AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons048_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944253182
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0271	64	hypothetical protein
#1	TM0272	74	pyruvate,orthophosphate dikinase
#2	TM0273	41	fructose-bisphosphate aldolase
#3	TM1131	155	aminotransferase, putative
#4	TM1754	102	butyrate kinase, putative

Motif 1
TCCTGTGTTATCATAAGTTTTGGTGAAGAAAAAAGAA	0	24	1
TTTGATTTTATAATAAATTCTTGGATACGAAAGGAAA	1	31	1
ATCCCTCCAGATAGAAGTATTTGCATACTTCAAAGTA	3	16	1
TGAGAATTTGATAGAAAAACTGGTATACTTTGAAGTA	3	41	0
TTCAACGTGTATTCGAAAAATTGAGAATTTGATAGAA	3	62	0
GAAAAATTATACACCAGTACTGGCGAAATTTCTGCAT	3	104	0
AGAAACATCAAGATCAAAATTTGTCAACATT      	4	4	0
ATGGAACATTACATAAAACTTTGTGTAATCTTTTGTC	4	57	1
          * *  ***  ***  **
MAP Score: 4.45969

Motif 2
TCATAAGTTTTGGTGAAGAAAAAAGAAGGAG	0	34	1
CGGTTTTGATTTTATAATAAATTCTTGGATA	1	27	1
AATAAATTCTTGGATACGAAAGGAAAAGGAG	1	42	1
AATTGAGAATTTGATAGAAAAACTGGTATAC	3	50	0
AAATTCAACGTGTATTCGAAAAATTGAGAAT	3	71	0
GCGAAATTTCTGCATTAAAATTCAACGTGTA	3	88	0
TCGCCAGTACTGGTGTATAATTTTTCAGAAG	3	115	1
TGTATAATTTTTCAGAAGAAAAGATATTCCA	3	128	1
        AATGTTGACAAATTTTGATCTTG	4	2	1
TCACCTCTTATGTTGACAAAAGATTACACAA	4	77	0
          ******* ***
MAP Score: 3.7403

Motif 3
GGTGTATAATTTTTCAGAAGAAAAGATATTCCA	3	126	1
TCACCAAAACTTATGATAACACAGGAAAGGAGG	0	17	0
AGTATACCAGTTTTTCTATCAAATTCTCAATTT	3	49	1
CAAGAATTTATTATAAAATCAAAACCGCACGAT	1	21	0
CGATCACCTCTTATGTTGACAAAAGATTACACA	4	78	0
TATCATAAGTTTTGGTGAAGAAAAAAGAAGGAG	0	32	1
AAATTCTCAATTTTTCGAATACACGTTGAATTT	3	69	1
ACTGGCGAAATTTCTGCATTAAAATTCAACGTG	3	90	0
          ****   ******
MAP Score: 1.6511