Markers + reference

Aulacospermum

2 species · Apiaceae · Apiales

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Species 2
Genome length 156–158 kb
Candidate markers 267
Primer pairs 95

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 365 0.3526 0.99 74.4 yes View details
trnK-UUU-rps16 LSC 899 0.1026 0.60 68.9 yes View details
rps16-trnQ-UUG LSC 1051 0.1996 0.92 84.6 yes View details
rpoB-trnC-GCA LSC 1221 0.0761 0.97 79.5 yes View details
petN-psbM LSC 1112 0.0834 0.97 79.4 yes View details
trnE-UUC-trnT-GGU LSC 824 0.1503 0.86 81.2 yes View details
accD-psaI LSC 651 0.1103 0.79 81.0 yes View details
ndhF-rpl32 SSC 1200 0.0832 0.51 67.0 yes View details
rpl32-trnL-UAG SSC 909 0.1072 0.94 83.6 yes View details
trnT-UGU-trnL-UAA LSC 783 0.0586 0.92 85.5 yes View details
trnC-GCA-petN LSC 609 0.0678 0.94 83.8 yes View details
ndhC-trnV-UAC LSC 678 0.0828 0.93 83.2 yes View details
trnW-CCA-trnP-UGG LSC 135 0.1172 0.95 82.8 yes View details
ycf3-trnS-GGA LSC 864 0.0708 0.93 82.7 yes View details
trnS-UGA-psbZ LSC 369 0.0745 0.95 82.4 yes View details
rrn4.5-rrn5 IRb 224 0.0938 1.00 82.1 yes View details
rrn5-rrn4.5 IRa 224 0.0938 1.00 82.1 yes View details
trnF-GAA-ndhJ LSC 404 0.0878 0.93 81.5 yes View details
petA-psbJ LSC 1009 0.0700 0.89 79.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGCTTAGTTTCCGTCTGGG 809–1056 1.000 87.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 815–1062 1.000 87.0
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGAGCTTAGTTTCCGTCTGG 810–1057 1.000 87.0
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAGCTTAGTTTCCGTCTG 811–1058 1.000 87.0
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 823–1070 1.000 87.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 880–1236 1.000 88.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 941–1297 1.000 87.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 940–1296 1.000 87.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AGAACAAGGAAACGCCCTTT 1625 0.500 59.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGAACAAGGAAACGCCCTTT 1624 0.500 59.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT TTTCTCGCAGCTATCCAACC 2000–2323 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAAGGGCGTTTCCTTGTTCT TTTCTCGCAGCTATCCAACC 2352 0.500 59.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAAGGGCGTTTCCTTGTTCT CGCAGCTATCCAACCAAGAT 2347 0.500 59.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAAGGGCGTTTCCTTGTTCT CTTACAGCAGCTTGCCAAAC 2209 0.500 59.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT CGCAGCTATCCAACCAAGAT 1995 0.500 59.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GATCGGGAAGTCGTGATAGC 1980–2006 1.000 85.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CTTACCACTCGGCCATATCG 1755–1775 1.000 85.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG GATCGGGAAGTCGTGATAGC 2172–2198 1.000 85.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CTTACCACTCGGCCATATCG 1947–1967 1.000 85.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG TAGAGTGGGATCGGGAAGTC 2180 0.500 59.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 665–757 1.000 86.3
trnC-GCA-petN_p2 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGCCCAAGCGAGACTTACTA 705–797 1.000 86.0
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 683–775 1.000 84.0
trnC-GCA-petN_p4 trnC-GCA-petN GATATGGCCGAGTGGTAAGG AGCCCAAGCGAGACTTACTA 704–796 1.000 82.9
trnC-GCA-petN_p5 trnC-GCA-petN CGATATGGCCGAGTGGTAAG GCCCAAGCGAGACTTACTAT 704–796 1.000 80.1
petN-psbM_p1 petN-psbM CGTCGTATGGGGAAGAAGTG TCCCCTTCTTACTCCGGTTT 1588–1612 1.000 86.6
petN-psbM_p2 petN-psbM GCTATCACGACTTCCCGATC TCCCCTTCTTACTCCGGTTT 2103 0.500 59.3
petN-psbM_p3 petN-psbM GCTATCACGACTTCCCGATC TTTTCGTTTCGCCCTTCTCA 2379 0.500 59.2
petN-psbM_p4 petN-psbM GCTATCACGACTTCCCGATC CTTTCCCTTTTCGTTTCGCC 2386 0.500 59.2
petN-psbM_p5 petN-psbM GACTTCCCGATCCCACTCTA TCCCCTTCTTACTCCGGTTT 2095 0.500 59.2

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
Aulacospermum anomalum OP425125.1 155948 View on NCBI ↗
Aulacospermum tianschanicum NC_071815.1 158142 View on NCBI ↗