Markers + reference

Colobanthus

7 species · Caryophyllaceae · Caryophyllales

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Species 7
Genome length 151–151 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

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF-rpl32 SSC 881 0.0067 1.00 40.2 yes View details
ycf1 SSC 5538 0.0043 1.00 36.1 yes View details
trnH-GUG-psbA LSC 263 0.0246 1.00 72.1 yes View details
trnK-UUU-rps16 LSC 555 0.0123 1.00 55.9 yes View details
petN-psbM LSC 586 0.0111 0.98 52.1 yes View details
psbM-trnD-GUC LSC 715 0.0115 1.00 54.7 yes View details
trnE-UUC-trnT-GGU LSC 542 0.0141 0.94 63.5 yes View details
petA-psbJ LSC 963 0.0090 0.98 48.4 yes View details
clpP LSC 2008 0.0044 1.00 49.3 yes View details
psbT-psbN LSC 71 0.0602 1.00 84.9 yes View details
rpl33-rps18 LSC 281 0.0130 0.95 66.6 yes View details
psaA-ycf3 LSC 1108 0.0068 1.00 64.8 yes View details
trnM-CAU-atpE LSC 254 0.0135 0.99 62.6 yes View details
psbE-petL LSC 1258 0.0065 0.99 61.2 yes View details
trnL-CAA-trnL-CAA LSC 182 0.0194 0.99 59.9 yes View details
trnG-GCC-trnfM-CAU LSC 200 0.0154 0.94 59.6 yes View details
trnS-GCU-trnG-UCC LSC 764 0.0067 1.00 56.7 yes View details
trnG-UCC-trnR-UCU LSC 162 0.0100 0.98 55.3 yes View details
rps4-trnT-UGU LSC 414 0.0061 0.98 55.1 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
ndhF-rpl32_p1 ndhF-rpl32 GCGTATTGGTATATATGTTCCA AGACTTTTTGGAAATAGAAGTACGT 945–950 1.000 41.4
ndhF-rpl32_p2 ndhF-rpl32 GCGTATTGGTATATATGTTCCA GACTTTTTGGAAATAGAAGTACGT 944–949 1.000 41.4
ndhF-rpl32_p3 ndhF-rpl32 GCGTATTGGTATATATGTTCCA AGACTTTTTGGAAATAGAAGTACGTT 945–950 1.000 41.4
ndhF-rpl32_p4 ndhF-rpl32 GCGTATTGGTATATATGTTCCAT AGACTTTTTGGAAATAGAAGTACGT 945–950 1.000 41.4
ndhF-rpl32_p5 ndhF-rpl32 GCGTATTGGTATATATGTTCCA ACTTTTTGGAAATAGAAGTACGT 943–948 1.000 41.4
ycf1_p1 ycf1 CCATGTGATTAGGGATTGTCGA AGTTTACAAAGAAATGGTTTCGA 225 1.000 43.2
ycf1_p2 ycf1 ACCATGTGATTAGGGATTGTCG AGTTTACAAAGAAATGGTTTCGA 226 1.000 43.2
ycf1_p3 ycf1 CCATGTGATTAGGGATTGTCGA AAGTTTACAAAGAAATGGTTTCGA 226 1.000 43.2
ycf1_p4 ycf1 ACCATGTGATTAGGGATTGTCG AAGTTTACAAAGAAATGGTTTCGA 227 1.000 43.2
ycf1_p5 ycf1 CCATGTGATTAGGGATTGTCG AGTTTACAAAGAAATGGTTTCGA 225 1.000 43.2
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 309–334 1.000 86.5
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCGAT 306–331 1.000 86.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 323–348 1.000 86.3
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 322–347 1.000 86.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 324–349 1.000 86.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA CGCTCAACCAACAGAAACTG 725–866 1.000 78.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC CGCTCAACCAACAGAAACTG 726–867 1.000 78.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA ATTCAAAAAGGCGCTCAACC 736–877 1.000 78.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC ATTCAAAAAGGCGCTCAACC 737–878 1.000 78.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTGTAGACGAATCCC CGCTCAACCAACAGAAACTG 737–878 1.000 77.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG CCGAGAGACCCCCTAACTAT 922–928 1.000 75.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG ACCGAGAGACCCCCTAACTA 923–929 1.000 75.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AAACCGAGAGACCCCCTAAC 925–931 1.000 75.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG CAAACCGAGAGACCCCCTAA 926–932 1.000 75.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CCGAGAGACCCCCTAACTAT 921–927 1.000 75.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 238–242 1.000 66.7
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 241–245 1.000 66.4
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 244–248 1.000 65.9
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 247–251 1.000 65.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 242–246 1.000 64.2

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
Colobanthus acicularis NC_053724.1 151050 View on NCBI ↗
Colobanthus affinis NC_053722.1 151314 View on NCBI ↗
Colobanthus apetalus NC_036424.1 151228 View on NCBI ↗
Colobanthus lycopodioides NC_053721.1 151462 View on NCBI ↗
Colobanthus nivicola NC_053720.1 151209 View on NCBI ↗
Colobanthus pulvinatus NC_053719.1 151132 View on NCBI ↗
Colobanthus subulatus NC_053723.1 151259 View on NCBI ↗