Looking for binding sites clustered in MIN_LENGTH bp
 Matrices are OK .....now reading sequences/mouse_pir.pir file
 11310 nt.  score: 300   CACAGGGGCAAAGCTGAAAA+		  hnf4_01 M00134
 11458 nt.  score: 162   AAACAAACAAACAACCTTGA-		  hnf3b_01 M00131
+-+-+-+-+-+-+-+-+--+-+-+
 11798 nt.  score: 163   ATTTATTTATTTATTTTCTA+		  hnf3b_01 M00131
 12054 nt.  score: 194   GCTGTTAATCATTTCACAAA+		  HNF1
+-+-+-+-+-+-+-+-+--+-+-+
 16998 nt.  score: 178   AGAGACTTGTTTGCTTCCCA+		  hnf3b_01 M00131
 17174 nt.  score: 164   AACAAAACAAACATAAAATA-		  hnf3b_01 M00131
 17431 nt.  score: 163   TCAGAGCTGTTTGCTCCTGG+		  hnf3b_01 M00131
+-+-+-+-+-+-+-+-+--+-+-+
 17820 nt.  score: 283   AAGTGGCCTTTTCTCCTGCC-		  hnf4_01 M00134
 17875 nt.  score: 189   ACTGTTAATCATTTCAGAAC+		  HNF1
 17981 nt.  score: 169   TGGAATTTATTTACTTACCA+		  hnf3b_01 M00131
+-+-+-+-+-+-+-+-+--+-+-+
 19674 nt.  score: 163   AGGAGAGTAAATATGCAGGG-		  hnf3b_01 M00131
 19952 nt.  score: 168   TCAATTCTGTTTGCTTCTAC+		  hnf3b_01 M00131
+-+-+-+-+-+-+-+-+--+-+-+
 22258 nt.  score: 192   AGGGTTATTTGTTACACAGC+		  HNF1
 22400 nt.  score: 286   TTGAAGTTCAAAGTACCTGT+		  hnf4_01 M00134
+-+-+-+-+-+-+-+-+--+-+-+
14+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
C;LOCUS       AB001489    29392 bp    DNA             ROD       21-JAN-1998
C;DEFINITION  Mus musculus DNA for polyimmunoglobulin receptor, complete cds.
C;ACCESSION   AB001489
C;NID         g2804245
C;KEYWORDS    polyimmunoglobulin receptor.
C;SOURCE      Mus musculus (strain:129SVJ) female liver DNA. . . . 


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