<MAF version="1" scoring="multiz">
<ALI score="0.128">
 <S seq="human_hoxa" seqSize="100257" strand="+" start="100" size="9">ACA-TTACT</S>
 <S seq="horse_hoxa" seqSize="98892" strand="-" start="120" size="10">ACAATTGCT</S>
 <S seq="fugu_hoxa" seqSize="90788" strand="+" start="100" size="8">ACA--TGCT</S>
</ALI>
<ALI score="0.071">
 <S seq="human_unc" seqSize="10998" strand="+" start="9077" size="8">ACAGTATT</S>
 <S seq="horse_unc" seqSize="5099" strand="0" start="4555" size="6">ACA--ATT</S>
 <S seq="fugu_unc" seqSize="4038" strand="+" start="4000" size="4">AC----TT</S>
</ALI>
</MAF>
