AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons025_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238274
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcp_1	135	O-Sialoglycoprotein Endopeptidase
#1	rs21	178	S21 Ribosomal Protein
#2	dnaJ	35	Heat Shock Protein J
#3	proS	299	Prolyl tRNA Synthetase
#4	hrcA	91	HTH Transcriptional Repressor
#5	dnaK	29	Heat Shock Protein-70
#6	CPn0849	285	SWI/SNF family helicase_2

Motif 1
TATCTGAATAAATTAAAACAATAAATGTTTTCA	0	41	1
ACAAAAATATAATTAAAATAATACATAATCCTG	3	89	1
CTACACCCGCAAAGAAAAGAATAGTTTAGATTT	6	105	1
TAAATTTCTAAATAAAAACAAAAATATAATTAA	3	72	1
GGCCTTCTATAAACACAATAATAATCTTCTTAC	1	117	0
  AGTACTACAATTACAAAAATAAAAGATTAAT	3	8	1
AACCCCTTTTAATCAAATAAAAATGAAAGAAAT	0	73	0
AATAAAAATGAAAGAAATGAAAACATTTATTGT	0	58	0
CGGAAGCAACAATGTAAAAAATATTTAGAAAAT	1	15	0
TCGATTTTTGATATAAAAAAATAAACTATACCA	0	109	0
TACCCATGCTAAATCAATGAAAAATTTTATCAA	6	211	0
TTTTCCTTTCAAGTCTAATAAAAAGGGTTGTCT	6	11	0
          **  **** ****
MAP Score: 15.1737

Motif 2
ATGTCTTTTAGAAGAGCCTCGATTGTACCACT	1	84	0
TATAAAATCGCAATAGCCTGTAATTTTTTCTA	3	234	1
GATTGATCGTCAAGAGTCTATAGAAAAAATTA	3	254	0
CCGAGAAGGTCAAGAGAATTTAGCACTCGAAT	4	55	0
AAAAGCGGGTGATGAGGCTTGAACTCACGACC	6	40	1
GCAAAGAAAAGAATAGTTTAGATTTTTGAAGA	6	113	1
TTAGATTTTTGAAGAGTTTTTAGCAACGACTA	6	130	1
TTAGCAACGACTAGAGTCTTTAGTATCATAGA	6	149	1
TTCTCAGGGGGAAGAGACACGAATTTCTATGA	6	174	0
TTCCCCCTGAGAAGGGCTTTGATAAAATTTTT	6	193	1
          ****** ** **
MAP Score: 11.9406

Motif 3
AACATTTATTGTTTTAATTTATTCAGATACAT	0	38	0
AACAATAAATGTTTTCATTTCTTTCATTTTTA	0	57	1
ATTTCTTTCATTTTTATTTGATTAAAAGGGGT	0	73	1
TGTTGGTATAGTTTATTTTTTTATATCAAAAA	0	106	1
          TTTGTATTTTCTAAATATTTTT	1	0	1
TCTAAATATTTTTTACATTGTTGCTTCCGAAT	1	19	1
AGGCCAGAGATTTGTTATTTATTGCGTAATAA	1	145	1
CTTATTAATCTTTTATTTTTGTAATTGTAGTA	3	12	0
TTAATTATAAGTTGAGATTATTAAATTTCTAA	3	51	1
TAATTATATTTTTGTTTTTATTTAGAAATTTA	3	72	0
GAAAAGAATAGTTTAGATTTTTGAAGAGTTTT	6	118	1
TTTGATAAAATTTTTCATTGATTTAGCATGGG	6	210	1
          ***** **** *
MAP Score: 11.1882