AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242614
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT053	300	hypothetical protein
#1	dnaJ	28	Heat Shock Protein J
#2	rs21	196	S21 Ribosomal Protein
#3	CT343	300	O-Sialoglycoprotein Endopeptidase family
#4	proS	200	Prolyl tRNA Synthetase
#5	hrcA	68	HTH Transcriptional Repressor
#6	dnaK	25	HSP-70
#7	CT708	300	SWF/SNF family helicase
#8	alaS	300	Alanyl tRNA Synthetase

Motif 1
TTTATTTTTCAAAAAAAGCAAACTTTGCTTT	0	34	1
CGATACTTAAAAAAAAAGCAAAGTTTGCTTT	0	48	0
TCTTTTGCTCAGACAGAGCAAAAAGTGAGCA	0	198	0
AGATTGATTTAGACAAAGGATTATAACCGTT	3	266	0
TTTAAGAAACAAACAAAAGAAACATCAAGTT	4	51	1
AGTTATTAAGAAATAAAGAATCTGAACTAGT	4	78	1
CACCCGCGAGAAGAAGAGCATTCTAGATAAT	7	53	1
TAAAACCTACAAGCAAAGGATTGCGAAAAAC	7	91	0
AAGAGGTGGTAAAAAAAGAAAAATTGGACTG	7	158	1
AAACAGCTTTAAAAAGGGGAAAAATAGAGGA	7	190	1
AAAAGGGGAAAAATAGAGGAAGAAGAGAGGG	7	201	1
CCCTCGTTCGAAAGAAAGCTACATCTTATGC	8	50	1
GGTGCATAAAAAATAGGGGATAGCATAAGAT	8	72	0
AAAAAGAAAAAAAGAGAGGAAAATTTTGTTT	8	186	0
AGGATGAGCAAAAAAAAGAAAAAAAGAGAGG	8	198	0
CAAAAAAATCGAAGAGAGGAAGGGTAGGATG	8	223	0
TGGAGCGCTAAAAAAAAGAATTTCGACAAAA	8	249	0
          *** *******
MAP Score: 21.9888

Motif 2
TTTTTGAAAAATAAAAATTTTGCTATGGGAAT	0	17	0
TTTTCAAAAAAAGCAAACTTTGCTTTTTTTTT	0	39	1
TATCAGTTGAACAAATACTTTGGAATGAGTAT	0	126	1
          AAAAAATCTTTGTTAGTGGTGT	1	0	1
AAACAAGTAAACAAAACTCTTGAAAAGTTGTT	2	29	0
GGCAACTAGTTCAAAATCCTTGGAAGAGCAAG	3	12	1
AAACATGTGCACACAACCCTTGCTCTTCCAAG	3	30	0
GCTGCAATTGATAAAAACCCTGCTATACTTTC	3	122	0
TTAAGCGTTTTTGCAAATTTTGTTTTTAAATC	4	13	0
GTTGCGAGCGCTAAAATTCTTGACCAGTGGAG	5	19	1
GGGGAGTTTTTCGCAATCCTTTGCTTGTAGGT	7	86	1
TAGGTTTTACAAAAAAACTTTGGAAAAAGGTT	7	113	1
TCACCTTCTCAAAAAACCTTTTTCCAAAGTTT	7	127	0
CGCTAAATCAATGAAAATTTTGACCCTCTCTT	7	223	0
TCAACTCCCCAAAAAACCCTTTTTCTTAACCT	8	112	1
AAAAAAAGAGAGGAAAATTTTGTTTTATAAAA	8	179	0
GATTTTTTTGTCGAAATTCTTTTTTTTAGCGC	8	244	1
          * **** *****
MAP Score: 18.145

Motif 3
TAGCAAAATTTTTATTTTTCAAAAAAAGCAAA	0	24	1
GCAAACTTTGCTTTTTTTTTAAGTATCGAATA	0	51	1
TCTCTCCTGATCTATTTGTTTATGCCTGCTCA	0	172	1
GTTTTGTTTACTTGTTTGGTAATTTTTATAAT	2	44	1
CGTAATTGGTTTTATTTAATAACGCGCGCCTA	2	160	0
TATAAATGAGCTTTTTTAGTAAAGTCGGTTTT	3	192	1
TTTTGCAAATTTTGTTTTTAAATCTCC     	4	5	0
GTTTCTTTTGTTTGTTTCTTAAAATTAATTTA	4	42	0
GTTCAGATTCTTTATTTCTTAATAACTTGATG	4	73	0
TTTTCCAAAGTTTTTTTGTAAAACCTACAAGC	7	108	0
CAGTCCAATTTTTCTTTTTTTACCACCTCTTC	7	157	0
TATGCTATCCCCTATTTTTTATGCACCTATTT	8	76	1
TTTTTATGCACCTATTTTTTATCAACTCCCCA	8	91	1
CCCAAAAAACCCTTTTTCTTAACCTCTCAATT	8	119	1
AGAGGAAAATTTTGTTTTATAAAAAGTGTTAA	8	171	0
CCTCTCTTTTTTTCTTTTTTTTGCTCATCCTA	8	198	1
TTGTCGAAATTCTTTTTTTTAGCGCTCCAAAC	8	251	1
          *** *** ****
MAP Score: 17.0634

Motif 4
AAGAGTTTTGTTTACTTGTTTGGTAATTTTT	2	40	1
TGATGTTTCTTTTGTTTGTTTCTTAAAATTA	4	47	0
AAAAGCAAACTTTGCTTTTTTTTTAAGTATC	0	47	1
GCAGTCCAATTTTTCTTTTTTTACCACCTCT	7	159	0
TCCTCTCTTTTTTTCTTTTTTTTGCTCATCC	8	197	1
AAAAGCAAAGTTTGCTTTTTTTGAAAAATAA	0	35	0
ATCTCTGTGATTTTTTTGTTCTTATTGGATT	4	112	0
TCTCTCCTGATCTATTTGTTTATGCCTGCTC	0	172	1
TGAGAGCCAATTTACTTGCTTCCTACCAAGG	0	238	0
AGCTTACATCTTGGCTTGTTCTAATT     	8	284	1
CTTCCTCTCTTCGATTTTTTTGTCGAAATTC	8	232	1
TTTTGTCGAAATTCTTTTTTTTAGCGCTCCA	8	249	1
CATAGCAAAATTTTTATTTTTCAAAAAAAGC	0	22	1
          *** *******
MAP Score: 13.2433

Motif 5
ACACAACCCTTGCTCTTCCAAGGATTTTGAA	3	21	0
TATGCTAAGATGCTCTTCCACACGAAACAAT	4	160	1
GGCAACGTGGCGCTCTACCACTGAGCTACAC	7	25	1
TTATCTAGAATGCTCTTCTTCTCGCGGGTGT	7	52	0
AATTTTGACCCTCTCTTCTTCCTCTATTTTT	7	209	0
          TTCTCCTCTAAAACATAGGGG	7	289	0
CTATCGCGCCCTCTCATCCACGTAAGAGGCC	8	10	1
TTCTTTTTTTTGCTCATCCTACCCTTCCTCT	8	209	1
          ***** *****
MAP Score: 9.12087

Motif 6
AAAAGCAAAGTTTGCTTTTTTTGAAAAATAAA	0	34	0
AAAAAGCAAACTTTGCTTTTTTTTTAAGTATC	0	46	1
TACCCTAGCCTCCTGACTTCTTACAAAAGCTA	0	81	1
CCAAAATCTCTCCTGATCTATTTGTTTATGCC	0	166	1
TGTTTATGCCTGCTCACTTTTTGCTCTGTCTG	0	188	1
        AGTGTTTTCCTTTTGGGACAACAA	2	2	1
TCAAGAGTTTTGTTTACTTGTTTGGTAATTTT	2	38	1
ATGTTTCTTTTGTTTGTTTCTTAAAATTAATT	4	44	0
TAGTTCAGATTCTTTATTTCTTAATAACTTGA	4	75	0
CTGTGATTTTTTTGTTCTTATTGGATTTTAAC	4	107	0
GCAGTCCAATTTTTCTTTTTTTACCACCTCTT	7	158	0
CTTCCTCTATTTTTCCCCTTTTTAAAGCTGTT	7	191	0
AAAATTTTGACCCTCTCTTCTTCCTCTATTTT	7	210	0
AGACCTGTTACTTGTACCTTTTTACTTCCGCT	7	251	0
CCCTATTTTTTATGCACCTATTTTTTATCAAC	8	85	1
TAAAACAAAATTTTCCTCTCTTTTTTTCTTTT	8	184	1
TCCTCTCTTTTTTTCTTTTTTTTGCTCATCCT	8	197	1
CTCATCCTACCCTTCCTCTCTTCGATTTTTTT	8	221	1
CAAGCTTACATCTTGGCTTGTTCTAATT    	8	282	1
          ***** *** **
MAP Score: 8.23117

Motif 7
TTGAAAAATAAAAATTTTGCTATGGGAATTTTCTAA     	0	5	0
CAGTTGAACAAATACTTTGGAATGAGTATTTTATTAGCCAA	0	129	1
       AAAAAATCTTTGTTAGTGGTGTTTCGTC      	1	3	1
CAACTTTTCAAGAGTTTTGTTTACTTGTTTGGTAATTTTTA	2	31	1
ATTAATTTAAGCGTTTTTGCAAATTTTGTTTTTAAATCTCC	4	10	0
ATCTAGAAACACTCCTATGCTAAGATGCTCTTCCACACGAA	4	145	1
AGTTTTTCGCAATCCTTTGCTTGTAGGTTTTACAAAAAAAC	7	90	1
GTTTTACAAAAAAACTTTGGAAAAAGGTTTTTTGAGAAGGT	7	116	1
TAAATCAATGAAAATTTTGACCCTCTCTTCTTCCTCTATTT	7	211	0
TTTATAAAACAAAATTTTCCTCTCTTTTTTTCTTTTTTTTG	8	180	1
CCTCTCTTCGATTTTTTTGTCGAAATTCTTTTTTTTAGCGC	8	235	1
          *   *****      *  ***
MAP Score: 6.50019

Motif 8
CACAACCCTTGCTCTTCCAAGGATTTTGAAC	3	20	0
ACAATATAAAGCACTTCCTTCCCT       	4	186	1
AAGAATTTTAGCGCTCGCAACTAAAGAGTG 	5	9	0
AAGAAAAATTGGACTGCAAACAGCTTTAAAA	7	173	1
ACAAGTAACAGGTCTGTCAACCCCCTATGTT	7	268	1
   CTATCGCGCCCTCTCATCCACGTAAGAG	8	7	1
CCACGTAAGAGGCCTTCCTTCAACCCTCGTT	8	27	1
TCTTTTTTTTGCTCATCCTACCCTTCCTCTC	8	210	1
CTTTTTTTTAGCGCTCCAAACAAGCTTACAT	8	262	1
          ** ********
MAP Score: 2.24777