Markers + reference

Eutreptiella

2 species · Eutreptiaceae · Eutreptiales

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Species 2
Genome length 68–105 kb
Candidate markers 201
Primer pairs 90

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 11 remaining regions by MarkerSeek score (out of 201 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
OF286_pgp042 LSC 1056 0.4824 0.92 82.8 yes View details
trnfM-trnS LSC 108 0.4699 0.77 72.2 yes View details
OF286_pgp032 LSC 1850 0.4722 0.67 75.0 yes View details
OF286_pgp030 LSC 375 0.5093 0.72 72.4 yes View details
OF286_pgp009 LSC 1512 0.4812 0.62 74.4 yes View details
trnC-OF286_pgp004 LSC 1122 0.4660 0.60 74.0 yes View details
OF286_pgp004 LSC 3462 0.4522 0.53 69.1 yes View details
OF286_pgp002 LSC 2967 0.4668 0.63 71.5 yes View details
OF286_pgp025-OF286_pgp024 LSC 687 0.2149 0.95 84.6 yes View details
OF286_pgp043-OF286_pgp042 LSC 610 0.4657 0.93 83.1 yes View details
OF286_pgp058 LSC 1428 0.1471 0.92 82.9 yes View details
OF286_pgp052 LSC 666 0.3230 0.97 81.6 yes View details
rrn16 IRa 1497 0.1624 0.97 81.2 yes View details
OF286_pgp025 LSC 1344 0.4727 0.79 81.0 yes View details
OF286_pgp060-OF286_pgp059 LSC 1102 0.1762 0.84 80.9 yes View details
OF286_pgp037-trnL LSC 2008 0.2292 0.89 80.9 yes View details
OF286_pgp055 LSC 834 0.2691 0.99 79.9 yes View details
OF286_pgp048 LSC 540 0.2758 0.99 78.8 yes View details
rrn16 IRb 1497 NA 0.00 32.6 no 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
OF286_pgp060-OF286_pgp059_p1 OF286_pgp060-OF286_pgp059 AGTCAAATTCGTGCTTGGGT ACTAACGCAAAACCACCCAT 1857 0.500 59.8
OF286_pgp060-OF286_pgp059_p2 OF286_pgp060-OF286_pgp059 AGTCAAATTCGTGCTTGGGT TAACGCAAAACCACCCATCA 1855 0.500 59.7
OF286_pgp060-OF286_pgp059_p3 OF286_pgp060-OF286_pgp059 AGTCAAATTCGTGCTTGGGT GCCCTGTCAGAGTTGGAAAA 1739 0.500 59.7
OF286_pgp060-OF286_pgp059_p4 OF286_pgp060-OF286_pgp059 AGTCAAATTCGTGCTTGGGT TCCTGCGCCTGTTTTAGTTT 2356 0.500 59.7
OF286_pgp060-OF286_pgp059_p5 OF286_pgp060-OF286_pgp059 AGTCAAATTCGTGCTTGGGT TTCCGCAGCTTTCTCAAACT 1975 0.500 59.6
OF286_pgp058_p1 OF286_pgp058 ATGGGTGGTTTTGCGTTAGT CAGTACCACCAGTAGCGTTC 2853 0.500 59.9
OF286_pgp058_p2 OF286_pgp058 ATGGGTGGTTTTGCGTTAGT GTACCACCAGTAGCGTTCAG 2851 0.500 59.9
OF286_pgp058_p3 OF286_pgp058 ATGGGTGGTTTTGCGTTAGT CGTATACTGCACGACCGTAG 2685 0.500 59.8
OF286_pgp058_p4 OF286_pgp058 TGATGGGTGGTTTTGCGTTA CAGTACCACCAGTAGCGTTC 2855 0.500 59.8
OF286_pgp058_p5 OF286_pgp058 TGATGGGTGGTTTTGCGTTA GTACCACCAGTAGCGTTCAG 2853 0.500 59.8
OF286_pgp055_p1 OF286_pgp055 GTCGCGTGACACCTTAGTAG CGCTCTTAACATGACCACGA 1536 0.500 59.1
OF286_pgp055_p2 OF286_pgp055 GTCGCGTGACACCTTAGTAG TCGCTCTTAACATGACCACG 1537 0.500 59.1
OF286_pgp055_p3 OF286_pgp055 TATATTCGTCGCGTGACACC CGCTCTTAACATGACCACGA 1543 0.500 59.0
OF286_pgp055_p4 OF286_pgp055 TATATTCGTCGCGTGACACC TCGCTCTTAACATGACCACG 1544 0.500 59.0
OF286_pgp055_p5 OF286_pgp055 GTCGCGTGACACCTTAGTAG GACACTACGCTTCTCACCAG 1367 0.500 59.0
OF286_pgp052_p1 OF286_pgp052 CGTGGTCATGTTAAGAGCGA TCCCCATCACTTCCTGGAAT 1594 0.500 59.8
OF286_pgp052_p2 OF286_pgp052 TCGTGGTCATGTTAAGAGCG TCCCCATCACTTCCTGGAAT 1595 0.500 59.8
OF286_pgp052_p3 OF286_pgp052 GGTCGTGGATTTCCGATTCA TCCCCATCACTTCCTGGAAT 1212 0.500 59.7
OF286_pgp052_p4 OF286_pgp052 CGTGGTCATGTTAAGAGCGA GCTACCGCCAAAGTCCATAA 1768 0.500 59.7
OF286_pgp052_p5 OF286_pgp052 TCGTGGTCATGTTAAGAGCG GCTACCGCCAAAGTCCATAA 1769 0.500 59.7
OF286_pgp048_p1 OF286_pgp048 GGGTGTTGCGGAGTTAGTAG ACAGACGCACGAACTTTCAT 1860 0.500 58.9
OF286_pgp048_p2 OF286_pgp048 CGGATGTTGTTAAGGCCGTA ACAGACGCACGAACTTTCAT 1485 0.500 58.8
OF286_pgp048_p3 OF286_pgp048 CTGAAGGTGCTCCAAAAGGT ACAGACGCACGAACTTTCAT 1383 0.500 58.8
OF286_pgp048_p4 OF286_pgp048 CGAATGGGTTCTGGTAAGGG ACAGACGCACGAACTTTCAT 1937 0.500 58.6
OF286_pgp048_p5 OF286_pgp048 TACTCCCAACATGCCTCTGA ACAGACGCACGAACTTTCAT 1511 0.500 58.5
OF286_pgp043-OF286_pgp042_p1 OF286_pgp043-OF286_pgp042 TCTGACGGTATGCCTCTAGG CCGAGTGTGTGGGACTATTG 1886 0.500 59.8
OF286_pgp043-OF286_pgp042_p2 OF286_pgp043-OF286_pgp042 AACGCTCACAACTTCCCATT CCGAGTGTGTGGGACTATTG 1388 0.500 59.8
OF286_pgp043-OF286_pgp042_p3 OF286_pgp043-OF286_pgp042 TCTGACGGTATGCCTCTAGG ATTCGAAGGACGTGACGAAG 1325 0.500 59.7
OF286_pgp043-OF286_pgp042_p4 OF286_pgp043-OF286_pgp042 AACGCTCACAACTTCCCATT ATTCGAAGGACGTGACGAAG 827 0.500 59.7
OF286_pgp043-OF286_pgp042_p5 OF286_pgp043-OF286_pgp042 GGTGTTTTCGGTGGTTCTCT CCGAGTGTGTGGGACTATTG 1781 0.500 59.6

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
Eutreptiella eupharyngea NC_066976.1 105379 View on NCBI ↗
Eutreptiella gymnastica NC_017754.2 67623 View on NCBI ↗