Markers + reference

Guinardia

2 species · Rhizosoleniaceae · Rhizosoleniales

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Species 2
Genome length 122–124 kb
Candidate markers 341
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 341 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
bas1 IRb 612 0.4858 0.75 78.0 yes View details
ycf45 IRb 1380 0.4796 0.87 81.3 yes View details
acpP IRb 237 0.4800 0.74 71.4 yes View details
rns IRb 1484 0.5147 0.82 80.1 yes View details
rnl IRb 2867 0.4850 0.85 77.8 yes View details
psbA IRb 1083 0.4979 0.89 81.8 yes View details
psbA IRa 1083 0.0074 1.00 49.5 no View details
rnl IRa 2867 0.0122 1.00 49.5 no View details
rns IRa 1484 0.0094 1.00 49.8 no View details
acpP IRa 237 0.1525 1.00 72.9 no View details
ycf45 IRa 1380 0.1486 1.00 78.8 no View details
bas1 IRa 612 0.1291 1.00 78.8 no View details
rnl-trnA(tgc) IRa 63 0.1639 0.97 85.3 yes View details
psbA-rrn5 IRa 485 0.4021 0.98 84.4 yes View details
trnI(gat)-rns IRa 64 0.1053 0.89 81.8 yes View details
trnP(tgg)-acpP IRa 495 0.2352 0.95 81.2 yes View details
trnS(tga)-petB LSC 88 0.2771 0.94 81.1 yes View details
ycf89 IRa 906 0.2514 0.98 80.7 yes View details
trnM(cat)-trnR(ccg) LSC 344 0.1235 0.97 80.5 yes View details
ycf89 IRb 906 0.4914 0.83 80.3 yes View details
trnK(ttt)-ycf12 LSC 336 0.2663 0.96 80.2 yes View details
rrn5-psbA IRb 485 0.4289 0.88 79.4 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
trnM(cat)-trnR(ccg)_p1 trnM(cat)-trnR(ccg) ATTATGAGTCCGGTGCCTTC GGTTCGATTCCCTTCATGCT 406–424 1.000 84.9
trnM(cat)-trnR(ccg)_p2 trnM(cat)-trnR(ccg) GATTATGAGTCCGGTGCCTT GGTTCGATTCCCTTCATGCT 407–425 1.000 84.9
trnM(cat)-trnR(ccg)_p3 trnM(cat)-trnR(ccg) TATGAGTCCGGTGCCTTCAA GGTTCGATTCCCTTCATGCT 404–422 1.000 84.1
trnM(cat)-trnR(ccg)_p4 trnM(cat)-trnR(ccg) TTATGAGTCCGGTGCCTTCA GGTTCGATTCCCTTCATGCT 405–423 1.000 84.1
trnM(cat)-trnR(ccg)_p5 trnM(cat)-trnR(ccg) ATTATGAGTCCGGTGCCTTC GGGGTTCGATTCCCTTCATG 408–426 1.000 82.6
trnK(ttt)-ycf12_p1 trnK(ttt)-ycf12 TCGAACCCAGAACAAATCGG AGCTGACCTAAAACTTGCCA 422–429 1.000 83.6
trnK(ttt)-ycf12_p2 trnK(ttt)-ycf12 GGACTCGAACCCAGAACAAA AGCTGACCTAAAACTTGCCA 426–433 1.000 83.2
trnK(ttt)-ycf12_p3 trnK(ttt)-ycf12 CGAACCCAGAACAAATCGGT AGCTGACCTAAAACTTGCCA 421–428 1.000 81.3
trnK(ttt)-ycf12_p4 trnK(ttt)-ycf12 TCGAACCCAGAACAAATCGG ACCGGTTGCTACTAGCTGA 435–442 1.000 80.6
trnK(ttt)-ycf12_p5 trnK(ttt)-ycf12 TCGAACCCAGAACAAATCGG CACCGGTTGCTACTAGCTG 436–443 1.000 80.4
trnS(tga)-petB_p1 trnS(tga)-petB GATGGCAGAGTTGGTCGATT TCGTTCTTCAAACCAATCGT 202–204 1.000 70.8
trnS(tga)-petB_p2 trnS(tga)-petB TGGTCGATTGCGTCTGATTT TCGTTCTTCAAACCAATCGT 191–193 1.000 70.4
trnS(tga)-petB_p3 trnS(tga)-petB TTGGTCGATTGCGTCTGATT TCGTTCTTCAAACCAATCGT 192–194 1.000 70.3
trnS(tga)-petB_p4 trnS(tga)-petB ATGGCAGAGTTGGTCGATTG TCGTTCTTCAAACCAATCGT 201–203 1.000 68.9
trnS(tga)-petB_p5 trnS(tga)-petB GGTCGATTGCGTCTGATTTG TCGTTCTTCAAACCAATCGT 190–192 1.000 67.6
bas1_p1 bas1 AGAAGCTCCTGCAAAACCTG ACGTTTCCGCGTTTAACTCT 976 0.500 55.8
bas1_p2 bas1 AGAAGCTCCTGCAAAACCTG AGACGAGAATGTGCTCCTCT 1042 0.500 55.7
bas1_p3 bas1 AGAAGCTCCTGCAAAACCTG GACGTTTCCGCGTTTAACTC 977 0.500 55.3
bas1_p4 bas1 AGAAGCTCCTGCAAAACCTG CGTTTCCGCGTTTAACTCTG 975 0.500 55.3
bas1_p5 bas1 AGAAGCTCCTGCAAAACCTG TTCCGCGTTTAACTCTGACC 972 0.500 55.2
ycf45_p1 ycf45 GGTCAGAGTTAAACGCGGAA CCTGCCGCCTCATCATTAAT 2211 0.500 57.5
ycf45_p2 ycf45 GGTCAGAGTTAAACGCGGAA AGGTGTAGATGGACGAAGCT 2003 0.500 57.1
ycf45_p3 ycf45 ATGGTCAGAGTTAAACGCGG CCTGCCGCCTCATCATTAAT 2213 0.500 57.0
ycf45_p4 ycf45 GGTCAGAGTTAAACGCGGAA GGTGTAACTTGGTCTGCCTC 2103 0.500 56.8
ycf45_p5 ycf45 TGCGGCGTCAAAACTAAATG CCTGCCGCCTCATCATTAAT 2016 0.500 56.6
acpP_p1 acpP AAGAAGCAAAACGACGAGGT TGTCACTTCAAAAGCAGCCA 1229 0.500 57.7
acpP_p2 acpP AAGAAGCAAAACGACGAGGT CGTTACTCCCAGTTGCTGAG 1716 0.500 57.3
acpP_p3 acpP AAGAAGCAAAACGACGAGGT ATAGCGTCCTGGACCGTTAT 1288 0.500 57.2
acpP_p4 acpP AAGAAGCAAAACGACGAGGT AGGTAACCGTTACTCCCAGT 1723 0.500 57.1
acpP_p5 acpP AGCTTCGTCCATCTACACCT TGTCACTTCAAAAGCAGCCA 529 0.500 56.9

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
Guinardia delicatula NC_069611.1 123772 View on NCBI ↗
Guinardia striata NC_037998.1 122145 View on NCBI ↗