Markers + reference

Emblica

2 species · Phyllanthaceae · Malpighiales

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Species 2
Genome length 156–158 kb
Candidate markers 266
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1168 0.0366 0.98 71.2 yes View details
ycf4-cemA LSC 1061 0.0462 0.98 72.9 yes View details
petA-psbJ LSC 913 0.0627 0.98 81.7 yes View details
ndhF-rpl32 SSC 943 0.0574 0.76 74.7 yes View details
rpl32-trnL-UAG SSC 1057 0.0604 0.97 79.5 yes View details
ndhA SSC 2241 0.0318 0.98 62.6 yes View details
ycf1 SSC 5640 0.0428 1.00 63.5 yes View details
ycf1 SSC 1851 0.0482 1.00 71.1 no View details
rps15-ycf1 SSC 391 0.0472 0.97 81.3 yes View details
trnD-GUC-trnY-GUA LSC 431 0.0565 0.99 78.9 yes View details
trnH-GUG-psbA LSC 206 0.0955 0.97 78.3 yes View details
ndhD-psaC SSC 106 0.0943 1.00 77.4 yes View details
trnF-GAA-ndhJ LSC 505 0.0483 0.98 76.9 yes View details
lhbA-trnG-UCC LSC 754 0.0468 0.94 75.2 yes View details
petL-petG LSC 174 0.0479 0.96 75.2 yes View details
trnG-UCC-trnR-UCU LSC 411 0.0475 0.87 75.0 yes View details
atpH-atpI LSC 1130 0.0365 0.97 74.8 yes View details
psaI-ycf4 LSC 400 0.0630 0.99 74.7 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 85 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 CCTCTAGACCTAGCTGCTGT 273–328 1.000 85.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 276–331 1.000 85.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 287–342 1.000 85.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 286–341 1.000 85.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 288–343 1.000 85.0
rps16_p1 rps16 TGGTTATAAATTATCCACACCCTCT ACCGGTTCAAAATTCAAGGA 1231 0.500 20.0
rps16_p2 rps16 TGGTTATAAATTATCCACACCCTCT ACCGGTTCAAAATTCAAGGAA 1231 0.500 20.0
rps16_p3 rps16 TGGTTATAAATTATCCACACCCTC ACCGGTTCAAAATTCAAGGA 1231 0.500 20.0
rps16_p4 rps16 TGGTTATAAATTATCCACACCCT ACCGGTTCAAAATTCAAGGA 1231 0.500 20.0
rps16_p5 rps16 TGGTTATAAATTATCCACACCCTC ACCGGTTCAAAATTCAAGGAA 1231 0.500 20.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 453–491 1.000 70.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 456–494 1.000 70.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 459–497 1.000 69.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 462–500 1.000 69.3
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 457–495 1.000 67.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1184–1217 1.000 83.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGG 1158–1191 1.000 83.2
atpH-atpI_p3 atpH-atpI CAGTACCTTGACCAACTCCG TTTTGCAACTTTAGCTGCGG 1243–1276 1.000 82.9
atpH-atpI_p4 atpH-atpI CAGTACCTTGACCAACTCCG TAGGTGAATCCATGGAGGGG 1217–1250 1.000 82.7
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTGCAACTTTAGCTGCGG 1222–1255 1.000 82.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATTTGGATCTGTCGGGAC GGGGACGGACTGTAAATTCG 580–588 1.000 80.9
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GGATTTGGATCTGTCGGGAC GGGACGGACTGTAAATTCGT 579–587 1.000 80.8
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATTTGGATCTGTCGGGAC GATTCTTCCTGGGTCGATGC 613–621 1.000 80.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GGATTTGGATCTGTCGGGAC CGGACTGTAAATTCGTTGGC 575–583 1.000 79.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTTGGATCTGTCGGGACTGA GGGGACGGACTGTAAATTCG 577–585 1.000 78.4
lhbA-trnG-UCC_p1 lhbA-trnG-UCC TTTTCTGGCTCGGCTATTCC CTTGAGGTCACGGGTTCAAA 1743–1755 1.000 85.2
lhbA-trnG-UCC_p2 lhbA-trnG-UCC TTTTCTGGCTCGGCTATTCC GGGGCGTATTCAATCCTTGT 1836–1847 1.000 84.8
lhbA-trnG-UCC_p3 lhbA-trnG-UCC TTTTCTGGCTCGGCTATTCC CCGAGAGCTAACTACCGAGA 2057–2058 1.000 84.3
lhbA-trnG-UCC_p4 lhbA-trnG-UCC TTTTCTGGCTCGGCTATTCC CGTCTCCGCAACATTGAAAC 1732 0.500 59.3
lhbA-trnG-UCC_p5 lhbA-trnG-UCC CGAATAGGACACGGCCATAG CTTGAGGTCACGGGTTCAAA 1522 0.500 59.2

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
Emblica officinalis NC_047477.1 156208 View on NCBI ↗
Emblica urinaria NC_060522.1 157673 View on NCBI ↗