AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238160
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ytgA	300	Solute Protein Binding Family
#1	CPn0533	255	CT406 hypothetical protein
#2	dksA	24	DnaK Suppressor
#3	CPn0541	300	Solute binding protein

Motif 1
ACAAAAGCAGTTTGATAAGATGATCTATTA	3	279	0
AACCCGTTTGTTTTATAAGAAAACAAAATG	0	129	0
TGTTTTGAATTTTGTTAAGAAACAAAAAGA	0	64	0
TCTAGAAGCATTTTTTAAGATCCATTAAAA	0	277	0
ATGAGAATTTTTTCCTAAGATCACCGCTTC	3	208	1
AAAATTCGGTTTTTCTTAGACTACCTTAAC	1	219	1
CCTAAAGCCGTTTCTTTAGAGAAGTATTTC	1	125	1
     TTGAATTTTATAAGGAGCAAGGTT 	2	5	1
TGCAAAGTTTTTTTCTAGGAAATCAAGGGT	1	159	0
TAAAATATATTTTGAATAGAACTTGTTTTT	0	230	1
GCAAAGCAATTTTGCACAGAAATTTAAGAT	1	85	1
GTTTTCTAATTTTTTTAAAACTATCCTGAA	0	156	1
GTATCCTCAATTTCATAAAATCTTTAATTG	3	12	0
AAGAAATATCTTTGTTCAGGATAGTTTTAA	0	170	0
TTTAAGTGGTTTTTAATGGATCTTAAAAAA	0	267	1
TGGGGCATAATTTTAATAAAGAACGAATAT	3	243	0
AAAGAACGAATATCCTAAGAAGCGGTGATC	3	226	0
          **********
MAP Score: 15.995

Motif 2
TTGCAAGTTCTCCTTTTTGCAATATTTTTCCTCTCAGGATCT	0	25	1
ATAAAAATCGTAAAGTAAAGAAGATTTTTTCTATAACATTTT	0	93	1
TTTTGTTTTCTTATAAAACAAACGGGTTTTCTAATTTTTTTA	0	131	1
GAAAAACAAGTTCTATTCAAAATATATTTTATCCAGCAAGAA	0	219	0
AACAACAGAATCTTTACAACAAAAGCTTTCCTAGAGTAGAGT	1	22	1
TATCTTAAATTTCTGTGCAAAATTGCTTTGCTTATTGAGACG	1	74	0
CCTAAAGCCGTTTCTTTAGAGAAGTATTTCCTCTACCCTTGA	1	125	1
TATAAGAGACTATAGTTGCAAAGTTTTTTTCTAGGAAATCAA	1	163	0
CTCCGTATCCTCAATTTCATAAAATCTTTAATTGTA      	3	4	0
TTGATAAAAATGGAAAGGTTAAGATATGTTCTCGGCAAGTCT	3	153	0
CAACATCCGTCTTACTATGAGAATTTTTTCCTAAGATCACCG	3	192	1
AATAATAGATCATCTTATCAAACTGCTTTTGTC         	3	277	1
          *    *    **  * *** **
MAP Score: 14.1055

Motif 3
ACATAAATTATATTGCAAGTTCTCCTTTTTGCAATATTTT	0	13	1
GCAATATTTTTCCTCTCAGGATCTTTTTGTTTCTTAACAA	0	43	1
ACTTTACGATTTTTATGTTTTGAATTTTGTTAAGAAACAA	0	69	0
GTAAAGAAGATTTTTTCTATAACATTTTGTTTTCTTATAA	0	107	1
TTTCTTTCATTTCTATTAGTTGTATTTCTTGCTGGATAAA	0	194	1
GGATAAAATATATTTTGAATAGAACTTGTTTTTCTGGTAC	0	227	1
GTTTTTCTGGTACTTTAAGTGGTTTTTAATGGATCTTAAA	0	254	1
AAACATACTCTACTCTAGGAAAGCTTTTGTTGTAAAGATT	1	30	0
TAAAGCCGTTTCTTTAGAGAAGTATTTCCTCTACCCTTGA	1	127	1
AAAATTCGGTTTTTCTTAGACTACCTTAACCTAGGAGGTA	1	219	1
GGTTAAGATATGTTCTCGGCAAGTCTTTTTGCCTGGAAAA	3	139	0
ACATCCGTCTTACTATGAGAATTTTTTCCTAAGATCACCG	3	194	1
TAATAGATCATCTTATCAAACTGCTTTTGTC         	3	279	1
          * ** * **     ***  *
MAP Score: 11.8426

Motif 4
AAAAAGGAGAACTTGCAATATAATTTATGTTCG        	0	2	0
TTTGCAATATTTTTCCTCTCAGGATCTTTTTGTTTCTTAAC	0	40	1
ACTTTACGATTTTTATGTTTTGAATTTTGTTAAGAAACAAA	0	68	0
TAAAGAAGATTTTTTCTATAACATTTTGTTTTCTTATAAAA	0	108	1
CAAAGATATTTCTTTCATTTCTATTAGTTGTATTTCTTGCT	0	186	1
GATAAAATATATTTTGAATAGAACTTGTTTTTCTGGTACTT	0	228	1
AACTTGTTTTTCTGGTACTTTAAGTGGTTTTTAATGGATCT	0	249	1
CTAGGAAAGCTTTTGTTGTAAAGATTCTGTTGTTAAATGGG	1	15	0
TTAGAGAAGTATTTCCTCTACCCTTGATTTCCTAGAAAAAA	1	140	1
AACTATAGTCTCTTATATTTATCCTGATCTAAAAATTCGGT	1	188	1
CGAGAACATATCTTAACCTTTCCATTTTTATCAACATCCGT	3	161	1
TCAACATCCGTCTTACTATGAGAATTTTTTCCTAAGATCAC	3	191	1
GATCACCGCTTCTTAGGATATTCGTTCTTTATTAAAATTAT	3	226	1
GAATAATAGATCATCTTATCAAACTGCTTTTGTC       	3	276	1
          ****    *     *  ****
MAP Score: 6.97265

Motif 5
TGCAATATTTTTCCTCTCAGGATCTTTTTGTTTCTTAA	0	42	1
AAACAAAATGTTATAGAAAAAATCTTCTTTACTTTACG	0	101	0
AAAGAAATATCTTTGTTCAGGATAGTTTTAAAAAAATT	0	163	0
TCTTTCATTTCTATTAGTTGTATTTCTTGCTGGATAAA	0	196	1
GTATTTCTTGCTGGATAAAATATATTTTGAATAGAACT	0	215	1
         CTCTCTAGAAGCATTTTTTAAGATCCATT	0	281	0
CCCACCCCATTTAACAACAGAATCTTTACAACAAAAGC	1	10	1
AAAGCTTTCCTAGAGTAGAGTATGTTTTTTTCGTCTCA	1	43	1
TATCTTAAATTTCTGTGCAAAATTGCTTTGCTTATTGA	1	78	0
AAGCCGTTTCTTTAGAGAAGTATTTCCTCTACCCTTGA	1	129	1
GCAAAAAGACTTGCCGAGAACATATCTTAACCTTTCCA	3	147	1
AACATCCGTCTTACTATGAGAATTTTTTCCTAAGATCA	3	193	1
          **      ** ** ****
MAP Score: 6.88924

Motif 6
TTTTGCAATATTTTTCCTCTCAGGATCTTTTTGTT	0	39	1
AGGATCTTTTTGTTTCTTAACAAAATTCAAAACAT	0	60	1
GTAAAGAAGATTTTTTCTATAACATTTTGTTTTCT	0	107	1
TATAACATTTTGTTTTCTTATAAAACAAACGGGTT	0	124	1
GGGTTTTCTAATTTTTTTAAAACTATCCTGAACAA	0	154	1
CAAAATATATTTTATCCAGCAAGAAATACAACTAA	0	209	0
AATAGAACTTGTTTTTCTGGTACTTTAAGTGGTTT	0	244	1
AGAGTATGTTTTTTTCGTCTCAATAAGCAAAGCAA	1	59	1
TTTAGAGAAGTATTTCCTCTACCCTTGATTTCCTA	1	139	1
CTCTACCCTTGATTTCCTAGAAAAAAACTTTGCAA	1	155	1
GTCTCTTATATTTATCCTGATCTAAAAATTCGGTT	1	195	1
TAAAAATTCGGTTTTTCTTAGACTACCTTAACCTA	1	217	1
ATATTTATAGATTTTCCAGGCAAAAAGACTTGCCG	3	128	1
CTATGAGAATTTTTTCCTAAGATCACCGCTTCTTA	3	206	1
          ********   *  *
MAP Score: 5.68784