AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251982
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0012	161	NADP-reducing hydrogenase, subunit A
#1	TM0198	215	ATP-dependent Clp protease, ATPase subunit
#2	TM0228	300	NADP-reducing hydrogenase, subunit C
#3	TM1095	300	adenylosuccinate lyase
#4	TM1205	300	conserved hypothetical protein
#5	TM1208	26	conserved hypothetical protein
#6	TM1420	255	hypothetical protein

Motif 1
       ATGTTTCACCTCCTTAGCTTTTG	6	3	1
        TTTTTTCCCTCCTTTCGAGAAA	1	2	1
        CTTTTTCCCTCCCAAACAGATC	3	288	0
GAGTCTGATCTTTCTCCTCGTCCTCGAGGG	3	32	1
        ATTGTCACCTCCAGATTTCAAA	0	2	1
TTGTGAAAACTTTCTCTTTCAATCCCGAGG	4	269	1
GCTTTGACCACTTCTCTTCCGTTTTCAACA	2	94	0
TTATCACGTATTTTCCTTCGGTTTTGTCGA	2	39	0
TGGAATCGACTTTTACGTCCAGAAAACGAA	4	100	1
TACCATGTTACTTTCCTTCCATATCAAAAA	6	33	0
        AGTATCACCTCCGGGTCTTCCA	1	203	0
GATCGTAATCTGTCCCTTTCAAATATTCGA	3	64	0
GCTTTTCTGGTTTCTCGTTGCGATGGCGTT	3	182	1
CTGATATTTTTTTCACATTCACCATAGTCG	0	132	0
GTTCACGGTTTTTTTCTTTGCGAAACTGGT	3	138	0
          CGTTCCTTTCAAATCGTGAA	6	245	0
          **********
MAP Score: 15.1058

Motif 2
AAATCGTTTGAAATCTGGAGGTGACAAT     	0	5	0
TCATCATATGACAGTGAGAGGTGTTATAATCGA	0	102	1
TGAAATTGGAAGACCCGGAGGTGATACT     	1	197	1
GTGTGAAAAGACCATCAGAAGTGGTCTGTCCGA	2	150	0
TTCACACTCGAAATGACGAGTTGTCTGGGTCTT	2	176	1
TCTCATAGATAGACTGAGAGGTGAGTCGCT   	2	280	1
TCGAACCCCTCGAGGACGAGGAGAAAGATCAGA	3	35	0
ATGTCAAGCGACATCCCGAGGAGATTTTCAACG	4	48	1
ACAGTTTCGAAGAGAACGAAGAGGGAAATTTAG	4	170	0
CTTTCTCTTTCAATCCCGAGGAGGTGTGATGA 	4	278	1
CAAAAACAAAAGCTAAGGAGGTGAAACAT    	6	6	0
          ***   *******
MAP Score: 11.2071

Motif 3
TTTTCATCATATGACAGTGAGAGGTGTTATAAT	0	99	1
ATCGACTATGGTGAATGTGAAAAAAATATCAGA	0	130	1
AGTCTGCCGTGTCATGTTGAAAACGGAAGAGAA	2	80	1
AGCCCTCAAAGAAATTCTGAAAATCGACTTCGG	2	121	1
TGCACCGGTGATCATGGTGAACGACGAGTATTA	2	217	1
GGATCTCATAGATAGACTGAGAGGTGAGTCGCT	2	277	1
CGCAAAGAAAAAAACCGTGAACATACCTCTCAA	3	146	1
ATACGTAAACGTTACCGTGAAAGTTACCGTGAT	4	17	1
TTATTTGGAAATAACGTTGAAAATCTCCTCGGG	4	62	0
CTCTTGTGTTGTGATTGTGAAAACTTTCTCTTT	4	255	1
GAAGGAAAGTAACATGGTAAGAGTGTAATGTAA	6	44	1
CTTGAAATATATGACTGTAAAAACGTGATATAA	6	89	0
CTTCTCCTGAAAAATAGTGAAAAATATAACGTG	6	206	1
TAGTGAAAAATATAACGTGAAAAGGTTCACGAT	6	220	1
          ** *  *******
MAP Score: 10.035

Motif 4
GGGGTTCGAATATTTGAAAGGGACAGATTACGA	3	59	1
ATCGCCACCAGTTTCGCAAAGAAAAAAACCGTG	3	132	1
CCAGAAAAGCGATTTGAGAGGTATGTTCACGGT	3	159	0
TTGCGATGGCGTTGTGGAAGGTAGCGAGCATTA	3	199	1
CGAGAGATCTGTTTGGGAGGGAAAAAG      	3	283	1
ATAAAAAACAGTTTCGAAGAGAACGAAGAGGGA	4	177	0
ACCTCCTCGGGATTGAAAGAGAAAGTTTTCACA	4	270	0
TTTTGTTTTTGATATGGAAGGAAAGTAACATGG	6	28	1
AAAAGAAAACTATTGGTAAAGCACTTGAAATAT	6	112	0
TACTTCACAAGTTTTGTAAACAAACTGATTCAC	6	147	0
AAAGGTTCACGATTTGAAAGGAACG        	6	240	1
          **** * **** *
MAP Score: 9.84325

Motif 5
CACCTCCAGATTTCAAACGATTTCAAGAATTAATCCCC	0	15	1
ATCACGTATTTTCCTTCGGTTTTGTCGAAAACATGGTG	2	29	0
GATGGTCTTTTCACACTCGAAATGACGAGTTGTCTGGG	2	167	1
CTTTGTGGTGTTGCACCGGTGATCATGGTGAACGACGA	2	206	1
AGTCTGATCTTTCTCCTCGTCCTCGAGGGGTTCGAATA	3	33	1
TGGTTTCTCGTTGCGATGGCGTTGTGGAAGGTAGCGAG	3	189	1
TTTCCTGTTGTTGCGCTCGTGTTCACGAGAGATCTGTT	3	258	1
CTCCTCGGGATGTCGCTTGACATCACGGTAACTTTCAC	4	33	0
TTGTGAAAACTTTCTCTTTCAATCCCGAGGAGGTGTGA	4	269	1
ACGTTATATTTTTCACTATTTTTCAGGAGAAGTCAAGG	6	200	0
          ** * ** *   **  **
MAP Score: 3.57457

Motif 6
AACACTTTGTGACTGTTTCTTTTCTTTTCA	0	75	1
AGAGAACTTTGAACATTTCTGAAAGATGTT	1	146	1
TGAGGGCTTTGACCACTTCTCTTCCGTTTT	2	99	0
ACTTCGGACAGACCACTTCTGATGGTCTTT	2	147	1
TCCAGAAAACGAATATTTCTGTGTTTCGTT	4	117	1
          **********
MAP Score: 2.97593

Motif 7
TCATATGACAGTGAGAGGTGTTATAATCGAC	0	105	1
TATGGTGAATGTGAAAAAAATATCAGATAAA	0	136	1
CCCTCCTTTCGAGAAAAGTGTCGTTTAAATT	1	16	1
CTTTACTTCTGAGAGAACTTTGAACATTTCT	1	135	1
AGGAAAATACGTGATAAGGGTTTGTGAGAGT	2	52	1
TCGTGTTCACGAGAGATCTGTTTGGGAGGGA	3	274	1
TGTTGTGATTGTGAAAACTTTCTCTTTCAAT	4	261	1
CTGAAAAATAGTGAAAAATATAACGTGAAAA	6	212	1
AAAATATAACGTGAAAAGGTTCACGATTTGA	6	226	1
          ********* *
MAP Score: 2.39774