AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242603
 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	proS	200	Prolyl tRNA Synthetase
#4	hrcA	68	HTH Transcriptional Repressor
#5	dnaK	25	HSP-70
#6	CT708	300	SWF/SNF family helicase
#7	alaS	300	Alanyl tRNA Synthetase

Motif 1
AAAGCAAAGTTTGCTTTTTTTGAAAAATAAA	0	34	0
AAAGCAAACTTTGCTTTTTTTTTAAGTATCG	0	48	1
TGCTCACTTTTTGCTCTGTCTGAGCAAAAGA	0	198	1
TTTCAAGAGTTTTGTTTACTTGTTTGGTAAT	2	36	1
TGATGTTTCTTTTGTTTGTTTCTTAAAATTA	3	47	0
ACTAGTTCAGATTCTTTATTTCTTAATAACT	3	78	0
ATTATCTAGAATGCTCTTCTTCTCGCGGGTG	6	53	0
GTTTTTCGCAATCCTTTGCTTGTAGGTTTTA	6	91	1
CAGTCCAATTTTTCTTTTTTTACCACCTCTT	6	158	0
TCCTCTATTTTTCCCCTTTTTAAAGCTGTTT	6	190	0
CCCTCTCTTCTTCCTCTATTTTTCCCCTTTT	6	201	0
GCATAAGATGTAGCTTTCTTTCGAACGAGGG	7	50	0
ATCTTATGCTATCCCCTATTTTTTATGCACC	7	72	1
AAACAAAATTTTCCTCTCTTTTTTTCTTTTT	7	186	1
CCTCTCTTTTTTTCTTTTTTTTGCTCATCCT	7	198	1
CATCCTACCCTTCCTCTCTTCGATTTTTTTG	7	223	1
TTTTGTCGAAATTCTTTTTTTTAGCGCTCCA	7	249	1
          ******* ***
MAP Score: 22.5911

Motif 2
ATTCCCATAGCAAAATTTTTATTTTTCAAAAAA	0	17	1
AAAAAAAAAGCAAAGTTTGCTTTTTTTGAAAAA	0	38	0
ATACTCATTCCAAAGTATTTGTTCAACTGATAA	0	125	0
         AAAAAATCTTTGTTAGTGGTGTTT	1	1	1
AACAACTTTTCAAGAGTTTTGTTTACTTGTTTG	2	29	1
AGCGTTTTTGCAAATTTTGTTTTTAAATCTCC 	3	9	0
TTAACTAGTTCAGATTCTTTATTTCTTAATAAC	3	79	0
AAACCTTTTTCCAAAGTTTTTTTGTAAAACCTA	6	113	0
AAAACTTTGGAAAAAGGTTTTTTGAGAAGGTGA	6	126	1
TGTTTGCAGTCCAATTTTTCTTTTTTTACCACC	6	162	0
AAGAGAGGGTCAAAATTTTCATTGATTTAGCGG	6	223	1
GAGGTTAAGAAAAAGGGTTTTTTGGGGAGTTGA	7	112	0
AAAAGAGAGGAAAATTTTGTTTTATAAAAAGTG	7	175	0
TTTTTTTGTCGAAATTCTTTTTTTTAGCGCTCC	7	246	1
          **** * *** **
MAP Score: 18.0376

Motif 3
TTTGCTTTTTTTGAAAAATAAAAATTTTGCTA	0	24	0
TATTCGATACTTAAAAAAAAAGCAAAGTTTGC	0	51	0
TGAGCAGGCATAAACAAATAGATCAGGAGAGA	0	172	0
ATTATAAAAATTACCAAACAAGTAAACAAAAC	2	44	0
TAGGCGCGCGTTATTAAATAAAACCAATTACG	2	160	1
     GGAGATTTAAAAACAAAATTTGCAAAA	3	5	1
TAAATTAATTTTAAGAAACAAACAAAAGAAAC	3	42	1
CATCAAGTTATTAAGAAATAAAGAATCTGAAC	3	73	1
GCTTGTAGGTTTTACAAAAAAACTTTGGAAAA	6	108	1
GAAGAGGTGGTAAAAAAAGAAAAATTGGACTG	6	157	1
TGCAAACAGCTTTAAAAAGGGGAAAAATAGAG	6	187	1
AAATAGGTGCATAAAAAATAGGGGATAGCATA	7	76	0
TGGGGAGTTGATAAAAAATAGGTGCATAAAAA	7	91	0
AATTGAGAGGTTAAGAAAAAGGGTTTTTTGGG	7	119	0
TTAACACTTTTTATAAAACAAAATTTTCCTCT	7	171	1
ATGAGCAAAAAAAAGAAAAAAAGAGAGGAAAA	7	194	0
TTTGGAGCGCTAAAAAAAAGAATTTCGACAAA	7	250	0
          **** *** ***
MAP Score: 16.9449

Motif 4
TGCTCTGTCTGAGCAAAAGATGCAGTTACC	0	209	1
GTTTCAATCATAGAACAGGACTATTTACGA	0	280	1
  GGAGATTTAAAAACAAAATTTGCAAAAA	3	8	1
TTTAAGAAACAAACAAAAGAAACATCAAGT	3	51	1
AAAATCCAATAAGAACAAAAAAATCACAGA	3	110	1
CTACACCCGCGAGAAGAAGAGCATTCTAGA	6	50	1
GAAGAGGTGGTAAAAAAAGAAAAATTGGAC	6	157	1
AAACAGCTTTAAAAAGGGGAAAAATAGAGG	6	190	1
ACACTTTTTATAAAACAAAATTTTCCTCTC	7	174	1
AAAAAAAAGAAAAAAAGAGAGGAAAATTTT	7	190	0
TAGGATGAGCAAAAAAAAGAAAAAAAGAGA	7	200	0
TTGGAGCGCTAAAAAAAAGAATTTCGACAA	7	251	0
          **********
MAP Score: 4.17498