Markers + reference

Enkianthus

14 species · Ericaceae · Ericales

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Species 14
Genome length 158–160 kb
Candidate markers 267
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD LSC 1953 0.0141 1.00 54.2 yes View details
rbcL-atpB LSC 1227 0.0372 0.89 70.8 yes View details
trnN-GUU-ndhF IRb 1174 0.0440 0.96 87.9 yes View details
ycf1 SSC 6582 0.0228 0.99 61.2 yes View details
ycf1-trnN-GUU IRa 1832 0.0222 0.97 59.0 yes View details
trnH-GUG-psbA LSC 707 0.0174 0.98 64.0 yes View details
rps16-trnQ-UUG LSC 1426 0.0071 0.99 61.9 yes View details
ndhC-accD LSC 1456 0.0111 0.99 59.7 yes View details
ndhF-rpl32 SSC 909 0.0114 0.97 59.7 yes View details
trnC-GCA-petN LSC 604 0.0095 0.98 57.8 yes View details
psbE-petL LSC 1279 0.0070 1.00 57.5 yes View details
ycf2-trnI-CAU IRa 216 0.0222 1.00 56.8 yes View details
trnT-GGU-psbD LSC 1468 0.0060 1.00 56.6 yes View details
petN-psbM LSC 1221 0.0098 1.00 56.0 yes View details
trnK-UUU-rps16 LSC 869 0.0081 0.94 55.7 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA AATCATAACCCTGGGCGAAC TCGTATTCCAAGCTGAGCAC 1265–1311 1.000 86.0
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCATAACCCTGGGCGAAC ATTCCAAGCTGAGCACAACA 1261–1307 1.000 86.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCATAACCCTGGGCGAAC TTCCAAGCTGAGCACAACAT 1260–1306 1.000 86.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCATAACCCTGGGCGAAC CTGATGGGATGCCTCTAGGA 1310–1356 1.000 85.9
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCATAACCCTGGGCGAAC TCTGATGGGATGCCTCTAGG 1311–1357 1.000 85.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AGGCGGAGATTTTTAAGGAAGT 920–986 1.000 67.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AGGCGGAGATTTTTAAGGAAGT 921–987 1.000 67.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC AGGCGGAGATTTTTAAGGAAGT 925–991 1.000 67.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AGGCGGAGATTTTTAAGGAAGT 923–989 1.000 67.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGCGGAGATTTTTAAGGAAGT 871–937 1.000 66.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG AAGGTTCGAATCCTTCCGTC 1473–1523 1.000 82.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TTGGTCCCGTTATTCGAAGG 1489–1539 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GGTCCCGTTATTCGAAGGTT 1487–1537 1.000 82.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA AAGGTTCGAATCCTTCCGTC 1474–1524 1.000 81.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA TTGGTCCCGTTATTCGAAGG 1490–1540 1.000 81.3
trnC-GCA-petN_p1 trnC-GCA-petN GGGTGTCGCCTAATCAACAA AGCCCAAGCGAGACTTACTA 637–652 1.000 82.3
trnC-GCA-petN_p2 trnC-GCA-petN TTGTATCCTTTTGGCGGCAT AGCCCAAGCGAGACTTACTA 709–724 1.000 82.0
trnC-GCA-petN_p3 trnC-GCA-petN GACTGCAACTCCTCTTTCCC AGCCCAAGCGAGACTTACTA 669–684 1.000 82.0
trnC-GCA-petN_p4 trnC-GCA-petN GGACTGCAACTCCTCTTTCC AGCCCAAGCGAGACTTACTA 670–685 1.000 82.0
trnC-GCA-petN_p5 trnC-GCA-petN GGGACTGCAACTCCTCTTTC AGCCCAAGCGAGACTTACTA 671–686 1.000 82.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1383–1406 1.000 69.5
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1322–1345 1.000 68.0
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1383–1406 1.000 65.3
petN-psbM_p4 petN-psbM GGGGACAGAATTCACATGGA TGCTACTGCACTGTTCATTCT 1405–1428 1.000 64.3
petN-psbM_p5 petN-psbM AGGGGACAGAATTCACATGG TGCTACTGCACTGTTCATTCT 1406–1429 1.000 64.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1617–1637 1.000 78.8
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1620–1640 1.000 78.6
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CAAAAACGAAACGGTCCCTC 1616–1636 1.000 77.6
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG AGAGCAATAAACCCGACCAG 1640–1660 1.000 77.5
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CAAAAACGAAACGGTCCCTC 1619–1639 1.000 77.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Enkianthus campanulatus PP722976.1 158033 View on NCBI ↗
Enkianthus cernuus PP727291.1 159575 View on NCBI ↗
Enkianthus cernuus f. rubens PP737347.1 159558 View on NCBI ↗
Enkianthus chinensis PP727289.1 159697 View on NCBI ↗
Enkianthus deflexus PP727292.1 159586 View on NCBI ↗
Enkianthus nudipes PP727296.1 158300 View on NCBI ↗
Enkianthus quinqueflorus PP727290.1 158689 View on NCBI ↗
Enkianthus quinqueflorus var. ciliatoserrulatus PP737348.1 158683 View on NCBI ↗
Enkianthus ruber PP737349.1 159852 View on NCBI ↗
Enkianthus serotinus PP727294.1 158992 View on NCBI ↗
Enkianthus serrulatus PP727288.1 159277 View on NCBI ↗
Enkianthus sikokianus PP737350.1 159197 View on NCBI ↗
Enkianthus subsessilis PP727295.1 158288 View on NCBI ↗
Enkianthus tubulatus PP727297.1 159300 View on NCBI ↗