AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID060_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391786
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	brnQ	300	branched chain amino acid transport system II carrier protein
#1	proY	75	proline permease transport protein
#2	malZ	155	maltodextrin glucosidase
#3	malF	153	part of maltose permease, periplasmic
#4	malE	300	periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis

Motif 1
TCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTAAAATT	0	187	1
AAATCATACTGCCTGTGGATGTGGTGTTGTAACGTTAAAT	0	270	0
CGTTCTGTAAGCCGGTTCAGGAGGAAATCCTGATCCGGCT	2	16	1
TTTCGGAATAGCCGGATCAGGATTTCCTCCTGAACCGGCT	2	25	0
GGGGGAGGAGGACGGGGGCGGATAACTTTCGGAATAGCCG	2	51	0
CTGAAGGATATTTGGGGGAGGAGGACGGGGGCGGATAACT	2	64	0
GCTGTGAAATGCCGGATGCGGCGTGAACGCCTTGTCCGGC	3	11	1
GGTTTTGTAGGCCGGACAAGGCGTTCACGCCGCATCCGGC	3	21	0
ACGTATGTAGGCCTGATAAGACGCGTCAGCGTCGCATCAG	3	64	1
GACAACAACTGCCTGATGCGACGCTGACGCGTCTTATCAG	3	76	0
GGCAGTTGTTGTCGGATAAGGCGTGAAAGCCTTATCCGTC	3	103	1
CTCATTCCAGGACGGATAAGGCTTTCACGCCTTATCCGAC	3	113	0
AAAAAAGCCAGGGGGTGGAGGATTTAAGCCATCTCCTGAT	4	10	0
CTGGCTTTTTTATGGGGGAGGAGGCGGGAGGATGAGAACA	4	39	1
GGGGGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAA	4	52	1
AAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGA	4	198	1
AGAAACTAGAGTCCGTTTAGGTGTTTTCACGAGCACTTCA	4	251	1
          * *** * *** *      *
MAP Score: 35.2242

Motif 2
TGAAAAAGACATGGCTAATCATGCG         	0	1	0
AAGCGTTTAAATTGCGCTTCAGGTGCTGTCATAC	0	120	1
AGCGGGAAATACTCCCAACCAGGCGCGGCGAAGA	0	187	0
TGCGTTCTGTAAGCCGGTTCAGGAGGAAATCCTG	2	14	1
TTCAGGAGGAAATCCTGATCCGGCTATTCCGAAA	2	31	1
 TGCTGTGAAATGCCGGATGCGGCGTGAACGCCT	3	9	1
TGCGGCGTGAACGCCTTGTCCGGCCTACAAAACC	3	27	1
AAACGTATGTAGGCCTGATAAGACGCGTCAGCGT	3	62	1
AGACGCGTCAGCGTCGCATCAGGCAGTTGTTGTC	3	82	1
TAAGGCTTTCACGCCTTATCCGACAACAACTGCC	3	103	0
TAAGGCGTGAAAGCCTTATCCGTCCTGGAATGAG	3	119	1
TGGAGGATTTAAGCCATCTCCTGAT         	4	1	0
AACTAAACCGAGGTCATGTAAGGAATTTCGTGAT	4	90	1
          * ***   ******
MAP Score: 19.6097

Motif 3
         CGCATGATTAGCCATGTCTTTTTCAC	0	1	1
AATGCAGTCAGTATGACAGCACCTGAAGCGCAATT	0	129	0
CTGTCATACTGACTGCATTAACGCGGTAAATCGAA	0	145	1
AATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGG	0	173	1
CAATCCCTGGGGATGATACAGCGGTATATTTAAAC	0	227	0
TTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTA	1	27	1
ATTTGGGGGAGGAGGACGGGGGCGGATAACTTTCG	2	60	0
TGATCCTGCATTAGGCTATGGCAAGGTGATCAGAT	2	112	1
GCTGTGAAATGCCGGATGCGGCGTGAACGCCTTGT	3	11	1
GGTTTTGTAGGCCGGACAAGGCGTTCACGCCGCAT	3	26	0
ACGTATGTAGGCCTGATAAGACGCGTCAGCGTCGC	3	64	1
GACAACAACTGCCTGATGCGACGCTGACGCGTCTT	3	81	0
GGCAGTTGTTGTCGGATAAGGCGTGAAAGCCTTAT	3	103	1
CTCATTCCAGGACGGATAAGGCTTTCACGCCTTAT	3	118	0
GCTTTTTTATGGGGGAGGAGGCGGGAGGATGAGAA	4	42	1
GCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAA	4	201	1
          * ****   **** *
MAP Score: 10.5854

Motif 4
TCGCTATATACCTCTGGTTTTTAGATCCCTC	0	71	1
CTGGTTTTTAGATCCCTCCTTGCTTTAAAAC	0	84	1
GCTGTATCATCCCCAGGGATTGGCACAAAAA	0	240	1
GGGCATCGCAGCCCCGTGGTTAAAACAAATG	1	19	0
GGGCTGCGATGCCCCGTGGTTTTTTATTGTG	1	36	1
AGGAAATCCTGATCCGGCTATTCCGAAAGTT	2	37	1
AAGTTATCCGCCCCCGTCCTCCTCCCCCAAA	2	63	1
GATGATGAGTGATCCTGCATTAGGCTATGGC	2	103	1
AAAATCTGATCACCTTGCCATAGCCTAATGC	2	119	0
GTTCACGCCGCATCCGGCATTTCACAGCA  	3	8	0
GTCAGCGTCGCATCAGGCAGTTGTTGTCGGA	3	88	1
AAATCCTCCACCCCCTGGCTTTTTTATGGGG	4	25	1
GTGTTCTCATCCTCCCGCCTCCTCCCCCATA	4	49	0
TTCCTTACATGACCTCGGTTTAGTTCACAGA	4	84	0
          ******** **
MAP Score: 7.5811