Markers + reference

Fragaria

15 species · Rosaceae · Rosales

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Species 15
Genome length 130–156 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 294 0.0081 1.00 40.8 yes View details
rps16-trnQ-UUG LSC 973 0.0067 0.99 61.9 yes View details
trnQ-UUG-psbK LSC 441 0.0052 1.00 51.9 yes View details
trnS-GCU-trnG-GCC LSC 612 0.0091 1.00 50.6 yes View details
trnR-UCU-atpA LSC 613 0.0119 1.00 53.7 yes View details
trnT-GGU-psbD LSC 1361 0.0051 1.00 54.1 yes View details
trnT-UGU-trnL-UAA LSC 944 0.0066 0.99 52.2 yes View details
rbcL LSC 1428 0.0059 1.00 43.5 yes View details
trnP-UGG-psaJ LSC 441 0.0161 0.98 64.8 yes View details
ycf1 IRb 1104 0.0030 1.00 33.5 yes View details
rpl32-trnL-UAG SSC 626 0.0077 1.00 67.1 yes View details
ycf1 SSC 5751 0.0030 1.00 59.5 yes View details
rpl2-trnH-GUG IRa 88 0.1053 0.72 76.4 no View details
ndhF-rpl32 SSC 613 0.0067 1.00 67.4 yes View details
ycf1-ndhF SSC 20 0.0522 1.00 61.1 yes View details
psbE-petL LSC 1221 0.0047 0.99 59.7 yes View details
ycf3-trnS-GGA LSC 868 0.0052 1.00 59.4 yes View details
accD-psaI LSC 499 0.0054 0.99 58.8 yes View details
rps4-trnT-UGU LSC 381 0.0070 1.00 58.7 yes View details
matK-trnK-UUU LSC 733 0.0051 1.00 58.2 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 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 340–374 1.000 85.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 354–388 1.000 85.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 353–387 1.000 85.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 355–389 1.000 85.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 343–377 1.000 85.2
matK-trnK-UUU_p1 matK-trnK-UUU CGATCATGAGCAAGGGCATA ATTGTGGTGTGCCCTTCAAT 943–950 1.000 84.1
matK-trnK-UUU_p2 matK-trnK-UUU AACCACGATCATGAGCAAGG ATTGTGGTGTGCCCTTCAAT 948–955 1.000 83.4
matK-trnK-UUU_p3 matK-trnK-UUU CGATCATGAGCAAGGGCATA AACGGTAGAGTACTCGGCTT 857–864 1.000 82.7
matK-trnK-UUU_p4 matK-trnK-UUU CGATCATGAGCAAGGGCATA ACGGTAGAGTACTCGGCTTT 856–863 1.000 82.7
matK-trnK-UUU_p5 matK-trnK-UUU CGATCATGAGCAAGGGCATA TGTGGTGTGCCCTTCAATTT 941–948 1.000 82.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 952–1133 1.000 85.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 950–1131 1.000 85.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATGTAAGACTCCACAGCGG GAGGTTCGAATCCTTCCGTC 966–1147 1.000 85.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATGTAAGACTCCACAGCG GAGGTTCGAATCCTTCCGTC 967–1148 1.000 85.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 934–1115 1.000 84.8
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA CGTAAGCTTCGGGCAATTTG 570–724 1.000 79.2
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GTAAGCTTCGGGCAATTTGG 569–723 1.000 77.8
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC CGTAAGCTTCGGGCAATTTG 579–724 1.000 77.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AAAACCCGTTGCCTTACCAC CGTAAGCTTCGGGCAATTTG 566–725 1.000 76.9
trnQ-UUG-psbK_p5 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC CGTAAGCTTCGGGCAATTTG 569–725 1.000 76.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 673–2062 1.000 57.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 672–2064 1.000 57.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 676–2065 1.000 56.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 675–2064 1.000 56.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 674–2066 1.000 56.5
trnR-UCU-atpA_p1 trnR-UCU-atpA ATTGGAGTGAAAAGCGTCCA CGTTTTCTACTTCAGGAACAGG 713–860 1.000 60.9
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT CGTTTTCTACTTCAGGAACAGG 711–858 1.000 60.9
trnR-UCU-atpA_p3 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT CGTTTTCTACTTCAGGAACAGG 712–859 1.000 60.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT GGAACGTTTTCTACTTCAGGAAC 715–862 1.000 58.1
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT GGAACGTTTTCTACTTCAGGAAC 716–863 1.000 58.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Fragaria chiloensis NC_019601.1 155603 View on NCBI ↗
Fragaria chinensis NC_058802.1 155806 View on NCBI ↗
Fragaria daltoniana NC_058804.1 155829 View on NCBI ↗
Fragaria iinumae NC_024258.1 155554 View on NCBI ↗
Fragaria iturupensis NC_062836.1 155637 View on NCBI ↗
Fragaria mandshurica NC_018767.1 129805 View on NCBI ↗
Fragaria moschata NC_062593.1 155601 View on NCBI ↗
Fragaria moupinensis NC_058805.1 155626 View on NCBI ↗
Fragaria nilgerrensis NC_058806.1 155783 View on NCBI ↗
Fragaria nubicola NC_058807.1 155608 View on NCBI ↗
Fragaria pentaphylla NC_034347.1 155640 View on NCBI ↗
Fragaria vesca subsp. bracteata NC_018766.1 129788 View on NCBI ↗
Fragaria vesca subsp. vesca NC_015206.1 155691 View on NCBI ↗
Fragaria virginiana NC_019602.1 155621 View on NCBI ↗
Fragaria viridis NC_048474.1 155458 View on NCBI ↗