Markers + reference

Ardisia

8 species · Primulaceae · Ericales

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Species 8
Genome length 155–157 kb
Candidate markers 273
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbM-trnD-GUC LSC 916 0.0224 0.99 69.6 yes View details
trnT-GGU-psbD LSC 1286 0.0299 1.00 83.7 yes View details
ndhC-trnV-UAC LSC 491 0.0237 1.00 63.1 yes View details
rpl22 LSC 495 0.0238 1.00 56.0 yes View details
rpl2 IRb 1480 0.0042 1.00 43.4 no View details
trnL-CAA-ndhB IRb 570 0.0195 0.99 70.5 yes View details
rpl32-trnL-UAG SSC 762 0.0297 0.99 69.2 yes View details
ccsA-ndhD SSC 249 0.0394 1.00 76.7 yes View details
ndhD SSC 1524 0.0053 1.00 48.9 yes View details
ndhB-trnL-CAA IRa 570 0.0205 0.99 71.1 yes View details
rpl2 IRa 1480 0.0042 1.00 43.4 yes View details
rpl2-trnH-GUG IRa 267 0.0497 0.38 65.5 yes View details
ndhF-rpl32 SSC 918 0.0135 0.97 62.6 yes View details
trnE-UUC-trnT-GGU LSC 781 0.0081 1.00 62.3 yes View details
ycf1-ndhF IRb 13 0.2005 1.00 62.3 yes View details
rps15-ycf1 SSC 421 0.0201 0.99 61.7 yes View details
rps16-trnQ-UUG LSC 1486 0.0106 0.99 61.6 yes View details
petL-petG LSC 172 0.0230 1.00 61.0 yes View details
trnS-GCU-trnG-UCC LSC 738 0.0115 1.00 60.7 yes View details
trnH-GUG-psbA LSC 427 0.0124 1.00 60.1 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 CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 458–503 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 459–504 1.000 84.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 451–496 1.000 83.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TAGACCTAGCTGCGGTTGAA 451–496 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 480–525 0.875 76.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCATGTCTTTCAAGCCGCA GAGGTTCGAATCCTTCCGTC 1571–1916 1.000 81.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GATCATGTCTTTCAAGCCGC GAGGTTCGAATCCTTCCGTC 1572–1917 1.000 79.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGGATGTAAGTCCACAACGG GAGGTTCGAATCCTTCCGTC 1591–1936 1.000 79.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCTTTCAAGCCGCA AAATTTAAATGGGGCGTGGC 1628–1973 1.000 78.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCTTCATCCTT GAGGTTCGAATCCTTCCGTC 1622–1967 1.000 78.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AACCGAAAGACCCCTTAACT 613–835 1.000 68.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GATTCGAACCCTCGGTACAA AACCGAAAGACCCCTTAACT 664–886 1.000 67.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AAACCGAAAGACCCCTTAACT 614–836 1.000 66.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATTCGAACCCTCGGTACAA AAACCGAAAGACCCCTTAACT 665–887 1.000 65.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAAAGAGAGGGATTCGAA AACCGAAAGACCCCTTAACT 676–898 1.000 65.3
psbM-trnD-GUC_p1 psbM-trnD-GUC ACGAGAACGAACAATGCAGT TCAATTGGTTAGAGCACCGC 1029–1290 1.000 80.1
psbM-trnD-GUC_p2 psbM-trnD-GUC CACGAGAACGAACAATGCAG TCAATTGGTTAGAGCACCGC 1030–1291 1.000 79.4
psbM-trnD-GUC_p3 psbM-trnD-GUC GTAGGCACGAGAACGAACAA TCAATTGGTTAGAGCACCGC 1035–1296 1.000 79.3
psbM-trnD-GUC_p4 psbM-trnD-GUC CAGTAGGCACGAGAACGAAC TCAATTGGTTAGAGCACCGC 1037–1298 1.000 75.8
psbM-trnD-GUC_p5 psbM-trnD-GUC ACGAGAACGAACAATGCAGT AATTGGTTAGAGCACCGCC 1027–1288 1.000 75.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AAGAGAGATGTCCTGGACCG GAACCGATGACTTACGCCTT 715–995 1.000 81.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTGTAGTACCCTACCCCCAG GAACCGATGACTTACGCCTT 764–1044 1.000 81.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AAGAGAGATGTCCTGGACCG CCATGGCGTTACTCTACCAC 694–974 1.000 81.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AAGAGAGATGTCCTGGACCG TGGCGTTACTCTACCACTGA 691–971 1.000 80.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTGTAGTACCCTACCCCCAG CCATGGCGTTACTCTACCAC 743–1023 1.000 80.6
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1313–1545 1.000 89.6
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1316–1548 1.000 89.4
trnT-GGU-psbD_p3 trnT-GGU-psbD CGACATAGCGGCTCCATTAA GGACCAGCCTACAAAAACGA 1364–1596 1.000 88.7
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1303–1535 1.000 88.5
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1306–1538 1.000 88.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Ardisia bullata NC_054287.1 155088 View on NCBI ↗
Ardisia crenata var. bicolor NC_061215.1 156538 View on NCBI ↗
Ardisia gigantifolia NC_059912.1 156216 View on NCBI ↗
Ardisia japonica NC_058736.1 155996 View on NCBI ↗
Ardisia mamillata NC_057115.1 156757 View on NCBI ↗
Ardisia polysticta NC_021121.1 156506 View on NCBI ↗
Ardisia silvestris PV608499.1 156640 View on NCBI ↗
Ardisia solanacea NC_045098.1 156518 View on NCBI ↗