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. 2006 Jun 8;7:292. doi: 10.1186/1471-2105-7-292

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Copyright © 2006 Wang et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Alignments of real non-coding DNA sequences from mouse and rat produced by AVID, CLUSTALW and MCALIGN2. The scale is shown below the alignments, and proportion of matched bases in the alignment is shown on the right. There are three cases (a) alignments of intronic DNA sequence from the Fshb gene, (b) alignments of intronic DNA sequences from the Omd gene and (c) alignments of small pieces of intronic DNA sequences from Omd, in which MCALIGN2 performed quite differently from the others.