AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons028_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242989
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	kdsB	300	CMP-2-keto-3-deoxyoctulosonic acid synthetase
#1	accA	132	AcCoA Carboxylase/Transferase Alpha
#2	himD	219	Integration Host Factor Alpha

Motif 1
ATAGGCTCTCTTCGTTCCTATATTCGACACCTCCCGC	0	67	1
CCTCCCGCGTTTCATTCGTGAAAAATAATCAAATACA	0	96	1
AAATTAAAATTGTTTGCGTGAAACAAAGGTCATTATA	1	24	1
AAAAAAGAGTTATTTTAATACAAACAATAATCAAAAA	1	84	0
CGTAGCACGCTCCCTTCTTATAAAAAAGAGTTATTTT	1	105	0
GTAGATTTTGTGCGTTCATGGAAAAGATAAAAAAAGT	2	98	1
AATACCGCAATATATGCGTATAATATGCATTCATCCT	2	146	0
TGGTAACCCTTGCGTCCCTAAATACCGCAATATATGC	2	166	0
          * * * * ** ** * *
MAP Score: 3.18462

Motif 2
TATATTCGACACCTCCCGCGTTTCATTCGTG	0	85	1
TACACAGAACCCGACCATCCTAACAAGGAGA	0	189	0
CCCATTAATGACGTCCCACCTAAGAAGCAAA	0	273	0
          CGCACCCCCATTAATGACGTC	0	289	0
   CGTAGCACGCTCCCTTCTTATAAAAAAG	1	114	0
TTAAAGCCCTCCCTCCCCCGGA         	2	1	0
          ******* ***
MAP Score: 1.96507

Motif 3
TGTTAACGATCTCCTTGTTAGGATGGTCGGGTTCTG	0	180	1
GAAGTTTTGCTTCTTAGGTGGGACGTCATTAATGGG	0	268	1
TTAAAATTGTTTGCGTGAAACAAAGGTCATTATAAT	1	27	1
AAAATAACTCTTTTTTATAAGAAGGGAGCGTGCTAC	1	105	1
          TCCGGGGGAGGGAGGGCTTTAACAAG	2	0	1
AACAAGACCTTTAAGTGCTCGAAAGGATATTCGTAG	2	30	1
CGAAAGGATATTCGTAGTGGAGAAGGTTTCGGTTGA	2	49	1
TATTGCGGTATTTAGGGACGCAAGGGTTACCACTTT	2	171	1
          **  * *  **** **
MAP Score: 1.17867

Motif 4
AACGATCTCCTTGTTAGGATGGTCGGGTTCT	0	184	1
GAAATTAAAATTGTTTGCGTGAAACAAAGGT	1	23	1
TAGTTGGTTTTTGGTTGTTTTTGATTATTGT	1	67	1
TTTTTGATTATTGTTTGTATTAAAATAACTC	1	84	1
GGAGAAGGTTTCGGTTGAGTGCAACTCGTGG	2	67	1
TATGCATTCATCCTTTGGATTCAAGACTTTT	2	129	0
          ******* ***
MAP Score: 0.677034