Markers + reference

Thalassiosira

2 species · Thalassiosiraceae · Thalassiosirales

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Species 2
Genome length 130–132 kb
Candidate markers 355
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 355 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaE Genome 198 0.2552 0.97 75.4 yes View details
ycf45-ffs Genome 721 0.4238 0.91 84.4 yes View details
petA-chlI Genome 1034 0.3742 0.93 83.2 yes View details
ycf89-rns Genome 563 0.2745 0.93 82.7 yes View details
thiS-psb28 Genome 397 0.2589 0.99 75.3 yes View details
groEL-dnaK Genome 484 0.4126 0.89 79.6 yes View details
rns-ycf89 Genome 563 0.2745 0.93 82.7 yes View details
dnaB Genome 1362 0.1079 1.00 80.3 yes View details
rns-trnI-GAU Genome 59 0.1034 0.98 79.7 yes View details
trnI-GAU-rns Genome 59 0.1034 0.98 79.7 yes View details
trnY-GUA-petG Genome 209 0.1841 0.96 79.6 yes View details
psaM-rps14 Genome 137 0.1240 0.94 79.3 yes View details
ycf90 Genome 1422 0.1434 1.00 79.3 yes View details
rpl2 Genome 828 0.1002 1.00 79.2 yes View details
thiG Genome 810 0.1173 1.00 79.2 yes View details
rps4 Genome 618 0.1100 1.00 79.0 yes View details
trnQ-UUG-trnR-ACG Genome 68 0.1324 1.00 79.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psaE_p1 psaE CAAGCAGAAGGTCACAGGTT ACAAGCTTGTCCTGGGTTTT 1109–1158 1.000 90.1
psaE_p2 psaE GCAGAAGGTCACAGGTTCAA ACAAGCTTGTCCTGGGTTTT 1106–1155 1.000 90.1
psaE_p3 psaE TCGTCTAACGGATCAGGACA ACAAGCTTGTCCTGGGTTTT 1051–1100 1.000 89.6
psaE_p4 psaE AACTCAGCGGTAGAGTGTCT ACAAGCTTGTCCTGGGTTTT 1135–1184 1.000 89.5
psaE_p5 psaE GAGTGTCTGCCTTACAAGCA ACAAGCTTGTCCTGGGTTTT 1123–1172 1.000 88.9
ycf45-ffs_p1 ycf45-ffs TACTCAGCCTTTCAGCTTGC TCCACTGCTCTACCAACTGA 1477 0.500 58.4
ycf45-ffs_p2 ycf45-ffs AGAAGCTAAACGGAGAGGGA TCCACTGCTCTACCAACTGA 1526 0.500 58.1
ycf45-ffs_p3 ycf45-ffs TACTCAGCCTTTCAGCTTGC CATCGTAATGGTCCGCTAGG 1601 0.500 58.0
ycf45-ffs_p4 ycf45-ffs AGAAGCTAAACGGAGAGGGA CATCGTAATGGTCCGCTAGG 1650 0.500 57.6
ycf45-ffs_p5 ycf45-ffs GAAGCTAAACGGAGAGGGAC TCCACTGCTCTACCAACTGA 1525 0.500 57.5
dnaB_p1 dnaB TCAGTTGGTAGAGCAGTGGA GGACTTGAACCCTCGACATC 1571–1577 1.000 87.6
dnaB_p2 dnaB TCAGTTGGTAGAGCAGTGGA GAAGGACTTGAACCCTCGAC 1574–1580 1.000 87.0
dnaB_p3 dnaB TCAGTTGGTAGAGCAGTGGA CTGAAGGACTTGAACCCTCG 1576–1582 1.000 87.0
dnaB_p4 dnaB ACGAAACCCAATCAACGACA GGACTTGAACCCTCGACATC 2150 0.500 59.6
dnaB_p5 dnaB TCAGTTGGTAGAGCAGTGGA AGGTGCAGGTGTAGCTTTTC 1843 0.500 59.1
petA-chlI_p1 petA-chlI AGCAGAGCAACCGTTAAACA GCAAAAGCACATGCAGCATA 1398 0.500 59.7
petA-chlI_p2 petA-chlI AGCAGAGCAACCGTTAAACA GGTATGCATGCCGAAATTCG 1662 0.500 59.4
petA-chlI_p3 petA-chlI AGCAGAGCAACCGTTAAACA CAGCATACAATGGTCGGGAA 1385 0.500 59.4
petA-chlI_p4 petA-chlI AGCAGAGCAACCGTTAAACA GATCGCTTTGGTATGCATGC 1671 0.500 59.4
petA-chlI_p5 petA-chlI ACTCAAGCAGGGCAAGTTAC GCAAAAGCACATGCAGCATA 1541 0.500 59.2
psaM-rps14_p1 psaM-rps14 GCGACATAAACTTGAAAATCAGT AGGGGTTACTAAATCAAGTTGGT 183–191 1.000 50.3
psaM-rps14_p2 psaM-rps14 GCGACATAAACTTGAAAATCAGT CAGGGGTTACTAAATCAAGTTGG 184–192 1.000 50.2
psaM-rps14_p3 psaM-rps14 GCGACATAAACTTGAAAATCAGT CCAGGGGTTACTAAATCAAGTTG 185–193 1.000 50.2
psaM-rps14_p4 psaM-rps14 GCGACATAAACTTGAAAATCAGT ACCAGGGGTTACTAAATCAAGT 186–194 1.000 50.1
psaM-rps14_p5 psaM-rps14 GCGACATAAACTTGAAAATCAGT ACCAGGGGTTACTAAATCAAGTT 186–194 1.000 50.1
trnY-GUA-petG_p1 trnY-GUA-petG GTAAATCCGCTGCGTTATGC TCGTCGTGGAAATCAATTTGA 278–286 1.000 67.7
trnY-GUA-petG_p2 trnY-GUA-petG AAATCCGCTGCGTTATGCTA TCGTCGTGGAAATCAATTTGA 276–284 1.000 67.5
trnY-GUA-petG_p3 trnY-GUA-petG TAAATCCGCTGCGTTATGCT TCGTCGTGGAAATCAATTTGA 277–285 1.000 67.5
trnY-GUA-petG_p4 trnY-GUA-petG AAGGGGGCGGATTGTAAATC TCGTCGTGGAAATCAATTTGA 291–299 1.000 67.2
trnY-GUA-petG_p5 trnY-GUA-petG TGCGTTATGCTACGTTGGTT TCGTCGTGGAAATCAATTTGA 268–276 1.000 66.3

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
Thalassiosira punctigera PV423710.1 130071 View on NCBI ↗
Thalassiosira tumida PV423687.1 131788 View on NCBI ↗