Markers + reference

Ajania

6 species · Asteraceae · Asterales

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Species 6
Genome length 151–151 kb
Candidate markers 273
Primer pairs 105

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-GGU-psbD LSC 1209 0.0034 0.98 57.7 yes View details
psaA-ycf3 LSC 730 0.0055 1.00 65.0 yes View details
trnT-UGU-trnL-UAA LSC 502 0.0088 1.00 51.0 yes View details
petA-psbJ LSC 745 0.0052 0.99 51.9 yes View details
psbE-petL LSC 1258 0.0046 1.00 59.3 yes View details
ycf1 IRb 591 0.0078 1.00 40.4 no View details
ndhF SSC 2223 0.0019 1.00 44.0 yes View details
rpl32-trnL-UAG SSC 881 0.0076 0.99 61.0 yes View details
ndhD SSC 1500 0.0007 1.00 33.7 yes View details
ycf1 SSC 3714 0.0035 1.00 36.3 yes View details
ycf1-trnN-GUU IRa 1656 0.0024 1.00 53.0 yes View details
rps16-trnQ-UUG LSC 888 0.0032 1.00 61.3 yes View details
ndhF-rpl32 SSC 989 0.0039 0.99 60.8 yes View details
ycf3-trnS-GGA LSC 807 0.0030 1.00 59.1 yes View details
trnR-UCU-trnG-UCC LSC 210 0.0096 0.98 58.2 yes View details
ycf1-ndhF SSC 6 0.1111 1.00 56.9 yes View details
petN-psbM LSC 529 0.0053 0.99 55.8 yes View details
trnK-UUU-rps16 LSC 847 0.0031 1.00 55.2 yes View details
atpB-rbcL LSC 728 0.0023 1.00 54.9 yes View details
clpP LSC 1997 0.0021 1.00 54.6 yes View details
ndhC-trnV-UAC LSC 1153 0.0029 1.00 54.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GGGCGTGTCAACCAATATCT CGTTGGATTTGATACCCGGA 2953–2991 0.833 72.2
trnK-UUU_p2 trnK-UUU GGGCGTGTCAACCAATATCT TCGTTGGATTTGATACCCGG 2954–2992 0.833 72.2
trnK-UUU_p3 trnK-UUU TGGGCGTGTCAACCAATATC CGTTGGATTTGATACCCGGA 2954–2992 0.833 70.4
trnK-UUU_p4 trnK-UUU TGGGCGTGTCAACCAATATC TCGTTGGATTTGATACCCGG 2955–2993 0.833 70.4
trnK-UUU_p5 trnK-UUU ATGGGCGTGTCAACCAATAT CGTTGGATTTGATACCCGGA 2955–2993 0.833 69.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GGTGCTCAACCTACAGGAAC 1001–1002 1.000 78.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC GGTGCTCAACCTACAGGAAC 1000–1001 1.000 78.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 940–941 1.000 77.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 939–940 1.000 77.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC GGTGCTCAACCTACAGGAAC 1025–1026 1.000 77.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 961 1.000 78.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 972 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACACCGGATCATGTCCTTC GAGGTTCGAATCCTTCCGTC 981 1.000 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 979 1.000 76.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1032 1.000 76.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 686–691 1.000 60.7
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 686–691 1.000 59.0
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 687–692 1.000 54.8
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 678–683 1.000 54.7
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 672–677 1.000 53.9
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 278–292 1.000 68.5
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 281–295 1.000 68.2
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 284–298 1.000 67.8
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 287–301 1.000 67.5
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 282–296 1.000 66.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGACCCGTTCAGGAATTCA GAAACGGTCCCTACGTAACC 1373–1399 1.000 80.6
trnT-GGU-psbD_p2 trnT-GGU-psbD CAGTGACCCGTTCAGGAATT GAAACGGTCCCTACGTAACC 1375–1401 1.000 80.5
trnT-GGU-psbD_p3 trnT-GGU-psbD TAATCCCACGGTAAGGCGTA GAAACGGTCCCTACGTAACC 1316–1342 1.000 80.3
trnT-GGU-psbD_p4 trnT-GGU-psbD GAGTAATCCCACGGTAAGGC GAAACGGTCCCTACGTAACC 1319–1345 1.000 80.2
trnT-GGU-psbD_p5 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT GAAACGGTCCCTACGTAACC 1300–1326 1.000 80.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Ajania fruticulosa NC_079653.1 151064 View on NCBI ↗
Ajania khartensis NC_079654.1 151095 View on NCBI ↗
Ajania nematoloba NC_079655.1 151092 View on NCBI ↗
Ajania pacifica NC_050690.1 151059 View on NCBI ↗
Ajania sericea PX316520.1 151054 View on NCBI ↗
Ajania tenuifolia NC_079657.1 151073 View on NCBI ↗