Markers + reference

Detonula

2 species · Thalassiosiraceae · Thalassiosirales

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Species 2
Genome length 131–132 kb
Candidate markers 355
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 10 remaining regions by MarkerSeek score (out of 355 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petA-chlI Genome 492 0.3156 0.95 81.3 yes View details
trnT-UGU-ycf33 Genome 499 0.2272 0.94 81.3 yes View details
psbY-rpl32 Genome 675 0.1673 0.81 82.3 yes View details
psbA-ycf35 Genome 476 0.3341 0.91 84.7 yes View details
thiS-psb28 Genome 527 0.2629 0.84 79.2 yes View details
rps6-ccsA Genome 936 0.1627 0.54 74.5 yes View details
ycf35-psbA Genome 476 0.3341 0.91 84.7 yes View details
rpl32-psbY Genome 675 0.1673 0.81 82.3 yes View details
psbX-rbcS Genome 521 0.1423 0.92 84.6 yes View details
trnA-UGC-rnl Genome 60 0.0667 1.00 83.3 yes View details
rnl-trnA-UGC Genome 60 0.0667 1.00 83.3 yes View details
psbT-pbf1 Genome 26 0.1923 1.00 82.4 yes View details
psbH-trnV-UAC Genome 284 0.1956 0.95 81.8 yes View details
ccs1-psbA Genome 93 0.1075 1.00 81.7 yes View details
psbA-ccs1 Genome 93 0.1075 1.00 81.7 yes View details
trnQ-UUG-trnR-ACG Genome 66 0.1077 0.98 79.9 yes View details
ycf45-ffs Genome 499 0.1595 0.98 79.2 yes View details
trnY-GUA-petG Genome 358 0.1462 0.96 78.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbX-rbcS_p1 psbX-rbcS CCTGCTGTTAAACTCGCGAT CCCTGAAGGTAGCCGTTACT 544–587 1.000 80.4
psbX-rbcS_p2 psbX-rbcS CCTGCTGTTAAACTCGCGAT CAGTGTTCAAGCTAACCCTGA 559–602 1.000 77.9
psbX-rbcS_p3 psbX-rbcS CCTGCTGTTAAACTCGCGAT TGTTCAAGCTAACCCTGAAGG 556–599 1.000 77.8
psbX-rbcS_p4 psbX-rbcS CCTGCTGTTAAACTCGCGAT ACAGTGTTCAAGCTAACCCTG 560–603 1.000 77.7
psbX-rbcS_p5 psbX-rbcS CCTGCTGTTAAACTCGCGAT ACAGTGTTCAAGCTAACCCT 560–603 1.000 76.3
psbT-pbf1_p1 psbT-pbf1 TCTTTGCTGTATTCTTCCGTGA TACTGCTTTTGGACCTGCTT 134 1.000 59.6
psbT-pbf1_p2 psbT-pbf1 TCTTTGCTGTATTCTTCCGTGA ACTGCTTTTGGACCTGCTTC 133 1.000 59.5
psbT-pbf1_p3 psbT-pbf1 TCTTTGCTGTATTCTTCCGTGA ATACTGCTTTTGGACCTGCT 135 1.000 57.7
psbT-pbf1_p4 psbT-pbf1 CTTTGCTGTATTCTTCCGTGA TACTGCTTTTGGACCTGCTT 133 1.000 56.0
psbT-pbf1_p5 psbT-pbf1 TCTTTGCTGTATTCTTCCGTG TACTGCTTTTGGACCTGCTT 134 1.000 56.0
psbH-trnV-UAC_p1 psbH-trnV-UAC AGATGTTGATTGGGCAAATGC AACCTGTGACCTTCTGCTTG 354–367 1.000 80.6
psbH-trnV-UAC_p2 psbH-trnV-UAC GATGTTGATTGGGCAAATGCT AACCTGTGACCTTCTGCTTG 353–366 1.000 80.6
psbH-trnV-UAC_p3 psbH-trnV-UAC AGATGTTGATTGGGCAAATGC TTGAACCTGTGACCTTCTGC 357–370 1.000 80.6
psbH-trnV-UAC_p4 psbH-trnV-UAC GATGTTGATTGGGCAAATGCT TTGAACCTGTGACCTTCTGC 356–369 1.000 80.6
psbH-trnV-UAC_p5 psbH-trnV-UAC GATGTTGATTGGGCAAATGCT AGACACTCTACCGCTGAGTT 327–340 1.000 80.4
ycf45-ffs_p1 ycf45-ffs AGCTTGCGATCGAAGTCAAT TCCACTGCTCTACCAACTGA 1478–1488 1.000 88.6
ycf45-ffs_p2 ycf45-ffs TTTCAGCTTGCGATCGAAGT TCCACTGCTCTACCAACTGA 1482–1492 1.000 87.1
ycf45-ffs_p3 ycf45-ffs AGCTTGCGATCGAAGTCAAT AACTGAGCTATCCGGGCTTA 1464–1474 1.000 87.0
ycf45-ffs_p4 ycf45-ffs AGCCAAAAACCCTTGGTTCA TCCACTGCTCTACCAACTGA 1244 0.500 58.9
ycf45-ffs_p5 ycf45-ffs CTGCATTTCAGCTTGCGATC TCCACTGCTCTACCAACTGA 1487 0.500 58.5
petA-chlI_p1 petA-chlI CTGTTGTTGCACCTGATCCT GCAAAAGCACATGCAGCATA 1133–1187 1.000 88.8
petA-chlI_p2 petA-chlI CCGTGGTCAAGTTTACCCAA GCAAAAGCACATGCAGCATA 1054 0.500 59.8
petA-chlI_p3 petA-chlI TGGTCAAGTTTACCCAACGG GCAAAAGCACATGCAGCATA 1051 0.500 59.8
petA-chlI_p4 petA-chlI CCGTGGTCAAGTTTACCCAA TTGGTATGCACGCAGAGATC 1320 0.500 59.3
petA-chlI_p5 petA-chlI TGGTCAAGTTTACCCAACGG TTGGTATGCACGCAGAGATC 1317 0.500 59.3
trnT-UGU-ycf33_p1 trnT-UGU-ycf33 TCGAATTGTTTGTGGACGGT CGACCTTGGGCTTATGAGTC 1489–1538 1.000 88.8
trnT-UGU-ycf33_p2 trnT-UGU-ycf33 TCGAATTGTTTGTGGACGGT TAGTAGATGGCTCTGGTGGG 1520–1569 1.000 88.6
trnT-UGU-ycf33_p3 trnT-UGU-ycf33 AGAAGCTTGAACGATCGCAT CGACCTTGGGCTTATGAGTC 1453 0.500 59.4
trnT-UGU-ycf33_p4 trnT-UGU-ycf33 AGAAGCTTGAACGATCGCAT TAGTAGATGGCTCTGGTGGG 1484 0.500 59.2
trnT-UGU-ycf33_p5 trnT-UGU-ycf33 AGAAGCTTGAACGATCGCAT ACCTACGACCTTGGGCTTAT 1458 0.500 58.9

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
Detonula confervacea PV423704.1 132214 View on NCBI ↗
Detonula pumila PV423673.1 131480 View on NCBI ↗