Markers + reference

Meeboldia

4 species · Apiaceae · Apiales

Back to catalogue

Species 4
Genome length 155–156 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 39.1 yes View details
trnE-UUC-trnT-GGU LSC 720 0.0125 1.00 55.8 yes View details
trnF-GAA-ndhJ LSC 386 0.0117 1.00 62.5 yes View details
psaJ-rpl33 LSC 474 0.0097 0.98 64.9 yes View details
rps11 LSC 417 0.0024 1.00 36.1 yes View details
ndhF SSC 2232 0.0031 1.00 45.1 yes View details
ndhF-rpl32 SSC 958 0.0070 1.00 67.2 yes View details
rpl32-trnL-UAG SSC 852 0.0092 1.00 65.2 yes View details
ndhI SSC 504 0.0023 1.00 35.5 yes View details
ndhH SSC 1182 0.0027 1.00 45.8 yes View details
trnH-GUG-psbA LSC 185 0.0378 1.00 70.9 yes View details
ycf4-cemA LSC 644 0.0054 0.99 66.8 yes View details
rpl2-trnH-GUG IRa 166 0.0030 1.00 65.8 no View details
rpl33-rps18 LSC 211 0.0142 1.00 65.2 yes View details
ycf3-trnS-GGA LSC 905 0.0057 0.97 64.8 yes View details
petA-psbJ LSC 972 0.0037 0.98 63.1 yes View details
rps11-rpl36 LSC 118 0.0339 1.00 63.0 yes View details
rps16 LSC 1018 0.0015 0.97 62.9 yes View details
petN-psbM LSC 1130 0.0044 1.00 62.3 yes View details
trnT-UGU-trnL-UAA LSC 748 0.0047 1.00 62.0 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 CCTCTAGACCTAGCTGCTGT 252 1.000 83.5
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 302 1.000 82.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 316 1.000 82.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 315 1.000 82.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 317 1.000 82.7
psbA_p1 psbA ACTCGTATAGACTAAGACCCCA AAATTCGTGTGCTTGGGAGT 1137 1.000 57.7
psbA_p2 psbA ACTCGTATAGACTAAGACCCCA TGCTTGGGAGTCCCTGATAA 1128 1.000 57.6
psbA_p3 psbA AACTCGTATAGACTAAGACCCCA AAATTCGTGTGCTTGGGAGT 1138 1.000 55.0
psbA_p4 psbA AACTCGTATAGACTAAGACCCCA TGCTTGGGAGTCCCTGATAA 1129 1.000 54.9
psbA_p5 psbA ACTCGTATAGACTAAGACCCCA AATTCGTGTGCTTGGGAGTC 1136 1.000 54.0
rps16_p1 rps16 ACCCCTTTCTATTTCTTTATTTCCT TGTATCGACGGAACCAATGAC 1122–1155 1.000 42.7
rps16_p2 rps16 ACCCCTTTCTATTTCTTTATTTCCT GTATCGACGGAACCAATGACT 1121–1154 1.000 42.7
rps16_p3 rps16 ACCCCTTTCTATTTCTTTATTTCCT TGTATCGACGGAACCAATGA 1122–1155 1.000 42.7
rps16_p4 rps16 ACCCCTTTCTATTTCTTTATTTCC TGTATCGACGGAACCAATGAC 1122–1155 1.000 42.7
rps16_p5 rps16 ACCCCTTTCTATTTCTTTATTTCCTT TGTATCGACGGAACCAATGAC 1122–1155 1.000 42.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1299–1308 1.000 68.4
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1238–1247 1.000 66.9
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACTGCTTTTCTGCT 1278–1287 1.000 65.5
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1299–1308 1.000 64.3
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGCT 1217–1226 1.000 63.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 372–797 1.000 83.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTGTAGTACCCTACCCCCAG TACCGCTGAGTTAAAAGGGC 407–832 1.000 80.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CCGTTGCCTCCTTGAAAGAG TACCGCTGAGTTAAAAGGGC 373–798 1.000 78.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTGTAGTACCCTACCCCCA TACCGCTGAGTTAAAAGGGC 408–833 1.000 76.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG TACCGCTGAGTTAAAAGGGC 344–769 1.000 76.4
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 940–994 1.000 75.7
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 961–1015 1.000 75.3
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTCAA 911–965 1.000 75.0
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA AGTTCCAATGCTACGCCTTC 913–967 1.000 74.4
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACCCTCGGTAAACAAAAGCC 941–995 1.000 73.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Meeboldia delavayi NC_054296.1 155552 View on NCBI ↗
Meeboldia linearis NC_086814.1 155535 View on NCBI ↗
Meeboldia microloba NC_054297.1 155709 View on NCBI ↗
Meeboldia yunnanensis NC_054360.1 154865 View on NCBI ↗