Markers + reference

Cyananthus

2 species · Campanulaceae · Asterales

Back to catalogue

Species 2
Genome length 166–168 kb
Candidate markers 276
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE(UUC)-trnT(GGU) LSC 1956 0.0136 0.90 57.6 yes View details
trnT(UGU)-psbM LSC 1044 0.0216 0.98 71.0 yes View details
psbK-trnQ(UUG) LSC 583 0.0223 1.00 56.4 yes View details
clpP-petA LSC 1343 0.0204 0.99 71.9 yes View details
trnN(GUU)-ycf1 IRb 697 0.0409 0.98 69.0 yes View details
ycf1 IRb 7353 0.0230 0.98 52.5 yes View details
ycf1 IRa 7353 0.0195 0.98 50.2 no View details
ycf1-trnN(GUU) IRa 697 0.0409 0.98 69.0 yes View details
trnQ(UUG) LSC 73 0.5075 0.92 76.4 yes View details
ndhD-ccsA SSC 237 0.0295 1.00 69.5 yes View details
rpl32-ndhF SSC 945 0.0127 1.00 66.3 yes View details
rps16-trnD(GUC) LSC 951 0.0106 0.99 65.5 yes View details
trnL(UAG)-rpl32 SSC 855 0.0119 0.98 64.9 yes View details
psaA-ycf3 LSC 730 0.0082 1.00 63.5 yes View details
trnR(UCU)-trnG(UCC) LSC 167 0.0180 1.00 61.9 yes View details
trnH(GUG)-psbA LSC 337 0.0148 1.00 61.8 yes View details
matK-trnK(UUU) LSC 728 0.0082 1.00 61.6 yes View details
rpoA LSC 1008 0.0050 1.00 61.6 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
trnH(GUG)-psbA_p1 trnH(GUG)-psbA TCACAATCCACTGCCTTGTC TAACCGGGCTAACCTTGGTA 475 1.000 79.6
trnH(GUG)-psbA_p2 trnH(GUG)-psbA TTCACAATCCACTGCCTTGT TAACCGGGCTAACCTTGGTA 476 1.000 77.5
trnH(GUG)-psbA_p3 trnH(GUG)-psbA TCACAATCCACTGCCTTGTC ATTAACCGGGCTAACCTTGG 477 1.000 76.6
trnH(GUG)-psbA_p4 trnH(GUG)-psbA TTGTCCACTTGGCTACATCC TAACCGGGCTAACCTTGGTA 460 1.000 76.5
trnH(GUG)-psbA_p5 trnH(GUG)-psbA CCTTGTCCACTTGGCTACAT TAACCGGGCTAACCTTGGTA 462 1.000 76.5
matK-trnK(UUU)_p1 matK-trnK(UUU) CCATGATCATGAGCAAGTGC AACGGTAGAGTACTCGGCTT 859 1.000 73.0
matK-trnK(UUU)_p2 matK-trnK(UUU) CCATGATCATGAGCAAGTGC ACGGTAGAGTACTCGGCTTT 858 1.000 73.0
matK-trnK(UUU)_p3 matK-trnK(UUU) CCATGATCATGAGCAAGTGC GGGTTTGATTGCCTCGTCTA 941 1.000 71.1
matK-trnK(UUU)_p4 matK-trnK(UUU) CCATGATCATGAGCAAGTGC TAGGGTTTGATTGCCTCGTC 943 1.000 71.1
matK-trnK(UUU)_p5 matK-trnK(UUU) CCATGATCATGAGCAAGTGC GGGTTGCTAACTCAACGGTA 872 1.000 70.7
rps16-trnD(GUC)_p1 rps16-trnD(GUC) TTCCTTCTCTTCGGGATCGA TTCAATTGGTCAGAGCACCG 1099–1106 1.000 76.3
rps16-trnD(GUC)_p2 rps16-trnD(GUC) CGGTGCTTTTTACCACATCG TTCAATTGGTCAGAGCACCG 1049–1056 1.000 75.5
rps16-trnD(GUC)_p3 rps16-trnD(GUC) CGGGATCGAACATCAATTGC TTCAATTGGTCAGAGCACCG 1088–1095 1.000 74.3
rps16-trnD(GUC)_p4 rps16-trnD(GUC) ATAAGTCGCACGGTGCTTTT TTCAATTGGTCAGAGCACCG 1059–1066 1.000 73.6
rps16-trnD(GUC)_p5 rps16-trnD(GUC) CTTCCTTCTCTTCGGGATCG TTCAATTGGTCAGAGCACCG 1100–1107 1.000 73.4
trnE(UUC)-trnT(GGU)_p1 trnE(UUC)-trnT(GGU) CGTTGCCTCCTTGAAAGAGA GGACTTACGCCTTACCATGG 1869–2054 1.000 83.2
trnE(UUC)-trnT(GGU)_p2 trnE(UUC)-trnT(GGU) TGTCCTGAACCACTAGACGA GGACTTACGCCTTACCATGG 1847–2032 1.000 82.3
trnE(UUC)-trnT(GGU)_p3 trnE(UUC)-trnT(GGU) CGTTGCCTCCTTGAAAGAGA ACTTACGCCTTACCATGGTG 1867–2052 1.000 80.4
trnE(UUC)-trnT(GGU)_p4 trnE(UUC)-trnT(GGU) CCTGAACCACTAGACGATGG GGACTTACGCCTTACCATGG 1844–2029 1.000 79.9
trnE(UUC)-trnT(GGU)_p5 trnE(UUC)-trnT(GGU) CTGAACCACTAGACGATGGG GGACTTACGCCTTACCATGG 1843–2028 1.000 79.9
psaA-ycf3_p1 psaA-ycf3 TGAAAAATGACCCGGTCTGG ATCAAGCCGCTGAGTATTGG 927 1.000 79.4
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 908 1.000 79.3
psaA-ycf3_p3 psaA-ycf3 TGAAAAATGACCCGGTCTGG CGATCAAGCCGCTGAGTATT 929 1.000 78.6
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT CGATCAAGCCGCTGAGTATT 910 1.000 78.5
psaA-ycf3_p5 psaA-ycf3 TGAAAAATGACCCGGTCTGG TTGAAGATCACGAGGCGTTT 856 1.000 78.5
trnT(UGU)-psbM_p1 trnT(UGU)-psbM AAGCCTACTCTCGGAATCGA AAAATGAACAGTGCCGTAGC 1156–1165 1.000 75.0
trnT(UGU)-psbM_p2 trnT(UGU)-psbM AGCCTACTCTCGGAATCGAA AAAATGAACAGTGCCGTAGC 1155–1164 1.000 75.0
trnT(UGU)-psbM_p3 trnT(UGU)-psbM CGATGACCTCCGCATTACAA AAAATGAACAGTGCCGTAGC 1134–1143 1.000 74.9
trnT(UGU)-psbM_p4 trnT(UGU)-psbM GCCTACTCTCGGAATCGAAC AAAATGAACAGTGCCGTAGC 1154–1163 1.000 74.4
trnT(UGU)-psbM_p5 trnT(UGU)-psbM GAATCGAACCGATGACCTCC AAAATGAACAGTGCCGTAGC 1143–1152 1.000 74.3

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
Cyananthus flavus MT074354.1 165675 View on NCBI ↗
Cyananthus macrocalyx PQ584750.1 167964 View on NCBI ↗