Markers + reference

Loeseneriella

2 species · Celastraceae · Celastrales

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Species 2
Genome length 158–158 kb
Candidate markers 275
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1027 0.0111 0.96 57.2 yes View details
trnS-GCU-trnG-UCC LSC 832 0.0185 0.98 68.5 yes View details
atpH-atpI LSC 1264 0.0073 0.98 64.7 yes View details
trnM-CAU-atpE LSC 254 0.0329 0.96 64.3 yes View details
psaI-ycf4 LSC 471 0.0193 0.99 67.9 yes View details
petA-psbJ LSC 1057 0.0246 1.00 72.9 yes View details
trnN-GUU-ndhF IRb 2102 0.0138 1.00 53.5 yes View details
ccsA-ndhD SSC 257 0.0251 0.93 63.2 yes View details
ycf1 SSC 5691 0.0059 0.99 46.1 yes View details
psbC-trnS-UGA LSC 240 0.0292 1.00 69.3 yes View details
trnH-GUG-psbA LSC 562 0.0116 0.92 68.5 yes View details
trnT-GGU-psbD LSC 1474 0.0056 0.97 64.4 yes View details
psbM-trnD-GUC LSC 1126 0.0063 0.99 63.7 yes View details
trnR-ACG-trnN-GUU IRb 597 0.0084 1.00 63.5 yes View details
trnN-GUU-trnR-ACG IRa 597 0.0084 1.00 63.5 yes View details
matK LSC 1527 0.0059 0.99 62.7 yes View details
petL-petG LSC 171 0.0175 1.00 62.6 yes View details
trnC-GCA-petN LSC 860 0.0072 0.98 62.0 yes View details
psbZ-trnG-GCC LSC 700 0.0087 0.98 61.3 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 GCGCTAACCTTGGTATGGAA 664–679 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 678–693 1.000 83.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 677–692 1.000 83.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 679–694 1.000 83.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACAATCCACTGCCTT GCGCTAACCTTGGTATGGAA 684–699 1.000 83.4
matK_p1 matK ACTCCGTTTTTGAACCCGTA TGCTTTGACTGTATCGCACT 1695–1704 1.000 72.3
matK_p2 matK TACTCCGTTTTTGAACCCGT TGCTTTGACTGTATCGCACT 1696–1705 1.000 72.3
matK_p3 matK TCCGTTTTTGAACCCGTACT TGCTTTGACTGTATCGCACT 1693–1702 1.000 72.3
matK_p4 matK ACTCCGTTTTTGAACCCGTA ACCTTTTCCCTTCGGTTCAA 1646–1655 1.000 70.0
matK_p5 matK TCCGTTTTTGAACCCGTACT ACCTTTTCCCTTCGGTTCAA 1644–1653 1.000 70.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCGTTGTTTTCGACCACACT GAGGTTCGAATCCTTCCGTC 1067–1093 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGTTTTCGACCACACTG GAGGTTCGAATCCTTCCGTC 1066–1092 1.000 82.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCGTTGTTTTCGACCACACT AATAGAATATGGGGCGTGGC 1124–1150 1.000 81.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GACCACACTGTCTCAAACGA GAGGTTCGAATCCTTCCGTC 1056–1082 1.000 81.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGTTTTCGACCACACTG AATAGAATATGGGGCGTGGC 1123–1149 1.000 81.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TATGAATCCAACCGAGGGAC 948–972 1.000 72.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TATGAATCCAACCGAGGGAC 947–971 1.000 72.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATGAATCCAACCGAGGGACC 947–971 1.000 71.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATGAATCCAACCGAGGGACC 946–970 1.000 71.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC TATGAATCCAACCGAGGGAC 950–974 1.000 69.6
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTGCAACTTTAGCCGCAG 1349–1406 1.000 80.0
atpH-atpI_p2 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTGCAACTTTAGCCGCAG 1359–1416 1.000 79.4
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGACCGACGG TTTTGCAACTTTAGCCGCAG 1385–1442 1.000 78.4
atpH-atpI_p4 atpH-atpI CCGGGTCCAATAGAAGCAAG TTTTGCAACTTTAGCCGCAG 1393–1450 1.000 78.1
atpH-atpI_p5 atpH-atpI ATGCCTTCTACAGCTTGACC TTTTGCAACTTTAGCCGCAG 1435–1492 1.000 77.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 901–916 1.000 80.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 962–977 1.000 78.8
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 919–934 1.000 78.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 980–995 1.000 76.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 900–915 1.000 74.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Loeseneriella lenticellata NC_065724.1 158035 View on NCBI ↗
Loeseneriella merrilliana NC_065720.1 158332 View on NCBI ↗