Markers + reference

Pleurosigma

2 species · Pleurosigmataceae · Naviculales

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Species 2
Genome length 155–174 kb
Candidate markers 321
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

2 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 321 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-ycf35 SSC 3163 0.4314 0.97 78.0 yes View details
rps6-tRNA-His SSC 5820 0.4361 0.56 67.0 yes View details
groEL SSC 1590 0.4374 0.98 80.6 yes View details
ycf35-groEL SSC 834 0.4127 0.98 80.5 yes View details
rbcR SSC 924 0.1288 1.00 79.5 yes View details
tRNA-Gln-dnaK SSC 564 0.3907 0.99 79.3 yes View details
5S ribosomal RNA-23S ribosomal RNA IRb 120 0.0714 0.70 79.1 yes View details
rps16-clpC SSC 614 0.2850 1.00 79.0 yes View details
secY SSC 1248 0.0721 1.00 78.3 yes View details
tRNA-Ala-tRNA-Ile IRb 2 0.5000 1.00 78.2 yes View details
tRNA-Pro-atpA IRb 468 0.1895 0.98 78.1 yes View details
ycf88 SSC 522 0.1098 0.99 77.9 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
rbcR_p1 rbcR GGTAGACGCGCTAGGTTTAG CGTACTACCCGCACCTTTTT 1487 0.500 57.5
rbcR_p2 rbcR GTAGACGCGCTAGGTTTAGG CGTACTACCCGCACCTTTTT 1486 0.500 57.5
rbcR_p3 rbcR GGTAGACGCGCTAGGTTTAG TTTTTCGTACTACCCGCACC 1492 0.500 57.4
rbcR_p4 rbcR GTAGACGCGCTAGGTTTAGG TTTTTCGTACTACCCGCACC 1491 0.500 57.4
rbcR_p5 rbcR TGAAAGATAACGGGTGTGGC CGTACTACCCGCACCTTTTT 1513 0.500 56.9
psbA-ycf35_p1 psbA-ycf35 GGGGAATTTCAGGTTCCTCC GCTTCAGGGTCTTCCTTGTC 562 0.500 57.4
psbA-ycf35_p2 psbA-ycf35 GGGGAATTTCAGGTTCCTCC TCAGGGTCTTCCTTGTCCAA 559 0.500 57.4
psbA-ycf35_p3 psbA-ycf35 GGGGAATTTCAGGTTCCTCC TTCAGGGTCTTCCTTGTCCA 560 0.500 57.4
psbA-ycf35_p4 psbA-ycf35 GGGGAATTTCAGGTTCCTCC TGAGCAACTTCCAAGCGAAA 287 0.500 56.2
psbA-ycf35_p5 psbA-ycf35 GGGGAATTTCAGGTTCCTCC TTGAGCAACTTCCAAGCGAA 288 0.500 56.2
ycf35-groEL_p1 ycf35-groEL AAAAGTCTCCGTCATGGCAG AAGCTCGACGAGTTTTGGTT 2034 0.500 58.1
ycf35-groEL_p2 ycf35-groEL CCGTCATGGCAGAGACTTTT AAGCTCGACGAGTTTTGGTT 2026 0.500 58.1
ycf35-groEL_p3 ycf35-groEL AAAAGTCTCCGTCATGGCAG TGCGGGAATTAATGGTCCAG 1613 0.500 58.1
ycf35-groEL_p4 ycf35-groEL CCGTCATGGCAGAGACTTTT TGCGGGAATTAATGGTCCAG 1605 0.500 58.1
ycf35-groEL_p5 ycf35-groEL CCGTCATGGCAGAGACTTTT GCGGGAATTAATGGTCCAGT 1604 0.500 58.1
groEL_p1 groEL ACTTGTTTGACCTTAGCCACT TGGCGACACCCCAAAATTTA 2153 0.500 47.4
groEL_p2 groEL ACTTTGGTACGGAATAAGCGA TGGCGACACCCCAAAATTTA 2074 0.500 47.2
groEL_p3 groEL TGGTACGGAATAAGCGAAGA TGGCGACACCCCAAAATTTA 2070 0.500 47.0
groEL_p4 groEL ACTTGTTTGACCTTAGCCACT ACCTACGAATGGTGGAGTCA 2193 0.500 46.8
groEL_p5 groEL ACTTGTTTGACCTTAGCCACT CGAACCTACGAATGGTGGAG 2196 0.500 46.8
tRNA-Gln-dnaK_p1 tRNA-Gln-dnaK GCAGCTTGACGAATCAGAGA GCAGGTATTTTAGCGGGTGA 1876 0.500 59.7
tRNA-Gln-dnaK_p2 tRNA-Gln-dnaK TAAATTTTGGGGTGTCGCCA GCAGGTATTTTAGCGGGTGA 1360 0.500 59.7
tRNA-Gln-dnaK_p3 tRNA-Gln-dnaK AGCAGCTTGACGAATCAGAG GCAGGTATTTTAGCGGGTGA 1877 0.500 59.7
tRNA-Gln-dnaK_p4 tRNA-Gln-dnaK GCAGCTTGACGAATCAGAGA AGCAGGTATTTTAGCGGGTG 1877 0.500 59.7
tRNA-Gln-dnaK_p5 tRNA-Gln-dnaK TAAATTTTGGGGTGTCGCCA AGCAGGTATTTTAGCGGGTG 1361 0.500 59.7
ycf88_p1 ycf88 CGACCATTAACTCCATGGGG AGCACGTGGTCGAATTCTTT 1400–1419 1.000 85.8
ycf88_p2 ycf88 AGGTCCGTTTGTTGCCTATC AGCACGTGGTCGAATTCTTT 1248–1267 1.000 85.6
ycf88_p3 ycf88 AATGAACCCTTGTGACCACC AGCACGTGGTCGAATTCTTT 1480 0.500 59.0
ycf88_p4 ycf88 TCCAACAGTTCGTGGTTCAG AGCACGTGGTCGAATTCTTT 1501 0.500 58.6
ycf88_p5 ycf88 CCCAAATCGAGGTGGTCAAA AGCACGTGGTCGAATTCTTT 1711 0.500 58.3

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
Pleurosigma inscriptura OR464349.1 154970 View on NCBI ↗
Pleurosigma intermedium NC_066077.1 174382 View on NCBI ↗