AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242732
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ytgA	300	Solute Protein Binding Family
#1	CT406	300	hypothetical protein
#2	yebL	300	Solute-binding protein

Motif 1
AGGAGCTCCCCCTCCAAAAAAAGAACCTCG	0	119	0
AGGATACAAGCCTCCTGTAAGGAGCTCCCC	0	138	0
     AAGAGCCTCCAGATAATCGATACGG	0	285	0
TCTTGAGCGTCCTGCAGATATTAGGCGACT	1	145	1
TACGATAGGCCCTTCAGAAATGAAAGAAAG	1	238	0
  GGGAGATTCCTCCTAAAATTCAAATATT	1	282	0
AAACTACTACTCTCCAAACAACTCGGCTAT	2	10	1
TCGGCTATCGCCGGCAAAAAGACAGTAGAA	2	32	1
AATGGCTTGTCTTCCAAACAATTTCATTCT	2	225	0
          **********
MAP Score: 10.3411

Motif 2
AAATTATTTAGAATTGTCTCTTCGAGATGAGAAAC	0	20	1
TAACAGAATGAATTTATATCCTCAACCAAAAGGAA	0	65	0
GCGATAAGCGAGGTTCTTTTTTTGGAGGGGGAGCT	0	111	1
CCTTACAGGAGGCTTGTATCCTTTAAAATAGAGTT	0	146	1
CCTTTAAAATAGAGTTTTTCTTATGATCCCATGTG	0	165	1
AATATCGGTTGGTTTTTGTCCTTAGGGGATCGTAT	0	231	1
CTTCTTAGAAAGGTTTTCTCTACGGGCGGTCTCGG	1	54	0
TTCTAAGAAGAGGTTCTTTTCAACACAAGACACAG	1	79	1
ACAAGACACAGGATTTTATCCATTAAAATAAAAAC	1	103	1
GATTTGTGGTGATTTTTTTTCAAAAGTCGCCTAAT	1	164	0
AAAACTAAGAATATTCTTTCTACTGTCTTTTTGCC	2	44	0
TAGTTTTTTAAGATTTTATCTCCAGCTTTTTTCGT	2	72	1
CGTTTTCTAAAGCTTCTCTGCTCTGAACCCCATAT	2	146	1
TTTGTTCAATGGCTTGTCTTCCAAACAATTTCATT	2	227	0
          ** ** * *** * *
MAP Score: 9.92672

Motif 3
ATACCACGGTTTTTATTTTAATGGATAAAAT	1	115	0
AGAATATTCTTAGTTTTTTAAGATTTTATCT	2	62	1
TTTGTGGTGATTTTTTTTCAAAAGTCGCCTA	1	166	0
GGTTCGTTGTTAATATTTTAAGATAAT    	2	283	1
GGGGATCGTATACTTTTTCAAAGTATGTCCC	0	255	1
          TTAGTTGTTAAAATTATTTAG	0	0	1
GGGTGAGGAACAGTTTTTTAAAGAAAAAGCA	2	115	0
ATAAGAAAAACTCTATTTTAAAGGATACAAG	0	158	0
CGGAGTATAATTATTTTTTGATTATAAGTAA	1	26	0
ACTAAAAAATTTATATGTGAATGATTTAACG	2	182	1
AACAAGGATCTAATATTTGAATTTTAGGAGG	1	271	1
AAGCGAGGTTCTTTTTTTGGAGGGGGAGCTC	0	116	1
          ** ********
MAP Score: 7.66951

Motif 4
ATATCCTCAACCAAAAGGAAAATCTAGCGCGTTTC	0	50	0
AGCTCCCCCTCCAAAAAAAGAACCTCGCTTATCGC	0	111	0
CACATGGGATCATAAGAAAAACTCTATTTTAAAGG	0	165	0
GGTCTAGCGCCGATAGTAGAAATATCGGTTGGTTT	0	211	1
TATACGATCCCCTAAGGACAAAAACCAACCGATAT	0	232	0
CCGAGACCGCCCGTAGAGAAAACCTTTCTAAGAAG	1	54	1
GGATTTTATCCATTAAAATAAAAACCGTGGTATCT	1	113	1
TATTAGGCGACTTTTGAAAAAAAATCACCACAAAT	1	163	1
GGCAAAAAGACAGTAGAAAGAATATTCTTAGTTTT	2	44	1
CGCGATTTCCCTAAAGAATGAAATTGTTTGGAAGA	2	211	1
GGAAGACAAGCCATTGAACAAAATTACTCAACAAT	2	240	1
AATTACTCAACAATAGAATAATGGTTCGTTGTTAA	2	261	1
          *  ***** ***  *
MAP Score: 6.02005

Motif 5
TCTTCGAGATGAGAAACGCGCTAGATTTTC	0	38	1
AAGTATCTTTGCGATAAGCGAGGTTCTTTT	0	101	1
TATTTTAAAGGATACAAGCCTCCTGTAAGG	0	146	0
ATCCCATGTGGCGATAGGCCGGGTCTAGCG	0	190	1
CGATATTTCTACTATCGGCGCTAGACCCGG	0	208	0
     TCAAGGCAAACAGCGGTTACTTATA	1	5	1
ATTATACTCCGAGACCGCCCGTAGAGAAAA	1	46	1
CTTGTTTACTACGATAGGCCCTTCAGAAAT	1	247	0
CTTTTTGCCGGCGATAGCCGAGTTGTTTGG	2	23	0
AATTGTTTGGAAGACAAGCCATTGAACAAA	2	232	1
          **********
MAP Score: 5.38038

Motif 6
TTTTTTTGGAGGGGGAGCTCCTTACAGGAG	0	127	1
GAGCTCCTTACAGGAGGCTTGTATCCTTTA	0	141	1
TATCGATTATCTGGAGGCTCTT        	0	288	1
TTTTCTCTACGGGCGGTCTCGGAGTATAAT	1	46	0
AATAAAAACCGTGGTATCTTGAGCGTCCTG	1	129	1
CTAATATCTGCAGGACGCTCAAGATACCAC	1	139	0
GAGGTAGCTTGGGGGATCTAGTAACACAAT	1	209	0
ATGAAAGAAAGAGGTAGCTTGGGGGATCTA	1	219	0
TGAATTTTAGGAGGAATCTCCC        	1	288	1
          **********
MAP Score: 4.05981