AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252460
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0181	83	hypothetical protein
#1	TM0238	67	hypothetical protein
#2	TM0239	39	glucose-1-phosphate adenylyltransferase
#3	TM0362	35	deoxyribonuclease IV
#4	TM0666	163	serine acetyltransferase
#5	TM0759	159	acyltransferase, putative
#6	TM0802	141	3-oxoacyl-(acyl carrier protein) synthase II
#7	TM0888	55	conserved hypothetical protein
#8	TM0889	64	conserved hypothetical protein
#9	TM1631	62	conserved hypothetical protein
#10	TM1655	36	response regulator DrrA
#11	TM1656	62	hypothetical protein
#12	TM1658	73	S-adenosylmethionine synthetase
#13	TM1666	104	succinyl-diaminopimelate desuccinylase, putative
#14	TM1840	250	alpha-amylase

Motif 1
AAAGTGTTATTATTTGGATAGTGAGGAGGTGAAAAT  	0	8	0
CAAAGCGTGTTAAAATCACCATGAGAGGTGATTGT   	0	58	1
TATTTAAAGCTTTTCCAGACAGGAGGTAAGAAAA    	1	43	1
TAGAATTCTTTAGTGAACGAAGGAAGAGAGGTGTGAAG	2	10	1
   CGTTTCATTATATCACCGGGAAAGGGGTAAGAAGC	3	7	1
TTTGTGTAGTATATTAACACAGGAGGAGGGATATTTCA	4	10	0
TTCCATTGAATCAAACGATCTGGAGGTGGTGGATATGG	4	128	1
GGGAAGTAAGAATACTCACACGGAGGTGAGTAGGTC  	5	8	0
TCTTTCCAGATAATCCGAGAGGGAGGCTGGATT     	5	136	1
ACTCTCCAGGTGATAACATATTGAGGAGAAGGAGGGAA	6	14	0
TCATGCCAGATTTTTTTGTCAGGAGGTGGTATT     	6	118	1
GGCCCTGATATAATTCTATCAGGAGGCG          	7	0	0
TATCAGGGCCTTGAACGAGAAGGAGGAGTAGAAATCC 	7	28	1
GTCACGATAGAAGTGAAGAAGGGAGGTTTGATCTACTT	8	33	1
TCAATATGTATTGTACAACACTGTGGAGGAACAGAAA 	9	9	0
CAATACATATTGAATCCCTCCGGAAGGAGACACAACGA	9	34	1
GGGGCATTTCTGATTTTAAAGGGAGGGA          	11	44	1
TGATTGATAGAAAAAATTTAGGGAGGTGTTTAC     	13	5	0
TTTAGGATATACTTGAATCTGGGAGGTGTTTTCA    	13	80	1
GTAAACTCTTTGTAATCTAAAGGAGGTGTCC       	14	3	0
          * **     * ***** *
MAP Score: 31.6849

Motif 2
CAATTTCAAAGTGTTATTATTTGGATAGTG	0	23	0
TTCTCAAAGCGTGTTAAAATCACCATGAGA	0	54	1
TTTAAATAAAGTGTTAAAATTCCTTCAGAG	1	21	0
CCCTTTCCCGGTGATATAATGAAACG    	3	6	0
CCCTCCTCCTGTGTTAATATACTACACAAA	4	18	1
AGGGATTTTAATGTTAAATTTTTGTAACGA	5	92	1
AACGACATGGGTGGTAAAATCTTTCCAGAT	5	117	1
TACTCTCCAGGTGATAACATATTGAGGAGA	6	23	0
ATGTGAGATTATGGTATAATCATGCCAGAT	6	99	1
          ATGTTAAAATAGTATAGAAA	10	0	1
AAGAAAGATTGTGATAAACTATCAAGGCTG	12	24	1
CGAAAATTCGGTGTTAAAATCCTTAGTGAA	14	63	0
TATGAATTGGGTGTTAATATAAACAGACGG	14	186	1
AGACGGATTTGTGTTAATTTATTGATCGTG	14	210	1
          **********
MAP Score: 27.461

Motif 3
CTTTTCCAGACAGGAGGTAAGAAAA      	1	52	1
GTGAACGAAGGAAGAGAGGTGTGAAGA    	2	22	1
ATTATATCACCGGGAAAGGGGTAAGAAGC  	3	16	1
TATATTAACACAGGAGGAGGGATATTTCA  	4	8	0
ATCAAACGATCTGGAGGTGGTGGATATGGTA	4	137	1
ATTTTTGTAACGACATGGGTGGTAAAATCTT	5	109	1
CCAGATAATCCGAGAGGGAGGCTGGATT   	5	141	1
AACATATTGAGGAGAAGGAGGGAATAGG   	6	7	0
ATTTTTTTGTCAGGAGGTGGTATT       	6	127	1
GGGCCTTGAACGAGAAGGAGGAGTAGAAATC	7	33	1
CGATAGAAGTGAAGAAGGGAGGTTTGATCTA	8	37	1
GTGTCTCCTTCCGGAGGGATTCAATATGTAT	9	36	0
CAGAAATGCCCCGCAAGGGGGCCAGCTTTCA	11	25	0
TCAGCGAAAGGAGGATGGGAG          	12	62	1
TACTTGAATCTGGGAGGTGTTTTCA      	13	89	1
          * *********
MAP Score: 12.6361

Motif 4
GAAATTGTTTCTCAAAGCGTGTTAAAATCACCATGAGAGGTGATTG	0	46	1
AGAACCACCTCTGAAGGAATTTTAACACTTTATTTAAAGCTTTTCC	1	13	1
TAATATACTACACAAAGGCTTTTGTGAAAAAAGTGAAGAGGTTCAC	4	32	1
TTGGTTTTAACAATTAGGTTGATATAATTCCATTGAATCAAACGAT	4	101	1
CGGGACAGGGAAGTAAGAATACTCACACGGAGGTGAGTAGGTC   	5	7	0
CATTAAAATCCCTAAAGCCTCTTCCGATTAAAGATAATGGAAAGCC	5	59	0
TCCAGCCTCCCTCTCGGATTATCTGGAAAGATTTTACCACCCATGT	5	121	0
    CGCCTCCTGATAGAATTATATCAGGGCCTTGAACGAGAAGGA	7	6	1
TGAAATGATACCCCAAGATTTTATATAATTGATTGATAGAAAAAAT	13	26	0
GGTATCATTTCAAATATTTTTTTAGGATATACTTGAATCTGGGAGG	13	60	1
CTTTAGATTACAAAGAGTTTACCGTCAGAAAATTCACAAAATGTTT	14	19	1
CAAAATGTTTCACTAAGGATTTTAACACCGAATTTTCGTGATGTCA	14	55	1
TCAACTGTTTCATTCAGAAATATCGAAATTCCGTTAACCCTATCGA	14	135	1
TTAATATAAACAGACGGATTTGTGTTAATTTATTGATCGTGGAATG	14	199	1
          *    **  *  *   *     ****
MAP Score: 11.7456

Motif 5
AGCGTGTTAAAATCACCATGAGAGGTGATTGT     	0	61	1
TAAAGTGTTAAAATTCCTTCAGAGGTGGTTCTACT  	1	8	0
CGTTTCATTATATCACCGGGAAAGGGGTAAGAAGC  	3	10	1
TGTAGTATATTAACACAGGAGGAGGGATATTTCA   	4	7	0
AAGAAACCTTTTCATCACAGAAAGGTGAACCTCTTCA	4	65	0
GGAAGTAAGAATACTCACACGGAGGTGAGTAGGTC  	5	8	0
AAATCTTTCCAGATAATCCGAGAGGGAGGCTGGATT 	5	133	1
        GCAACGAAGCTGTGAGGGATAGAGTCACG	8	2	1
ATACATATTGAATCCCTCCGGAAGGAGACACAACGA 	9	36	1
TTAAAATCAGAAATGCCCCGCAAGGGGGCCAGCTTTC	11	26	0
AGGCTGTTATAAGATCAGCGAAAGGAGGATGGGAG  	12	48	1
GATTGATAGAAAAAATTTAGGGAGGTGTTTAC     	13	5	0
          **   * * * **** *
MAP Score: 8.13562

Motif 6
TTGGATAGTGAGGAGGTGAAAAT       	0	3	0
GTTTCTCAAAGCGTGTTAAAATCACCATGA	0	52	1
TCACCATGAGAGGTGATTGT          	0	73	1
TTTTCCAGACAGGAGGTAAGAAAA      	1	53	1
GAAGGAAGAGAGGTGTGAAGA         	2	28	1
ACCCCTTTCCCGGTGATATAATGAAACG  	3	8	0
GTTCACCTTTCTGTGATGAAAAGGTTTCTT	4	72	1
AACGATCTGGAGGTGGTGGATATGGTATCG	4	141	1
AATACTCACACGGAGGTGAGTAGGTC    	5	6	0
GTAACGACATGGGTGGTAAAATCTTTCCAG	5	115	1
TTTTGTCAGGAGGTGGTATT          	6	131	1
AAGTGAAGAAGGGAGGTTTGATCTACTTCA	8	43	1
TGTCTCCTTCCGGAGGGATTCAATATGTAT	9	36	0
AAACTATCAAGGCTGTTATAAGATCAGCGA	12	39	1
AAAAAATTTAGGGAGGTGTTTAC       	13	3	0
ACTTGAATCTGGGAGGTGTTTTCA      	13	90	1
CACGAAAATTCGGTGTTAAAATCCTTAGTG	14	65	0
GGATTCGAATCGGTGTTTTTAAATTACTCA	14	105	1
GTTATGAATTGGGTGTTAATATAAACAGAC	14	184	1
          **********
MAP Score: 4.13207

Motif 7
TTGAAATTGTTTCTCAAAGCGTGTTAAAATCACC	0	44	1
GCGTGTTAAAATCACCATGAGAGGTGATTGT   	0	62	1
    AGTAGAACCACCTCTGAAGGAATTTTAACA	1	6	1
GTTTCATTATATCACCGGGAAAGGGGTAAGAAGC	3	11	1
 GACCTACTCACCTCCGTGTGAGTATTCTTACTT	5	9	1
AAATTTTTGTAACGACATGGGTGGTAAAATCTTT	5	107	1
TTTCCAGATAATCCGAGAGGGAGGCTGGATT   	5	138	1
TCAATATGTTATCACCTGGAGAGTAAATTTCTCA	6	28	1
TACATATTGAATCCCTCCGGAAGGAGACACAACG	9	37	1
TTGAAAGCTGGCCCCCTTGCGGGGCATTTCTGAT	11	24	1
          *** **  * ****
MAP Score: 3.37792

Motif 8
ATTTGGATAGTGAGGAGGTGAAAAT      	0	4	0
TAAAATCACCATGAGAGGTGATTGT      	0	68	1
TTAAAATTCCTTCAGAGGTGGTTCTACT   	1	7	0
AAAGCTTTTCCAGACAGGAGGTAAGAAAA  	1	48	1
TTTAGTGAACGAAGGAAGAGAGGTGTGAAGA	2	18	1
ATTATATCACCGGGAAAGGGGTAAGAAGC  	3	16	1
AGGCTTTTGTGAAAAAAGTGAAGAGGTTCAC	4	47	1
CTTTTCATCACAGAAAGGTGAACCTCTTCAC	4	64	0
AATCAAACGATCTGGAGGTGGTGGATATGGT	4	136	1
AGAATACTCACACGGAGGTGAGTAGGTC   	5	7	0
AGCCCGGCGCCGGGACAGGGAAGTAAGAATA	5	32	0
ATTATCTTTAATCGGAAGAGGCTTTAGGGAT	5	67	1
AACATATTGAGGAGAAGGAGGGAATAGG   	6	7	0
GATTTTTTTGTCAGGAGGTGGTATT      	6	126	1
ATATCAGGGCCTTGAACGAGAAGGAGGAGTA	7	27	1
TTGAATCCCTCCGGAAGGAGACACAACGA  	9	43	1
GCATTTCTGATTTTAAAGGGAGGGA      	11	47	1
TATAAGATCAGCGAAAGGAGGATGGGAG   	12	55	1
AGAAAAAATTTAGGGAGGTGTTTAC      	13	4	0
ATACTTGAATCTGGGAGGTGTTTTCA     	13	88	1
CTCTTTGTAATCTAAAGGAGGTGTCC     	14	5	0
          * *********
MAP Score: 3.26165

Motif 9
GCTTCTTACCCCTTTCCCGGTGATATAATGAAA	3	12	0
   ACAATCACCTCTCATGGTGATTTTAACACG	0	63	0
TTCTTACTTCCCTGTCCCGGCGCCGGGCTTTCC	5	34	1
TGAGAAATTTACTCTCCAGGTGATAACATATTG	6	29	0
GGTGGTAAAATCTTTCCAGATAATCCGAGAGGG	5	126	1
CTGATATAATTCTATCAGGAGGCG         	7	1	0
ACATATTGAATCCCTCCGGAAGGAGACACAACG	9	38	1
TTTCTTACCTCCTGTCTGGAAAAGCTTTAAATA	1	43	0
ATCCCGATGTTCTCTCATGTTAAGGAAATGAGA	6	57	0
AAGTAAGAATACTCACACGGAGGTGAGTAGGTC	5	10	0
GGTTCACCTTTCTGTGATGAAAAGGTTTCTTTG	4	71	1
ATTGTGATAAACTATCAAGGCTGTTATAAGATC	12	31	1
          *** *** ** **
MAP Score: 2.22245