AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons021_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238193
 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
CATACGAACAAAAAGGTTAACAGCAAAGTA	0	82	0
ATGCTAAGATAATAGGTTACCTTTCCTAGG	0	109	1
GTATACTGAGAAAAGTTGCACAAAGTGCTC	0	148	0
TAGGTCCTTGGGTAGTATACTGAGAAAAGT	0	162	0
      TTAGGATAGGTTAACTATCAAAAT	1	4	1
TCAGGTTTGCACAAGTTGACATTTTTCATT	1	31	0
ACCTTTTATTGCAAGTTTCCAAATCTATAG	1	106	0
AACTTGCAATAAAAGGTTCTGAGCAGTTCC	1	119	1
TCCCTCAAGTGCTAGTTGCTCAGAGAGATT	1	154	0
GATACTTCTAGATAGGTTATGTTATCTAGC	1	189	0
TAACCTATCTAGAAGTATCCTAAACCCTCA	1	200	1
TAATTGTGATGAAAGTATACTCGCTTTTTA	2	68	0
CACAATTATAGAAAGGTGATTT        	2	90	1
TACAGTTACCAAAAGGAGAAGAAAAGGACT	3	58	0
TCTTCTTACAAGAAGGATATACGTTCAATT	3	101	1
  ATGGCTTGAGAAGTTTCTGAAATAATTT	4	8	1
AGACAGATAGAGTAGTTTATTATCCTTAAG	4	54	0
          **********
MAP Score: 8.02391

Motif 2
         AAACTTCCAGAATTGTATATAA	0	1	1
CGATGAAACAAAGTATTGCAACTACAAAATA	0	53	1
ATAATAGGTTACCTTTCCTAGGACAATAGCC	0	117	1
ATACTGAGAAAAGTTGCACAAAGTGCTCGGC	0	145	0
CTACCCAAGGACCTAGTAAAACT        	0	177	1
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: 5.98443

Motif 3
ATACTTTGTTTCATCGTTCACATTACAGTTTCTAATT	0	32	0
ACAAAATACTTTGCTGTTAACCTTTTTGTTCGTATGC	0	76	1
TATGCTAAGATAATAGGTTACCTTTCCTAGGACAATA	0	108	1
ATAGCCGAGCACTTTGTGCAACTTTTCTCAGTATACT	0	142	1
TTTTTCATTTTGATAGTTAACCTATCCTAA       	1	3	0
CTCAGAGAGATTTTCGAGGAACTGCTCAGAACCTTTT	1	129	0
CTCGAAAATCTCTCTGAGCAACTAGCACTTGAGGGAT	1	148	1
GAGGGATATATGCTAGATAACATAACCTATCTAGAAG	1	178	1
TGGACAAATCTACTGGTGTACCTCTCCCCTCTCCTCC	1	254	1
CCACTAAAATTATTTCAGAAACTTCTCAAGCCAT   	4	7	0
          *  * * * ****  **
MAP Score: 4.58052

Motif 4
ATACTTTGCTGTTAACCTTTTTGTTCGTATG	0	81	1
TCCTAGGAAAGGTAACCTATTATCTTAGCAT	0	109	0
CATTTTGATAGTTAACCTATCCTAA      	1	4	0
AAAAAAGGAAGGCAATCTCTTAAAATTCACC	1	65	1
AGGAACTGCTCAGAACCTTTTATTGCAAGTT	1	119	0
GCAGTTCCTCGAAAATCTCTCTGAGCAACTA	1	141	1
TGCTAGATAACATAACCTATCTAGAAGTATC	1	188	1
AAATCTACTGGTGTACCTCTCCCCTCTCCTC	1	259	1
CCTCGAGACTGACAATCTCTGTCGAGCTAAA	2	36	1
          ** ********
MAP Score: 3.76938

Motif 5
AATTTTATATACAATTCTGGAAGTTT          	0	0	0
TTTGCTGTTAACCTTTTTGTTCGTATGCTAAGATAA	0	85	1
AGATAACATAACCTATCTAGAAGTATCCTAAACCCT	1	192	1
CTTCTAATGGACAAATCTACTGGTGTACCTCTCCCC	1	247	1
     AAATCACCTTTCTATAATTGTGATGAAAGTA	2	81	0
AGGATAATAAACTACTCTATCTGTCTGTGTTTAGGA	4	58	1
          ** * ****   ** *
MAP Score: 3.11901

Motif 6
CTTAAAATTCACCTCTGAACTCCCTATAGATTTG	1	83	1
TCTGAGCAGTTCCTCGAAAATCTCTCTGAGCAAC	1	136	1
TCTAGAAGTATCCTAAACCCTCACGAATTACGAA	1	207	1
CTACTGGTGTACCTCTCCCCTCTCCTCCTCATTC	1	263	1
TTAGCTTTACACCTCGAGACTGACAATCTCTGTC	2	25	1
   TAAAAACTCCTAAACACAGACAGATAGAGTA	4	70	0
          *****   **** *
MAP Score: 2.42716

Motif 7
TGTTAACCTTTTTGTTCGTATGCTAAGATAATAGGTTAC	0	90	1
TTGTGCAACTTTTCTCAGTATACTACCCAAGGACCTAGT	0	155	1
CATTTTTCATTTTGATAGTTAACCTATCCTAA       	1	3	0
AAATGAAAAATGTCAACTTGTGCAAACCTGACAAGAAAA	1	30	1
AGAGGTGAATTTTAAGAGATTGCCTTCCTTTTTTCTTGT	1	60	0
AGAACCTTTTATTGCAAGTTTCCAAATCTATAGGGAGTT	1	100	0
TTGAGGGATATATGCTAGATAACATAACCTATCTAGAAG	1	176	1
ACATAACCTATCTAGAAGTATCCTAAACCCTCACGAATT	1	197	1
TCGAACCTCCGATGCACGGTACCAAAAACCGCT      	3	4	0
AGGACTCTGGGGTGGAAGGATTCGAACCTCCGATGCACG	3	25	0
TTAGGGAAAGTATTGACTTTTTCCAAACTGGAGATATAA	3	137	1
CCAAACATATTTTCTTAGAGGGCCAATCACTGTCATGTC	3	208	0
CTATGCATTCACTCTGAGAGTCCAAACATATTTTCTTAG	3	229	0
ATCCTTAAGATATCTCAGTCCACTAAAATTATTTCAGAA	4	24	0
          * *   ***   * ** **
MAP Score: 1.61258

Motif 8
TTCGTATGCTAAGATAATAGGTTACCTTTCCTA	0	104	1
TACCTTTCCTAGGACAATAGCCGAGCACTTTGT	0	126	1
AGAAAAAAGGAAGGCAATCTCTTAAAATTCACC	1	63	1
CTAGCACTTGAGGGATATATGCTAGATAACATA	1	169	1
TTCTTACAAGAAGGATATACGTTCAATTCTTTA	3	103	1
AGTTTGGAAAAAGTCAATACTTTCCCTAATTAA	3	133	0
TTGGCCCTCTAAGAAAATATGTTTGGACTCTCA	3	221	1
AGATATCTTAAGGATAATAAACTACTCTATCTG	4	48	1
          **** ****  **
MAP Score: 1.50662

Motif 9
GCTAGTTGCTCAGAGAGATTTTCGAGGAAC	1	144	0
ATTTTAGCTCGACAGAGATTGTCAGTCTCG	2	39	0
TCCAAGACATGACAGTGATTGGCCCTCTAA	3	203	1
TTTGGACTCTCAGAGTGAATGCATAGCGCA	3	242	1
AATTTTAGTGGACTGAGATATCTTAAGGAT	4	33	1
CTCCTAAACACAGACAGATAGAGTAGTTTA	4	65	0
          **********
MAP Score: 0.847265

Motif 10
TATATACAATTCTGGAAGTTT          	0	0	0
TACTAGGTCCTTGGGTAGTATACTGAGAAAA	0	164	0
ACATAACCTATCTAGAAGTATCCTAAACCCT	1	197	1
AACTGTATTCTTTAGTTGTCTCTTCTTACAA	3	81	1
TAATTTTGCCTCGAAAACTGTCGATAGACGT	3	173	1
     ATGGCTTGAGAAGTTTCTGAAATAAT	4	5	1
CACAGACAGATAGAGTAGTTTATTATCCTTA	4	56	0
TCTGTCTGTGTTTAGGAGTTTTTA       	4	77	1
          ********* *
MAP Score: 0.495827