Markers + reference

Bougainvillea

15 species · Nyctaginaceae · Caryophyllales

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Species 15
Genome length 154–155 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 460 0.0212 0.98 68.2 yes View details
trnK-UUU-rps16 LSC 641 0.0183 0.99 63.1 yes View details
rps16-trnQ-UUG LSC 754 0.0230 0.98 72.1 yes View details
trnS-GCU-trnG-UCC LSC 1000 0.0233 0.95 65.9 yes View details
psbM-trnD-GUC LSC 994 0.0158 0.97 68.5 yes View details
ycf3-trnS-GGA LSC 827 0.0122 0.98 66.0 yes View details
petA-psbJ LSC 1004 0.0145 0.99 55.6 yes View details
ycf1 IRb 1377 0.0061 1.00 43.9 no View details
ndhF-rpl32 SSC 866 0.0150 0.97 61.8 yes View details
rpl32-trnL-UAG SSC 894 0.0142 0.99 63.0 yes View details
ycf1 SSC 5658 0.0119 1.00 46.1 yes View details
rpl14-rpl16 LSC 146 0.0186 0.99 65.9 yes View details
atpH-atpI LSC 727 0.0075 1.00 65.6 yes View details
rps18-rpl20 LSC 235 0.0168 1.00 64.5 yes View details
ndhC-trnV-UAC LSC 943 0.0102 0.98 64.0 yes View details
petN-psbM LSC 1132 0.0036 0.99 63.2 yes View details
trnF-GAA-ndhJ LSC 683 0.0068 0.99 61.3 yes View details
rpl20-rps12 LSC 790 0.0068 1.00 60.5 yes View details
trnT-GGU-psbD LSC 1304 0.0097 0.99 60.4 yes View details
trnT-UGU-trnL-UAA LSC 727 0.0121 0.98 60.1 yes View details
psbK-psbI LSC 411 0.0153 1.00 58.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 578–799 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 592–813 1.000 85.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 591–812 1.000 85.0
trnH-GUG-psbA_p4 trnH-GUG-psbA TGTTATGGACGTTATGGGCG CCGTGCTAACCTTGGTATGG 647–868 0.867 79.1
trnH-GUG-psbA_p5 trnH-GUG-psbA TGTTATGGACGTTATGGGCG ACCGTGCTAACCTTGGTATG 648–869 0.867 78.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GGCGGGAGTTTTGGAAGAAT 645–792 1.000 84.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGCGGGAGTTTTGGAAGAAT 605–752 1.000 82.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC ATTTTAAGGAGGGCGGGAGT 656–803 1.000 82.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 GAATCCCTTGCTTCATCCGA GGCGGGAGTTTTGGAAGAAT 643–790 1.000 81.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC GGCGGGAGTTTTGGAAGAAT 610–757 1.000 81.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 842–887 1.000 88.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 816–861 1.000 87.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 832–877 1.000 87.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TAAGGCATCGGGTTTTGGTC 872–917 1.000 87.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA TAAGGCATCGGGTTTTGGTC 846–891 1.000 86.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGCCCTGGATCAT 520–538 1.000 83.9
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCGCGTCCAGGATTAC 532–550 1.000 83.6
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGATTACGCCCTGGATCAT 517–535 1.000 81.9
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGATTACGCCCTGGATCAT 518–536 1.000 81.9
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGATTACGCCCTGGATCAT 519–537 1.000 81.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC ACGAATCACACTTTTACCACT 874–1059 1.000 56.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AACGAATCACACTTTTACCACT 875–1060 1.000 54.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TTTCGTCCACTCAGCCATCT ACGAATCACACTTTTACCACT 873–1058 1.000 53.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 868–1053 1.000 52.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TACCACTAAACTATACCCGC 860–1045 1.000 52.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 771–811 1.000 83.4
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA CGAATCCATGGAGGGTCATC 787–827 1.000 82.4
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 772–812 1.000 82.2
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 831–871 1.000 81.9
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 827–867 0.933 78.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Bougainvillea arborea NC_065344.1 154828 View on NCBI ↗
Bougainvillea berberidifolia NC_065346.1 154561 View on NCBI ↗
Bougainvillea buttiana OR344367.1 154542 View on NCBI ↗
Bougainvillea campanulata NC_065350.1 154529 View on NCBI ↗
Bougainvillea hybrid cultivar NC_056256.1 154520 View on NCBI ↗
Bougainvillea infesta NC_065349.1 154385 View on NCBI ↗
Bougainvillea modesta NC_065345.1 154457 View on NCBI ↗
Bougainvillea pachyphylla NC_056255.1 154062 View on NCBI ↗
Bougainvillea peruviana NC_049005.1 154465 View on NCBI ↗
Bougainvillea praecox NC_056254.1 154306 View on NCBI ↗
Bougainvillea spectabilis NC_041266.1 154541 View on NCBI ↗
Bougainvillea spectabilis x Bougainvillea glabra MW557548.1 154541 View on NCBI ↗
Bougainvillea spinosa NC_065348.1 154872 View on NCBI ↗
Bougainvillea stipitata NC_065347.1 154667 View on NCBI ↗
Bougainvillea stipitata var. grisebachiana OM044392.1 154679 View on NCBI ↗