Markers + reference

Brassaiopsis

3 species · Araliaceae · Apiales

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Species 3
Genome length 156–157 kb
Candidate markers 272
Primer pairs 85

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 894 0.0208 0.97 66.2 yes View details
rps16-trnQ-UUG LSC 1741 0.0125 0.99 66.2 yes View details
psbK-psbI LSC 419 0.0263 1.00 70.1 yes View details
atpF LSC 1278 0.0120 1.00 54.4 yes View details
psbM-trnD-GUC LSC 1158 0.0199 1.00 75.6 yes View details
trnT-GGU-psbD LSC 1366 0.0127 1.00 53.2 yes View details
ycf1 IRb 1524 0.0096 1.00 54.3 no View details
ndhF SSC 2247 0.0098 1.00 49.1 yes View details
ycf1 SSC 5622 0.0134 0.98 49.0 yes View details
rpl2-trnH-GUG IRa 120 0.0278 1.00 70.2 no View details
psbE-petL LSC 1165 0.0114 1.00 66.9 yes View details
petA-psbJ LSC 1029 0.0123 1.00 66.6 yes View details
psbI-trnS-GCU LSC 138 0.0290 1.00 66.3 yes View details
atpF-atpH LSC 373 0.0161 1.00 65.4 yes View details
trnC-GCA-petN LSC 679 0.0069 1.00 65.4 yes View details
ndhG-ndhI SSC 385 0.0125 0.97 65.0 yes View details
atpH-atpI LSC 1123 0.0101 1.00 64.9 yes View details
rpl32-trnL-UAG SSC 805 0.0157 1.00 64.7 yes View details
rpl14-rpl16 LSC 139 0.0240 1.00 64.4 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCTTCGCTTCATCCA TTCCTTGAAAAAGGCGCTCA 1021–1048 1.000 81.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 973–1000 1.000 80.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 972–999 1.000 80.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 988–1015 1.000 79.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 982–1009 1.000 79.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1799–1840 1.000 82.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1814–1855 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1813–1854 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1870–1911 1.000 79.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1803–1844 1.000 77.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 532–539 1.000 83.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 533–540 1.000 83.2
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 534–541 1.000 81.4
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 529–536 1.000 81.2
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 530–537 1.000 81.2
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TAAAGCGGCGGATTGCTAAT 246 1.000 81.1
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TAAAGCGGCGGATTGCTAAT 247 1.000 81.1
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA ATTGGGAGAGATGGCTGAGT 270 1.000 80.4
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT ATTGGGAGAGATGGCTGAGT 271 1.000 80.4
psbI-trnS-GCU_p5 psbI-trnS-GCU TCTAATGATCCGGGGCGTAA TAAAGCGGCGGATTGCTAAT 245 1.000 79.3
atpF_p1 atpF GGCTCGAATGGTTACCATGA AGTCTATCTATAAGAGGAGATCA 1373–1374 1.000 41.4
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA AGTCTATCTATAAGAGGAGATCA 1385–1386 1.000 41.4
atpF_p3 atpF GGCTCGAATGGTTACCATGA AGTCTATCTATAAGAGGAGATCAT 1373–1374 1.000 41.4
atpF_p4 atpF AATTTCGTCGGCTCGAATGG AGTCTATCTATAAGAGGAGATCA 1382–1383 1.000 41.4
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA AGTCTATCTATAAGAGGAGATCAT 1385–1386 1.000 41.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 484–490 1.000 79.5
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 486–492 1.000 78.2
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG CGGAGGGAAAAATACGAGGT 550–556 1.000 75.7
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GCGGAGGGAAAAATACGAGG 551–557 1.000 75.6
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG GGCGGAGGGAAAAATACGAG 552–558 1.000 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Brassaiopsis angustifolia NC_065370.1 156534 View on NCBI ↗
Brassaiopsis hainla NC_022811.1 156459 View on NCBI ↗
Brassaiopsis tripteris PP697969.1 156142 View on NCBI ↗