Markers + reference

Tetraselmis

2 species · Chlorodendraceae · Chlorodendrales

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Species 2
Genome length 92–96 kb
Candidate markers 248
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 12 remaining regions by MarkerSeek score (out of 248 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaA LSC 2256 0.4573 0.51 71.1 yes View details
psaB LSC 2205 0.4488 0.42 70.2 yes View details
clpP LSC 624 0.4742 0.62 74.4 yes View details
rpoB LSC 3756 0.4596 0.54 70.5 yes View details
rpoC1 LSC 2511 0.4599 0.60 71.7 yes View details
rpl22 LSC 558 0.4468 0.94 82.6 yes View details
tilS LSC 1149 0.4266 0.88 81.9 yes View details
ccsA IRb 879 0.2812 0.97 81.9 yes View details
petA LSC 960 0.4289 0.97 81.3 yes View details
ycf4 LSC 597 0.2371 0.97 81.2 yes View details
psbD LSC 1059 0.4139 0.98 81.1 yes View details
ycf3 LSC 504 0.4091 0.96 80.7 yes View details
chlI LSC 1065 0.4124 0.99 80.2 yes View details
ycf1 IRb 2376 0.3617 0.97 80.2 yes View details
rbcL-trnH-GTG LSC 427 0.3840 0.94 79.7 yes View details
ycf1 IRa 2376 0.2955 0.02 67.8 no View details
ccsA IRa 879 NA 0.00 46.2 no 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
psaA_p1 psaA AATGAAACCGCTTGTGGTCT TTGGTTTGTACGCATCCCAA 2898 0.500 59.7
psaA_p2 psaA ATGAAACCGCTTGTGGTCTT TTGGTTTGTACGCATCCCAA 2897 0.500 59.7
psaA_p3 psaA AATGAAACCGCTTGTGGTCT AAAGTTTCCTTGCCACGCTA 2721 0.500 59.7
psaA_p4 psaA ATGAAACCGCTTGTGGTCTT AAAGTTTCCTTGCCACGCTA 2720 0.500 59.7
psaA_p5 psaA ATGAAACCGCTTGTGGTCTT TAACAGGACCAGATGCTCCA 2838 0.500 59.5
psaB_p1 psaB GGACAACCTGGGCATTCTTT GCAGGACTTTCCATAAGCGA 2930 0.500 56.9
psaB_p2 psaB GGACAACCTGGGCATTCTTT AGCAGGACTTTCCATAAGCG 2931 0.500 56.8
psaB_p3 psaB CGGTGTTGCCCACTACTTAT GCAGGACTTTCCATAAGCGA 2962 0.500 56.6
psaB_p4 psaB CGGTGTTGCCCACTACTTAT AGCAGGACTTTCCATAAGCG 2963 0.500 56.6
psaB_p5 psaB TTGTCAAGTATCAGCGTGGG AGTTACCACTTAGGGCTGGA 2913 0.500 56.6
clpP_p1 clpP TGCCGCTACACCTTCATAAC GGTATGGCCAAGTGGTAAGG 1408 0.500 59.4
clpP_p2 clpP CCTGTTCTTGGGTCACGAAA GGTATGGCCAAGTGGTAAGG 1500 0.500 59.3
clpP_p3 clpP TGCCGCTACACCTTCATAAC GGTAAGGCAGAGGATTGCAA 1395 0.500 58.8
clpP_p4 clpP CCTGTTCTTGGGTCACGAAA GGTAAGGCAGAGGATTGCAA 1487 0.500 58.7
clpP_p5 clpP CACGATACCACGGTAATCCC GGTATGGCCAAGTGGTAAGG 1136 0.500 58.4
rpoB_p1 rpoB AAGGGCCAAATGCAGGTTTA ACTCGACCTTCTAAGCCAGT 436 0.500 59.2
rpoB_p2 rpoB ACACGTGAAACTGCTGGAAT ACTCGACCTTCTAAGCCAGT 515 0.500 59.1
rpoB_p3 rpoB AAGGGCCAAATGCAGGTTTA AAGGTGTTGCCCCAAAGATT 591 0.500 59.0
rpoB_p4 rpoB ACACGTGAAACTGCTGGAAT AAGGTGTTGCCCCAAAGATT 670 0.500 58.9
rpoB_p5 rpoB CGGGAGATTACCAGTTGACG ACTCGACCTTCTAAGCCAGT 822 0.500 58.8
rpoC1_p1 rpoC1 ATTCAAGGCCGACAACAAGT ACCAGCTCTTGTTGCTTGTT 2939 0.500 58.0
rpoC1_p2 rpoC1 CAGATGACATTCAAGGCCGA ACCAGCTCTTGTTGCTTGTT 2947 0.500 57.9
rpoC1_p3 rpoC1 TCAGATGACATTCAAGGCCG ACCAGCTCTTGTTGCTTGTT 2948 0.500 57.9
rpoC1_p4 rpoC1 AGATGACATTCAAGGCCGAC ACCAGCTCTTGTTGCTTGTT 2946 0.500 57.9
rpoC1_p5 rpoC1 ATGACATTCAAGGCCGACAA ACCAGCTCTTGTTGCTTGTT 2944 0.500 56.6
ycf4_p1 ycf4 GGGGTGAATGAAAACCGACA CTAGATTGTGGTCGCGACAA 1841 0.500 56.8
ycf4_p2 ycf4 TGGGGTGAATGAAAACCGAC CTAGATTGTGGTCGCGACAA 1842 0.500 56.8
ycf4_p3 ycf4 GGGGTGAATGAAAACCGACA GTGAAGGTGGACGAACTGTT 1947 0.500 56.5
ycf4_p4 ycf4 TGGGGTGAATGAAAACCGAC GTGAAGGTGGACGAACTGTT 1948 0.500 56.5
ycf4_p5 ycf4 GGGGTGAATGAAAACCGACA TGAAGGTGGACGAACTGTTG 1946 0.500 56.5

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
Tetraselmis marina NC_065695.1 96151 View on NCBI ↗
Tetraselmis suecica NC_067041.1 92103 View on NCBI ↗