Markers + reference

Lepocinclis

4 species · Phacaceae · Euglenales

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Species 4
Genome length 70–82 kb
Candidate markers 184
Primer pairs 65

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 184 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
EI144_pgp60 LSC 5693 0.3263 0.95 74.1 yes View details
trnS(UGA)-EI144_pgp28 LSC 412 0.4297 0.94 77.9 yes View details
EI144_pgp28 LSC 561 0.4351 0.98 82.9 yes View details
EI144_pgp08 LSC 1476 0.4002 0.98 83.6 yes View details
EI144_pgp62 LSC 1295 0.2214 0.98 84.2 yes View details
EI144_pgp15 LSC 1613 0.1552 0.99 84.2 yes View details
EI144_pgp35 LSC 964 0.3145 0.97 83.8 yes View details
EI144_pgp58 LSC 1362 0.3967 0.97 83.4 yes View details
EI144_pgp51 LSC 1030 0.3398 0.97 83.3 yes View details
EI144_pgp19 LSC 1110 0.2365 0.97 83.3 yes View details
EI144_pgp34 LSC 1492 0.3082 0.96 83.1 yes View details
EI144_pgp61 LSC 1438 0.1998 0.95 82.8 yes View details
EI144_pgp24 LSC 826 0.2872 0.94 82.8 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
EI144_pgp62_p1 EI144_pgp62 TCGGTCCATATCCGGTGTAA ACGCCAAAACTAGGAGCAAA 2544–2630 0.750 79.5
EI144_pgp62_p2 EI144_pgp62 TTCGGTCCATATCCGGTGTA ACGCCAAAACTAGGAGCAAA 2545–2631 0.750 79.5
EI144_pgp62_p3 EI144_pgp62 GAGAGGACCGAAAAGGACAC ACGCCAAAACTAGGAGCAAA 2490–2576 0.750 79.5
EI144_pgp62_p4 EI144_pgp62 TCGGTCCATATCCGGTGTAA CAAAAAGAGCAGCGCCTAAC 2688 0.250 49.2
EI144_pgp62_p5 EI144_pgp62 TTCGGTCCATATCCGGTGTA CAAAAAGAGCAGCGCCTAAC 2689 0.250 49.2
EI144_pgp61_p1 EI144_pgp61 GTCTTCCGTTGCTCCTAAGG ATCCAGTTAGGCAAGTCCTT 2346 0.250 34.9
EI144_pgp61_p2 EI144_pgp61 TGCTCCTAAGGGAAGGTCAA ATCCAGTTAGGCAAGTCCTT 2337 0.250 34.6
EI144_pgp61_p3 EI144_pgp61 TTGCTCCTAAGGGAAGGTCA ATCCAGTTAGGCAAGTCCTT 2338 0.250 34.6
EI144_pgp61_p4 EI144_pgp61 TCTGTCTTCCGTTGCTCCTA ATCCAGTTAGGCAAGTCCTT 2349 0.250 34.3
EI144_pgp61_p5 EI144_pgp61 GTCTTCCGTTGCTCCTAAGG AATCCAGTTAGGCAAGTCCTT 2347 0.250 33.1
EI144_pgp60_p1 EI144_pgp60 GGACTTGCCTAACTGGATTT TGACGCTGGAAACAAAACTG 1147 0.250 21.8
EI144_pgp60_p2 EI144_pgp60 GGACTTGCCTAACTGGATTTT TGACGCTGGAAACAAAACTG 1147 0.250 20.3
EI144_pgp60_p3 EI144_pgp60 GGACTTGCCTAACTGGATTT GACGCTGGAAACAAAACTGA 1146 0.250 19.6
EI144_pgp60_p4 EI144_pgp60 GGACTTGCCTAACTGGATTTTTC TGACGCTGGAAACAAAACTG 1147 0.250 18.8
EI144_pgp60_p5 EI144_pgp60 TGTCCCTTATTCTTTTATGCGGA TGACGCTGGAAACAAAACTG 725 0.250 18.4
EI144_pgp58_p1 EI144_pgp58 GGTGGTCGTGATCAAGAGTC CCAACCATCACCACCAAAGA 2189–2791 0.500 69.3
EI144_pgp58_p2 EI144_pgp58 GGTGGTCGTGATCAAGAGTC TCCAACCATCACCACCAAAG 2190–2792 0.500 69.3
EI144_pgp58_p3 EI144_pgp58 CAACTGGTTTTGCTTGGTGG CCAACCATCACCACCAAAGA 2170–2772 0.500 68.9
EI144_pgp58_p4 EI144_pgp58 CAACTGGTTTTGCTTGGTGG TCCAACCATCACCACCAAAG 2171–2773 0.500 68.9
EI144_pgp58_p5 EI144_pgp58 GGTGGTCGTGATCAAGAGTC CGATGGATTCAAAGTCGGGT 2141 0.250 49.8
EI144_pgp51_p1 EI144_pgp51 CGGAGTAGAGCAGTCTGGTA ACTGTAGGAGCAGGAGTTGT 1639–1671 0.500 71.0
EI144_pgp51_p2 EI144_pgp51 GGTTAATGTCGTGGGTTCGA ACTGTAGGAGCAGGAGTTGT 1688–1715 0.500 70.9
EI144_pgp51_p3 EI144_pgp51 AAAGCGGATGTAGCTCAGTG ACTGTAGGAGCAGGAGTTGT 1728 0.250 49.7
EI144_pgp51_p4 EI144_pgp51 GAATCCCATCATCCGCTTGT ACTGTAGGAGCAGGAGTTGT 1670 0.250 49.6
EI144_pgp51_p5 EI144_pgp51 AGGCTTAAAGCGGATGTAGC ACTGTAGGAGCAGGAGTTGT 1734 0.250 49.5
EI144_pgp35_p1 EI144_pgp35 CCAGTTCGAATCCGGGTATC AAAGATTGTCCGCTTCCAGG 1656 0.250 47.4
EI144_pgp35_p2 EI144_pgp35 CCAGTTCGAATCCGGGTATC TCATTTGTTGGCGCTCCTAA 1845 0.250 47.3
EI144_pgp35_p3 EI144_pgp35 CCAGTTCGAATCCGGGTATC TTGTTGGCGCTCCTAATTCA 1841 0.250 47.3
EI144_pgp35_p4 EI144_pgp35 CAGTTCGAATCCGGGTATCG AAAGATTGTCCGCTTCCAGG 1655 0.250 46.7
EI144_pgp35_p5 EI144_pgp35 GTTCGAATCCGGGTATCGTC AAAGATTGTCCGCTTCCAGG 1653 0.250 46.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Lepocinclis ovum NC_039928.1 69550 View on NCBI ↗
Lepocinclis playfairiana NC_039970.1 77415 View on NCBI ↗
Lepocinclis steinii NC_039971.1 82134 View on NCBI ↗
Lepocinclis tripteris NC_039968.1 81048 View on NCBI ↗