It is conserved in most of the CRT sequences, except for a group of plant CRTs (Figure S4).
As all sequences (except for those from Ciona intestinalis) were obtained from GenBank, only their accession numbers are provided.
Aside from the TTR copy number variation, all 43 MgPars showed homogeneous sequences except for the MgPar 7 in specimen 64.0 as described below.
Sequences (except for ITS2 sequences) were aligned using the ClustalW implemented in Bioedit 7.0.0 [88] and further modified manually using Bioedit.
The 8,000 lowest-energy designed sequences outperformed the random sequences, except for the R55 ones (55% identity to the caspase templates; see Table 2 and Figure 3).
All target genes had this core binding motif present in their upstream sequences except for two of the ten target genes, which had binding motifs that differed from the consensus binding motif in two nucleotides, namely, TTTTAAC and AGTTTCC.
The ABI sequencing resulted in extending the length of the sequence coverage for the genes to ≥95% 95% too 105%) when compared to the corresponding TIGR4 sequences except for the eleven sequences listed in Table S3 (1.4% of total sequences).
Somewhat surprisingly, the next closest set of matrices is that derived from mitochondrial sequences, except for the long evolutionary scale, when the rtREV model (derived from a viral reverse transcriptase protein alignment) becomes most similar to the HIV models.
The density of insertions/deletions increased with increasing GC of isochore families, essentially paralleling the densities of genes and Alu sequences, except for the lower values of the longest (>1000 bp, base pairs) insertions/deletions in H3 isochores.
Oligonucleotide sequences except for miRNA-specific forward primers are shown in Supplementary Table S4.
All of the M. truncatula sequences except for MtSERK3 have a predicted signal peptide.
