Markers + reference

Barnadesia

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 271
Primer pairs 95

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 935 0.0076 0.99 64.3 yes View details
psaA-ycf3 LSC 716 0.0056 1.00 62.0 yes View details
ycf3 LSC 1956 0.0031 0.99 49.3 yes View details
trnT-UGU-trnL-UAA LSC 529 0.0076 1.00 61.6 yes View details
rps11 LSC 411 0.0000 1.00 21.1 yes View details
rps8 LSC 405 0.0049 1.00 47.3 yes View details
ycf1 IRb 527 0.0000 1.00 23.9 no View details
ndhF-rpl32 SSC 1083 0.0105 0.96 67.5 yes View details
rpl32-trnL-UAG SSC 886 0.0045 1.00 61.3 yes View details
ndhE SSC 306 0.0000 1.00 20.2 yes View details
ycf1 SSC 5289 0.0030 0.99 54.9 yes View details
ycf1-ndhF SSC 45 0.0444 1.00 78.1 yes View details
rps8-rpl14 LSC 172 0.0233 1.00 65.9 yes View details
accD-psaI LSC 688 0.0045 0.97 64.1 yes View details
rpl2-rps19 IRa 59 0.0172 0.98 64.0 no View details
atpH-atpI LSC 982 0.0000 0.94 63.4 yes View details
ndhE-ndhG SSC 217 0.0184 1.00 63.1 yes View details
rps19-rpl2 IRb 59 0.0172 0.98 62.2 yes View details
trnE-UUC-trnT-GGU LSC 603 0.0000 0.87 61.4 yes View details
trnC-GCA-petN LSC 824 0.0015 0.82 60.8 yes View details
psbE-petL LSC 1223 0.0025 0.99 60.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 997–1008 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1008–1019 1.000 79.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACACCGGATCATGTCCTTC GAGGTTCGAATCCTTCCGTC 1017–1028 1.000 78.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1015–1026 1.000 77.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1013–1024 1.000 75.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GTGAATCCATGGAGGGTCAC 986–1040 1.000 83.3
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT GTGAATCCATGGAGGGTCAC 1042–1096 1.000 82.7
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA GTGAATCCATGGAGGGTCAC 1002–1056 1.000 82.5
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA GTGAATCCATGGAGGGTCAC 987–1041 1.000 82.2
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC GTGAATCCATGGAGGGTCAC 1046–1100 1.000 82.1
trnC-GCA-petN_p1 trnC-GCA-petN TCTCCTATCATTTTGGCGGC AGCCCAAGCGAGACTTACTA 799–936 1.000 82.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 743–880 1.000 82.2
trnC-GCA-petN_p3 trnC-GCA-petN CTCCTATCATTTTGGCGGCA AGCCCAAGCGAGACTTACTA 798–935 1.000 80.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 761–898 1.000 80.0
trnC-GCA-petN_p5 trnC-GCA-petN TCCTATCATTTTGGCGGCAT AGCCCAAGCGAGACTTACTA 797–934 1.000 80.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GAAGTCCTAACCGCTAGACG GAACCGATGACTTACGCCTT 620–686 1.000 80.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGAGAGAAGTCCTAACCGCT GAACCGATGACTTACGCCTT 625–691 1.000 79.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GAAGTCCTAACCGCTAGACG CCATGGCGTTACTCTACCAC 599–665 1.000 79.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CCCGTTGTCTCCTTGAAAGA GAACCGATGACTTACGCCTT 642–708 1.000 79.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCCCGTTGTCTCCTTGAAAG GAACCGATGACTTACGCCTT 643–709 1.000 79.6
psaA-ycf3_p1 psaA-ycf3 GAGAAATGACCCGGTCTAGC AGCCGCTGAGTATTGGAAAC 908–909 1.000 76.5
psaA-ycf3_p2 psaA-ycf3 GAGAAATGACCCGGTCTAGC CAAGCCGCTGAGTATTGGAA 910–911 1.000 76.4
psaA-ycf3_p3 psaA-ycf3 GAGAAATGACCCGGTCTAGC TGGTTGAAGATCACGAGACG 844–845 1.000 75.8
psaA-ycf3_p4 psaA-ycf3 GAGAAATGACCCGGTCTAGC GGTTGAAGATCACGAGACGT 843–844 1.000 75.8
psaA-ycf3_p5 psaA-ycf3 GAGAAATGACCCGGTCTAGC AAGCCGCTGAGTATTGGAAA 909–910 1.000 74.6
ycf3_p1 ycf3 TGATGGGGCCAACAAACAAT TCCCGCGAGAAGTAATGAGA 2082–2092 1.000 76.5
ycf3_p2 ycf3 TGATGGGGCCAACAAACAAT GGATCATTTTCCCGCGAGAA 2091–2101 1.000 75.7
ycf3_p3 ycf3 TGATGGGGCCAACAAACAAT ATCATTTTCCCGCGAGAAGT 2089–2099 1.000 75.2
ycf3_p4 ycf3 ATTTGACTGATGGGGCCAAC TCCCGCGAGAAGTAATGAGA 2089–2099 1.000 75.2
ycf3_p5 ycf3 ATTTGACTGATGGGGCCAAC GGATCATTTTCCCGCGAGAA 2098–2108 1.000 74.4

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
Barnadesia caryophylla NC_086793.1 152610 View on NCBI ↗
Barnadesia lehmannii MH341582.1 152771 View on NCBI ↗