AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238146
 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
AACTATCCTGAACAAAGATATTTCTTTCATTTC	0	174	1
TTTCTTATAAAACAAACGGGTTTTCTAATTTTT	0	137	1
TCAAGGGTAGAGGAAATACTTCTCTAAAGAAAC	1	134	0
CGGTGATCTTAGGAAAAAATTCTCATAGTAAGA	3	201	0
AATGGATCTTAAAAAATGCTTCTAGAGAG    	0	281	1
TACTTCTCTAAAGAAACGGCTTTAGGGATTCGT	1	118	0
TTGATTTCCTAGAAAAAAACTTTGCAACTATAG	1	163	1
TTTGTTAAGAAACAAAAAGATCCTGAGAGGAAA	0	51	0
CACCCCATTTAACAACAGAATCTTTACAACAAA	1	12	1
GAATCTTTACAACAAAAGCTTTCCTAGAGTAGA	1	29	1
AAAGTACCAGAAAAACAAGTTCTATTCAAAATA	0	237	0
CGTCTCAATAAGCAAAGCAATTTTGCACAGAAA	1	74	1
GTAGTCTAAGAAAAACCGAATTTTTAGATCAGG	1	210	0
AAAATGTTATAGAAAAAATCTTCTTTACTTTAC	0	102	0
TTTATCCAGCAAGAAATACAACTAATAGAAATG	0	201	0
AGATCCTGAGAGGAAAAATATTGCAAAAAGGAG	0	34	0
TTCTTGCTGGATAAAATATATTTTGAATAGAAC	0	219	1
TATTGAGACGAAAAAAACATACTCTACTCTAGG	1	51	0
AATTTTAATAAAGAACGAATATCCTAAGAAGCG	3	232	0
TTGTTTTATAAGAAAACAAAATGTTATAGAAAA	0	119	0
          ****** *  ***
MAP Score: 15.5034

Motif 2
TTGCAAAGTTTTTTTCTAGGAAATCAAGGGT	1	159	0
TATGAGAATTTTTTCCTAAGATCACCGCTTC	3	207	1
AAAAATTCGGTTTTTCTTAGACTACCTTAAC	1	218	1
ATGTTTTGAATTTTGTTAAGAAACAAAAAGA	0	64	0
     TTGAATTTTATAAGGAGCAAGGTT  	2	5	1
CGGCAAGTCTTTTTGCCTGGAAAATCTATAA	3	132	0
CCCTAAAGCCGTTTCTTTAGAGAAGTATTTC	1	124	1
AAACCCGTTTGTTTTATAAGAAAACAAAATG	0	129	0
GACAAAAGCAGTTTGATAAGATGATCTATTA	3	279	0
TAAGATCACCGCTTCTTAGGATATTCGTTCT	3	223	1
AGCAAAGCAATTTTGCACAGAAATTTAAGAT	1	84	1
CTTTAAGTGGTTTTTAATGGATCTTAAAAAA	0	266	1
ATAAAATATATTTTGAATAGAACTTGTTTTT	0	229	1
TACAACAAAAGCTTTCCTAGAGTAGAGTATG	1	36	1
TCAACATCCGTCTTACTATGAGAATTTTTTC	3	191	1
GGTTTTCTAATTTTTTTAAAACTATCCTGAA	0	155	1
TAAAGAAGATTTTTTCTATAACATTTTGTTT	0	108	1
CTCTAGAAGCATTTTTTAAGATCCATTAAAA	0	277	0
          **** ******
MAP Score: 14.9167

Motif 3
GGATCTTTTTGTTTCTTAACAAAATTCAAAACAT	0	61	1
ATAGAAAAAATCTTCTTTACTTTACGATTTTTAT	0	93	0
GTAAAGAAGATTTTTTCTATAACATTTTGTTTTC	0	107	1
ATAACATTTTGTTTTCTTATAAAACAAACGGGTT	0	125	1
GGTTTTCTAATTTTTTTAAAACTATCCTGAACAA	0	155	1
TTTAACAACAGAATCTTTACAACAAAAGCTTTCC	1	19	1
TACAACAAAAGCTTTCCTAGAGTAGAGTATGTTT	1	36	1
CCCTAAAGCCGTTTCTTTAGAGAAGTATTTCCTC	1	124	1
CTCTACCCTTGATTTCCTAGAAAAAAACTTTGCA	1	155	1
AAGAAAAACCGAATTTTTAGATCAGGATAAATAT	1	202	0
AAAAATTCGGTTTTTCTTAGACTACCTTAACCTA	1	218	1
     AACCTTGCTCCTTATAAAATTCAA     	2	5	0
TATGAGAATTTTTTCCTAAGATCACCGCTTCTTA	3	207	1
          * ******* *  *
MAP Score: 11.4895

Motif 4
ACATAAATTATATTGCAAGTTCTCCTTTTTGCAATATTTTTC	0	13	1
ATATTTTTCCTCTCAGGATCTTTTTGTTTCTTAACAAAATTC	0	46	1
ATAAAAATCGTAAAGTAAAGAAGATTTTTTCTATAACATTTT	0	93	1
TTTTGTTTTCTTATAAAACAAACGGGTTTTCTAATTTTTTTA	0	131	1
TTTTTAAAACTATCCTGAACAAAGATATTTCTTTCATTTCTA	0	167	1
TAAAATATATTTTGAATAGAACTTGTTTTTCTGGTACTTTAA	0	230	1
AACAACAGAATCTTTACAACAAAAGCTTTCCTAGAGTAGAGT	1	22	1
TTTTTTCGTCTCAATAAGCAAAGCAATTTTGCACAGAAATTT	1	68	1
CCTAAAGCCGTTTCTTTAGAGAAGTATTTCCTCTACCCTTGA	1	125	1
TATAAGAGACTATAGTTGCAAAGTTTTTTTCTAGGAAATCAA	1	163	0
ATATTTATCCTGATCTAAAAATTCGGTTTTTCTTAGACTACC	1	202	1
CTCGGACATCTCTCCATATTTATAGATTTTCCAGGCAAAAAG	3	113	1
GGTTAAGATATGTTCTCGGCAAGTCTTTTTGCCTGGAAAATC	3	137	0
TCAACATCCGTCTTACTATGAGAATTTTTTCCTAAGATCACC	3	191	1
GGGGCATAATTTTAATAAAGAACGAATATCCTAAGAAGCGGT	3	230	0
AAAAGCAGTTTGATAAGATGATCTATTATTCTATTGGGGCAT	3	265	0
          * *    *  *     ******
MAP Score: 10.3625

Motif 5
CGTAAAGTAAAGAAGATTTTTTCTATAACATTTTG	0	101	1
CTTATAAAACAAACGGGTTTTCTAATTTTTTTAAA	0	140	1
ACTATCCTGAACAAAGATATTTCTTTCATTTCTAT	0	175	1
    CTCTCTAGAAGCATTTTTTAAGATCCATTAA	0	279	0
CCATTTAACAACAGAATCTTTACAACAAAAGCTTT	1	16	1
AATCTTTACAACAAAAGCTTTCCTAGAGTAGAGTA	1	30	1
ATTTCTGTGCAAAATTGCTTTGCTTATTGAGACGA	1	73	0
CCGTTTCTTTAGAGAAGTATTTCCTCTACCCTTGA	1	132	1
GATTTCCTAGAAAAAAACTTTGCAACTATAGTCTC	1	165	1
     TACAATTAAAGATTTTATGAAATTGAGGAT	3	5	1
GCGTTAACGCACACACGCTTTCCAAGCGTGCTCCT	3	71	1
TTTTCCAGGCAAAAAGACTTGCCGAGAACATATCT	3	139	1
CGTCTTACTATGAGAATTTTTTCCTAAGATCACCG	3	199	1
          * ***  **** * *
MAP Score: 3.03668

Motif 6
ATTTTTCCTCTCAGGATCTTTTTGTTTCTTAACAAAATTC	0	48	1
ATAAAAATCGTAAAGTAAAGAAGATTTTTTCTATAACATT	0	93	1
GAAGATTTTTTCTATAACATTTTGTTTTCTTATAAAACAA	0	112	1
TTAAAACTATCCTGAACAAAGATATTTCTTTCATTTCTAT	0	170	1
TTTCTTTCATTTCTATTAGTTGTATTTCTTGCTGGATAAA	0	194	1
AAATATATTTTGAATAGAACTTGTTTTTCTGGTACTTTAA	0	232	1
CCCACCCCATTTAACAACAGAATCTTTACAACAAAAGCTT	1	10	1
CAACAGAATCTTTACAACAAAAGCTTTCCTAGAGTAGAGT	1	24	1
AAAGCTTTCCTAGAGTAGAGTATGTTTTTTTCGTCTCAAT	1	43	1
TAAAGCCGTTTCTTTAGAGAAGTATTTCCTCTACCCTTGA	1	127	1
GAGAAGTATTTCCTCTACCCTTGATTTCCTAGAAAAAAAC	1	143	1
TTTATCCTGATCTAAAAATTCGGTTTTTCTTAGACTACCT	1	205	1
CGGTACGCGTTAACGCACACACGCTTTCCAAGCGTGCTCC	3	65	1
GGTTAAGATATGTTCTCGGCAAGTCTTTTTGCCTGGAAAA	3	139	0
ACATCCGTCTTACTATGAGAATTTTTTCCTAAGATCACCG	3	194	1
          *    * *    * ******
MAP Score: 2.98232

Motif 7
TGTTTTGAATTTTGTTAAGAAACAAAAAGAT	0	63	0
AAATCGTAAAGTAAAGAAGATTTTTTCTATA	0	97	1
AACATTTTGTTTTCTTATAAAACAAACGGGT	0	127	1
TCAGGATAGTTTTAAAAAAATTAGAAAACCC	0	154	0
TCTAGAAGCATTTTTTAAGATCCATTAAAAA	0	276	0
GAAAGCTTTTGTTGTAAAGATTCTGTTGTTA	1	21	0
TGCACAGAAATTTAAGATAATACGAATCCCT	1	97	1
GTTAAGGTAGTCTAAGAAAAACCGAATTTTT	1	218	0
     TTGAATTTTATAAGGAGCAAGGTT  	2	5	1
GTATCCTCAATTTCATAAAATCTTTAATTGT	3	11	0
TAAGACGGATGTTGATAAAAATGGAAAGGTT	3	175	0
ATATTCGTTCTTTATTAAAATTATGCCCCAA	3	243	1
ACAAAAGCAGTTTGATAAGATGATCTATTAT	3	278	0
          *** *******
MAP Score: 2.77681