AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons025_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252576
 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
#5	TM1623	49	lepA protein

Motif 1
      GATTTAGCACTCCCTTCTTTTGAGT	1	4	1
GTTCCGAGAATCCCTCTTCCTTCTTGAATTC	1	65	0
TAGTACCAGCTTTCTCTTTCTAAAGTCAAGT	1	94	0
GCGTCTGCCATTCCGCCACCTCGGCCCTCCA	1	132	0
CGGGTTCAAGTCCCGCCCTCGGCACCACAGG	1	198	1
      AGGTTTTTCCCTCCTGATGTGATAC	1	253	0
       AAATCTCACCTCCGGTGTGTGGTA	2	3	1
ACCTCCTTGTTTTCCCTATCTATTCAATGAT	2	33	0
        AGTGTCACCTCCTTGTTTTCCCT	2	47	0
       ACCTCTCAGTTTCTTTCAAAAGAA	4	208	0
        GTTATCACCTCCTCATGAATGTA	5	2	1
TGAATGTATATCACACTCTCTATGAAAAAAC	5	25	1
          **** ******
MAP Score: 11.9748

Motif 2
    AGGATAATCCACCTCTCGTTAAATTTT	0	32	0
     GATTTAGCACTCCCTTCTTTTGAGTG	1	5	1
AGTTCCGAGAATCCCTCTTCCTTCTTGAATT	1	66	0
CCGCCACCTCGGCCCTCCATTATATATAGTA	1	120	0
CGCGTCTGCCATTCCGCCACCTCGGCCCTCC	1	133	0
GCGGGTTCAAGTCCCGCCCTCGGCACCACAG	1	197	1
        AAATCTCACCTCCGGTGTGTGGT	2	2	1
       AGTGTCACCTCCTTGTTTTCCCTA	2	46	0
AAACAGTAAAATCCCATTTTTGAAGGTCCAT	4	128	0
       GTTATCACCTCCTCATGAATGTAT	5	3	1
ATGAATGTATATCACACTCTCTATGAAAAAA	5	24	1
          ***** *****
MAP Score: 6.53869

Motif 3
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
      TTCGTTTTTTCATAGAGAGTGTGAT	5	34	0
          ********* *
MAP Score: 6.50877

Motif 4
CCGAGAATCCCTCTTCCTTCTTGAATTCTTTTAAA	1	58	0
ATAGTACCAGCTTTCTCTTTCTAAAGTCAAGTTCC	1	91	0
AAAGAGAAAGCTGGTACTATATATAATGGAGGGCC	1	106	1
CTCGGCACCACAGGGGCTCCGAAGAGCCCCTTTAT	1	215	1
GAAATCTTTTCAGGGACTTTGGAAAATACAACATA	4	22	1
TTCATAACGACTCTGGCTTCGAACATCGTTGTCGG	4	66	1
ATCTGGACAAATGGACCTTCAAAAATGGGATTTTA	4	118	1
TGGGATTTTACTGTTTATTTTCATAATTTTAGGAA	4	143	1
    ACCTCTCAGTTTCTTTCAAAAGAATTTTGAA	4	201	0
ATGTATATCACACTCTCTATGAAAAAACGAA    	5	28	1
          ****  ****  * *
MAP Score: 5.31858

Motif 5
TGAAAATTATATCACGTGGTAAAATTTAAC	0	12	1
CTGCCATTCCGCCACCTCGGCCCTCCATTA	1	129	0
CTGATTTTGAGTCAGCCGCGTCTGCCATTC	1	150	0
CTGACTCAAAATCAGCTGGGGGATAACCCC	1	165	1
CAGCTGGGGGATAACCCCGTGCGGGTTCAA	1	177	1
GCGGGTTCAAGTCCCGCCCTCGGCACCACA	1	197	1
TTTATTTTGTATCACATCAGGAGGGAAAAA	1	245	1
      AAATCTCACCTCCGGTGTGTGGTA	2	4	1
       AGTGTCACCTCCTTGTTTTCCCT	2	47	0
       GTTATCACCTCCTCATGAATGTA	5	3	1
          **********
MAP Score: 5.22238