Markers + reference

Nannochloropsis

4 species · Monodopsidaceae · Eustigmatales

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Species 4
Genome length 117–118 kb
Candidate markers 314
Primer pairs 80

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 314 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf34 Genome 252 0.1237 1.00 72.6 yes View details
P417_t011-P417_t012 Genome 172 0.1512 1.00 78.6 yes View details
clpC-I Genome 1344 0.1053 0.99 72.6 yes View details
thiG-rpl27 Genome 331 0.1853 0.57 68.2 yes View details
ycf54-secA Genome 2295 0.1028 0.97 80.7 yes View details
rbcS-psbA Genome 379 0.2315 0.94 80.3 yes View details
clpC-I Genome 1308 0.0959 1.00 78.9 no View details
P417_t002-P417_t003 Genome 652 0.0918 1.00 86.3 yes View details
P417_r006-psaC Genome 161 0.1201 0.99 81.4 yes View details
rpl32-psbV Genome 637 0.1049 1.00 80.2 yes View details
rps16-P417_t022 Genome 839 0.0747 1.00 80.2 yes View details
psaI-psbJ Genome 55 0.1848 1.00 79.7 yes View details
ycf49-psaL Genome 532 0.0711 1.00 79.7 yes View details
chlN Genome 1326 0.0588 1.00 79.5 yes View details
chlB Genome 1521 0.0602 1.00 79.4 yes View details
rpoA Genome 1323 0.0707 1.00 79.3 yes View details
chlI Genome 1236 0.0612 1.00 79.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
P417_t002-P417_t003_p1 P417_t002-P417_t003 GCTACCAATTTCGCCACATC TGGAGACCTACGTTCTACCA 707–732 1.000 79.7
P417_t002-P417_t003_p2 P417_t002-P417_t003 TACCAATTTCGCCACATCCG TGGAGACCTACGTTCTACCA 705–730 1.000 78.5
P417_t002-P417_t003_p3 P417_t002-P417_t003 GCTACCAATTTCGCCACATC TGGAGACCTACGTTCTACCAA 707–732 1.000 77.5
P417_t002-P417_t003_p4 P417_t002-P417_t003 GCTACCAATTTCGCCACATC TTGGAGACCTACGTTCTACCA 708–733 1.000 77.5
P417_t002-P417_t003_p5 P417_t002-P417_t003 GGCTACCAATTTCGCCACAT TGGAGACCTACGTTCTACCA 708–733 1.000 76.3
rpoA_p1 rpoA CCCACCACCAGAAACATCAA ACATAATGGGTGTCGTGCTC 2136 0.750 75.9
rpoA_p2 rpoA CCCACCACCAGAAACATCAA AAATGGACCTGGAAACGGTC 2229 0.500 63.7
rpoA_p3 rpoA CCCACCACCAGAAACATCAA CGACGTCACATACAGGGTTT 2657 0.500 63.6
rpoA_p4 rpoA CCCACCACCAGAAACATCAA GGCAGGAAGTAGCGGTTTTA 2349 0.500 63.6
rpoA_p5 rpoA CCCACCACCAGAAACATCAA ACGGTCGTGAAATTGCCATA 2215 0.500 61.8
ycf34_p1 ycf34 GGACTGAAGATCCGTGTGTC CTGTTGCGTTTGCCCTATTG 935–966 1.000 91.8
ycf34_p2 ycf34 GCAATGGACTGAAGATCCGT CTGTTGCGTTTGCCCTATTG 940–971 1.000 91.6
ycf34_p3 ycf34 GGACTGAAGATCCGTGTGTC CCCATACTGTTTGCAGGTGT 1174–1205 1.000 90.5
ycf34_p4 ycf34 GGACTGAAGATCCGTGTGTC TGCACCGTGTAATGCGATAA 1274–1305 0.750 80.6
ycf34_p5 ycf34 GCAATGGACTGAAGATCCGT TGCACCGTGTAATGCGATAA 1279–1310 0.750 80.3
chlI_p1 chlI CCATGGGTAGAACCACTTCG CGGTGATTTCTTTGCAGCTG 2350–2354 0.750 76.1
chlI_p2 chlI TGGGATTTACGTGCTCCATG CGGTGATTTCTTTGCAGCTG 2365–2369 0.750 75.9
chlI_p3 chlI GATTTACGTGCTCCATGGGT CGGTGATTTCTTTGCAGCTG 2362–2366 0.750 75.9
chlI_p4 chlI CCATGGGTAGAACCACTTCG GTGCCAAGATGAAAATCGCC 2372–2381 0.750 75.4
chlI_p5 chlI CCATGGGTAGAACCACTTCG GCCAAGATGAAAATCGCCAC 2370–2373 0.500 62.6
chlB_p1 chlB AGACGTCTAGTGGAACGACT ACACGCGCCTAGTTTTTACA 2325–2327 1.000 85.6
chlB_p2 chlB AGACGTCTAGTGGAACGACT GCCACAAATTGCTCGTGATC 2193–2194 0.750 74.5
chlB_p3 chlB CCGATTGCTCTACCACTGAG GCCACAAATTGCTCGTGATC 2435–2436 0.750 74.5
chlB_p4 chlB AGACGTCTAGTGGAACGACT AAAGCCACAAATTGCTCGTG 2196–2197 0.750 74.2
chlB_p5 chlB AGACGTCTAGTGGAACGACT ATTAGGCTCCGTGCTATTGC 2039–2040 0.500 61.1
P417_t011-P417_t012_p1 P417_t011-P417_t012 CGGAAACCATTACTTTATCCT TACCAAACTGCGCTACATCC 226–230 1.000 49.7
P417_t011-P417_t012_p2 P417_t011-P417_t012 CGGAAACCATTACTTTATCCTT TACCAAACTGCGCTACATCC 226–230 1.000 49.7
P417_t011-P417_t012_p3 P417_t011-P417_t012 CGGAAACCATTACTTTATCCT CTGTGACATTCTGCTCCCAA 257–261 1.000 49.5
P417_t011-P417_t012_p4 P417_t011-P417_t012 CGGAAACCATTACTTTATCCT AACCTGTGACATTCTGCTCC 260–264 1.000 49.5
P417_t011-P417_t012_p5 P417_t011-P417_t012 CGGAAACCATTACTTTATCCTT CTGTGACATTCTGCTCCCAA 257–261 1.000 49.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Nannochloropsis granulata NC_022259.1 117672 View on NCBI ↗
Nannochloropsis limnetica NC_022262.1 117806 View on NCBI ↗
Nannochloropsis oceanica NC_022263.1 117557 View on NCBI ↗
Nannochloropsis oculata NC_022260.1 117463 View on NCBI ↗