AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241600
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0042	63	polysaccharide ABC transporter, permease protein (rfbA-1)
#1	AF0968	205	3-ketoacyl-CoA thiolase (acaB-10)
#2	AF1136	103	ABC transporter, ATP-binding protein
#3	AF1843	163	cobalamin biosynthesis protein (cbiM-2)

Motif 1
AACTTAGAGCAAAATTTTTAATCAGCTTCGC	0	21	0
ACAAAAATATAAAAATAAAAAT         	1	1	0
AACAGCGTGTTAAAAACAAAAATATAAAAAT	1	16	0
AGAGCAAATGAAAAATCTAAACGCGTAAAAA	1	90	1
TCTAAACGCGTAAAAATTGAATATATCAAGT	1	105	1
TGCCGATTTAAAAATAGATAATCCGCCTGTA	1	156	0
GCACATTACGTAAAATTTAAGTATTAACGAA	1	184	1
GAAGCTGAGAAAAAATGGGAAATAGC     	2	5	0
AATTATGAATAAAAAAGAAAA          	3	0	0
TATTTTGGAGAAAATTATGAATAAAAAAGAA	3	12	0
AATTTTCTCCAAAATACTAAAATCAAAAACT	3	27	1
AGCACTTGTGAAAAATCTGAAAAAAAGTAAT	3	63	1
 CGCTATGCTAAGAATGTAAAACAAACCCGC	3	143	0
          ****** ****
MAP Score: 14.2491

Motif 2
TAGCGAAGCTGATTAAAAATTTTGCTCTAA	0	19	1
TTTGCTCTAAGTTTAAAAACATTGAGCTCA	0	39	1
AAAAATATAAAAATAAAAAT          	1	0	0
AGCGTGTTAAAAACAAAAATATAAAAATAA	1	14	0
TACGAGAGCAAATGAAAAATCTAAACGCGT	1	86	1
AAATCTAAACGCGTAAAAATTGAATATATC	1	102	1
TAATGTGCCGATTTAAAAATAGATAATCCG	1	162	0
TCGGCACATTACGTAAAATTTAAGTATTAA	1	181	1
TTAGGAAGCTGAGAAAAAATGGGAAATAGC	2	10	0
TGGTAGGGGAGAATATAAATGTTACCAAAT	2	74	0
AGAAAATTATGAATAAAAAAGAAAA     	3	5	0
AAAATACTAAAATCAAAAACTTTATTAGCA	3	37	1
          **********
MAP Score: 7.34595

Motif 3
GTTTTTAAACTTAGAGCAAAATTTTTAATCAGCTTCG	0	22	0
      AGACTGAGCTCAATGTTTTTAAACTTAGAGC	0	42	0
ATTTTTATTTTTATATTTTTGTTTTTAACACGCTGTT	1	10	1
CACGCTGTTTTTAGCGTACTGTATTTAGCTTTAATGT	1	38	1
TTGATATATTCAATTTTTACGCGTTTAGATTTTTCAT	1	97	0
      TTCGTTAATACTTAAATTTTACGTAATGTGC	1	184	0
TTCCTAATTGTCATCATAATGTATTTACCATATCACA	2	33	1
CAAGTGCTAATAAAGTTTTTGATTTTAGTATTTTGGA	3	34	0
TACCTCGATTTGAGCATAGCGGGTTTGTTTTACATTC	3	125	1
          * **  **  *  ****
MAP Score: 5.76432