Markers + reference

Gephyrocapsa

3 species · Noelaerhabdaceae · Isochrysidales

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Species 3
Genome length 105–107 kb
Candidate markers 291
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 291 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcS Genome 420 0.0016 1.00 29.7 yes View details
psbZ Genome 189 0.0000 1.00 20.9 yes View details
trnR-ACG-trnS-UGA Genome 326 0.0041 1.00 35.6 yes View details
rbcR-trnE-UUC Genome 182 0.0073 1.00 49.6 yes View details
secA Genome 2646 0.0008 1.00 30.8 yes View details
dfr Genome 1839 0.0025 1.00 52.8 yes View details
rpoA Genome 930 0.0036 1.00 61.0 yes View details
petG-secA Genome 51 0.0654 1.00 74.8 yes View details
petB-petD Genome 82 0.0163 1.00 62.9 yes View details
psbZ-trnN-GUU Genome 98 0.0340 1.00 61.7 yes View details
rps3 Genome 651 0.0020 1.00 60.1 yes View details
ycf39 Genome 921 0.0022 1.00 60.1 yes View details
atpA Genome 1500 0.0018 1.00 59.9 yes View details
secY Genome 1269 0.0016 1.00 59.8 yes View details
ycf80 Genome 1461 0.0009 1.00 59.3 yes View details
rbcL Genome 1467 0.0009 1.00 58.2 yes View details
rrnS-psbI Genome 241 0.0083 1.00 57.8 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
petB-petD_p1 petB-petD ATTACCCGTTGTAGCAGCAG TTATGGCCCATACCTTTCGC 235 1.000 80.3
petB-petD_p2 petB-petD ATTACCCGTTGTAGCAGCAG GCACGAAGTTTTGGATCAGC 208 1.000 80.3
petB-petD_p3 petB-petD TGACGCGTTTCTATAGTGCC GCACGAAGTTTTGGATCAGC 239 1.000 79.8
petB-petD_p4 petB-petD TGACGCGTTTCTATAGTGCC TTATGGCCCATACCTTTCGC 266 1.000 79.7
petB-petD_p5 petB-petD CGCGTTTCTATAGTGCCCAT TTATGGCCCATACCTTTCGC 263 1.000 79.3
rbcL_p1 rbcL GCATACATCTTAAACCAAGGAGG AGATATTCCGGGCTAAATGC 1554 1.000 40.1
rbcL_p2 rbcL GCATACATCTTAAACCAAGGAGG AAGATATTCCGGGCTAAATGC 1555 1.000 40.1
rbcL_p3 rbcL GCATACATCTTAAACCAAGGAGG GGAAAGAAAAGCATCCTTGAGT 1612 1.000 40.1
rbcL_p4 rbcL GCATACATCTTAAACCAAGGAGG AGGAAAGAAAAGCATCCTTGAGT 1613 1.000 40.1
rbcL_p5 rbcL GCATACATCTTAAACCAAGGAGG AGGAAAGAAAAGCATCCTTGAG 1613 1.000 40.1
rbcS_p1 rbcS TTCTAGCACGTAACGAAGGC GAGCTTGGTACTACAGCACC 1192 1.000 80.3
rbcS_p2 rbcS GTGGTCCTCTTCAAACTGCA GAGCTTGGTACTACAGCACC 1120 1.000 80.2
rbcS_p3 rbcS TGGATGCGTATGTCAGGTTG GAGCTTGGTACTACAGCACC 1526 1.000 80.1
rbcS_p4 rbcS GGATGCGTATGTCAGGTTGT GAGCTTGGTACTACAGCACC 1525 1.000 80.1
rbcS_p5 rbcS GTGGATGCGTATGTCAGGTT GAGCTTGGTACTACAGCACC 1527 1.000 80.1
rrnS-psbI_p1 rrnS-psbI GCATGTGTTAAGCATACCGC CCATCTAGAAACCCGAACCG 335 1.000 79.4
rrnS-psbI_p2 rrnS-psbI AAACTCTCGTTCGACTTGCA CCATCTAGAAACCCGAACCG 352 1.000 78.4
rrnS-psbI_p3 rrnS-psbI TGTGTTAAGCATACCGCCAG CCATCTAGAAACCCGAACCG 332 1.000 78.1
rrnS-psbI_p4 rrnS-psbI ACTCTCGTTCGACTTGCATG CCATCTAGAAACCCGAACCG 350 1.000 77.8
rrnS-psbI_p5 rrnS-psbI CTCTCGTTCGACTTGCATGT CCATCTAGAAACCCGAACCG 349 1.000 77.8
psbZ_p1 psbZ CACCACCTGGGAATTCTACG CACGATACCAAGGTAGTGCC 1423–1424 1.000 79.7
psbZ_p2 psbZ ACGTCAACAATTGGTCGGAA CACGATACCAAGGTAGTGCC 1105–1106 1.000 79.6
psbZ_p3 psbZ AACAATTGCGCTGTAAACCG CACGATACCAAGGTAGTGCC 1452–1453 1.000 79.5
psbZ_p4 psbZ TGCTACGCTGATCGACAAAA CACGATACCAAGGTAGTGCC 1314–1315 1.000 79.3
psbZ_p5 psbZ TTGCTACGCTGATCGACAAA CACGATACCAAGGTAGTGCC 1315–1316 1.000 79.3
psbZ-trnN-GUU_p1 psbZ-trnN-GUU TATTTTAGCGACGCCTGGTG AACCGGTTTGTCGTAGGTTC 250 1.000 77.7
psbZ-trnN-GUU_p2 psbZ-trnN-GUU TATTTTAGCGACGCCTGGTG CCGGTTTGTCGTAGGTTCAA 248 1.000 77.7
psbZ-trnN-GUU_p3 psbZ-trnN-GUU TTATTTTAGCGACGCCTGGT AACCGGTTTGTCGTAGGTTC 251 1.000 77.4
psbZ-trnN-GUU_p4 psbZ-trnN-GUU TTATTTTAGCGACGCCTGGT CCGGTTTGTCGTAGGTTCAA 249 1.000 77.4
psbZ-trnN-GUU_p5 psbZ-trnN-GUU TATTTTAGCGACGCCTGGTG CCTCAGTAGCTCAGGGGTAG 284 1.000 76.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Gephyrocapsa ericsonii NC_063784.1 105307 View on NCBI ↗
Gephyrocapsa oceanica NC_063782.1 107088 View on NCBI ↗
Gephyrocapsa parvula NC_063785.1 105309 View on NCBI ↗