Markers + reference

Ainsliaea

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 268
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 414 0.0024 1.00 56.3 yes View details
trnC-GCA-petN LSC 843 0.0024 1.00 60.3 yes View details
psbM-trnD-GUC LSC 660 0.0015 1.00 60.1 yes View details
trnT-GGU-psbD LSC 1247 0.0016 1.00 52.0 yes View details
trnT-UGU-trnL-UAA LSC 587 0.0102 1.00 64.4 yes View details
trnF-GAA-ndhJ LSC 600 0.0017 1.00 59.9 yes View details
ndhC LSC 363 0.0000 1.00 35.1 yes View details
accD-psaI LSC 702 0.0014 1.00 59.6 yes View details
petA-psbJ LSC 778 0.0013 1.00 59.6 yes View details
ycf1 IRb 579 0.0000 1.00 29.2 no View details
ccsA SSC 969 0.0010 1.00 49.7 yes View details
ndhD SSC 1521 0.0007 1.00 58.3 yes View details
ycf1 SSC 5109 0.0006 1.00 52.8 yes View details
cemA LSC 690 0.0014 1.00 59.6 yes View details
rpl16 LSC 1397 0.0014 1.00 59.6 yes View details
atpB-rbcL LSC 762 0.0013 1.00 59.5 yes View details
trnE-UUC-rpoB LSC 922 0.0011 1.00 59.4 yes View details
rpoA LSC 1008 0.0010 1.00 59.3 yes View details
psbE-petL LSC 1281 0.0008 1.00 59.2 yes View details
trnK-UUU-rps16 LSC 803 0.0000 1.00 58.9 yes View details
atpI-atpH LSC 1104 0.0000 1.00 58.8 yes View details
ndhI SSC 501 0.0020 1.00 57.8 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1000–1004 1.000 76.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 999–1003 1.000 76.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 939–943 1.000 76.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 938–942 1.000 76.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1024–1028 1.000 75.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 551 1.000 72.2
psbK-psbI_p2 psbK-psbI TATGCCAGTGATACCCCTGT TCTTCACGTCCAGGATTACG 591 1.000 71.1
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 548 1.000 70.2
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 549 1.000 70.2
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 550 1.000 70.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 897–899 1.000 78.5
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 915–917 1.000 76.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 896–898 1.000 72.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 905–907 1.000 72.5
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 954–956 1.000 71.8
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 774–777 1.000 50.8
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 768–771 1.000 50.4
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 771–774 1.000 49.4
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCAAGAGCACCG 775–778 1.000 48.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCA TTCAATAGGCAAGAGCACCG 775–778 1.000 47.9
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GAAGTCGTAACCACTGGACC AGTTCTTCTGTCAAACCCTGA 1029 1.000 61.8
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 1022 1.000 61.5
trnE-UUC-rpoB_p3 trnE-UUC-rpoB AACCCTCGTTATCTCCGTGA AGTTCTTCTGTCAAACCCTGA 1055 1.000 61.1
trnE-UUC-rpoB_p4 trnE-UUC-rpoB ACCCTCGTTATCTCCGTGAA AGTTCTTCTGTCAAACCCTGA 1054 1.000 61.1
trnE-UUC-rpoB_p5 trnE-UUC-rpoB TGAACCCTCGTTATCTCCGT AGTTCTTCTGTCAAACCCTGA 1057 1.000 61.1
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1240 1.000 77.7
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA TACCTTGACCAACTCCAGGT 1296 1.000 77.1
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1256 1.000 76.8
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1241 1.000 76.5
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA GCAGTACCTTGACCAACTCC 1300 1.000 76.5

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
Ainsliaea erectifolia PQ653531.1 152930 View on NCBI ↗
Ainsliaea laxiflora PQ653533.1 152946 View on NCBI ↗