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Very recently, this same TRP2 promoter element was predicted to bind an AP2 [29], and later observed to bind a T. gondii AP2, X1-3 (KimKim, personal communication, 2010).
One DRE-like element was predicted in the SiLEA14 promoter.
Similarly, primers described in Panels D and E yielded the expected amplicon of size 205 and 264 bp respectively, as the IS element was predicted to be absent in the 5 clinical isolates,.
Similar(57)
This element is predicted to be solid at room temperature, although it is so unstable that this quality is difficult to document.
In fact, out of the oxidation states the element is predicted to form, −1 is predicted to be the least common.
The 3-class SSE is predicted by PSIPRED [ 8] which is more accurate but contains less information, while the 8-class secondary structure element is predicted by RaptorX-SS8 [ 45] which is less accurate but contains more information.
The structure of BOX elements was generated from those elements with a canonical A1B1C1 sequence; notably, the folding of the boxB element is predicted to involve few interactions with the boxA and C elements that form the rest of the structure.
The cis-element was predicted by PLACE (http://www.dna.affrc.go.jp/PLACE/).jp/PLACE/
In general, EST specific alignments resulted in more positive RNAz predictions and the most structural RNA elements were predicted from both alignment sets [see Additional file 1, Figure S2].
Meanwhile, a number of putative cis-regulatory elements were predicted in PtAP1 promoter by bioinformatics analysis.
Subsequently, conserved elements were predicted in the multiple alignments using PhastCons with the following inputs and parameters: the neutral and conserved models, target coverage of input alignments = 0.3 and average length of conserved sequence = 45 bp.
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