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Candidate sequences (>80% sequency identity) were further analyzed using mFold and MiRscan.
Constraints imposed on candidate sequences following [15].
Also, the candidate sequences with fewer errors are favored.
High-scoring candidate sequences were identified after MAMA score calculation.
For each logic operator, 300 candidate sequences were generated.
For the 5% highest-scoring candidate sequences, similar and lower-scoring candidate sequences were grouped into the same motif group as the higher-scoring one.
These 300 candidate sequences were then filtered using the filter cascade shown in Table 4.
Candidate sequences were extracted from the 50 most highly upregulated genes from the microarray analyses.
Table 9 shows the overall result of generating candidate sequences for LG-T logic operators.
This method initially lists every 8-bp sequence upstream of regulated genes as candidate sequences.
For this purpose 50,000 candidate sequences were generated using the protocol.
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