AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241572
 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	AF1963	174	aconitase (acn)
#4	AF2199	82	3-isopropylmalate dehydratase, large subunit (leuC)

Motif 1
    AACCTTTTTTAATTCCGCCCCTACTTAGCTC 	0	6	1
AATTTTTGTTTGTGTACTCCTCCTCTTTCAAACCAA	1	20	1
ATGTAAACCCTTATTTTTCAGCCTACTATCCCTCCT	2	48	1
TCCCTCCTAATTTTTGCTGCCCCACCATGATGGTAT	2	76	1
GCTGATAACTTTTTTAATCCACCGGCTGTTCAGGTT	2	145	1
AACCAAAGCATTCAAGTCCCGCCTCCCGGATTTGAA	3	35	1
CCGGGGACCATGGGATCTCCGCCTGCCGCGGAGTGG	3	71	1
AGAGCGTGGGACTGTAGTCCGCCACTCCGCGGCAGG	3	92	0
          **  *  *** ** **
MAP Score: 5.92916

Motif 2
GAGCTAAGTAGGGGCGGAATTAAAAAAGGTT       	0	3	0
GTTTGAAAGAGGAGGAGTACACAAACAAAAATTGGAGG	1	15	0
          GGAGGGAGAGTGAGGGAAGGTATTAAAC	2	0	1
AGGAGGGATAGTAGGCTGAAAAATAAGGGTTTACATGA	2	46	0
TCATGGTGGGGCAGCAAAAATTAGGAGGGATAGTAGGC	2	68	0
AACCTGAACAGCCGGTGGATTAAAAAAGTTATCAGCTT	2	143	0
TAAAAAATGAGTAGGGATATAAACCAAAGCATTCAAGT	3	14	1
AGGCGGGTTCGATAGCTTACTGAGCGAATCTGCTTAAA	3	140	1
       TTTGAGAGTTCATTAAAAAAGTATTTAAGGC	4	3	1
CTAAGAAACAAACGGTTAACTTAAAAAGCACCGAACTA	4	45	1
          *  **   * * * ****
MAP Score: 5.00641

Motif 3
    AACCTTTTTTAATTCCGCCCCTACTTAGC	0	6	1
ATTTTTCAGCCTACTATCCCTCCTAATTTTTGC	2	60	1
CTCCTAATTTTTGCTGCCCCACCATGATGGTAT	2	79	1
GCTGATAACTTTTTTAATCCACCGGCTGTTCAG	2	145	1
AACCAAAGCATTCAAGTCCCGCCTCCCGGATTT	3	35	1
GAGTGGCGGACTACAGTCCCACGCTCTACCTCT	3	101	1
          **  ****** **
MAP Score: 3.63094

Motif 4
       AACCTTTTTTAATTCCGCCCCTACT	0	3	1
TGTACTCCTCCTCTTTCAAACCAAAAAGCTTA	1	32	1
AACTTTAATTGTCATGTAAACCCTTATTTTTC	2	35	1
AAGCTGATAACTTTTTTAATCCACCGGCTGTT	2	143	1
AAAATGAGTAGGGATATAAACCAAAGCATTCA	3	17	1
CCATGGTCCCCGGTTCAAATCCGGGAGGCGGG	3	52	0
          ** ** ******
MAP Score: 0.369801

Motif 5
GGAGGAGTACACAAACAAAAATTGGAGGGAT	1	12	0
TCCTCCTCTTTCAAACCAAAAAGCTTATTAT	1	37	1
GATAACTTTTTTAATCCACCGGCTGTTCAGG	2	148	1
GAGTAGGGATATAAACCAAAGCATTCAAGTC	3	22	1
GGCTTTTCTAAGAAACAAACGGTTAACTTAA	4	38	1
CGGTTAACTTAAAAAGCACCGAACTAACTTG	4	57	1
          * *********
MAP Score: 0.0252177