.00 60.9 yes View details
psbE-petL LSC 1379 0.0022 0.99 60.5 yes View details
psaJ-rpl33 LSC 415 0.0024 1.00 47.6 yes View details
ycf1 IRb 1035 0.0019 1.00 59.9 yes View details
rps15 SSC 267 0.0000 1.00 23.5 yes View details
ycf1 SSC 5316 0.0017 1.00 52.7 yes View details
ndhF-rpl32 SSC 849 0.0024 1.00 60.2 yes View details
petN-psbM LSC 551 0.0036 1.00 60.0 yes View details
trnE-GAA-trnT-ACC LSC 631 0.0016 1.00 60.0 yes View details
rpoA LSC 984 0.0020 1.00 59.9 yes View details
ycf3-trnS-UCC LSC 1083 0.0018 1.00 59.8 yes View details
accD-psaI LSC 650 0.0015 1.00 59.8 yes View details
rpl16 LSC 1505 0.0013 1.00 59.8 yes View details
trnT-ACA-trnL-UUA LSC 773 0.0013 1.00 59.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 395–405 1.000 80.9
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GAGGCTCCATCTACAAACGG 389–399 1.000 80.9
trnH-CAC-psbA_p3 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 396–406 1.000 80.7
trnH-CAC-psbA_p4 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GAGGCTCCATCTACAAACGG 390–400 1.000 80.7
trnH-CAC-psbA_p5 trnH-CAC-psbA AATCCACTTGGCTACATCCG GCTGTTGAGGCTCCATCTAC 388–398 1.000 79.4
trnK-AAA-rps16_p1 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 782–788 1.000 76.4
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 783–789 1.000 76.3
trnK-AAA-rps16_p3 trnK-AAA-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 769–775 1.000 74.0
trnK-AAA-rps16_p4 trnK-AAA-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 794–800 1.000 73.1
trnK-AAA-rps16_p5 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AGGCAGGGATTTTTACGGAA 744–750 1.000 72.4
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCA 684–718 1.000 54.7
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCA 682–716 1.000 54.4
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AGGGATTAAAGGAACGAATCACA 694–728 1.000 54.0
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC AGGGATTAAAGGAACGAATCACA 692–726 1.000 53.7
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCAC 684–718 1.000 53.6
trnR-AGA-atpA_p1 trnR-AGA-atpA AGCCTTCCAAGCTAACGATG CCAGTCAGGGGATGTTTCAG 1144 1.000 79.0
trnR-AGA-atpA_p2 trnR-AGA-atpA TTCTGTGAAAGCACCCAGAC CCAGTCAGGGGATGTTTCAG 1345 1.000 79.0
trnR-AGA-atpA_p3 trnR-AGA-atpA ACCCTTAGCCTTCCAAGCTA CCAGTCAGGGGATGTTTCAG 1150 1.000 79.0
trnR-AGA-atpA_p4 trnR-AGA-atpA CGACGTCGACTAAAACCCTT CCAGTCAGGGGATGTTTCAG 1164 1.000 78.8
trnR-AGA-atpA_p5 trnR-AGA-atpA AAACCCTTAGCCTTCCAAGC CCAGTCAGGGGATGTTTCAG 1152 1.000 78.6
rpoC2_p1 rpoC2 TTGTGGACGTTTCCTCACAA CCCCTTAGGAACAGCCATTC 269 1.000 76.9
rpoC2_p2 rpoC2 TTTGTGGACGTTTCCTCACA CCCCTTAGGAACAGCCATTC 270 1.000 76.9
rpoC2_p3 rpoC2 TGTGGACGTTTCCTCACAAT CCCCTTAGGAACAGCCATTC 268 1.000 75.1
rpoC2_p4 rpoC2 TTGTGGACGTTTCCTCACAA ATTAAAAACTCGTCGGGCCC 286 1.000 73.0
rpoC2_p5 rpoC2 TTTGTGGACGTTTCCTCACA ATTAAAAACTCGTCGGGCCC 287 1.000 73.0
rpoB-trnC-UGC_p1 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1185–1194 1.000 79.0
rpoB-trnC-UGC_p2 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAAAGGATTTGCAGTCCCCC 1167–1176 1.000 76.8
rpoB-trnC-UGC_p3 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC TCAAGTCTGTTGTTGAGGCG 1209–1218 1.000 76.3
rpoB-trnC-UGC_p4 rpoB-trnC-UGC TGTTCCCTCTTTTCCATCCC CCGGATTTGAACTGGGGAAA 1186–1195 1.000 73.0
rpoB-trnC-UGC_p5 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAGTCTGTTGTTGAGGCGG 1207–1216 1.000 71.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Leiospora eriocalyx NC_050796.1 154896 View on NCBI ↗
Leiospora pamirica NC_050797.1 154907 View on NCBI ↗