Markers + reference

Oreocnide

12 species · Urticaceae · Rosales

Back to catalogue

Species 12
Genome length 157–157 kb
Candidate markers 265
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 823 0.0068 0.94 60.0 yes View details
atpA LSC 1524 0.0006 1.00 30.3 yes View details
rpoB-trnC-GCA LSC 1213 0.0051 1.00 50.4 yes View details
trnT-UGU-trnL-UAA LSC 1088 0.0036 1.00 55.1 yes View details
petA-psbJ LSC 982 0.0044 1.00 54.1 yes View details
clpP LSC 2106 0.0027 1.00 43.4 yes View details
ndhF-rpl32 SSC 1263 0.0043 0.99 61.1 yes View details
rpl32-trnL-UAG SSC 860 0.0102 0.99 54.0 yes View details
ccsA-ndhD SSC 285 0.0302 1.00 64.8 yes View details
ycf1 SSC 5751 0.0021 1.00 44.6 yes View details
atpA-atpF LSC 68 0.0372 1.00 63.0 yes View details
psbE-petL LSC 1229 0.0033 1.00 57.8 yes View details
trnC-GCA-petN LSC 994 0.0032 0.98 57.6 yes View details
trnK-UUU-rps16 LSC 812 0.0032 0.99 54.1 yes View details
rps16 LSC 1198 0.0020 1.00 54.0 yes View details
atpF-atpH LSC 458 0.0040 1.00 53.8 yes View details
rps4-trnT-UGU LSC 501 0.0016 1.00 53.2 yes View details
psaJ-rpl33 LSC 457 0.0029 1.00 51.8 yes View details
rpl16-rps3 LSC 162 0.0067 0.99 51.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAGGCGGGTGT 976–995 1.000 82.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAGGCGGGTGT 975–994 1.000 82.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAGGCGGGTGT 893–912 1.000 81.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAGGCGGGTGT 892–911 1.000 81.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT ATTTCAAAGAAGGCGGGTGT 977–996 1.000 81.0
rps16_p1 rps16 CAATGGGCGTTTTTCAGTGG CCGACCGAACCAATGACTAT 1368–1396 1.000 75.3
rps16_p2 rps16 CAATGGGCGTTTTTCAGTGG GTACCGACCGAACCAATGAC 1371–1399 1.000 74.9
rps16_p3 rps16 AATGGGCGTTTTTCAGTGGA CCGACCGAACCAATGACTAT 1367–1395 1.000 74.6
rps16_p4 rps16 ATGGGCGTTTTTCAGTGGAA CCGACCGAACCAATGACTAT 1366–1394 1.000 74.6
rps16_p5 rps16 TGGGCGTTTTTCAGTGGAAT CCGACCGAACCAATGACTAT 1365–1393 1.000 74.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 818–896 1.000 84.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 833–911 1.000 83.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 832–910 1.000 83.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGGTGTAAGAATCCACAGC GAGGTTCGAATCCTTCCGTC 852–930 1.000 82.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 839–917 1.000 81.2
atpA_p1 atpA AGCCTTCCAAGCTAACGATG GTAATTGAGCGTGAGAGCCA 2429–2435 1.000 80.3
atpA_p2 atpA ACCCTTAGCCTTCCAAGCTA GTAATTGAGCGTGAGAGCCA 2435–2441 1.000 80.3
atpA_p3 atpA AGCCTTCCAAGCTAACGATG ATTCGTGTTTGGTTCGGGAA 2396–2402 1.000 80.2
atpA_p4 atpA ACCCTTAGCCTTCCAAGCTA ATTCGTGTTTGGTTCGGGAA 2402–2408 1.000 80.1
atpA_p5 atpA AGCCTTCCAAGCTAACGATG AAAAAGCCCAATCCCGCTTA 2239–2245 1.000 79.9
atpA-atpF_p1 atpA-atpF AATTTCATCGGCTCGAAGGG ACAAGGAGCTCTAGGAACTCT 203–206 1.000 68.8
atpA-atpF_p2 atpA-atpF AATTTCATCGGCTCGAAGGG AGGAGCTCTAGGAACTCTGA 200–203 1.000 68.4
atpA-atpF_p3 atpA-atpF ACTTGAAGTACGGTACCGGT ACAAGGAGCTCTAGGAACTCT 280–283 1.000 67.5
atpA-atpF_p4 atpA-atpF ACTTGAAGTACGGTACCGGT AGGAGCTCTAGGAACTCTGA 277–280 1.000 67.2
atpA-atpF_p5 atpA-atpF TCGCCTACTTGAAGTACGGT ACAAGGAGCTCTAGGAACTCT 286–289 1.000 66.8
atpF-atpH_p1 atpF-atpH GATGGCCAATAACCCAAGGA TGGTTGTGGCATTAGCACTT 545–558 1.000 81.0
atpF-atpH_p2 atpF-atpH GGATGGCCAATAACCCAAGG TGGTTGTGGCATTAGCACTT 546–559 1.000 79.9
atpF-atpH_p3 atpF-atpH GATGGCCAATAACCCAAGGA TGGACTGGTTGTGGCATTAG 550–563 1.000 79.4
atpF-atpH_p4 atpF-atpH TGGCCAATAACCCAAGGAAA TGGTTGTGGCATTAGCACTT 543–556 1.000 79.0
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTTCCGGC TGGTTGTGGCATTAGCACTT 566–579 1.000 78.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Oreocnide boniana NC_062324.1 157015 View on NCBI ↗
Oreocnide frutescens NC_062323.1 156955 View on NCBI ↗
Oreocnide frutescens subsp. frutescens NC_062322.1 157182 View on NCBI ↗
Oreocnide integrifolia NC_062321.1 157053 View on NCBI ↗
Oreocnide kwangsiensis NC_062320.1 156962 View on NCBI ↗
Oreocnide obovata var. paradoxa NC_062319.1 156986 View on NCBI ↗
Oreocnide pedunculata NC_062318.1 157046 View on NCBI ↗
Oreocnide rubescens NC_062317.1 157135 View on NCBI ↗
Oreocnide serrulata NC_062316.1 157015 View on NCBI ↗
Oreocnide tonkinensis NC_062315.1 156736 View on NCBI ↗
Oreocnide tonkinensis var. discolor NC_062314.1 156984 View on NCBI ↗
Oreocnide trinervis NC_062313.1 156793 View on NCBI ↗