AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons021_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238178
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ybbP	190	YbbP family hypothetical protein
#1	dnaB	300	Replicative DNA Helicase
#2	ung	102	Uracil DNA Glycosylase
#3	ctc	300	General Stress Protein
#4	rs6	91	S6 Ribosomal Protein

Motif 1
         AAACTTCCAGAATTGTATATAA	0	1	1
CGATGAAACAAAGTATTGCAACTACAAAATA	0	53	1
ATACTGAGAAAAGTTGCACAAAGTGCTCGGC	0	145	0
TTGATAGTTAACCTATCCTAA          	1	0	0
AGGATAGGTTAACTATCAAAATGAAAAATGT	1	12	1
GAAAAATGTCAACTTGTGCAAACCTGACAAG	1	34	1
CTTTTATTGCAAGTTTCCAAATCTATAGGGA	1	103	0
ACCTATCTAGAAGTATCCTAAACCCTCACGA	1	202	1
ATTAGAAGCGAACTTTCGTAATTCGTGAGGG	1	224	0
CCTCATTCGAAAGAATCGGAA          	1	289	1
ATGGCTTGAGAAGTTTCTGAAATAATTTTAG	4	10	1
          ******** **
MAP Score: 6.48403

Motif 2
GCATACGAACAAAAAGGTTAACAGCAAAGT	0	83	0
TATGCTAAGATAATAGGTTACCTTTCCTAG	0	108	1
AGTATACTGAGAAAAGTTGCACAAAGTGCT	0	149	0
CTAGGTCCTTGGGTAGTATACTGAGAAAAG	0	163	0
       TTAGGATAGGTTAACTATCAAAA	1	3	1
AAACTTGCAATAAAAGGTTCTGAGCAGTTC	1	118	1
GGATACTTCTAGATAGGTTATGTTATCTAG	1	190	0
ATAATTGTGATGAAAGTATACTCGCTTTTT	2	69	0
TCACAATTATAGAAAGGTGATTT       	2	89	1
GACTCTGGGGTGGAAGGATTCGAACCTCCG	3	32	0
CTCTTCTTACAAGAAGGATATACGTTCAAT	3	100	1
CTTTAATTAGGGAAAGTATTGACTTTTTCC	3	131	1
   ATGGCTTGAGAAGTTTCTGAAATAATT	4	7	1
CAGACAGATAGAGTAGTTTATTATCCTTAA	4	55	0
          **********
MAP Score: 4.25387

Motif 3
ATACTTTGTTTCATCGTTCACATTACAGTTTCTAAT	0	33	0
TATGCTAAGATAATAGGTTACCTTTCCTAGGACAAT	0	108	1
TTTTTCATTTTGATAGTTAACCTATCCTAA      	1	4	0
TCTGAGCAGTTCCTCGAAAATCTCTCTGAGCAACTA	1	136	1
GAGGGATATATGCTAGATAACATAACCTATCTAGAA	1	178	1
TGGACAAATCTACTGGTGTACCTCTCCCCTCTCCTC	1	254	1
          * ** *   **** **
MAP Score: 4.11329

Motif 4
ACAATAGCCGAGCACTTTGTGCAACTTTTCT	0	139	1
 AGTTTTACTAGGTCCTTGGGTAGTATACTG	0	170	0
TTCCTCGAAAATCTCTCTGAGCAACTAGCAC	1	145	1
GGAGAAGAAAAGGACTCTGGGGTGGAAGGAT	3	43	0
AGTCCTTTTCTTCTCCTTTTGGTAACTGTAT	3	58	1
GCGCTATGCATTCACTCTGAGAGTCCAAACA	3	240	0
CATAGCGCACAGCTCTTTTAGCTCAAGATTA	3	263	1
AAACTACTCTATCTGTCTGTGTTTAGGAGTT	4	66	1
          ********* *
MAP Score: 3.35902

Motif 5
TGTTCGTATGCTAAGATAATAGGTTACCTTT	0	102	1
GGGTAGTATACTGAGAAAAGTTGCACAAAGT	0	152	0
CTCTGTCGAGCTAAAATAAAAAGCGAGTATA	2	52	1
GATTGGCCCTCTAAGAAAATATGTTTGGACT	3	219	1
CTCAAGATTACGGAGAAAACAACATT     	3	284	1
TGAGAAGTTTCTGAAATAATTTTAGTGGACT	4	16	1
TTTTAGTGGACTGAGATATCTTAAGGATAAT	4	35	1
          ********* *
MAP Score: 3.00058

Motif 6
CACATTACAGTTTCTAATTTTATATACAATT	0	20	0
TATTGCAAGTTTCCAAATCTATAGGGAGTTC	1	99	0
AATTACGAAAGTTCGCTTCTAATGGACAAAT	1	232	1
          TTCCGATTCTTTCGAATGAGG	1	289	0
     AATAAGTCCTAATTTTTAGCTTTACA	2	5	1
TGCATCGGAGGTTCGAATCCTTCCACCCCAG	3	27	1
CCACCCCAGAGTCCTTTTCTTCTCCTTTTGG	3	49	1
AAGGATATACGTTCAATTCTTTAATTAGGGA	3	113	1
          **** ******
MAP Score: 1.43376

Motif 7
AGGAAAGGTAACCTATTATCTTAGCATACG	0	106	0
CAAAGTGCTCGGCTATTGTCCTAGGAAAGG	0	128	0
GTGAATTTTAAGAGATTGCCTTCCTTTTTT	1	65	0
AGTTGCTCAGAGAGATTTTCGAGGAACTGC	1	141	0
TTAGCTCGACAGAGATTGTCAGTCTCGAGG	2	36	0
AAGACATGACAGTGATTGGCCCTCTAAGAA	3	206	1
GAGAGTCCAAACATATTTTCTTAGAGGGCC	3	223	0
          **********
MAP Score: 0.371651

Motif 8
GTTCGTATGCTAAGATAATAGGTTACCTTTCCTA	0	103	1
TTACCTTTCCTAGGACAATAGCCGAGCACTTTGT	0	125	1
AAGAAAAAAGGAAGGCAATCTCTTAAAATTCACC	1	62	1
ACTAGCACTTGAGGGATATATGCTAGATAACATA	1	168	1
GCTAAAATAAAAAGCGAGTATACTTTCATCACAA	2	61	1
CTTCTTACAAGAAGGATATACGTTCAATTCTTTA	3	102	1
CAGTTTGGAAAAAGTCAATACTTTCCCTAATTAA	3	133	0
ATTGGCCCTCTAAGAAAATATGTTTGGACTCTCA	3	220	1
GAGATATCTTAAGGATAATAAACTACTCTATCTG	4	47	1
          ****  ****  **
MAP Score: 0.348074