Markers + reference

Xylosma

2 species · Salicaceae · Malpighiales

Back to catalogue

Species 2
Genome length 157–157 kb
Candidate markers 265
Primer pairs 100

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0056 1.00 50.9 yes View details
trnS-GCU-trnR-UCU LSC 1619 0.0188 0.99 63.0 yes View details
trnE-UUC-trnT-GGU LSC 230 0.0856 0.97 77.4 yes View details
trnS-UGA-lhbA LSC 339 0.0396 0.97 73.5 yes View details
ndhC-trnV-UAC LSC 1280 0.1124 0.95 90.5 yes View details
petA-psbJ LSC 932 0.0449 0.91 78.6 yes View details
ycf1 SSC 1821 0.0127 0.99 51.5 yes View details
ndhF-trnL-UAG SSC 678 0.0236 0.94 63.9 yes View details
ndhG-ndhI SSC 399 0.0125 1.00 47.4 yes View details
ycf1 SSC 3867 0.0130 0.99 52.9 no View details
trnN-GUU-trnR-ACG SSC 665 0.0271 1.00 74.3 yes View details
trnH-GUG-psbA LSC 252 0.0826 0.96 88.8 yes View details
ndhD-psaC SSC 109 0.0917 1.00 86.5 yes View details
psbI-trnS-GCU LSC 137 0.0299 0.98 71.7 yes View details
psbT-psbN LSC 60 0.0333 1.00 71.7 yes View details
rpl2-rps19 LSC 56 0.0893 1.00 71.5 yes View details
rps15-ycf1 SSC 450 0.0255 0.96 69.2 yes View details
petN-psbM LSC 1291 0.0106 0.95 67.8 yes View details
trnY-GUA-trnE-UUC LSC 58 0.0345 1.00 67.8 yes View details
atpH-atpI LSC 1020 0.0129 0.99 67.2 yes View details
trnR-ACG-trnN-GUU SSC 664 0.0122 0.98 67.2 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 AACCGTGCAAACCTTGGTAT 373–400 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AACCGTGCAAACCTTGGTAT 387–414 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AACCGTGCAAACCTTGGTAT 386–413 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AACCGTGCAAACCTTGGTAT 388–415 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GCGAATGACGGGAATTGAAC AACCGTGCAAACCTTGGTAT 425–540 1.000 83.5
psbA_p1 psbA AGCTCATACACACTAAGACCA AGAATTCGTGTGCTTGGGAG 1140–1175 1.000 55.7
psbA_p2 psbA AGCTCATACACACTAAGACCA AGAGAATTCGTGTGCTTGGG 1142–1177 1.000 55.7
psbA_p3 psbA AGCTCATACACACTAAGACCA GAGAATTCGTGTGCTTGGGA 1141–1176 1.000 55.7
psbA_p4 psbA AGCTCATACACACTAAGACCAA AGAATTCGTGTGCTTGGGAG 1140–1175 1.000 53.7
psbA_p5 psbA AGCTCATACACACTAAGACCAA AGAGAATTCGTGTGCTTGGG 1142–1177 1.000 53.7
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TAAAGCGCCGGATTGCTAAT 237–240 1.000 79.9
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT ATTGGGAGAGATGGCTGAGT 261–264 1.000 79.1
psbI-trnS-GCU_p3 psbI-trnS-GCU AATGATCCAGGGCGTAATCC TAAAGCGCCGGATTGCTAAT 238–241 1.000 77.5
psbI-trnS-GCU_p4 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT CGAGTTATTCGTACCGAGGG 209–212 1.000 77.4
psbI-trnS-GCU_p5 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT ATGGCTGAGTGGACTAAAGC 251–254 1.000 76.8
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGGCGCTTTA AGAAGACCTCTGTCCTATCCA 1695–1808 1.000 65.6
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ATCAACGGAACCGGAAAGAG AGAAGACCTCTGTCCTATCCA 1754–1867 1.000 65.1
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ATTAGCAATCCGGCGCTTTA AGGTTTAGAAGACCTCTGTCCT 1701–1814 1.000 64.9
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ATCAACGGAACCGGAAAGAG AGGTTTAGAAGACCTCTGTCCT 1760–1873 1.000 64.4
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CATCAACGGAACCGGAAAGA AGAAGACCTCTGTCCTATCCA 1755–1868 1.000 64.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GTGAATCCATGGAGGGACAC 1077–1078 1.000 81.1
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT GTGAATCCATGGAGGGACAC 1069–1070 1.000 80.9
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1106–1107 1.000 80.4
atpH-atpI_p4 atpH-atpI GTCCAATAGAAGCAAGCCCA GTGAATCCATGGAGGGACAC 1115–1116 1.000 80.3
atpH-atpI_p5 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 1098–1099 1.000 80.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1453–1473 1.000 71.6
petN-psbM_p2 petN-psbM CTTGGGCTGCTTTGATGGTA TGCTACTGCACTGTTCATTCT 1441–1461 1.000 71.6
petN-psbM_p3 petN-psbM TTGGGCTGCTTTGATGGTAG TGCTACTGCACTGTTCATTCT 1440–1460 1.000 71.6
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1392–1412 1.000 70.2
petN-psbM_p5 petN-psbM GGGGCCATAATTCACATGGA TGCTACTGCACTGTTCATTCT 1475–1495 1.000 69.7

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
Xylosma congesta NC_060653.1 156520 View on NCBI ↗
Xylosma longifolia NC_057050.1 156938 View on NCBI ↗