Markers + reference

Epilobium

15 species · Onagraceae · Myrtales

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Species 15
Genome length 161–161 kb
Candidate markers 271
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 395 0.0279 0.98 80.9 yes View details
trnK-UUU-rps16 LSC 758 0.0185 1.00 82.7 yes View details
rps16-trnQ-UUG LSC 1433 0.0144 1.00 69.2 yes View details
psbI-trnS-GCU LSC 191 0.0314 0.99 68.7 yes View details
trnS-GCU-trnG-UCC LSC 806 0.0177 0.99 69.3 yes View details
trnC-GCA-petN LSC 913 0.0126 1.00 65.7 yes View details
ycf2 IRb 6720 0.0020 0.99 48.9 yes View details
ndhF-rpl32 SSC 718 0.0335 0.98 82.5 yes View details
ccsA-ndhD SSC 429 0.0203 0.99 68.1 yes View details
ycf2 IRa 6720 0.0016 0.99 48.0 no View details
trnT-UGU-trnL-UAA LSC 1146 0.0092 1.00 72.3 yes View details
trnR-UCU-atpA LSC 223 0.0140 0.99 71.1 yes View details
atpF-atpH LSC 506 0.0127 0.99 70.5 yes View details
rpoB-trnC-GCA LSC 1269 0.0094 1.00 70.3 yes View details
ycf4-cemA LSC 872 0.0079 0.99 70.3 yes View details
trnG-GCC-trnM-CAU LSC 181 0.0165 0.97 69.5 yes View details
petN-psbM LSC 905 0.0125 0.99 69.0 yes View details
petA-psbJ LSC 998 0.0078 0.99 68.7 yes View details
trnD-GUC-trnY-GUA LSC 470 0.0113 1.00 65.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAAACCTCCGCCTTAATCCA CCTCTAGACCTAGCTGCTGT 264–490 1.000 90.5
trnH-GUG-psbA_p2 trnH-GUG-psbA AAACCTCCGCCTTAATCCAC CCTCTAGACCTAGCTGCTGT 263–489 1.000 90.5
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAAACCTCCGCCTTAATCC CCTCTAGACCTAGCTGCTGT 265–491 1.000 90.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CAAACCTCCGCCTTAATCCA TTCCCTCTAGACCTAGCTGC 267–493 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AAACCTCCGCCTTAATCCAC TTCCCTCTAGACCTAGCTGC 266–492 1.000 90.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAGGAGCTCAACCCACAG 854–908 1.000 87.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGAAAGCGGGGGTTTTTACC 813–867 1.000 84.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGAGCTCAACCCACA 855–909 1.000 83.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTGTAAAAGATGCTAGCCGC AAAAGGAGCTCAACCCACAG 870–924 1.000 83.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC AAAAGGAGCTCAACCCACAG 853–907 1.000 83.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT GAGGTTCGAATCCTTCCGTC 1020–1529 1.000 88.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCATGTCTGTCAAGTCGCG GAGGTTCGAATCCTTCCGTC 1038–1547 1.000 85.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT TTCGGAGGTTCGAATCCTTC 1024–1533 1.000 83.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT TAAGGCAACGGGTTTTGGTC 1050–1559 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT TAGAAATCGAAATGGGGCGT 1080–1589 1.000 83.1
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TCGAATCCCTCTCTTTCCGT 233–243 1.000 80.5
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 287–297 1.000 80.0
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 288–298 1.000 79.9
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTTTTCGTACCGAGGGTTCG 250–260 1.000 79.4
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 287–297 1.000 77.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CAAACCGAGCGATCCCTTAA 877–949 1.000 90.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CAAACCGAGCGATCCCTTAA 876–948 1.000 90.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACCGAGCGATCCCTTAAC 876–948 1.000 90.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAACCGAGCGATCCCTTAAC 875–947 1.000 90.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACTGAACGGAAAGAGAGGGA CAAACCGAGCGATCCCTTAA 936–1008 1.000 90.1
trnR-UCU-atpA_p1 trnR-UCU-atpA TCGGAATCAAAAAGGCGTCC CGCTATTCAGGAGCAGAAGG 352–385 1.000 79.3
trnR-UCU-atpA_p2 trnR-UCU-atpA TCGGAATCAAAAAGGCGTCC CACAAGCCCTTTTGAACGAC 371–404 1.000 79.2
trnR-UCU-atpA_p3 trnR-UCU-atpA TCGGAATCAAAAAGGCGTCC GAGCAGAAGGAACGCTTTCT 342–375 1.000 78.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TCGGAATCAAAAAGGCGTCC ATTCACCGAGGAAGCACAAG 385–418 1.000 78.5
trnR-UCU-atpA_p5 trnR-UCU-atpA TCGGAATCAAAAAGGCGTCC ACCGCAGTTCGAAGAAATCA 421–450 0.933 75.3

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
Epilobium alpestre PP335062.1 161214 View on NCBI ↗
Epilobium amurense subsp. amurense NC_061013.1 160748 View on NCBI ↗
Epilobium amurense subsp. cephalostigma NC_061015.1 161124 View on NCBI ↗
Epilobium ciliatum PP335063.1 160856 View on NCBI ↗
Epilobium collinum PP335064.1 161321 View on NCBI ↗
Epilobium cylindricum NC_061016.1 160773 View on NCBI ↗
Epilobium hirsutum NC_058317.1 161111 View on NCBI ↗
Epilobium minutiflorum NC_061011.1 160993 View on NCBI ↗
Epilobium palustre PP335065.1 160581 View on NCBI ↗
Epilobium parviflorum NC_066964.1 161284 View on NCBI ↗
Epilobium royleanum NC_061023.1 161129 View on NCBI ↗
Epilobium sikkimense NC_061019.1 161144 View on NCBI ↗
Epilobium tibetanum NC_061026.1 160771 View on NCBI ↗
Epilobium ulleungensis NC_039575.1 160912 View on NCBI ↗
Epilobium williamsii NC_061012.1 160837 View on NCBI ↗