AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252523
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0013	161	conserved hypothetical protein
#1	TM0015	90	pyruvate ferredoxin oxidoreductase, gamma subunit
#2	TM0033	300	hypothetical protein
#3	TM0034	87	iron-sulfur cluster-binding protein
#4	TM0402	300	ammonium transporter
#5	TM0404	47	deoxycytidylate deaminase, putative
#6	TM0880	45	oxaloacetate decarboxylase, beta subunit
#7	TM0882	135	O-acetylhomoserine sulfhydrylase
#8	TM1162	207	conserved hypothetical protein
#9	TM1754	102	butyrate kinase, putative

Motif 1
ATCATATGACAGTGAGAGGTGTTATAATCGA	0	46	0
ATCGTTTGAAATCTGGAGGTGACAAT     	0	145	1
ATCCATGTTGTCGAGGAGGTGCAATCGG   	1	72	1
CAGCAGGGCTCTCTTGAGGTGTATGATTTTT	3	29	0
CATATTTACCAAAAGGAGGTGTTTTT     	4	284	1
  GGTTTCCTTTCGGGAGGAGAAACCTCCTC	5	8	1
AGGCCGAAAAAAGGGGAGGAGGTTTCTCCTC	5	23	0
ACCATCTCAAATGTGGAGGTGATACTT    	7	6	0
AAAATTTTATCACGGGAGGTGGAGAGA    	7	118	1
AAAAAGCGGTCCGAGGAGGTGTGAAA     	8	5	0
CAGATGCTTTTTCGGGAGGTGATTTCTAAGT	8	60	0
TATAATCTAAAATGGGAGGTGGTAAC     	8	191	1
CTTTTGTCAACATAAGAGGTGATCGG     	9	86	1
          * *********
MAP Score: 28.2573

Motif 2
TTTCAAACGATTTCAAGAATTAATCCCCAT	0	126	0
TTGGAAAGAGCATCGGGAATAAAATCAGTT	2	114	0
ATTCTTCTCACTTTGAGAATGTCTTGAGCT	2	146	0
GGGGGTATAATCACGAGAAGAGGA      	2	286	1
ATCCCTCCTTTTTTGAGAATTAAAAAGAGA	3	63	0
CCGCTGTCAATTATGAGAATGTTTCAGTTT	4	57	0
CGGGAATAAATTTCTGGAGGATTTTATATG	4	111	0
TATTACTAATTTTCGGGAATAAATTTCTGG	4	124	0
GGGGTTCTTTTTTTTAGAGGGCACAAACCC	4	172	0
GTTTTTTGTTTTTCAAGAATATTGTTTATT	4	211	1
   GGTTTCCTTTCGGGAGGAGAAACCTCC	5	7	1
GAAAATTTTATCACGGGAGGTGGAGAGA  	7	117	1
GCAGATGCTTTTTCGGGAGGTGATTTCTAA	8	62	0
ATTATACTCTTTTCGGAAATTAACGTTGAA	8	167	0
          **********
MAP Score: 9.38736

Motif 3
ATTTTTATCTGATATTTTTTTCACATTCACCATA	0	11	1
TGATTTCGATGGATTTTTTGTTACACACATTCTT	2	170	0
TTCGATATGTTGTAATTTTAACAAAAAATAACGG	2	235	0
CTCTTGAGGTGTATGATTTTTCACTTAAATTCTA	3	16	0
TGGTGTTTGTTTTTTGTTTTTCAAGAATATTGTT	4	203	1
AGGTGTGTAAGAAATATTTTACACCATCTCAAAT	7	25	0
ACACACCTCTGAAACATTTGACACGAAGATATAG	7	51	1
GAGGACATCAGAAAATTTTATCACGGGAGGTGGA	7	107	1
AGTACAGAAAGAAAAATTTTTCAACGAACACATT	8	128	1
AACATCAAGATCAAAATTTGTCAACATT      	9	4	0
AAACTTTGTGTAATCTTTTGTCAACATAAGAGGT	9	72	1
          * **  *** ****
MAP Score: 9.35482

Motif 4
TCATATGATGAAAAGAAAAGAAACAGTCACAAAG	0	68	1
CTAACATGGAAAAAGAAGAACCCCGAAGGGGTTC	6	11	0
TTAATTTCCGAAAAGAGTATAATCTAAAATGGGA	8	174	1
TCTTGAAAAACAAAAAACAAACACCATGGGGTTC	4	195	0
AGTTGTAACTCAAAGAAAATATTAGAATTTGAAC	2	84	0
GTGCCCTCTAAAAAAAAGAACCCCATGGTGTTTG	4	178	1
GTAATTTTAACAAAAAATAACGGCAACCGATCAT	2	224	0
TACTAAATCTAAAAGAGGACATCAGAAAATTTTA	7	93	1
         TCAAAAAGTACAAACACGAGTAATA	2	1	1
GGTGAATGTGAAAAAAATATCAGATAAAAATT  	0	8	0
AAAAATTTTTCAACGAACACATTCCTTCTTCAAC	8	139	1
TTATGTTGACAAAAGATTACACAAAGTTTTATGT	9	67	0
AATTAATCTTAAAAGAGTCAACAAACATATTTAC	4	259	1
TTTGAGAATTAAAAAGAGAGCCCAGCAGGGCTCT	3	48	0
ATCACCTCCCGAAAAAGCATCTGCGTAGAACTAT	8	68	1
          ******* * *  *
MAP Score: 8.30073

Motif 5
CAGTGAGAGGTGTTATAATCGACTATGGTG	0	38	0
TTGCATGTAGTGATAGAATCAAATGGGGAT	0	104	1
ATTATGTATCTGATACAATAACGTGGGTTA	1	41	1
TCAAAGAAAATATTAGAATTTGAACTATAA	2	79	0
CGTTATTTTTTGTTAAAATTACAACATATC	2	236	1
       TTGTGGTAGAATTTAAGTGAAAA	3	3	1
TTTTTTGAATTGATAGTATTGAGACATATA	4	87	1
TCTTTTTCCATGTTAGAATAATAGTT    	6	29	1
CCACCTCCCGTGATAAAATTTTCTGATGTC	7	110	0
TCCGGTGTGATGTTAGAATAGTTCTACGCA	8	89	0
TGTTTCTGTATGGTAATATTCTTATGGAAC	9	34	1
          **********
MAP Score: 8.0133

Motif 6
   AATTTTTATCTGATATTTTTTTCACATTCACCATAG	0	7	1
CTTTGTGACTGTTTCTTTTCTTTTCATCATATGACAGTG	0	63	0
ATTATGAAATGCATTATGTATCTGATACAATAACGTGGG	1	29	1
CTATAATTCGAAATAATTCCTGTTATTCACTCATAATCA	2	46	0
TCAAATTCTAATATTTTCTTTGAGTTACAACTGATTTTA	2	86	1
TATGATTTCGATGGATTTTTTGTTACACACATTCTTCTC	2	167	0
ATTCACTTCGATATGTTGTAATTTTAACAAAAAATAACG	2	236	0
GCCCTGCTGGGCTCTCTTTTTAATTCTCAAAAAAGGAGG	3	51	1
TAAATTTCTGGAGGATTTTATATGTCTCAATACTATCAA	4	96	0
ACCCCATGGTGTTTGTTTTTTGTTTTTCAAGAATATTGT	4	197	1
TTTTTCAAGAATATTGTTTATTTGTATCATATTGATAGA	4	219	1
TTGAGATGGTGTAAAATATTTCTTACACACCTCTGAAAC	7	27	1
TTTCTGTATGGTAATATTCTTATGGAACATTACATAAAA	9	36	1
ATAAAACTTTGTGTAATCTTTTGTCAACATAAGAGGTGA	9	69	1
          **    * * * **  ***
MAP Score: 7.22987

Motif 7
ATGACAGTGAGAGGTGTTATAATCGACTAT	0	42	0
GGGCTCTCTTGAGGTGTATGATTTTTCACT	3	25	0
ATAATTGACAGCGGTTTTTTGAATTGATAG	4	73	1
AATCCAACATGGGGTTTGTGCCCTCTAAAA	4	161	1
CAAACACCATGGGGTTCTTTTTTTTAGAGG	4	182	0
AGAACCCCATGGTGTTTGTTTTTTGTTTTT	4	194	1
TTACCAAAAGGAGGTGTTTTT         	4	289	1
AAAAGGGGAGGAGGTTTCTCCTCCCGAAAG	5	16	0
GAACCCCTTCGGGGTTCTTCTTTTTCCATG	6	11	1
AAATGTTTCAGAGGTGTGTAAGAAATATTT	7	40	0
GCTTTTTCGGGAGGTGATTTCTAAGTGGAA	8	56	0
GTTCTACGCAGATGCTTTTTCGGGAGGTGA	8	69	0
TTTCTGTACTGGTGTTTCTTCCGGTGTGAT	8	108	0
TTTTGATCTTGATGTTTCTGTATGGTAATA	9	22	1
          **********
MAP Score: 6.02745

Motif 8
AATTCTGCATCAAAGGGGGTATAATCACGA	2	272	1
GGAGGCCGAAAAAAGGGGAGGAGGTTTCTC	5	26	0
TGATAGAATCAAATGGGGATTAATTCTTGA	0	114	1
ATCTAATCCAACATGGGGTTTGTGCCCTCT	4	157	1
CATATTTACCAAAAGGAGGTGTTTTT    	4	284	1
AAAACAAACACCATGGGGTTCTTTTTTTTA	4	186	0
TAATTCTCAAAAAAGGAGGGATTCAC    	3	71	1
AGAAGAACCCCGAAGGGGTTCT        	6	2	0
GTATAATCTAAAATGGGAGGTGGTAAC   	8	190	1
ACACCATCTCAAATGTGGAGGTGATACTT 	7	9	0
          **********
MAP Score: 5.7845