Markers + reference

Aphyllon

3 species · Orobanchaceae · Lamiales

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Species 3
Genome length 105–121 kb
Candidate markers 241
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

2 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 241 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
PS16_p038 LSC 51689 0.1087 0.73 69.1 yes View details
PS16_p039 SSC 56116 0.0696 0.93 75.1 yes View details
psaB-trnS-GGA LSC 650 0.2952 1.00 84.4 yes View details
rps16 LSC 1094 0.0880 0.99 83.0 yes View details
ycf4 LSC 558 0.1253 0.97 82.9 yes View details
matK-trnK-UUU LSC 702 0.0924 0.99 81.9 yes View details
PS16_r008-trnA-UGC SSC 546 0.0565 0.97 81.6 yes View details
ndhJ LSC 480 0.1565 0.95 81.5 yes View details
atpI LSC 744 0.0983 1.00 81.3 yes View details
atpB LSC 1500 0.0832 0.99 81.2 yes View details
clpP-psbB LSC 477 0.1301 0.95 80.9 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
PS16_p038_p1 PS16_p038 TGGGTTAGGGAGATGCAGAA TTGCGGGTTAGTTATTCGGG 1742 0.333 52.8
PS16_p038_p2 PS16_p038 TTGGGTTAGGGAGATGCAGA TTGCGGGTTAGTTATTCGGG 1743 0.333 52.8
PS16_p038_p3 PS16_p038 TGGGTTAGGGAGATGCAGAA GCGGGTTAGTTATTCGGGTT 1740 0.333 52.8
PS16_p038_p4 PS16_p038 TTGGGTTAGGGAGATGCAGA GCGGGTTAGTTATTCGGGTT 1741 0.333 52.8
PS16_p038_p5 PS16_p038 TTTCCCCATTCCCCACTACT TTGCGGGTTAGTTATTCGGG 2051 0.333 52.6
matK-trnK-UUU_p1 matK-trnK-UUU CCACGATCATGAGCAAATGC AACGGTAGAGTACTCGGCTT 832–833 0.667 73.2
matK-trnK-UUU_p2 matK-trnK-UUU CCACGATCATGAGCAAATGC ACGGTAGAGTACTCGGCTTT 831–832 0.667 73.2
matK-trnK-UUU_p3 matK-trnK-UUU GATTTCCGCATGGACAGAGT AACGGTAGAGTACTCGGCTT 1212 0.333 51.7
matK-trnK-UUU_p4 matK-trnK-UUU GATTTCCGCATGGACAGAGT ACGGTAGAGTACTCGGCTTT 1211 0.333 51.7
matK-trnK-UUU_p5 matK-trnK-UUU GATTTCCGCATGGACAGAGT TCGCGGTTTTATTAGCTCGT 1364 0.333 50.8
rps16_p1 rps16 TACAAGTTGCTACCCCCTTG TCTGCGATAGACCCTAACGT 1719 0.333 46.0
rps16_p2 rps16 TACAAGTTGCTACCCCCTTG TATGGACAGCTGAACCAACG 1201 0.333 45.6
rps16_p3 rps16 TACAAGTTGCTACCCCCTTG CCCCATACCGGTTCCAAATT 1153 0.333 45.1
rps16_p4 rps16 CAAGTTGCTACCCCCTTGG TCTGCGATAGACCCTAACGT 1717 0.333 44.6
rps16_p5 rps16 CAAGTTGCTACCCCCTTGG TATGGACAGCTGAACCAACG 1199 0.333 44.3
trnG-UCC_p1 trnG-UCC CAATCCGACGCTTTAGTCCA TTCAGGAACAAATGGACCGG 1538–1848 0.667 77.9
trnG-UCC_p2 trnG-UCC CAATCCGACGCTTTAGTCCA ATTGGAACTGGCGCAATTTG 1682–2177 0.667 77.6
trnG-UCC_p3 trnG-UCC AATCCGACGCTTTAGTCCAC ATTGGAACTGGCGCAATTTG 1681–2176 0.667 77.6
trnG-UCC_p4 trnG-UCC CAATCCGACGCTTTAGTCCA GAGGAAGCAGAAGCCCTTTT 1879 0.333 52.6
trnG-UCC_p5 trnG-UCC AATCCGACGCTTTAGTCCAC GAGGAAGCAGAAGCCCTTTT 1878 0.333 52.6
atpI_p1 atpI TTCCATTGCTTGGTTCCGAA AAGACTCAACCTCCTTCCGA 1674 0.333 53.2
atpI_p2 atpI TTCCATTGCTTGGTTCCGAA AGACTCAACCTCCTTCCGAA 1673 0.333 53.2
atpI_p3 atpI TTCCATTGCTTGGTTCCGAA TTGGTTTTTGGTGCAGCAAG 1880 0.333 53.1
atpI_p4 atpI TTCCATTGCTTGGTTCCGAA ATATATGGCCCTGCGAGAGT 1539 0.333 52.8
atpI_p5 atpI TTCCATTGCTTGGTTCCGAA TGGAACAAAAAGCGGGAAGA 1690 0.333 52.8
psaB-trnS-GGA_p1 psaB-trnS-GGA GTGCACTACTCCGTGGTAAG TGAAAGGCCTAACTGAGGGA 1189 0.333 53.0
psaB-trnS-GGA_p2 psaB-trnS-GGA GCTACCAAACTGCTCTACCC TGAAAGGCCTAACTGAGGGA 1504 0.333 52.8
psaB-trnS-GGA_p3 psaB-trnS-GGA AAGGTTATGAGCCTTGCGAG TGAAAGGCCTAACTGAGGGA 1523 0.333 52.8
psaB-trnS-GGA_p4 psaB-trnS-GGA GATGTTGCGGAGACAGGATT TGAAAGGCCTAACTGAGGGA 1558 0.333 52.8
psaB-trnS-GGA_p5 psaB-trnS-GGA GTGCACTACTCCGTGGTAAG GGGGTCAACAGGTCAAGTTT 1768 0.333 52.7

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
Aphyllon californicum NC_025651.1 120840 View on NCBI ↗
Aphyllon fasciculatum NC_039679.1 106796 View on NCBI ↗
Aphyllon uniflorum var. uniflorum MH580290.1 104640 View on NCBI ↗