AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons030_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249832
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0065	300	311aa long hypothetical protein

Motif 1
GAAATGATGAGAATGTCCTCGGAGAGGGGGGGAGTACTGGT	0	140	1
AGGAGAAGTCGATTGTGACTGCAATGGGGGGGCTCGA    	0	273	1
TCGACCTGGAGGGTCAGCAGGCTGTGGCGGAAATGATGAGA	0	111	1
          GGTTGACGAGCTTAGCGGGGGCAACATGCAG	0	0	1
GCGGCTGGGTTCATAGCAACCAGGAGGCGGGGCTTGAGCCA	0	65	0
GTCAAACAAGATTTACGTTGCGAGTGGCGGGATAGTCAAAG	0	214	1
TAGTCAAAGGGCCTTACCTGCCTACCGAGGAGAAGTCGATT	0	246	1
GCAACATGCAGAGGCTCGTACTAGCGAGGGAGCTCTGGCTC	0	30	1
ACGTAAATCTTGTTTGACACCCGGAGAAGGAAGTCTAGGTC	0	191	0
          *  *  *   *  * ** ***
MAP Score: 13.5171

Motif 2
TGAGAATGTCCTCGGAGAGGGGGGGAGTACT	0	147	1
GGTTGACGAGCTTAGCGGGGGCAACATGCAG	0	10	1
GCGGGGGCAACATGCAGAGGCTCGTACTAGC	0	24	1
ACAAGATTTACGTTGCGAGTGGCGGGATAGT	0	219	1
TTCATAGCAACCAGGAGGCGGGGCTTGAGCC	0	66	0
CTGGTCTCGACCTGGAGGGTCAGCAGGCTGT	0	105	1
TTGTTTGACACCCGGAGAAGGAAGTCTAGGT	0	192	0
AGAGGCTCGTACTAGCGAGGGAGCTCTGGCT	0	39	1
ATTGTGACTGCAATGGGGGGGCTCGA     	0	284	1
GCCTTACCTGCCTACCGAGGAGAAGTCGATT	0	256	1
CCAGGTCGAGACCAGCGGCTGGGTTCATAGC	0	89	0
          * *********
MAP Score: 12.7542

Motif 3
 GGTTGACGAGCTTAGCGGGGGCAACATGCAG	0	9	1
TTAGCGGGGGCAACATGCAGAGGCTCGTACTA	0	21	1
GAGGCTCGTACTAGCGAGGGAGCTCTGGCTCA	0	40	1
GGAGGCGGGGCTTGAGCCAGAGCTCCCTCGCT	0	52	0
TCATAGCAACCAGGAGGCGGGGCTTGAGCCAG	0	64	0
CAGGTCGAGACCAGCGGCTGGGTTCATAGCAA	0	87	0
CCGCTGGTCTCGACCTGGAGGGTCAGCAGGCT	0	102	1
CCTGGAGGGTCAGCAGGCTGTGGCGGAAATGA	0	115	1
ATGAGAATGTCCTCGGAGAGGGGGGGAGTACT	0	146	1
TGTTTGACACCCGGAGAAGGAAGTCTAGGTCT	0	190	0
ATTTACGTTGCGAGTGGCGGGATAGTCAAAGG	0	224	1
GACTTCTCCTCGGTAGGCAGGTAAGGCCCTTT	0	251	0
GATTGTGACTGCAATGGGGGGGCTCGA     	0	283	1
          * ** *******
MAP Score: 10.9783

Motif 4
   GGTTGACGAGCTTAGCGGGGGCAACATG	0	7	1
GGGCAACATGCAGAGGCTCGTACTAGCGAGG	0	28	1
CATAGCAACCAGGAGGCGGGGCTTGAGCCAG	0	64	0
AGGTCGAGACCAGCGGCTGGGTTCATAGCAA	0	87	0
CGCTGGTCTCGACCTGGAGGGTCAGCAGGCT	0	103	1
AGGGTCAGCAGGCTGTGGCGGAAATGATGAG	0	120	1
AGAATGTCCTCGGAGAGGGGGGGAGTACTGG	0	149	1
GATTTACGTTGCGAGTGGCGGGATAGTCAAA	0	223	1
ACTTCTCCTCGGTAGGCAGGTAAGGCCCTTT	0	251	0
AGGAGAAGTCGATTGTGACTGCAATGGGGGG	0	273	1
ATTGTGACTGCAATGGGGGGGCTCGA     	0	284	1
          *** *******
MAP Score: 2.5889

Motif 5
   GGTTGACGAGCTTAGCGGGGGCAACATGCAGAG	0	7	1
GGGTTCATAGCAACCAGGAGGCGGGGCTTGAGCCAG	0	64	0
ACAGCCTGCTGACCCTCCAGGTCGAGACCAGCGGCT	0	100	0
TGGAGGGTCAGCAGGCTGTGGCGGAAATGATGAGAA	0	117	1
TGATGAGAATGTCCTCGGAGAGGGGGGGAGTACTGG	0	144	1
ACCTAGACTTCCTTCTCCGGGTGTCAAACAAGATTT	0	192	1
CAAGATTTACGTTGCGAGTGGCGGGATAGTCAAAGG	0	220	1
AGTCGATTGTGACTGCAATGGGGGGGCTCGA     	0	279	1
          *  *   * *******
MAP Score: 0.881372