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Accordingly, the angle formed between the diagonal and the base in this sequence increases continually from just over 45° to just under 60°.
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The optimal (canonical) PAS consists of the AAUAAA motif and most base substitutions in this sequence, except the AUUAAA variant, have been shown to have a significantly reduced cleavage and polyadenylation efficiency (to almost 10% of those sequences with the canonical PAS).
This method assigns a probability distribution over labels to each base in the sequence considering ChIP-chip ratio and sequence information.
We therefore associate one variable y i with every base in the sequence.
The quality of each base in the sequence was assessed with the program Phred [ 54, 55].
The base of this sequence in the Arabian platform shows evidence of exposure and is the lower boundary of a second-order sequence (Vahrenkamp 2010; Van Buchem et al. 2010b) with an abrupt gamma ray increases probably due to uranium concentration by groundwater movement.
The core sequence of DBE is TGTT, and a single base-pair replacement in this sequence might significantly weaken its interaction with forkhead proteins.
As each 5 base sequence was encountered, the next two bases in the sequence were added.
All sequencing platform vendors provide quality scores for individual bases in the sequence reads.
Finally, any remaining ambiguous bases in the sequence were targeted for resequencing.
CAP3 may yield conflicting bases in the sequence generated for the contig.
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