AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons021_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242768
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	fliA	107	Sigma-28/WhiG Family
#1	rl13	222	L13 Ribosomal Protein
#2	rs9	25	S9 Ribosomal Protein
#3	CT398	255	hypothetical protein
#4	rpoD	148	RNA Polymerase Sigma-66
#5	CT793	62	hypothetical protein

Motif 1
TTAGCCTTATTTTTTAGTTTGTAAAAGAAATTTTT	0	79	1
    CTATTTTTTTTATTATGTAAATCATGATTCA	1	6	1
ATACAGCTGCTTTTTGTTTGGAAAAAATAATCATC	1	158	1
TAAGAAAATCTTTTTCAATGGGAGAAAGTCGGTCA	3	45	0
GTAAAGCACGTTTTGTTTAAGAAAATCTTTTTCAA	3	62	0
AAAGTGACAGTTTATCTTAAGAAAAACAAGAAATC	4	88	0
TTTTTGAAATTTTTTCTTTTCTAAATTCTTTAGAA	1	118	1
ATCAACAGGCTTTTTTTTATCTAAAAATCCCTAGA	4	55	1
ATCTCTTTTCTTTTTGCCTTCAAAAATAGCCTTAC	1	82	0
CCTAAAATATTTTTTCGAAAGAAGTGTAGAAGTGT	1	49	1
ATCGAAAAAATTTTTTATTCGTAGTAGGGGAACAG	5	31	1
GTTGATCAGATTTAGGCCTAGAAAAACCCCTCCCG	4	26	0
TTTTCTAAATTCTTTAGAAGGCAAATACAGCTGCT	1	134	1
AAACTTGCCGTTTCGTCTAGGCAGACTCGTCCGCG	3	116	1
CAAAACGTGCTTTACTTCTTGCAGAAAAATCGGTA	3	82	1
     AAGAGTTATTGATTAGGAGTTATGTGTTAG	0	5	1
TAAAAAATTTTTTCGATCACGCAATACTAGATAAA	5	13	0
          *****   * * ***
MAP Score: 21.8552

Motif 2
        GGAAATCTTTCCTTACCTTGAT	3	243	0
GGCGTTCCTCAGATTTTCCCGAGTTGGAGG	3	188	1
GATCTTTTTGAAATTTTTTCTTTTCTAAAT	1	114	1
TACGAATAAAAAATTTTTTCGATCACGCAA	5	24	0
TTGTTTAAGAAAATCTTTTTCAATGGGAGA	3	55	0
   ATCCTTCAAATTATTCCTTACATGAAT	3	7	1
TCATGATTCAAGAACTTCCCTAAAATATTT	1	31	1
TTTGTAAAAGAAATTTTTTTT         	0	96	1
AAAAGAAAAGAGATCTTTTTGAAATTTTTT	1	103	1
AACGCCTTCAAAAACTTCCTAAAAAGGGAG	3	164	0
TCTTTGTCACAAATTACCCCAAA       	2	3	0
GTCTTTTTTCAAAACTCCCTTTTTAGGAAG	3	150	1
CTTTCTAGGCCGATTTTTCCTTAGTTTTAA	4	119	1
GCAAGTTTACCGATTTTTCTGCAAGAAGTA	3	94	0
     AACTTAAATCACCTTATCAGAGGGA	1	207	0
GAACTTCCCTAAAATATTTTTTCGAAAGAA	1	42	1
          **********
MAP Score: 13.5355

Motif 3
GATATTGTTTAAAAATTTTATTTGATTTAGCC	0	53	1
TCCCATTGAAAAAGATTTTCTTAAACAAAACG	3	57	1
AGTTTGTAAAAGAAATTTTTTTT         	0	94	1
AACTTCCCTAAAATATTTTTTCGAAAGAAGTG	1	43	1
ACTACGAATAAAAAATTTTTTCGATCACGCAA	5	24	0
GATCTTTTTGAAATTTTTTCTTTTCTAAATTC	1	114	1
CAAAAAGAAAAGAGATCTTTTTGAAATTTTTT	1	101	1
AAAAATCCCTAGATTTCTTGTTTTTCTTAAGA	4	77	1
TTCCTTACATGAATTTTTTGTCTGACCGACTT	3	23	1
TCTGATCAACAGGCTTTTTTTTATCTAAAAAT	4	51	1
          *** ***** **
MAP Score: 12.3787

Motif 4
GTAAGGCTATTTTTGAAGGCAAAAAGAAAAGAG	1	82	1
TTCTAAATTCTTTAGAAGGCAAATACAGCTGCT	1	136	1
GATGATTATTTTTTCCAAACAAAAAGCAGCTGT	1	160	0
GTGCTTTACTTCTTGCAGAAAAATCGGTAAACT	3	88	1
ACTTGCCGTTTCGTCTAGGCAGACTCGTCCGCG	3	118	1
AAAAAGGGAGTTTTGAAAAAAGACGCGGACGAG	3	141	0
TTTAGGAAGTTTTTGAAGGCGTTCCTCAGATTT	3	171	1
CGGGAGGGGTTTTTCTAGGCCTAAATCTGATCA	4	26	1
TAAACTGTCACTTTCTAGGCCGATTTTTCCTTA	4	109	1
          ***** ****  *
MAP Score: 4.84275