Markers + reference

Monomorphina

2 species · Euglenaceae · Euglenales

Back to catalogue

Species 2
Genome length 75–80 kb
Candidate markers 182
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 182 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbC Genome 6228 0.2937 0.96 76.7 yes View details
orf240 Genome 825 0.4204 0.94 83.2 yes View details
rrs-trnL(caa) Genome 1538 0.4208 0.48 75.6 no View details
rpl23 Genome 719 0.3821 0.95 83.9 yes View details
rpl16 Genome 958 0.2778 0.95 83.6 yes View details
atpE Genome 1058 0.3214 0.95 83.5 yes View details
rps8 Genome 832 0.3167 0.94 83.5 yes View details
atpF Genome 868 0.3148 0.95 83.4 yes View details
psbT-psbH Genome 596 0.3195 0.93 83.0 yes View details
psbZ-trnS(uga) Genome 1152 0.3886 0.96 82.9 yes View details
tufA Genome 1330 0.1691 0.92 82.9 yes View details
rps3 Genome 1145 0.2979 0.96 82.8 yes View details
orf631 Genome 1896 0.3948 0.95 82.7 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbC_p1 psbC AGGTTTAGTTTCGCTGAAGC AGCCTTGAGAAACTTTGGCT 1351 0.500 43.9
psbC_p2 psbC AAGGTTTAGTTTCGCTGAAGC AGCCTTGAGAAACTTTGGCT 1352 0.500 41.8
psbC_p3 psbC TGGGATTCGTTAGGACTACC AGCCTTGAGAAACTTTGGCT 1139 0.500 41.4
psbC_p4 psbC TTGGGATTCGTTAGGACTACC AGCCTTGAGAAACTTTGGCT 1140 0.500 39.6
psbC_p5 psbC AAAGGTTTAGTTTCGCTGAAGC AGCCTTGAGAAACTTTGGCT 1353 0.500 39.2
orf631_p1 orf631 GCAATGTGCGTTTTAGCTTG GACTCTTGATCACGACCACC 2163 0.500 51.0
orf631_p2 orf631 GCAATGTGCGTTTTAGCTTG AGACCACCAAGCAAATCCTG 2185 0.500 50.4
orf631_p3 orf631 GCAATGTGCGTTTTAGCTTG CAGACCACCAAGCAAATCCT 2186 0.500 50.4
orf631_p4 orf631 GCAATGTGCGTTTTAGCTTG ACCACCAAGCAAATCCTGTT 2183 0.500 50.4
orf631_p5 orf631 GCAATGTGCGTTTTAGCTTG TCCAGACCACCAAGCAAATC 2188 0.500 50.3
psbT-psbH_p1 psbT-psbH CCTCGTGGATGGTTCACTTT CGAAACGCACAACCAATCAT 2042 0.500 55.9
psbT-psbH_p2 psbT-psbH TAGTCCTCGTGGATGGTTCA CGAAACGCACAACCAATCAT 2046 0.500 55.6
psbT-psbH_p3 psbT-psbH AAGTAGTCCTCGTGGATGGT CGAAACGCACAACCAATCAT 2049 0.500 55.5
psbT-psbH_p4 psbT-psbH AGTAGTCCTCGTGGATGGTT CGAAACGCACAACCAATCAT 2048 0.500 55.5
psbT-psbH_p5 psbT-psbH CCTCGTGGATGGTTCACTTT TGGAAAAGTTGCACCTGGAT 1444 0.500 55.5
atpE_p1 atpE ACAAGCAGGTTCCGAAGTTT TCCGGCTTTAAATCCAGCTC 2348 0.500 59.3
atpE_p2 atpE ACAAGCAGGTTCCGAAGTTT CGGCTTTAAATCCAGCTCCT 2346 0.500 59.2
atpE_p3 atpE ACAAGCAGGTTCCGAAGTTT CTCCGGCTTTAAATCCAGCT 2349 0.500 59.2
atpE_p4 atpE TCGTAGTTTGGTCGCGATTT TCCGGCTTTAAATCCAGCTC 1694 0.500 59.1
atpE_p5 atpE TCGTAGTTTGGTCGCGATTT CGGCTTTAAATCCAGCTCCT 1692 0.500 59.1
psbZ-trnS(uga)_p1 psbZ-trnS(uga) CAGCTTGGGCAGGATTAGTT GGATGTAGCGCAGTTTGGTA 1367 0.500 58.8
psbZ-trnS(uga)_p2 psbZ-trnS(uga) TCAGGCTTCTCTTCTAGCGT GGATGTAGCGCAGTTTGGTA 1486 0.500 58.6
psbZ-trnS(uga)_p3 psbZ-trnS(uga) CAGCTTGGGCAGGATTAGTT GGTTCGAATCCTGTCATCCC 1317 0.500 58.6
psbZ-trnS(uga)_p4 psbZ-trnS(uga) TCAGGCTTCTCTTCTAGCGT GGTTCGAATCCTGTCATCCC 1436 0.500 58.4
psbZ-trnS(uga)_p5 psbZ-trnS(uga) CAGCTTGGGCAGGATTAGTT TTTAAACGGGATGTAGCGCA 1375 0.500 58.2
atpF_p1 atpF CGATCTTTTTCTGAAGAGTCGG TCACAAGTGGTATTCAGGCG 2147 0.500 36.6
atpF_p2 atpF CGATCTTTTTCTGAAGAGTCGG GTACTGCTGCAGGTAAAGCT 1795 0.500 36.5
atpF_p3 atpF CGATCTTTTTCTGAAGAGTCGG GTCTTGCTCGTCAACCTGAA 1768 0.500 36.3
atpF_p4 atpF CGATCTTTTTCTGAAGAGTCGG TGAAGGTCTTGCTCGTCAAC 1773 0.500 36.3
atpF_p5 atpF CGATCTTTTTCTGAAGAGTCGG TCGTCAACCTGAAGCTGAAG 1761 0.500 36.1

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
Monomorphina aenigmatica NC_020018.1 74746 View on NCBI ↗
Monomorphina parapyrum NC_027287.1 80147 View on NCBI ↗