In the first set of data (Part2-Upstream1.txt), CLUSTALW did not find any matches.  DiAlign found a few matches in some of the strings.  The most promising seemed to be  the following pattern in four of the seven sequences:
 
MJ0564   230  -ATTTAATTAA
APE2166  115  -----------
TVN0819  108  GATTCCAAAAA 
Ta0849    55  GCTTTCACAAA
MTH1683   69  TATTTATAAAA
VNG2283G  28  -----------
AF2255    56  -----------   
 
 
In the second set of data (Part2-Upstream2.txt), CLUSTALW again did not find any matches.  DiAlign again found a few candidates, the most promising of which seemed to be:
 
Ta0946   30  AACTTTTTGCATTG
TVN1090  97  AACTTTTCACTATA
MJ1555  202  AATTATTAACCTTA
MTH226   62  AAATATTCACTTTA
PH1020   44  AATTTTTCA-----
PAB0646  40  GGTTCTTCA-----
 
 
In the third set of data (Part2-Upstream3.txt), CLUSTALW again did not find any matches.  DiAlign didn't find any really good candidates either.  It did find the pattern "AGCGATG CCAATGAGGA GGGATAGCCT TCTC" occuring almost identically in two of the five sequences (PAB1782 and PH0965), but they didn't occur in any of the other sequences.