AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID060_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391563
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	malZ	155	maltodextrin glucosidase
#1	malF	153	part of maltose permease, periplasmic
#2	malE	300	periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis

Motif 1
AGCCGGATCAGGATTTCCTCCTGAACCGGCTTACAGAACG	0	16	0
AGCCGGTTCAGGAGGAAATCCTGATCCGGCTATTCCGAAA	0	25	1
CGGCTATTCCGAAAGTTATCCGCCCCCGTCCTCCTCCCCC	0	51	1
GCCGGACAAGGCGTTCACGCCGCATCCGGCATTTCACAGC	1	11	0
GCCGGATGCGGCGTGAACGCCTTGTCCGGCCTACAAAACC	1	21	1
CTGATGCGACGCTGACGCGTCTTATCAGGCCTACATACGT	1	64	0
CTGATAAGACGCGTCAGCGTCGCATCAGGCAGTTGTTGTC	1	76	1
GACGGATAAGGCTTTCACGCCTTATCCGACAACAACTGCC	1	103	0
GTCGGATAAGGCGTGAAAGCCTTATCCGTCCTGGAATGAG	1	113	1
ATCAGGAGATGGCTTAAATCCTCCACCCCCTGGCTTTTTT	2	10	1
CCGTGTTCTCATCCTCCCGCCTCCTCCCCCATAAAAAAGC	2	42	0
          *      *****   *** *
MAP Score: 39.3882

Motif 2
TCAGGAGGAAATCCTGATCCGGCTATTCCG	0	32	1
TCCGAAAGTTATCCGCCCCCGTCCTCCTCC	0	58	1
CGCCCCCGTCCTCCTCCCCCAAATATCCTT	0	71	1
ATGATGAGTGATCCTGCATTAGGCTATGGC	0	104	1
TTCACGCCGCATCCGGCATTTCACAGCA  	1	8	0
TGAACGCCTTGTCCGGCCTACAAAACCGAA	1	34	1
TGAAAGCCTTATCCGTCCTGGAATGAGGAA	1	126	1
GATGGCTTAAATCCTCCACCCCCTGGCTTT	2	17	1
ATCCTCCCGCCTCCTCCCCCATAAAAAAGC	2	42	0
          **********
MAP Score: 8.69579

Motif 3
CGTTCTGTAAGCCGGTTCAGGAGGAAATCC	0	16	1
CAGGAGGAAATCCTGATCCGGCTATTCCGA	0	33	1
GGAGGACGGGGGCGGATAACTTTCGGAATA	0	55	0
GATATTTGGGGGAGGAGGACGGGGGCGGAT	0	68	0
GCAGGATCACTCATCATCTGAAGGATATTT	0	91	0
ATAGCCTAATGCAGGATCACTCATCATCTG	0	101	0
GCTGTGAAATGCCGGATGCGGCGTGAACGC	1	11	1
CGGCGTGAACGCCTTGTCCGGCCTACAAAA	1	29	1
ACGTATGTAGGCCTGATAAGACGCGTCAGC	1	64	1
ACGCGTCAGCGTCGCATCAGGCAGTTGTTG	1	84	1
GGCAGTTGTTGTCGGATAAGGCGTGAAAGC	1	103	1
AGGCGTGAAAGCCTTATCCGTCCTGGAATG	1	121	1
TCATCCTCCCGCCTCCTCCCCCATAAAAAA	2	44	0
GGAGGAGGCGGGAGGATGAGAACACGGCTT	2	55	1
ATTTTTGCAAGCAACATCACGAAATTCCTT	2	109	0
CGATTTTATGTGCGCATCTCCACATTACCG	2	144	1
          **********
MAP Score: 8.37888