AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252568
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0221	49	flagellar M-ring protein
#1	TM0852	268	conserved hypothetical protein
#2	TM1085	60	methionyl-tRNA synthetase
#3	TM1611	21	ATP synthase F1, subunit gamma
#4	TM1617	222	hypothetical protein

Motif 1
GGTAAAATTTAACGAGAGGTGGATTATCCT  	0	29	1
ATTAGCACTCAAAAGAAGGGAGTGCTAAATC 	1	9	0
AAAGAATTCAAGAAGGAAGAGGGATTCTCGGA	1	62	1
GACTTTAGAAAGAGAAAGCTGGTACTATATAT	1	98	1
CGGCTGACTCAAAATCAGCTGGGGGATAACCC	1	162	1
GATGTGATACAAAATAAAGGGGCTCTTCGGAG	1	231	0
TATTTTGTATCACATCAGGAGGGAAAAACCT 	1	247	1
ATAGATAGGGAAAACAAGGAGGTGACACT   	2	41	1
TAAAATTATGAAAATAAACAGTAAAATCCCAT	4	142	0
          **** **** **
MAP Score: 5.56512

Motif 2
AGCACTCCCTTCTTTTGAGTGCTAATAATAG	1	15	1
TCGGAACTTGACTTTAGAAAGAGAAAGCTGG	1	89	1
GTTTTCCCTATCTATTCAATGATACCACACA	2	25	0
TTTCCAGAAATCTTTTCAGGGACTTTGGAAA	4	16	1
ACTATGTTGTATTTTCCAAAGTCCCTGAAAA	4	28	0
GTAAAATCCCATTTTTGAAGGTCCATTTGTC	4	123	0
GTTTCAAAATTCTTTTGAAAGAAACTGAGAG	4	199	1
          ********* *
MAP Score: 5.49861