AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241579
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0629	31	3-isopropylmalate dehydratase, small subunit (leuD-1)
#1	AF0632	80	nifU protein (nifU-3)
#2	AF0633	173	isoleucyl-tRNA synthetase (ileS)
#3	AF1962	116	conserved hypothetical protein
#4	AF1963	174	aconitase (acn)
#5	AF2199	82	3-isopropylmalate dehydratase, large subunit (leuC)

Motif 1
   GAGCTAAGTAGGGGCGGAATTAAAAAA	0	14	0
AACAAAAATTGGAGGGATTT          	1	0	0
          GGAGGGAGAGTGAGGGAAGG	2	0	1
GCAAAAATTAGGAGGGATAGTAGGCTGAAA	2	63	0
ATACCATCATGGTGGGGCAGCAAAAATTAG	2	82	0
TTCGGCCCTCGGTGGGGCTGAAGCGTCGCC	3	83	1
TAAAAAATGAGTAGGGATATAAACCAAAGC	4	14	1
AAATCCGGGAGGCGGGACTTGAATGCTTTG	4	38	0
CGCCTGCCGCGGAGTGGCGGACTACAGTCC	4	90	1
AGAGGTAGAGCGTGGGACTGTAGTCCGCCA	4	104	0
          **********
MAP Score: 18.2751

Motif 2
      AACCTTTTTTAATTCCGCCCCTACTTAGC	0	4	1
CCAATTTTTGTTTGTGTACTCCTCCTCTTTCAAAC	1	18	1
AACCAAAAAGCTTATTATTTCCGTCAAGGGAAGAG	1	50	1
TAATACCTTCCCTCACTCTCCCTCC          	2	0	0
TCATGTAAACCCTTATTTTTCAGCCTACTATCCCT	2	46	1
CCCTCCTAATTTTTGCTGCCCCACCATGATGGTAT	2	77	1
AAGCTGATAACTTTTTTAATCCACCGGCTGTTCAG	2	143	1
AAGTCGGCGACGCTTCAGCCCCACCGAGGGCCGAA	3	83	0
TAAACCAAAGCATTCAAGTCCCGCCTCCCGGATTT	4	33	1
AACCGGGGACCATGGGATCTCCGCCTGCCGCGGAG	4	69	1
          * *   * *******
MAP Score: 12.7011

Motif 3
       AACCTTTTTTAATTCCGCCCCTACTT	0	3	1
TGTACTCCTCCTCTTTCAAACCAAAAAGCTTAT	1	32	1
ATGGTATATGCTTTTGCATGTCAAAATTCCGGA	2	105	1
AAGCTGATAACTTTTTTAATCCACCGGCTGTTC	2	143	1
ATACAGAATATTTTTTGAACAAAAACCGTTATC	3	36	0
GCCTTAAATACTTTTTTAATGAACTCTCAAA  	5	8	0
GTATTTAAGGCTTTTCTAAGAAACAAACGGTTA	5	30	1
TAGTTCGGTGCTTTTTAAGTTAACCGTTTGTTT	5	50	0
          ****** **  **
MAP Score: 6.25657