AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251953
 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
        ATTGTCACCTCCAGATTTCAAA	0	2	1
TGACTGTTTCTTTTCTTTTCATCATATGAC	0	84	1
        TTTTTTCCCTCCTTTCGAGAAA	1	2	1
TGAATCTAATTGTTACCTTTTGCTTTACTT	1	113	1
TTACCTTTTGCTTTACTTCTGAGAGAACTT	1	125	1
TTCTGAAAGATGTTATGTCCATAAGGGTGA	1	162	1
TTATCACGTATTTTCCTTCGGTTTTGTCGA	2	39	0
CCATCAGAAGTGGTCTGTCCGAAGTCGATT	2	142	0
CCACTTCTGATGGTCTTTTCACACTCGAAA	2	159	1
GATCGTAATCTGTCCCTTTCAAATATTCGA	3	64	0
GTTTCTGGTGCTGTCCTTCTTTCCTCTGAT	3	104	1
        CTTTTTCCCTCCCAAACAGATC	3	288	0
AGATTTTCAACGTTATTTCCAAATAATTTC	4	69	1
TGGAATCGACTTTTACGTCCAGAAAACGAA	4	100	1
TTTCCCTCTTCGTTCTCTTCGAAACTGTTT	4	175	1
CGAAACTGTTTTTTATCTCTACTAATTAGG	4	194	1
ATTGTGAAAACTTTCTCTTTCAATCCCGAG	4	268	1
       ATGTTTCACCTCCTTAGCTTTTG	6	3	1
TACCATGTTACTTTCCTTCCATATCAAAAA	6	33	0
TTACCAATAGTTTTCTTTTTAGTGAATCAG	6	126	1
          CGTTCCTTTCAAATCGTGAA	6	245	0
          **********
MAP Score: 14.5876

Motif 2
ATATGATGAAAAGAAAAGAAACAGTCACAA	0	81	0
TATGGTGAATGTGAAAAAAATATCAGATAA	0	136	1
AAAAAAATATCAGATAAAAATT        	0	149	1
TTCTCGAAAGGAGGGAAAAAA         	1	1	0
GACAAAACCGAAGGAAAATACGTGATAAGG	2	41	1
CATTTCGAGTGTGAAAAGACCATCAGAAGT	2	161	0
          GAGAAAAGACCCTGTTTCAT	3	0	1
GTGGCGATCAGAGGAAAGAAGGACAGCACC	3	110	0
CAGTTTCGCAAAGAAAAAAACCGTGAACAT	3	140	1
CAGGAAAAACAAGATAAGAAGCCGTTGGAT	3	235	0
AGCGCAACAACAGGAAAAACAAGATAAGAA	3	245	0
ATCTGTTTGGGAGGGAAAAAG         	3	289	1
CTAATTAGTAGAGATAAAAAACAGTTTCGA	4	193	0
TTTGATATGGAAGGAAAGTAACATGGTAAG	6	35	1
TTGACTTCTCCTGAAAAATAGTGAAAAATA	6	202	1
CTGAAAAATAGTGAAAAATATAACGTGAAA	6	212	1
          **********
MAP Score: 13.6265

Motif 3
TCACTGTCATATGATGAAAAGAAAAGAAAC	0	89	0
GACTATGGTGAATGTGAAAAAAATATCAGA	0	133	1
TTCTGAGAGAACTTTGAACATTTCTGAAAG	1	141	1
CTGCCGTGTCATGTTGAAAACGGAAGAGAA	2	83	1
CCTCAAAGAAATTCTGAAAATCGACTTCGG	2	124	1
CGTCATTTCGAGTGTGAAAAGACCATCAGA	2	164	0
ACCGGTGATCATGGTGAACGACGAGTATTA	2	220	1
AAAGAAAAAAACCGTGAACATACCTCTCAA	3	149	1
AAACAGATCTCTCGTGAACACGAGCGCAAC	3	267	0
CGTAAACGTTACCGTGAAAGTTACCGTGAT	4	20	1
TTTGGAAATAACGTTGAAAATCTCCTCGGG	4	62	0
TTGTGTTGTGATTGTGAAAACTTTCTCTTT	4	258	1
CCCTTGACTTCTCCTGAAAAATAGTGAAAA	6	199	1
CTCCTGAAAAATAGTGAAAAATATAACGTG	6	209	1
TGAAAAATATAACGTGAAAAGGTTCACGAT	6	223	1
TTCCTTTCAAATCGTGAACCTTTTCACGTT	6	233	0
          **********
MAP Score: 12.1349

Motif 4
TGCAACACTTTGTGACTGTTTCTTTTCTTTTCATCATATGA	0	72	1
TCGAATTCGGTGAATCTAATTGTTACCTTTTGCTTTACTTC	1	103	1
CTCACAAACCCTTATCACGTATTTTCCTTCGGTTTTGTCGA	2	39	0
ACTTCGGACAGACCACTTCTGATGGTCTTTTCACACTCGAA	2	147	1
CATGTTACCGTAATACTCGTCGTTCACCATGATCACCGGTG	2	219	0
CTGTTTCATGTGAGTCTGATCTTTCTCCTCGTCCTCGAGGG	3	21	1
ACAACTCGGCTCGATCGTAATCTGTCCCTTTCAAATATTCG	3	65	0
CGAGCCGAGTTGTTTCTGGTGCTGTCCTTCTTTCCTCTGAT	3	93	1
TTGAGAGGTATGTTCACGGTTTTTTTCTTTGCGAAACTGGT	3	138	0
GCATTAAATATCCAACGGCTTCTTATCTTGTTTTTCCTGTT	3	226	1
TTGGTCTAAATTTCCCTCTTCGTTCTCTTCGAAACTGTTTT	4	165	1
         ATGTTTCACCTCCTTAGCTTTTGTTTTTGATA	6	1	1
ATTTCAAGTGCTTTACCAATAGTTTTCTTTTTAGTGAATCA	6	114	1
GGTAACAACATAGAGCATTCCCTTGACTTCTCCTGAAAAAT	6	180	1
      CGTTCCTTTCAAATCGTGAACCTTTTCACGTTATA	6	230	0
          *    *   *  **  *****
MAP Score: 11.2513

Motif 5
AATCGTTTGAAATCTGGAGGTGACAAT      	0	4	0
CATCATATGACAGTGAGAGGTGTTATAATCGAC	0	103	1
GAAATTGGAAGACCCGGAGGTGATACT      	1	198	1
TGTCATGTTGAAAACGGAAGAGAAGTGGTCAAA	2	89	1
TGTGAAAAGACCATCAGAAGTGGTCTGTCCGAA	2	149	0
CTCATAGATAGACTGAGAGGTGAGTCGCT    	2	281	1
CGAACCCCTCGAGGACGAGGAGAAAGATCAGAC	3	34	0
TGTCAAGCGACATCCCGAGGAGATTTTCAACGT	4	49	1
CAGTTTCGAAGAGAACGAAGAGGGAAATTTAGA	4	169	0
TGACATTATTGATTCAGAAGAGTAAAATTACTC	4	225	1
TTTCTCTTTCAATCCCGAGGAGGTGTGATGA  	4	279	1
AAAAACAAAAGCTAAGGAGGTGAAACAT     	6	5	0
          **   ********
MAP Score: 10.5131

Motif 6
ACTTTGTGACTGTTTCTTTTCTTTTCATCATAT	0	78	1
          TTTTTTCCCTCCTTTCGAGAAAA	1	0	1
GTATCATGGATATTTCACCGGTTGTAGATCCGT	1	62	1
CGAATTCGATTTTTCGTACGGATCTACAACCGG	1	79	0
TTATCACGTATTTTCCTTCGGTTTTGTCGAAAA	2	36	0
TTTCAGAATTTCTTTGAGGGCTTTGACCACTTC	2	110	0
GTTGTCTGGGTCTTTGTGGTGTTGCACCGGTGA	2	195	1
GAAAAGACCCTGTTTCATGTGAGTCTGATCTTT	3	12	1
GTGAGTCTGATCTTTCTCCTCGTCCTCGAGGGG	3	30	1
CGAGCCGAGTTGTTTCTGGTGCTGTCCTTCTTT	3	93	1
GTGCTGTCCTTCTTTCCTCTGATCGCCACCAGT	3	111	1
CTTCTTATCTTGTTTTTCCTGTTGTTGCGCTCG	3	244	1
TAAATTTCCCTCTTCGTTCTCTTCGAAACTGTT	4	171	1
         ATGTTTCACCTCCTTAGCTTTTGT	6	1	1
TACAGTCATATATTTCAAGTGCTTTACCAATAG	6	103	1
          * ***** *** *
MAP Score: 9.83328

Motif 7
CACCTCTCACTGTCATATGATGAAAAGAAAAGAAACAGTCAC	0	83	0
TGTTCAAAGTTCTCTCAGAAGTAAAGCAAAAGGTAACAATTA	1	119	0
GAGTCTGCCGTGTCATGTTGAAAACGGAAGAGAAGTGGTCAA	2	79	1
CACAACGCCATCGCAACGAGAAACCAGAAAAGCGATTTGAGA	3	173	0
GTTACCGTGATGTCAAGCGACATCCCGAGGAGATTTTCAACG	4	39	1
CTAATTAGGTTGACATTATTGATTCAGAAGAGTAAAATTACT	4	215	1
AAGAGAAAGTTTTCACAATCACAACACAAGAGTAATTTTACT	4	245	0
TTGTGAAAACTTTCTCTTTCAATCCCGAGGAGGTGTGATGA 	4	269	1
ACGTTATATTTTTCACTATTTTTCAGGAGAAGTCAAGGGAAT	6	196	0
          *  **         * ******
MAP Score: 8.70962

Motif 8
CTCCAGATTTCAAACGATTTCAAGAATTAATCCCCATT	0	18	1
GAATTAATCCCCATTTGATTCTATCACTACATGCAACA	0	41	1
AGTGTCGTTTAAATTCGGTTCGATTAAATTGTATCATG	1	32	1
CAAAAGGTAACAATTAGATTCACCGAATTCGATTTTTC	1	97	0
GAAATTCTGAAAATCGACTTCGGACAGACCACTTCTGA	2	131	1
CCTCTGATCGCCACCAGTTTCGCAAAGAAAAAAACCGT	3	126	1
CATTAAATATCCAACGGCTTCTTATCTTGTTTTTCCTG	3	227	1
TCTGGACGTAAAAGTCGATTCCAGGAAATTATTTGGAA	4	85	0
GTAGAGATAAAAAACAGTTTCGAAGAGAACGAAGAGGG	4	178	0
TCAATAATGTCAACCTAATTAGTAGAGATAAAAAACAG	4	199	0
GTGTAATGTAAGAGCCGTTTCTATTATATCACGTTTTT	6	66	1
GTTTTGTAAACAAACTGATTCACTAAAAAGAAAACTAT	6	132	0
          *** * * ***    * *
MAP Score: 8.35494

Motif 9
CATTACACTCTTACCATGTTACTTTCCTTCCATATCAAAAAC	6	32	0
TACGTAAACGTTACCGTGAAAGTTACCGTGATGTCAAGCGAC	4	18	1
TATCACGTATTTTCCTTCGGTTTTGTCGAAAACATGGTGTAG	2	26	0
TTGGTCTAAATTTCCCTCTTCGTTCTCTTCGAAACTGTTTTT	4	165	1
AATCTAATTGTTACCTTTTGCTTTACTTCTGAGAGAACTTTG	1	115	1
GGGCGTCATGTTACCGTAATACTCGTCGTTCACCATGATCAC	2	224	0
AACATAGAGCATTCCCTTGACTTCTCCTGAAAAATAGTGAAA	6	186	1
TTCAACGTTATTTCCAAATAATTTCCTGGAATCGACTTTTAC	4	74	1
CGTGAACCTTTTCACGTTATATTTTTCACTATTTTTCAGGAG	6	209	0
GTCAAGCGACATCCCGAGGAGATTTTCAACGTTATTTCCAAA	4	50	1
TTTCAAGTGCTTTACCAATAGTTTTCTTTTTAGTGAATCAGT	6	115	1
       AGTATCACCTCCGGGTCTTCCAATTTCATTATATC	1	190	0
          ** ** *     ** **    *
MAP Score: 3.38929

Motif 10
TATAATCGACTATGGTGAATGTGAAAAAAATAT	0	126	1
AAAAATCGAATTCGGTGAATCTAATTGTTACCT	1	98	1
TGATAAGGGTTTGTGAGAGTCTGCCGTGTCATG	2	63	1
AGACCCTGTTTCATGTGAGTCTGATCTTTCTCC	3	16	1
ATTACTCTTGTGTTGTGATTGTGAAAACTTTCT	4	251	1
TAGTTTTCTTTTTAGTGAATCAGTTTGTTTACA	6	133	1
          *  ***** ****
MAP Score: 0.388594