for BLAST, save the result as XML. And use the following XSLT stylesheet. It only prints the Hsp_qseq and the Hsp_hseq of the first hit and first hsp.

<xsl:stylesheet xmlns:xsl="&lt;a href=" <a="" href="http://www.w3.org/1999/XSL/Transform" rel="nofollow">http://www.w3.org/1999/XSL/Transform" "="" rel="nofollow">http://www.w3.org/1999/XSL/Transform' version='1.0' >
<xsl:output method="text"/>
<xsl:template match="/">
<xsl:apply-templates select="BlastOutput/BlastOutput_iterations/Iteration/Iteration_hits/Hit[1]/Hit_hsps/Hsp[1]"/>
</xsl:template>
<xsl:template match="Hsp">
<xsl:value-of select="Hsp_qseq"/><xsl:text>
</xsl:text><xsl:value-of select="Hsp_hseq"/><xsl:text>
</xsl:text>
</xsl:template>
</xsl:stylesheet>

.usage:

$ xsltproc --novalid stylesheet.xsl blast.xml

.

IDVWTEER-KGTLNRDLLFD
ID--TEERLKGVI--DLIFE

There are many multiple alignment programs and most of them use global alignment. Almost all of them output results (alignment) in more than one type (see types here). Just select the format you want and use the program of your choice to get your job done!