Markers + reference

Pelargonium

13 species · Geraniaceae · Geraniales

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Species 13
Genome length 166–173 kb
Candidate markers 292
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 292 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnD-GUC LSC 3262 0.3233 0.64 70.9 yes View details
trnD-GUC-trnG-GCC LSC 672 0.3644 0.64 74.2 yes View details
petD-rpoA IRb 921 0.2549 0.98 78.9 yes View details
rpoA-petD IRa 921 0.2565 0.98 78.9 yes View details
psbE-petL LSC 870 0.0506 1.00 88.6 yes View details
trnS-GCU-trnG-UCC LSC 895 0.0530 0.99 85.8 yes View details
atpH-atpI LSC 938 0.1218 1.00 85.2 yes View details
rpoB-trnC-GCA LSC 1105 0.0457 0.99 85.1 yes View details
trnK-UUU-rps16 LSC 608 0.0577 0.98 84.8 yes View details
rpoA IRb 885 0.2022 1.00 84.1 yes View details
rpoA IRa 885 0.1976 1.00 84.0 yes View details
psbM-trnD-GUC LSC 1106 0.0582 0.99 83.7 yes View details
petA-psbJ LSC 1107 0.0450 0.99 82.9 yes View details
ndhF IRa 2235 0.1641 1.00 82.5 yes View details
ndhF IRb 2235 0.1644 1.00 82.1 no 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGGTCTTACAAACCCTACCG GGATCTTCGAAAGGTGGGTC 892–905 0.846 85.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCAACCCCTAATCGAATGGG GGATCTTCGAAAGGTGGGTC 1240–1255 0.846 83.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGTGGGGAATTTCTTGGGTT GGATCTTCGAAAGGTGGGTC 1508–1520 0.615 70.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGACGGTATGGACGAATCTC GGATCTTCGAAAGGTGGGTC 875–887 0.538 68.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CTTACAAACCCTACCGACGG GGATCTTCGAAAGGTGGGTC 889–900 0.308 56.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CACTTTTACCACTAAACTATACCCG 914–994 1.000 52.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CACTTTTACCACTAAACTATACCCG 913–993 1.000 52.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACTTTTACCACTAAACTATACCCG 913–993 1.000 52.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACTTTTACCACTAAACTATACCCG 912–992 1.000 52.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC CACTTTTACCACTAAACTATACCCG 916–996 1.000 52.0
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA ATGGAGGGTCATCATTGA 985–1242 1.000 52.0
atpH-atpI_p2 atpH-atpI GCAGAAATAACAGAAGCGGC ATGGAGGGTCATCATTGA 993–1250 1.000 52.0
atpH-atpI_p3 atpH-atpI GGCCAACCCAGCAGAAATAA ATGGAGGGTCATCATTGA 1003–1260 1.000 52.0
atpH-atpI_p4 atpH-atpI AGAAGCGGCAGAAATCAGTG ATGGAGGGTCATCATTGA 982–1239 1.000 52.0
atpH-atpI_p5 atpH-atpI CAGAAGCGGCAGAAATCAGT ATGGAGGGTCATCATTGA 983–1240 1.000 52.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTTCATTTCTATCGCCAAGC AGGATTTGCAGTCCCCCG 935–1190 1.000 52.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GGGATTGTAGCCATTCCTTCA AGGATTTGCAGTCCCCCG 950–1205 0.923 52.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGGGATTGTAGCCATTCCTTC AGGATTTGCAGTCCCCCG 951–1206 0.923 49.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GGGATTGTAGCCATTCCTTCA CTTACCGCTCGGCCATGT 931–1186 0.923 48.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GGGATTGTAGCCATTCCTTCA TTACCGCTCGGCCATGTC 930–1185 0.923 48.9
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTGACTTCCA TTCAATTGGTCAGAGCACCG 550–1271 0.846 53.9
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGCGAGAATATTGACTTCCA TTCAATTGGTCAGAGCACCG 551–1272 0.846 50.8
psbM-trnD-GUC_p3 psbM-trnD-GUC TGCGAGAATATTGACTTCCAT TTCAATTGGTCAGAGCACCG 550–1271 0.846 50.8
psbM-trnD-GUC_p4 psbM-trnD-GUC TGCGAGAATATTGACTTCCA GTTCAATTGGTCAGAGCACC 551–1272 0.846 49.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGCGAGAATATTGACTTCCA TTCAATTGGTCAGAGCACCG 552–1273 0.846 49.0
trnE-UUC-trnD-GUC_p1 trnE-UUC-trnD-GUC ATGCGTTGTGCCATTTCATG ATCATAATGTTTCCGCCCCC 1855 0.077 43.0
trnE-UUC-trnD-GUC_p2 trnE-UUC-trnD-GUC ATGCGTTGTGCCATTTCATG GGCCATTTCCGAAATTGTGG 1881 0.077 43.0
trnE-UUC-trnD-GUC_p3 trnE-UUC-trnD-GUC ATGCGTTGTGCCATTTCATG TCAAGGAAAAAGCGAGCACT 2295 0.077 42.8
trnE-UUC-trnD-GUC_p4 trnE-UUC-trnD-GUC ATGCGTTGTGCCATTTCATG GTCAAGGAAAAAGCGAGCAC 2296 0.077 42.8
trnE-UUC-trnD-GUC_p5 trnE-UUC-trnD-GUC ATGCGTTGTGCCATTTCATG CAAGGAAAAAGCGAGCACTG 2294 0.077 42.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Pelargonium alternans NC_023261.1 173374 View on NCBI ↗
Pelargonium australe NC_028053.1 165508 View on NCBI ↗
Pelargonium citronellum NC_031194.1 171223 View on NCBI ↗
Pelargonium cotyledonis NC_028052.1 166111 View on NCBI ↗
Pelargonium cucullatum NC_031193.1 170963 View on NCBI ↗
Pelargonium echinatum NC_031197.1 170212 View on NCBI ↗
Pelargonium exhibens NC_031196.1 171665 View on NCBI ↗
Pelargonium exstipulatum NC_031198.1 168732 View on NCBI ↗
Pelargonium fulgidum NC_031199.1 171502 View on NCBI ↗
Pelargonium incrassatum NC_031200.1 173196 View on NCBI ↗
Pelargonium nanum NC_031202.1 173496 View on NCBI ↗
Pelargonium quercifolium NC_031203.1 170569 View on NCBI ↗
Pelargonium tetragonum NC_031205.1 173410 View on NCBI ↗