Markers + reference

Cyathula

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–152 kb
Candidate markers 267
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 4110 0.0002 1.00 54.0 yes View details
rpoC1 LSC 2801 0.0004 1.00 56.2 yes View details
psbM-trnD-GUC LSC 996 0.0000 1.00 26.8 yes View details
psbZ-trnG-GCC LSC 308 0.0032 1.00 54.5 yes View details
petB LSC 1389 0.0000 1.00 40.0 yes View details
petD LSC 1247 0.0008 1.00 59.2 yes View details
rpl16 LSC 1404 0.0007 1.00 59.2 yes View details
trnN-GUU-ndhF IRb 2093 0.0022 0.86 47.2 yes View details
ndhF SSC 2238 0.0004 0.99 52.2 yes View details
trnR-UCU LSC 72 0.0139 1.00 60.5 yes View details
trnD-GUC LSC 74 0.0135 1.00 60.3 yes View details
trnI-CAU IRb 74 0.0135 1.00 60.3 yes View details
trnI-CAU IRa 74 0.0135 1.00 60.3 yes View details
rps15 SSC 273 0.0037 1.00 54.6 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
matK LSC 1512 0.0000 1.00 40.0 yes View details
matK-trnK-UUU LSC 725 0.0000 1.00 40.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACCAACTTCTTGCCAGAACA TGCTTGGGAGTCCCTGATAA 1190 1.000 76.2
psbA_p2 psbA ACCAACTTCTTGCCAGAACA ATTCATGTGCTTGGGAGTCC 1197 1.000 75.4
psbA_p3 psbA ACCAACTTCTTGCCAGAACA GGATTCATGTGCTTGGGAGT 1199 1.000 75.4
psbA_p4 psbA GAACAAGAAACCGGCATTGC TGCTTGGGAGTCCCTGATAA 1175 1.000 75.1
psbA_p5 psbA GGCATTGCCCCTTTACTTTC TGCTTGGGAGTCCCTGATAA 1163 1.000 74.3
matK_p1 matK TACTCAATGGCTTCAACCCC CCTTGTTTTGACTGTATCGCA 1710 1.000 58.6
matK_p2 matK TACTCAATGGCTTCAACCCC ACCTTGTTTTGACTGTATCGC 1711 1.000 58.6
matK_p3 matK TACTCAATGGCTTCAACCCC CCTTGTTTTGACTGTATCGCAC 1710 1.000 58.4
matK_p4 matK CTCAATGGCTTCAACCCCTA CCTTGTTTTGACTGTATCGCA 1708 1.000 56.2
matK_p5 matK CTCAATGGCTTCAACCCCTA ACCTTGTTTTGACTGTATCGC 1709 1.000 56.2
matK-trnK-UUU_p1 matK-trnK-UUU TGTTGCCAAGACCTATCTAGT AACGGTAGAGTACTCGGCTT 796 1.000 55.3
matK-trnK-UUU_p2 matK-trnK-UUU TGTTGCCAAGACCTATCTAGT ACGGTAGAGTACTCGGCTTT 795 1.000 55.3
matK-trnK-UUU_p3 matK-trnK-UUU TGTTGCCAAGACCTATCTAGTTC AACGGTAGAGTACTCGGCTT 796 1.000 54.0
matK-trnK-UUU_p4 matK-trnK-UUU TGTTGCCAAGACCTATCTAGTTC ACGGTAGAGTACTCGGCTTT 795 1.000 54.0
matK-trnK-UUU_p5 matK-trnK-UUU TGCCAAGACCTATCTAGTTCTCT ACGGTAGAGTACTCGGCTTT 792 1.000 53.6
trnG-UCC_p1 trnG-UCC TCAGTGTTCGACAAAAGTTCT TCGGATTGTATGTGATGTGAGA 917 1.000 40.0
trnG-UCC_p2 trnG-UCC TTCAGTGTTCGACAAAAGTTCT TCGGATTGTATGTGATGTGAGA 918 1.000 40.0
trnG-UCC_p3 trnG-UCC ACATCAAATTTCAGTGTTCGACA TCGGATTGTATGTGATGTGAGA 927 1.000 40.0
trnG-UCC_p4 trnG-UCC TCAGTGTTCGACAAAAGTTCT CGGATTGTATGTGATGTGAGA 916 1.000 40.0
trnG-UCC_p5 trnG-UCC TCAGTGTTCGACAAAAGTTCT TCGGATTGTATGTGATGTGAG 917 1.000 40.0
trnR-UCU_p1 trnR-UCU TCTCACATCACATACAATCCGA TCAAGAACAGAAGGAACGCT 247 1.000 49.0
trnR-UCU_p2 trnR-UCU TCTCACATCACATACAATCCGA TCAAGAACAGAAGGAACGCTT 247 1.000 46.8
trnR-UCU_p3 trnR-UCU TCTCACATCACATACAATCCGA TTCAAGAACAGAAGGAACGCT 248 1.000 46.8
trnR-UCU_p4 trnR-UCU TCTCACATCACATACAATCCGA GGAACGCTTTCTACTTCAGGA 235 1.000 45.8
trnR-UCU_p5 trnR-UCU TCTCACATCACATACAATCCGA AGGAACGCTTTCTACTTCAGG 236 1.000 45.8
rpoC2_p1 rpoC2 ACTACTTCGACAAGCCTTCG TCGGGAGCTAGAGGAAATGT 230 1.000 76.3
rpoC2_p2 rpoC2 ACTACTTCGACAAGCCTTCG CGGGAGCTAGAGGAAATGTG 229 1.000 75.7
rpoC2_p3 rpoC2 CTACTTCGACAAGCCTTCGC TCGGGAGCTAGAGGAAATGT 229 1.000 71.0
rpoC2_p4 rpoC2 CTACTTCGACAAGCCTTCGC CGGGAGCTAGAGGAAATGTG 228 1.000 70.4
rpoC2_p5 rpoC2 TTCTTTCCGGCATCATACCA TCGGGAGCTAGAGGAAATGT 316 1.000 70.2

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
Cyathula capitata NC_041262.1 151557 View on NCBI ↗
Cyathula officinalis NC_066401.1 151518 View on NCBI ↗