Markers + reference

Sloanea

5 species · Elaeocarpaceae · Oxalidales

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Species 5
Genome length 158–158 kb
Candidate markers 269
Primer pairs 100

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 10 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 468 0.0034 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 1022 0.0051 0.97 66.2 yes View details
rpoB-trnC-GCA LSC 1216 0.0053 1.00 47.2 yes View details
trnC-GCA-petN LSC 914 0.0037 1.00 39.1 yes View details
rps8 LSC 402 0.0010 1.00 25.8 yes View details
trnR-ACG-trnN-GUU IRb 581 0.0048 1.00 46.6 yes View details
trnN-GUU-ndhF IRb 1528 0.0061 1.00 45.6 yes View details
ndhF-trnL-UAG SSC 1113 0.0066 0.99 53.0 yes View details
ycf1 SSC 5808 0.0015 1.00 53.6 yes View details
trnN-GUU-trnR-ACG IRa 581 0.0048 1.00 46.6 yes View details
psbF-psbE LSC 9 0.0444 1.00 70.0 yes View details
ndhK-ndhC LSC 73 0.0167 0.99 60.3 yes View details
trnT-UGU-trnL-UAA LSC 1005 0.0018 1.00 60.0 yes View details
rps8-rpl14 LSC 209 0.0153 0.97 59.9 yes View details
ycf3 LSC 1947 0.0008 1.00 59.0 yes View details
psbZ-trnG-GCC LSC 436 0.0023 1.00 57.7 yes View details
rps16-trnQ-UUG LSC 621 0.0023 1.00 52.9 yes View details
ycf4-cemA LSC 886 0.0016 1.00 52.5 yes View details
atpB-rbcL LSC 776 0.0013 1.00 52.4 yes View details
matK LSC 1515 0.0015 1.00 52.3 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 100 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 CCGTGCTAACCTTGGTATGG 586 1.000 76.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 600 1.000 76.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 599 1.000 76.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 601 1.000 76.6
trnH-GUG-psbA_p5 trnH-GUG-psbA TATTTATGGGCGAACGACGG CCGTGCTAACCTTGGTATGG 647 1.000 76.5
matK_p1 matK GGGATAATTTCTATTTAGAAGGTCTCA TCCCCTACCTTTGGTTCAAA 1580 1.000 40.3
matK_p2 matK AGGGATAATTTCTATTTAGAAGGTCTC TCCCCTACCTTTGGTTCAAA 1581 1.000 40.3
matK_p3 matK GGGATAATTTCTATTTAGAAGGTCTCA AATCCCCTACCTTTGGTTCA 1582 1.000 40.3
matK_p4 matK GGGATAATTTCTATTTAGAAGGTCTCA ATCCCCTACCTTTGGTTCAA 1581 1.000 40.3
matK_p5 matK AGGGATAATTTCTATTTAGAAGGTCT TCCCCTACCTTTGGTTCAAA 1581 1.000 40.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1060–1156 1.000 83.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1059–1155 1.000 83.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCAAAGAAGGCGGGGG 1026–1122 1.000 82.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAAAGAAGGCGGGGG 1025–1121 1.000 82.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1069–1165 1.000 82.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 712–727 1.000 79.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 710–725 1.000 79.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 689–704 1.000 77.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGCGGATCATGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 711–726 1.000 77.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCCTCATTTCT GAGGTTCGAATCCTTCCGTC 764–779 1.000 75.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCATTTCCATCCCCCAGCAT CCGGATTTGAACTGGGGAAA 1298–1302 1.000 71.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCCTCATTTCCATCCCCC CCGGATTTGAACTGGGGAAA 1303–1307 1.000 71.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1304–1308 1.000 71.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCGGGTATTGTAGACATTCC CCGGATTTGAACTGGGGAAA 1320–1324 1.000 71.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGGGTATTGTAGACATTCCC CCGGATTTGAACTGGGGAAA 1319–1323 1.000 71.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TACCATTAAAGCAGCCCAGG 982 1.000 76.4
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TACCATTAAAGCAGCCCAGG 1000 1.000 74.2
trnC-GCA-petN_p3 trnC-GCA-petN CCAATCCAAGCAAAAGGGGA TACCATTAAAGCAGCCCAGG 1071 1.000 74.2
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAGGCGAGATTTACTAT 969 1.000 73.2
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GACTACCATTAAAGCAGCCCA 985 1.000 71.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Sloanea cordifolia MW242789.1 158059 View on NCBI ↗
Sloanea dasycarpa MW242790.1 157966 View on NCBI ↗
Sloanea hemsleyana NC_058626.1 158085 View on NCBI ↗
Sloanea longiaculeata MW242791.1 157918 View on NCBI ↗
Sloanea sinensis NC_056387.1 158001 View on NCBI ↗