AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241220
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0433	122	conserved hypothetical protein
#1	AF0641	51	ISA1214-3, ISORF2
#2	AF0982	300	osmoprotection protein (proX)
#3	AF1391	50	branched-chain amino acid ABC transporter, periplasmic binding protein (braC-4)
#4	AF1768	300	dipeptide ABC transporter, permease protein (dppB)

Motif 1
ACAAAGAACAGTAAATTTATGAGAAGAAAAA	0	21	0
AGACTGAAGATTAAAATTTTGGTTTTTGGTG	0	64	0
TCTTCATCTTTTAAAATTTTGCTCTCTAATT	2	93	1
AAATGTAATTGTAAAATTTGAGATATCACGC	2	215	1
CCGAGCTTTAGTAAAGTTTTAAAATTTTAAC	3	15	1
TTATACAACGTTAAAATTTTAAAACTTTACT	3	24	0
GATTAGCCCATTAAATTTTTGCCAGATACAC	4	39	0
          ***** *****
MAP Score: 10.1862

Motif 2
         TTTTCTTTCAATTTTTCTTCTCATAAATTTAC	0	1	1
TCAGTCTGCCATTAGCACAGTTGTTAGTAACACCACACAAA	0	88	1
GTTTTTCTTCATCTTTTAAAATTTTGCTCTCTAATTGAAAG	2	88	1
TTGAAAGCGCATCCCATAATATCTTTGTACCCCCAACAAGA	2	122	1
CAAAAATTTAATGGGCTAATCTTTTTATCGCTCCGGCTGGG	4	49	1
TAGTGCCACTCTTCCGTTAATTATTTCTCCCGAAATCGACA	4	167	1
TTCTCCCGAAATCGACATGGTTCTTTTTCACTATCGTTTTC	4	191	1
          **    * *  * **  ** *
MAP Score: 2.34296

Motif 3
GTAACCTTTGGTAACACCAAAAACCAAAAT	0	50	1
ACAGTTGTTAGTAACACCACACAAAAAG  	0	104	1
TAATATCTTTGTACCCCCAACAAGATTGCC	2	138	1
         CTTACCACCTCTTTCAATTTA	2	289	0
GATTAGTTTCGTAACCTCTCCAATGAATCT	4	96	0
AAGAGAGGCTTTAGCATCAACGTGTAGTGC	4	143	1
GCATCAACGTGTAGTGCCACTCTTCCGTTA	4	156	1
          **********
MAP Score: 0.860952