Markers + reference

Euonymus

15 species · Celastraceae · Celastrales

Back to catalogue

Species 15
Genome length 157–158 kb
Candidate markers 273
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 478 0.0722 0.82 71.8 yes View details
trnK-UUU-rps16 LSC 634 0.0297 0.98 69.4 yes View details
petN-psbM LSC 884 0.0282 0.95 71.5 yes View details
psbZ-trnG-GCC LSC 734 0.0429 0.96 84.4 yes View details
accD LSC 1491 0.0140 1.00 52.9 yes View details
psbE-petL LSC 1215 0.0228 0.96 70.2 yes View details
rps19 LSC 279 0.0024 1.00 26.0 yes View details
trnN-GUU-ndhF IRb 2130 0.0161 1.00 59.6 yes View details
ndhF-rpl32 SSC 1034 0.0301 0.93 73.2 yes View details
ccsA-ndhD SSC 260 0.0617 0.95 71.8 yes View details
ycf1 SSC 5631 0.0198 1.00 58.9 yes View details
rps19-rpl2 IRb 65 0.0414 1.00 80.0 yes View details
trnT-UGU-trnL-UAA LSC 953 0.0231 0.98 78.4 yes View details
trnG-GCC-trnfM-CAU LSC 167 0.0454 0.95 72.7 yes View details
atpH-atpI LSC 1187 0.0158 0.95 72.3 yes View details
psbI-trnS-GCU LSC 230 0.0264 1.00 71.5 yes View details
psbM-trnD-GUC LSC 468 0.0232 1.00 69.8 yes View details
rps16-trnQ-UUG LSC 1009 0.0205 0.99 69.5 yes View details
psbC-trnS-UGA LSC 252 0.0278 1.00 68.7 yes View details
trnG-UCC-trnR-UCU LSC 392 0.0288 1.00 68.6 yes View details
trnT-GGU-psbD LSC 1449 0.0204 0.98 68.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACAATCCACTGCCTT GCGCTAACCTTGGTATGGAA 505–693 0.933 88.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACAATCCACTGCCTT TCAGTGCTATGCATGGTTCC 841–1029 0.933 87.9
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACAATCCACTGCCTT ATTTCTTCCTAGCCGCTTGG 658–846 0.933 87.9
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACAATCCACTGCCTT CAGTGCTATGCATGGTTCCT 840–1028 0.933 87.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ATCCACAATCCACTGCCTTG GCGCTAACCTTGGTATGGAA 504–692 0.933 87.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTCATCTCCACCCCCTAA CGATCGCGAAGAGAAGGAAA 1281–1355 1.000 88.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTCATCTCCACCCCCTAA TTAGAACCCCCAACCCTCAT 1655–1738 0.933 85.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG CGATCGCGAAGAGAAGGAAA 1045–1101 0.867 83.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG TTAGAACCCCCAACCCTCAT 1409–1487 0.800 80.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG TTTAGAACCCCCAACCCTCA 1410–1488 0.800 79.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TAGTTCGTTGCTTTCGACCA GAGGTTCGAATCCTTCCGTC 897–1247 1.000 85.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATAGTTCGTTGCTTTCGACCA GAGGTTCGAATCCTTCCGTC 898–1248 1.000 81.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGTTCGTTGCTTTCGACCAC GAGGTTCGAATCCTTCCGTC 896–1246 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTCGTTGCTTTCGACCACA GAGGTTCGAATCCTTCCGTC 894–1244 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TAGTTCGTTGCTTTCGACCA TTCGGAGGTTCGAATCCTTC 901–1251 1.000 80.9
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA GTTCTTCGTACCGAGGGTTC 274–346 1.000 80.8
psbI-trnS-GCU_p2 psbI-trnS-GCU AATCCCGGACGCGAAGAATA TGGACTAAAGCGTCGGATTG 311–383 1.000 80.1
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA TGGACTAAAGCGTCGGATTG 310–382 1.000 80.1
psbI-trnS-GCU_p4 psbI-trnS-GCU AATCCCGGACGCGAAGAATA GTGGACTAAAGCGTCGGATT 312–384 1.000 80.1
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA GTGGACTAAAGCGTCGGATT 311–383 1.000 80.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGTCCTATCCATTAGACAATG 462–581 1.000 52.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGTCCTATCCATTAGACAATG 465–584 1.000 52.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGTCCTATCCATTAGACAATG 466–585 1.000 52.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGTCCTATCCATTAGACAATG 451–570 1.000 52.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU TAACGATGCGGGTTCGATTC TGTCCTATCCATTAGACAATG 450–569 1.000 52.0
atpH-atpI_p1 atpH-atpI AATCACAGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1126–1301 1.000 84.1
atpH-atpI_p2 atpH-atpI ATCACAGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1125–1300 1.000 84.0
atpH-atpI_p3 atpH-atpI AATCACAGAAGCGGCAGAAA TAGGTGAATCCATGGAGGGT 1099–1274 1.000 83.7
atpH-atpI_p4 atpH-atpI ATCACAGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 1098–1273 1.000 83.6
atpH-atpI_p5 atpH-atpI AATAGAAGCAAGACCGACGG TTTTTGCAACTTTAGCCGCG 1159–1334 1.000 82.5

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
Euonymus acanthocarpus NC_065712.1 157113 View on NCBI ↗
Euonymus centidens NC_065711.1 158359 View on NCBI ↗
Euonymus europaeus NC_060645.1 157263 View on NCBI ↗
Euonymus fortunei NC_057058.1 157611 View on NCBI ↗
Euonymus hamiltonianus NC_037518.1 157360 View on NCBI ↗
Euonymus japonicus NC_028067.1 157637 View on NCBI ↗
Euonymus kiautschovicus PQ397793.1 157611 View on NCBI ↗
Euonymus maackii NC_057059.1 156860 View on NCBI ↗
Euonymus macropterus NC_062702.1 157377 View on NCBI ↗
Euonymus microcarpus ON611716.1 157542 View on NCBI ↗
Euonymus oxyphyllus NC_062703.1 157861 View on NCBI ↗
Euonymus phellomanus NC_057060.1 157543 View on NCBI ↗
Euonymus sachalinensis NC_062704.1 157290 View on NCBI ↗
Euonymus schensianus NC_036019.1 157702 View on NCBI ↗
Euonymus yunnanensis MW770452.1 156881 View on NCBI ↗