Markers + reference

Santalum

10 species · Santalaceae · Santalales

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Species 10
Genome length 144–144 kb
Candidate markers 253
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 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 367 0.0229 1.00 75.9 yes View details
rps16 LSC 1111 0.0085 1.00 62.3 yes View details
ycf3-trnS-GGA LSC 756 0.0096 1.00 67.2 yes View details
petA-psbJ LSC 819 0.0125 1.00 64.5 yes View details
trnP-UGG-psaJ LSC 370 0.0077 1.00 39.9 yes View details
infA LSC 239 0.0150 1.00 41.8 yes View details
rpl22 LSC 480 0.0063 1.00 35.9 yes View details
trnL-UAG-rpl32 SSC 788 0.0147 1.00 64.9 yes View details
ycf1 SSC 5697 0.0069 1.00 45.7 yes View details
trnN-GUU-trnR-ACG SSC 517 0.0146 0.99 66.0 yes View details
petN-psbM LSC 1084 0.0092 1.00 65.0 yes View details
rps2-rpoC2 LSC 157 0.0183 1.00 62.5 yes View details
ycf4-cemA LSC 710 0.0042 1.00 61.4 yes View details
rbcL-accD LSC 643 0.0059 0.99 61.0 yes View details
trnT-GGU-psbD LSC 1356 0.0054 1.00 59.3 yes View details
ndhD-psaC SSC 99 0.0364 1.00 58.4 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0169 1.00 57.6 yes View details
trnK-UUU-rps16 LSC 793 0.0070 0.95 57.5 yes View details
atpF-atpH LSC 165 0.0098 1.00 57.3 yes View details
trnR-ACG-rrn5S IRa 407 0.0069 0.97 57.2 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 CAATCCACTGCCTTGATCCA CTGTTGAAGTTCCGTCCACA 349–447 1.000 87.9
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTGTTGAAGTTCCGTCCACA 348–446 1.000 87.9
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTGTTGAAGTTCCGTCCACA 350–448 1.000 87.9
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TAACCGTGCTAACCTGGGTA 420–518 1.000 87.1
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TAACCGTGCTAACCTGGGTA 419–517 1.000 87.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GGGCGGAGGTTTTTAAGGAA 871–910 1.000 84.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GGGCGGAGGTTTTTAAGGAA 872–911 1.000 84.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC GGGCGGAGGTTTTTAAGGAA 876–915 1.000 84.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT GGGCGGAGGTTTTTAAGGAA 874–913 1.000 84.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC GGGCGGAGGTTTTTAAGGAA 883–922 1.000 84.5
rps16_p1 rps16 TGTTGTTATAGGACGTGGGA TGGGTACTAGTTAAAGCAATGACT 1309–1314 0.900 37.3
rps16_p2 rps16 GACGTGGGATTTTAAACAAGCA TGGGTACTAGTTAAAGCAATGACT 1298–1303 0.900 37.3
rps16_p3 rps16 TTGTTGTTATAGGACGTGGGA TGGGTACTAGTTAAAGCAATGACT 1310–1315 0.900 37.3
rps16_p4 rps16 ACGTGGGATTTTAAACAAGCA TGGGTACTAGTTAAAGCAATGACT 1297–1302 0.900 37.3
rps16_p5 rps16 GGACGTGGGATTTTAAACAAGC TGGGTACTAGTTAAAGCAATGACT 1299–1304 0.900 37.3
atpF-atpH_p1 atpF-atpH TATTAAACCCGAAACCCCCG GCAGAGGGAAAGATACGAGG 343–358 1.000 77.1
atpF-atpH_p2 atpF-atpH GGCAGATGACCAGTGACCTA GCAGAGGGAAAGATACGAGG 324–339 1.000 74.3
atpF-atpH_p3 atpF-atpH GCAGATGACCAGTGACCTAA GCAGAGGGAAAGATACGAGG 323–338 1.000 72.2
atpF-atpH_p4 atpF-atpH TATTAAACCCGAAACCCCCG CCGAAGCAGAGGGAAAGATAC 348–363 1.000 72.0
atpF-atpH_p5 atpF-atpH ACACCGAGCACTACACTTAG GCAGAGGGAAAGATACGAGG 392–407 1.000 71.8
rps2-rpoC2_p1 rps2-rpoC2 AAAATGCACTCCTGCTTCCA TTTTGTTCTACCACAGAGGA 318–323 1.000 48.2
rps2-rpoC2_p2 rps2-rpoC2 AAATGCACTCCTGCTTCCAT TTTTGTTCTACCACAGAGGA 317–322 1.000 46.4
rps2-rpoC2_p3 rps2-rpoC2 AATGCACTCCTGCTTCCATC TTTTGTTCTACCACAGAGGA 316–321 1.000 46.3
rps2-rpoC2_p4 rps2-rpoC2 AAAATGCACTCCTGCTTCCA TTGTTCTACCACAGAGGATT 316–321 1.000 46.3
rps2-rpoC2_p5 rps2-rpoC2 AAAATGCACTCCTGCTTCCA TTTGTTCTACCACAGAGGAT 317–322 1.000 46.3
petN-psbM_p1 petN-psbM ATCGCTTGGGCTGCTTTAAT ATTGCTACTGCGCTGTTCAT 1248–1295 1.000 79.5
petN-psbM_p2 petN-psbM ATGGGGGAGAAATGGACTCT ATTGCTACTGCGCTGTTCAT 1195–1242 1.000 79.1
petN-psbM_p3 petN-psbM GTATCGCTTGGGCTGCTTTA ATTGCTACTGCGCTGTTCAT 1250–1297 1.000 78.6
petN-psbM_p4 petN-psbM CACTCGTAGTATGGGGGAGA ATTGCTACTGCGCTGTTCAT 1205–1252 1.000 78.6
petN-psbM_p5 petN-psbM ATCGCTTGGGCTGCTTTAAT TATTGCTACTGCGCTGTTCA 1249–1296 1.000 78.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Santalum album NC_048953.1 144101 View on NCBI ↗
Santalum boninense NC_077481.1 144263 View on NCBI ↗
Santalum ellipticum NC_077482.1 144250 View on NCBI ↗
Santalum ellipticum var. littorale MW464920.1 144255 View on NCBI ↗
Santalum lanceolatum NC_077483.1 143801 View on NCBI ↗
Santalum leptocladum NC_077480.1 143923 View on NCBI ↗
Santalum paniculatum NC_077484.1 144239 View on NCBI ↗
Santalum pyrularium NC_077485.1 143895 View on NCBI ↗
Santalum spicatum NC_077487.1 143638 View on NCBI ↗
Santalum yasi NC_077486.1 144019 View on NCBI ↗