AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons016_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252281
 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
       ACATCCACCTCCATTTGAAAATGGTTTT	0	3	1
  ATTCTCTGCCTCCCTGATTTTCTTCTTTGTCTA	0	78	0
         CCCTCCTGATATGTGATATTTAATCA	1	46	0
CAACCCCTCCCCTTGCTTAATGTCTTCAAAACATA	2	12	1
CAAAACATATTCTACCAATTTTTCTGCGAAAGTGT	2	38	1
TTTAACTTTACCTTCAAGTTTGTATGGTAAAATTT	2	129	1
TTTCCCAAAGCCCTCCTTCATTTTTAATCGTTCCA	2	161	1
    AATAACACCTCCGTGTTGTATAACTATACAC	2	196	0
TTCCTAAAAACCCCCCGTGATTTATTTATTATTCC	3	104	1
ATCTCACCTGCCTTTCTGGATTTTTACCACGAAAT	4	56	0
          *** **   **** *
MAP Score: 9.65808

Motif 2
TTGAGAAAACCATTTTCAAATGGAGGTGGATGT 	0	9	0
TATTTAATCATATTTCAAAAAAACAAAAACCATA	1	22	0
TTTTTTGAAATATGATTAAATATCACATATCAGG	1	34	1
TAATGCTTTTCATTTCAAAAAAGATTTAACACTT	2	67	0
TTCAAGTTTGTATGGTAAAATTTCCCAAAGCCCT	2	141	1
TTTACATTTTCATGATAAAAATGCTACTTCTAAC	3	22	1
GTATATCACTCACTTTAAAATGTCAAGTTGTTGA	3	68	0
AGTGATATACCATTCCTAAAAACCCCCCGTGATT	3	92	1
TAATTTCCTTTGTGTTAAAATTCCTTAAAAGGGG	4	12	0
TTCCTCATTTCGTGGTAAAAATCCAGAAAGGCAG	4	50	1
          **** * ****  *
MAP Score: 9.51618

Motif 3
     ACATCCACCTCCATTTGAAAATGGTTTTCTCAAAA	0	5	1
ATTCTCTGCCTCCCTGATTTTCTTCTTTGTCTACAATCAA	0	71	0
        AACCCGCAGATTTATGGTTTTTGTTTTTTTGA	1	2	1
         CCCTCCTGATATGTGATATTTAATCATATTT	1	41	0
     TTCAACCCCTCCCCTTGCTTAATGTCTTCAAAACA	2	5	1
TCCCAAAGCCCTCCTTCATTTTTAATCGTTCCAGTGTATA	2	163	1
   AATAACACCTCCGTGTTGTATAACTATACACTGGAAC	2	190	0
CCTAAAAACCCCCCGTGATTTATTTATTATTCCAGGTCTG	3	106	1
      TCCTCTCGGAGATTGAATGATTATACCAGACCTG	3	138	0
          CCCCCCTTTTAAGGAATTTTAACACAAAGG	4	0	1
     GATCTCACCTGCCTTTCTGGATTTTTACCACGAAA	4	57	0
          ****    ***    * * *
MAP Score: 7.79057

Motif 4
AATCAATTATAATAATACCATGAAGATTTTC	0	46	0
ATTTCAAAAAAGATTTAACACTTTCGCAGAA	2	59	0
AGTACTGTTTAACTTTACCTTCAAGTTTGTA	2	122	1
GGCTTTGGGAAATTTTACCATACAAACTTGA	2	142	0
TCCAGTGTATAGTTATACAACACGGAGGTGT	2	192	1
 CTTATCCTAAATTTTACATTTTCATGATAA	3	9	1
TAGAAGTAGCATTTTTATCATGAAAATGTAA	3	23	0
CCTTTTAAGGAATTTTAACACAAAGGAAATT	4	14	1
AAAGGAAATTAGTTATTCCTCATTTCGTGGT	4	35	1
GCCTTTCTGGATTTTTACCACGAAATGAGGA	4	51	0
          * *********
MAP Score: 7.1487