Markers + reference

Phacus

2 species · Phacaceae · Euglenales

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Species 2
Genome length 58–91 kb
Candidate markers 178
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 178 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
EI075_pgp60 Genome 1047 0.4519 0.92 82.9 yes View details
EI075_pgp33 Genome 580 0.3922 0.97 82.0 yes View details
EI075_pgp21 Genome 948 0.3478 0.75 78.2 yes View details
rrn16-trnL(CAA) Genome 1149 0.4141 0.96 82.5 no View details
EI075_pgp57-trnS(GCU) Genome 1572 0.1711 0.95 84.2 yes View details
EI075_pgp40 Genome 951 0.2562 0.93 83.0 yes View details
EI075_pgp57 Genome 1377 0.3263 0.96 82.5 yes View details
EI075_pgp59 Genome 1404 0.1779 0.97 82.1 yes View details
EI075_pgp01 Genome 612 0.2764 0.98 81.1 yes View details
EI075_pgp42 Genome 2124 0.2474 0.96 80.9 yes View details
EI075_pgp24 Genome 1107 0.2143 0.99 80.2 yes View details
EI075_pgp02 Genome 557 0.2807 0.98 80.2 yes View details
EI075_pgp37 Genome 558 0.2418 0.98 80.0 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
EI075_pgp60_p1 EI075_pgp60 TGGCCTAACAGAGCTTCTCT TGAGCTTCAGGTCCCCATAA 2002 0.500 59.3
EI075_pgp60_p2 EI075_pgp60 CGATCGGTCTCGTTTTAGCA TGAGCTTCAGGTCCCCATAA 2193 0.500 59.0
EI075_pgp60_p3 EI075_pgp60 TGGCCTAACAGAGCTTCTCT CTGACCAGCCTACGAAAACA 1467 0.500 58.2
EI075_pgp60_p4 EI075_pgp60 CGATCGGTCTCGTTTTAGCA CTGACCAGCCTACGAAAACA 1658 0.500 57.9
EI075_pgp60_p5 EI075_pgp60 GCTTTACCCTGGCCTAACAG TGAGCTTCAGGTCCCCATAA 2011 0.500 57.7
EI075_pgp59_p1 EI075_pgp59 ATTCTGCTGCATCAGGATGG ATTCTTGATCACGACCACCG 2094 0.500 59.8
EI075_pgp59_p2 EI075_pgp59 CTGCTGCATCAGGATGGAAT ATTCTTGATCACGACCACCG 2091 0.500 59.8
EI075_pgp59_p3 EI075_pgp59 CTGGCTCAGGCAAATAGAGG ATTCTTGATCACGACCACCG 2173 0.500 59.6
EI075_pgp59_p4 EI075_pgp59 ATTCTGCTGCATCAGGATGG ATAGCTTCATGTGCTGGCTC 2712 0.500 59.6
EI075_pgp59_p5 EI075_pgp59 CTGCTGCATCAGGATGGAAT ATAGCTTCATGTGCTGGCTC 2709 0.500 59.6
EI075_pgp57_p1 EI075_pgp57 CGGTGGTCGTGATCAAGAAT AAAACTTCACCACCAGGACC 1905–2083 1.000 91.4
EI075_pgp57_p2 EI075_pgp57 CGGTGGTCGTGATCAAGAAT AGCAATCCATCCATCACCAC 2263 0.500 59.4
EI075_pgp57_p3 EI075_pgp57 TGATGGGTGTAGCTGGTGTA AGCAATCCATCCATCACCAC 2745 0.500 59.1
EI075_pgp57_p4 EI075_pgp57 CGGTGGTCGTGATCAAGAAT CACCAAATCCTAGAACGGCA 1973 0.500 59.1
EI075_pgp57_p5 EI075_pgp57 TGATGGGTGTAGCTGGTGTA AAAACTTCACCACCAGGACC 2387 0.500 59.0
EI075_pgp57-trnS(GCU)_p1 EI075_pgp57-trnS(GCU) AGTCTGGTTTGTTTCCTTCT GTCTGAGTGGCCTAAAGAGC 2370 0.500 31.0
EI075_pgp57-trnS(GCU)_p2 EI075_pgp57-trnS(GCU) AGTCTGGTTTGTTTCCTTCT TCTGAGTGGCCTAAAGAGCT 2369 0.500 30.6
EI075_pgp57-trnS(GCU)_p3 EI075_pgp57-trnS(GCU) AGTCTGGTTTGTTTCCTTCT CCCTGTCATTCGTAGGTTCG 2431 0.500 30.5
EI075_pgp57-trnS(GCU)_p4 EI075_pgp57-trnS(GCU) AGTCTGGTTTGTTTCCTTCT TTTGGCCCTGTCATTCGTAG 2436 0.500 30.2
EI075_pgp57-trnS(GCU)_p5 EI075_pgp57-trnS(GCU) AGTCTGGTTTGTTTCCTTCT GGTGTAGCCAAGTGGTAAGG 2464 0.500 30.2
EI075_pgp42_p1 EI075_pgp42 ATTTCCTCTTGCGCCTGAAA CCAAAACCACAAGTACCGGA 2793 0.500 59.0
EI075_pgp42_p2 EI075_pgp42 ATTTCCTCTTGCGCCTGAAA TGAAGCATTTGGATGTGCCT 2902 0.500 58.7
EI075_pgp42_p3 EI075_pgp42 TTCCTCTTGCGCCTGAAAAA CCAAAACCACAAGTACCGGA 2791 0.500 57.3
EI075_pgp42_p4 EI075_pgp42 TTTCCTCTTGCGCCTGAAAA CCAAAACCACAAGTACCGGA 2792 0.500 57.3
EI075_pgp42_p5 EI075_pgp42 TTCCTCTTGCGCCTGAAAAA TGAAGCATTTGGATGTGCCT 2900 0.500 56.9
EI075_pgp40_p1 EI075_pgp40 GCGATATGGCCAAGTGGTAA TTCACCATTGGGCAACTCAA 1623 0.500 59.1
EI075_pgp40_p2 EI075_pgp40 CGAATCTGGGTGTCGTCTTT TTCACCATTGGGCAACTCAA 1571 0.500 58.7
EI075_pgp40_p3 EI075_pgp40 GCGATATGGCCAAGTGGTAA CAAGTGCCCCAGACCAATTA 1588 0.500 58.0
EI075_pgp40_p4 EI075_pgp40 CGAATCTGGGTGTCGTCTTT CAAGTGCCCCAGACCAATTA 1536 0.500 57.6
EI075_pgp40_p5 EI075_pgp40 GCGATATGGCCAAGTGGTAA AGCCAAACCTGCAGTTGTAT 1668 0.500 57.4

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
Phacus inflexus NC_039967.1 58112 View on NCBI ↗
Phacus pleuronectes NC_039927.1 90869 View on NCBI ↗