Markers + reference

Galdieria

2 species · Galdieriaceae · Galdieriales

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Species 2
Genome length 168–168 kb
Candidate markers 467
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 467 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf80 Genome 1779 0.2489 1.00 78.5 yes View details
carA Genome 1200 0.2452 1.00 79.2 yes View details
Gsul_orf2 Genome 795 0.3178 1.00 79.0 yes View details
ycf23 Genome 804 0.2458 0.95 83.5 yes View details
minD Genome 801 0.2326 0.99 80.8 yes View details
ycf60 Genome 939 0.2418 0.97 81.4 yes View details
ccsA Genome 912 0.1691 0.97 81.7 yes View details
Gsul_orf1 Genome 762 0.1413 0.98 80.3 yes View details
cysT Genome 816 0.2289 0.99 80.2 yes View details
cobA Genome 783 0.2171 0.99 79.9 yes View details
thiG Genome 837 0.1966 0.99 79.8 yes View details
accA Genome 1032 0.1760 0.99 79.7 yes View details
chlI Genome 1041 0.1802 0.99 79.6 yes View details
accB Genome 552 0.1400 0.98 79.4 yes View details
ilvH Genome 555 0.1593 0.98 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
accB_p1 accB TCTTACCGACACCTGGTCTT AATCGTGAGCATCTGCATGT 1606 0.500 59.7
accB_p2 accB TCTTACCGACACCTGGTCTT AATCCTCCACCAACATCAGC 1835 0.500 58.9
accB_p3 accB TCTTACCGACACCTGGTCTT CCTCCACCAACATCAGCATT 1832 0.500 58.7
accB_p4 accB TCTTACCGACACCTGGTCTT TGATTCCTGAGGCTCTCCAT 1891 0.500 58.5
accB_p5 accB TCTTACCGACACCTGGTCTT CGTGAGCATCTGCATGTAGA 1603 0.500 58.2
Gsul_orf1_p1 Gsul_orf1 ACAATGGGTATTGGGAGGGA CTACCAGTTTCGCCACCTAC 1563 0.500 59.9
Gsul_orf1_p2 Gsul_orf1 ACAATGGGTATTGGGAGGGA TGATGCGTCTACCAGTTTCG 1571 0.500 59.9
Gsul_orf1_p3 Gsul_orf1 ACAATGGGTATTGGGAGGGA TCTACCAGTTTCGCCACCTA 1564 0.500 59.4
Gsul_orf1_p4 Gsul_orf1 ACAATGGGTATTGGGAGGGA GTGTGATGCGTCTACCAGTT 1574 0.500 59.3
Gsul_orf1_p5 Gsul_orf1 ACAATGGGTATTGGGAGGGA GAGTGTGATGCGTCTACCAG 1576 0.500 59.3
ilvH_p1 ilvH GTGCTACTGGTGGTTCTGTT GGTATGGCCAAGTGGTAAGG 1066 0.500 57.5
ilvH_p2 ilvH GTGCTACTGGTGGTTCTGTT GGTAAGGCAGAGGATTGCAA 1053 0.500 56.9
ilvH_p3 ilvH TACGTGCTACTGGTGGTTCT GGTATGGCCAAGTGGTAAGG 1069 0.500 56.6
ilvH_p4 ilvH GTGCTACTGGTGGTTCTGTT AAGGGGATGTGTTGGAATGG 984 0.500 56.1
ilvH_p5 ilvH GTGCTACTGGTGGTTCTGTT AAGTCTTAAAGCGCGCAATG 1661 0.500 56.0
ycf80_p1 ycf80 AGTCGGCAGTGCAACATTTA ACCACCACACCTATCGGTAA 2345 0.500 58.7
ycf80_p2 ycf80 AGTCGGCAGTGCAACATTTA ACTATACCAGCTGCTAGGCA 2518 0.500 58.4
ycf80_p3 ycf80 GCATAAAACAGGGAGGCTGT ACCACCACACCTATCGGTAA 2276 0.500 58.2
ycf80_p4 ycf80 TAAAACAGGGAGGCTGTTCG ACCACCACACCTATCGGTAA 2273 0.500 58.1
ycf80_p5 ycf80 GCATAAAACAGGGAGGCTGT ACTATACCAGCTGCTAGGCA 2449 0.500 58.0
chlI_p1 chlI GCAGATGGTCACTGGTTCAA GCAGAAGGCAATCCAGCTAT 1739 0.500 59.0
chlI_p2 chlI GCAGATGGTCACTGGTTCAA TTCCAGCCGTTTTAGCACTT 1326 0.500 59.0
chlI_p3 chlI GCCTTACAAGCAGATGGTCA GCAGAAGGCAATCCAGCTAT 1748 0.500 58.9
chlI_p4 chlI TGCCTTACAAGCAGATGGTC GCAGAAGGCAATCCAGCTAT 1749 0.500 58.9
chlI_p5 chlI GCCTTACAAGCAGATGGTCA TTCCAGCCGTTTTAGCACTT 1335 0.500 58.9
carA_p1 carA ACGAGATTCAAACTCAAAACGC AGCTCCTATAGGTCATTTGCC 1549 0.500 28.8
carA_p2 carA ACGAGATTCAAACTCAAAACGC GCTCCTATAGGTCATTTGCCT 1548 0.500 28.8
carA_p3 carA CGAGATTCAAACTCAAAACGCT AGCTCCTATAGGTCATTTGCC 1548 0.500 28.7
carA_p4 carA CGAGATTCAAACTCAAAACGCT GCTCCTATAGGTCATTTGCCT 1547 0.500 28.7
carA_p5 carA ACGAGATTCAAACTCAAAACGC GCTCCTATAGGTCATTTGCCTT 1548 0.500 26.3

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
Galdieria phlegrea NC_072236.1 168452 View on NCBI ↗
Galdieria sulphuraria NC_024665.1 167741 View on NCBI ↗