AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248819
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0383	267	hypothetical protein
#1	PAB0751	105	hypothetical protein
#2	PAB0754	37	PAB0754
#3	infB	52	PAB0755
#4	PAB1054	58	hypothetical protein
#5	PAB1055	229	hypothetical protein
#6	nrd	168	PAB1057
#7	PAB1182	31	PAB1182
#8	PAB1179	87	hypothetical protein
#9	PAB1176	78	PAB1176

Motif 1
AATCCAGTTTATTTATAAAAGCAAAGGATTTATAAA	0	79	1
AAAGCAAAGGATTTATAAACTTTTTGTCGTCAGATT	0	96	1
TACATATTACCATTAACAATGTAATGGCAATCTGAC	0	124	0
CAAATTTCAAAACTGACAATTACTTGGTAAAGTTAA	0	160	1
TTACTTGGTAAAGTTAAAATTCATGGAGAATTTTTT	0	179	1
TCAACTTAACATTTAAAAATTGCTTGGACGATGGTT	0	224	1
AAATTACACCATATGTAAATTACATGCCATGTAATA	1	12	1
TAATGAAGGTATATAAAAATTTATCGATTTGTGCTT	1	61	0
 CTTTCCAAACTTTTAAAACCTGTAGGATAGCCTTT	3	9	1
AAGGTGGTAAATTTTAAAATATTTTGTGAAGGTGGT	4	24	0
AGTATCCACGCTGTTAAAAATAAAAGCATGTAATCT	5	11	0
TAATAGTCTGAGGTCAAAATCATTAGGCGCTGTAAA	6	93	1
GATTTTACTTATTTAAAGACAAAATGACAGGGGTGT	6	138	1
CTGTCCCCGTATATCACAATCATCGGGGGAG     	8	66	1
GAATGATATTAAATTAAAACTTTATGCTCAACGATT	9	28	1
          ** * *****   * *
MAP Score: 10.2531

Motif 2
AGTTGCCACAACAAGCAAAGTATAAGTTAA	0	47	1
GTTTATTTATAAAAGCAAAGGATTTATAAA	0	85	1
CCCCCTAAAAAAGAGGAAAGGGTAAAAGAG	2	10	0
TGCACTAGCAACGAGCAAAGTCGACGTATT	5	53	1
CAACTCTGCAGAGAGCAAAGTATAATAGTC	6	71	1
ATTTAAAGACAAAATGACAGGGGTGTTAGT	6	148	1
CCTCCTAAGGAAATGGAAAGGAA       	7	3	0
CCATTTCCTTAGGAGGACAGAAAA      	7	17	1
ATTGTGATATACGGGGACAGATATGTGAAT	8	56	0
          **********
MAP Score: 9.13121

Motif 3
CATGAATTTTAACTTTACCAAGTAATTGTCA	0	173	0
        TTCTCATCCCCAAGAATAACCAT	0	254	0
       TTCCTCACCACCAAACTAAAGGCT	3	38	0
CCCATCTAACCACCTTCACAAAATATTTTAA	4	16	1
TAAAATTTACCACCTTCCCACCCG       	4	44	1
CCCAACGGTTCTCACTATCAATATTCCAATT	5	98	0
TTGAAAGGAACTCGCTCCCAACGGTTCTCAC	5	114	0
GAAGGATAACCTCTCTCCCATAATAGAGATT	5	152	1
ATCTTCCAGTCAAGCTACCAACTATTAATCC	6	22	1
          *** *******
MAP Score: 7.23333

Motif 4
GCCACAACAAGCAAAGTATAAGTTAAATAAT	0	51	1
GGTAATATGTACAAATTTCAAAACTGACAAT	0	149	1
CAATTACTTGGTAAAGTTAAAATTCATGGAG	0	176	1
CATCGTCCAAGCAATTTTTAAATGTTAAGTT	0	226	0
          GTAAATTACACCATATGTAAA	1	0	1
TACACCATATGTAAATTACATGCCATGTAAT	1	16	1
TGGGAAGGTGGTAAATTTTAAAATATTTTGT	4	33	0
CTAGCAACGAGCAAAGTCGACGTATTCTTAA	5	57	1
TCTGCAGAGAGCAAAGTATAATAGTCTGAGG	6	75	1
ATTAGGCGCTGTAAATATTACAGCGATTTTA	6	114	1
ATGAATGATATTAAATTAAAACTTTATGCTC	9	26	1
          ******** **
MAP Score: 4.94836

Motif 5
TGTTAATGGTAATATGTACAAATTTCAAAA	0	142	1
TGCTCAACTTAACATTTAAAAATTGCTTGG	0	221	1
TAAATTACACCATATGTAAATTACATGCCA	1	11	1
   CTTTCCAAACTTTTAAAACCTGTAGGA	3	7	1
ACCTTCACAAAATATTTTAAAATTTACCAC	4	27	1
GCTTGACTGGAAGATTTAAAAGCAGGA   	6	7	0
AAATCGCTGTAATATTTACAGCGCCTAATG	6	113	0
TTTGTCTTTAAATAAGTAAAATCGCTGTAA	6	131	0
TTTGAGAAAAAATATTTTAAGCGAATTCAC	8	32	1
          **********
MAP Score: 4.48451

Motif 6
AGAACTAGTGTTTGTGGCAAGCAAGTTGCCACA	0	24	1
TTATAAACTTTTTGTCGTCAGATTGCCATTACA	0	108	1
ATGGTTATTCTTGGGGATGAGAA          	0	254	1
TTTCCTCTTTTTTAGGGGGAACAACT       	2	21	1
AGCCTTTAGTTTGGTGGTGAGGAA         	3	38	1
AATTGGAATATTGATAGTGAGAACCGTTGGGAG	5	98	1
GTGAGAACCGTTGGGAGCGAGTTCCTTTCAAAG	5	114	1
AATCTCTATTATGGGAGAGAGGTTATCCTTCTG	5	150	0
GACTGGAAGATTTAAAAGCAGGA          	6	0	0
ATATGACAACTCTGCAGAGAGCAAAGTATAATA	6	65	1
AGTATAATAGTCTGAGGTCAAAATCATTAGGCG	6	89	1
ATTTTACTTATTTAAAGACAAAATGACAGGGGT	6	139	1
TCCATTTCCTTAGGAGGACAGAAAA        	7	16	1
          **** ** *** *
MAP Score: 3.76401

Motif 7
AAAATTCATGGAGAATTTTTTCGTCGATGC	0	194	1
AAACCTGTAGGATAGCCTTTAGTTTGGTGG	3	25	1
TATTGATAGTGAGAACCGTTGGGAGCGAGT	5	106	1
CGTTGGGAGCGAGTTCCTTTCAAAGAGACA	5	122	1
GAGACAGAAGGATAACCTCTCTCCCATAAT	5	146	1
ATATCGCCAGGAGAATCTCTATTATGGGAG	5	166	0
TTCTCCTGGCGATATTCGTTATAATAGTGC	5	181	1
          **********
MAP Score: 0.668849