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Table 1 Consensus derived from binding sites aligned using ClustalW2 (left) and simple sorted (right) multiple sequence alignment algorithms

From: Effect of positional dependence and alignment strategy on modeling transcription factor binding sites

ClustalW2 Alignment

Simple Sorted Alignment

-------ATTACACCAAGTACC

-------ACCTAAGCTG--

----GGAATTTCCTGTTGATCC

----ATTACACCAAGTACC

-------ACCTAA-GCTG----

-GGAATTTCCTGTTGATCC

CTAAAGGACGTCACATTGC---

CTAAAGGACGTCACATTGC

-------A--TCA---TG----

----A--AC-T-A--T--C