AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252271
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0065	101	transcriptional regulator, IclR family
#1	TM0066	62	2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
#2	TM0290	217	citrate synthase
#3	TM0548	162	acetolactate synthase, large subunit
#4	TM1155	82	glucose-6-phosphate 1-dehydrogenase

Motif 1
AACCATTTTCAAATGGAGGTGGATGT      	0	4	0
CTCAAAAAGAAAATCTTCATGGTATTATTATA	0	38	1
ACAAAGAAGAAAATCAGGGAGGCAGAGAAT  	0	81	1
CAAAAACCATAAATCTGCGGGTT         	1	1	0
TAAATATCACATATCAGGAGGG          	1	50	1
TTTTACCATACAAACTTGAAGGTAAAGTTAAA	2	129	0
GAACGATTAAAAATGAAGGAGGGCTTTGGGAA	2	162	0
GTATAGTTATACAACACGGAGGTGTTATT   	2	198	1
AATAATAAATAAATCACGGGGGGTTTTTAGGA	3	105	0
TATAATCATTCAATCTCCGAGAGGA       	3	147	1
TTCGTGGTAAAAATCCAGAAAGGCAGGTGAGA	4	58	1
          *****  *****
MAP Score: 12.4734

Motif 2
GAAGATTTTCTTTTTGAGAAAACCATTTTCAAATGG	0	20	0
TCTACAATCAATTATAATAATACCATGAAGATTTTC	0	46	0
TTTTGAAATATGATTAAATATCACATATCAGGAGGG	1	36	1
TGAAATGAAAAGCATTAAAATGCCAGCCTGTGCCAT	2	84	1
CATGCAGTACTGTTTAACTTTACCTTCAAGTTTGTA	2	117	1
AGGAGGGCTTTGGGAAATTTTACCATACAAACTTGA	2	142	0
CCCTCCTTCATTTTTAATCGTTCCAGTGTATAGTTA	2	171	1
       CTTATCCTAAATTTTACATTTTCATGATA	3	3	1
AAAAATTCGATTCAACAACTTGACATTTTAAAGTGA	3	57	1
CCCCCGTGATTTATTTATTATTCCAGGTCTGGTATA	3	115	1
TCTCGGAGATTGAATGATTATACCAGACCTGGAATA	3	133	0
TAATTTCCTTTGTGTTAAAATTCCTTAAAAGGGGGG	4	10	0
          **  * *  ** ****
MAP Score: 11.0325

Motif 3
     ACATCCACCTCCATTTGAAAATGGTTTTCTCAAAA	0	5	1
AAAAGAAAATCTTCATGGTATTATTATAATTGATTGTAGA	0	42	1
  ATTCTCTGCCTCCCTGATTTTCTTCTTTGTCTACAATC	0	73	0
         CCCTCCTGATATGTGATATTTAATCATATTT	1	41	0
     TTCAACCCCTCCCCTTGCTTAATGTCTTCAAAACA	2	5	1
TGTTTAACTTTACCTTCAAGTTTGTATGGTAAAATTTCCC	2	127	1
TTCCCAAAGCCCTCCTTCATTTTTAATCGTTCCAGTGTAT	2	162	1
     AATAACACCTCCGTGTTGTATAACTATACACTGGA	2	192	0
GTAGCATTTTTATCATGAAAATGTAAAATTTAGGATAAG 	3	9	0
AGGAATGGTATATCACTCACTTTAAAATGTCAAGTTGTTG	3	69	0
TTCCTAAAAACCCCCCGTGATTTATTTATTATTCCAGGTC	3	104	1
         TCCTCTCGGAGATTGAATGATTATACCAGAC	3	141	0
          CCCCCCTTTTAAGGAATTTTAACACAAAGG	4	0	1
ATTAGTTATTCCTCATTTCGTGGTAAAAATCCAGAAAGGC	4	42	1
          **** *    **  **   *
MAP Score: 10.219

Motif 4
TCTACAATCAATTATAATAATACCATGAAGATT	0	49	0
ATTTAATCATATTTCAAAAAAACAAAAACCATA	1	22	0
TTTTTGAAATATGATTAAATATCACATATCAGG	1	35	1
AATGCTTTTCATTTCAAAAAAGATTTAACACTT	2	67	0
TCAAGTTTGTATGGTAAAATTTCCCAAAGCCCT	2	142	1
TTACATTTTCATGATAAAAATGCTACTTCTAAC	3	23	1
TATATCACTCACTTTAAAATGTCAAGTTGTTGA	3	68	0
GTGATATACCATTCCTAAAAACCCCCCGTGATT	3	93	1
AATTTCCTTTGTGTTAAAATTCCTTAAAAGGGG	4	12	0
TCCTCATTTCGTGGTAAAAATCCAGAAAGGCAG	4	51	1
          *** ******  *
MAP Score: 9.23998

Motif 5
        ACATCCACCTCCATTTGAAAAT	0	2	1
        TTCAACCCCTCCCCTTGCTTAA	2	2	1
AAAAAAGATTTAACACTTTCGCAGAAAAAT	2	55	0
GTTTGTATGGTAAAATTTCCCAAAGCCCTC	2	146	1
AAAATTTCCCAAAGCCCTCCTTCATTTTTA	2	157	1
        AATAACACCTCCGTGTTGTATA	2	205	0
AGTGAGTGATATACCATTCCTAAAAACCCC	3	88	1
TACCATTCCTAAAAACCCCCCGTGATTTAT	3	99	1
GGTATAATCATTCAATCTCCGAGAGGA   	3	145	1
TTCCTTTGTGTTAAAATTCCTTAAAAGGGG	4	12	0
          **********
MAP Score: 1.70808