Markers + reference

Tetrataenium

2 species · Apiaceae · Apiales

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Species 2
Genome length 142–143 kb
Candidate markers 253
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petA-psbJ Genome 953 0.0336 1.00 78.3 yes View details
trnH-GUG-rrn16 Genome 1205 0.0705 1.00 82.9 yes View details
ndhF Genome 2238 0.0050 0.99 47.2 yes View details
ndhF-rpl32 Genome 990 0.0206 0.98 60.8 yes View details
rrn16-trnH-GUG Genome 1205 0.0463 0.59 67.2 yes View details
trnH-GUG-trnK-UUU Genome 1440 0.0451 0.74 68.4 no View details
trnE-UUC-trnT-GGU Genome 772 0.0120 0.98 68.0 yes View details
psbE-petL Genome 1002 0.0136 0.81 67.1 yes View details
psbT-psbN Genome 86 0.0349 1.00 65.9 yes View details
rps2-rpoC2 Genome 220 0.0239 0.95 65.0 yes View details
trnF-GAA-ndhJ Genome 397 0.0176 1.00 64.7 yes View details
atpF-atpH Genome 339 0.0162 0.91 64.5 yes View details
ycf1-ndhF Genome 85 0.4500 0.24 64.5 yes View details
rrn23-rrn4.5 Genome 98 0.0204 1.00 64.2 yes View details
rrn4.5-rrn23 Genome 98 0.0204 1.00 64.2 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 429–455 1.000 82.0
atpF-atpH_p2 atpF-atpH CCAGTGGCCTAAAGAAACGA GCCTGGTTGTAGCATTAGCA 402–428 1.000 81.5
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 431–457 1.000 80.6
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGAGGCGGAGGGAAAAATAC 500–526 1.000 80.5
atpF-atpH_p5 atpF-atpH CCAGTGGCCTAAAGAAACGA TGAGGCGGAGGGAAAAATAC 473–499 1.000 80.1
rps2-rpoC2_p1 rps2-rpoC2 AATGAACTCCGGCCTTCATC GCCTTTCAAACAATTTCCACG 337–346 1.000 66.4
rps2-rpoC2_p2 rps2-rpoC2 CCGGCCTTCATCATCTCTTC GCCTTTCAAACAATTTCCACG 329–338 1.000 65.8
rps2-rpoC2_p3 rps2-rpoC2 CGGCCTTCATCATCTCTTCC GCCTTTCAAACAATTTCCACG 328–337 1.000 65.8
rps2-rpoC2_p4 rps2-rpoC2 AATGAACTCCGGCCTTCATC GCCTTTCAAACAATTTCCACGA 337–346 1.000 65.1
rps2-rpoC2_p5 rps2-rpoC2 CGGCCTTCATCATCTCTTCC GCCTTTCAAACAATTTCCACGA 328–337 1.000 64.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 874–876 1.000 81.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GTGTAGTACCCTACCCCCAG GAACCGATGACTTACGCCTT 909–911 1.000 80.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GGCGTTACTCTACCGTTGAG 849–851 1.000 80.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GTGTAGTACCCTACCCCCAG GGCGTTACTCTACCGTTGAG 884–886 1.000 80.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 871–873 1.000 80.0
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA TGGATAGGATGGCCTTTACG 536–543 1.000 71.2
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA GGATAGGATGGCCTTTACGT 535–542 1.000 71.2
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGGATAGGATGGCCTTTACG 500–507 1.000 70.9
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GGATAGGATGGCCTTTACGT 499–506 1.000 70.9
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA TGAAAGTTGGATAGGATGGCC 543–550 1.000 70.6
petA-psbJ_p1 petA-psbJ CTTACGTGTCCAAGGCCTTT GCTGGTATTCTTGTGATCGGT 1143–1165 1.000 72.7
petA-psbJ_p2 petA-psbJ GGCCTTTTGTTCTTCTTGGC GCTGGTATTCTTGTGATCGGT 1130–1152 1.000 72.4
petA-psbJ_p3 petA-psbJ CTTACGTGTCCAAGGCCTTT AGCTGGTATTCTTGTGATCGG 1144–1166 1.000 72.0
petA-psbJ_p4 petA-psbJ GGCCTTTTGTTCTTCTTGGC AGCTGGTATTCTTGTGATCGG 1131–1153 1.000 71.7
petA-psbJ_p5 petA-psbJ GATCCCTTACGTGTCCAAGG GCTGGTATTCTTGTGATCGGT 1148–1170 1.000 71.1
psbE-petL_p1 psbE-petL CAACCCGCAATGAATAGGGA GGTTACCGTTAAAGCCGCTA 969–1160 1.000 84.3
psbE-petL_p2 psbE-petL ACTGACGAATAACCAACCCG GGTTACCGTTAAAGCCGCTA 982–1173 1.000 84.0
psbE-petL_p3 psbE-petL CAACCCGCAATGAATAGGGA TGAGGTTACCGTTAAAGCCG 972–1163 1.000 83.7
psbE-petL_p4 psbE-petL AGAACGTTCTCCTGTGCTTC GGTTACCGTTAAAGCCGCTA 892–1083 1.000 83.6
psbE-petL_p5 psbE-petL ACTGACGAATAACCAACCCG TGAGGTTACCGTTAAAGCCG 985–1176 1.000 83.4

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
Tetrataenium nepalense NC_086727.1 142034 View on NCBI ↗
Tetrataenium yunnanense NC_045183.1 142714 View on NCBI ↗