AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons074_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944253673
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0984	199	hypothetical protein
#1	TM0987	50	conserved hypothetical protein
#2	TM0990	121	conserved hypothetical protein

Motif 1
TTTTGTGAAAAAAATCTCAATCCTCGTGAAAA	0	31	1
AATCCTCGTGAAAATAATAATATTCTAATGTT	0	49	1
AATGTTACATAGACGTTGAATAATATTACGAT	0	75	1
AAAGAAAATCAGAAGATCAATCTTTAAACGTG	0	128	0
TCACGTTTTTAAAATGTTAATACTATGATACC	0	168	0
TCCCTCGAACAGAAGGAGAATAGAAGCTTTCA	2	70	1
          ***** * ****
MAP Score: 3.74539

Motif 2
TTTTGTGAAAAAAATCTCAATCCTCGTGAAAATA	0	31	1
AATCCTCGTGAAAATAATAATATTCTAATGTTAC	0	49	1
AATGTTACATAGACGTTGAATAATATTACGATAT	0	75	1
AAAGAAAATCAGAAGATCAATCTTTAAACGTGAT	0	126	0
TCACGTTTTTAAAATGTTAATACTATGATACCAC	0	166	0
TCCCTCGAACAGAAGGAGAATAGAAGCTTTCAAG	2	70	1
          *****   **** *
MAP Score: 2.64908

Motif 3
TGATCACGTTTAAAGATTGATCTTCTGATTT	0	124	1
TTTTCTTTCGTTAAGTGGTATCATAGTATTA	0	152	1
TTAAAAACGTGAAAGAGGGGG          	0	188	1
TGTGTACAATTTAAGTTGGATACAGCAAATC	1	13	1
ACAGCAAATCCAAAGGGGGATGTACA     	1	34	1
AGGAATAAAAGAGAGCGGGATTGCTCAGTGT	2	29	0
          ***** *****
MAP Score: 1.64057