AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252477
 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
TTTTTTTGTCAGGAGGTGGTATT       	6	128	1
ATATTAACACAGGAGGAGGGATATTTCA  	4	8	0
AAAAAATTTAGGGAGGTGTTTAC       	13	3	0
ACTTGAATCTGGGAGGTGTTTTCA      	13	90	1
AATACTCACACGGAGGTGAGTAGGTC    	5	6	0
AAGTGAAGAAGGGAGGTTTGATCTACTTCA	8	43	1
AACGAAGGAAGAGAGGTGTGAAGA      	2	25	1
TGTAATCTAAAGGAGGTGTCC         	14	1	0
TCAAACGATCTGGAGGTGGTGGATATGGTA	4	138	1
TTGGATAGTGAGGAGGTGAAAAT       	0	3	0
GATCAGCGAAAGGAGGATGGGAG       	12	60	1
TTGAACGAGAAGGAGGAGTAGAAATCC   	7	38	1
AAATCACCATGAGAGGTGATTGT       	0	70	1
TAATCCGAGAGGGAGGCTGGATT       	5	146	1
AAAATTCCTTCAGAGGTGGTTCTACT    	1	6	0
TTTTCCAGACAGGAGGTAAGAAAA      	1	53	1
CATATTGAGGAGAAGGAGGGAATAGG    	6	6	0
GAATCCCTCCGGAAGGAGACACAACGA   	9	45	1
          **********
MAP Score: 31.0638

Motif 2
CACTATCCAAATAATAACACTTTGAAATTG	0	23	1
TCTCATGGTGATTTTAACACGCTTTGAGAA	0	54	0
CTCTGAAGGAATTTTAACACTTTATTTAAA	1	21	1
    CGTTTCATTATATCACCGGGAAAGGG	3	6	1
TTTGTGTAGTATATTAACACAGGAGGAGGG	4	18	0
TCGTTACAAAAATTTAACATTAAAATCCCT	5	92	0
ATCTGGAAAGATTTTACCACCCATGTCGTT	5	117	0
TCTCCTCAATATGTTATCACCTGGAGAGTA	6	23	1
ATCTGGCATGATTATACCATAATCTCACAT	6	99	0
TTTCTATACTATTTTAACAT          	10	0	0
CAGCCTTGATAGTTTATCACAATCTTTCTT	12	24	0
TTCACTAAGGATTTTAACACCGAATTTTCG	14	63	1
CCGTCTGTTTATATTAACACCCAATTCATA	14	186	0
CACGATCAATAAATTAACACAAATCCGTCT	14	210	0
          **********
MAP Score: 27.461

Motif 3
AGAAACAATTTCAAAGTGTTATTATTTGGATAGTGAGGAGGTGAAA	0	12	0
GTTTCTCAAAGCGTGTTAAAATCACCATGAGAGGTGATTGT     	0	52	1
GCTTTAAATAAAGTGTTAAAATTCCTTCAGAGGTGGTTCTACT   	1	7	0
       TAGAATTCTTTAGTGAACGAAGGAAGAGAGGTGTGAAGA	2	3	1
         CGTTTCATTATATCACCGGGAAAGGGGTAAGAAGC  	3	1	1
AAAAGCCTTTGTGTAGTATATTAACACAGGAGGAGGGATATTTCA 	4	9	0
TTAACAATTAGGTTGATATAATTCCATTGAATCAAACGATCTGGAG	4	107	1
CGCCGGGACAGGGAAGTAAGAATACTCACACGGAGGTGAGTAGGTC	5	10	0
TTCCGATTAAAGATAATGGAAAGCCCGGCGCCGGGACAGGGAAGTA	5	38	0
TTTAATGTTAAATTTTTGTAACGACATGGGTGGTAAAATCTTTCCA	5	98	1
CTCCTTCTCCTCAATATGTTATCACCTGGAGAGTAAATTTCTCATT	6	18	1
CCTCCTGATAGAATTATATCAGGGCCTTGAACGAGAAGGAGGAGTA	7	12	1
TGTTGTACAATACATATTGAATCCCTCCGGAAGGAGACACAACGA 	9	27	1
CCCCTTGCGGGGCATTTCTGATTTTAAAGGGAGGGA          	11	36	1
AAACTATCAAGGCTGTTATAAGATCAGCGAAAGGAGGATGGGAG  	12	39	1
CCTTAGTGAAACATTTTGTGAATTTTCTGACGGTAAACTCTTTGTA	14	27	0
AACAGTTGATGAGTAATTTAAAAACACCGATTCGAATCCAGATTGA	14	98	0
TAAACAGACGGATTTGTGTTAATTTATTGATCGTGGAATGTTTCGA	14	205	1
          *  *  *   *   *   **  * **
MAP Score: 13.3178

Motif 4
TCAAAGTGTTATTATTTGGATAGTGAGGAGGTG	0	15	0
GCGTGTTAAAATCACCATGAGAGGTGATTGT  	0	62	1
GTTTCATTATATCACCGGGAAAGGGGTAAGAAG	3	11	1
TGGAAAGCCCGGCGCCGGGACAGGGAAGTAAGA	5	35	0
TCCCTCTCGGATTATCTGGAAAGATTTTACCAC	5	127	0
TCAATATGTTATCACCTGGAGAGTAAATTTCTC	6	28	1
AACATGAGAGAACATCGGGATTGTAACCCAATG	6	69	1
AGATTATGGTATAATCATGCCAGATTTTTTTGT	6	104	1
TGTGAGGGATAGAGTCACGATAGAAGTGAAGAA	8	20	1
TAAAATCAGAAATGCCCCGCAAGGGGGCCAGCT	11	29	0
TGATCTTATAACAGCCTTGATAGTTTATCACAA	12	32	0
CCCAATTCATAACATGTCGATAGGGTTAACGGA	14	164	0
          * **** *** **
MAP Score: 9.56159

Motif 5
   ATTTTCACCTCCTCACTATCCAAATAATAACAC	0	7	1
   AGTAGAACCACCTCTGAAGGAATTTTAACACTT	1	7	1
  TTTTCTTACCTCCTGTCTGGAAAAGCTTTAAATA	1	43	0
 TGAAATATCCCTCCTCCTGTGTTAATATACTACAC	4	9	1
GTGAAGAGGTTCACCTTTCTGTGATGAAAAGGTTTC	4	64	1
ACCATATCCACCACCTCCAGATCGTTTGATTCAATG	4	131	0
   GACCTACTCACCTCCGTGTGAGTATTCTTACTT	5	7	1
  AATCCAGCCTCCCTCTCGGATTATCTGGAAAGAT	5	135	0
ATTCCCTCCTTCTCCTCAATATGTTATCACCTGGAG	6	13	1
CAATATGTTATCACCTGGAGAGTAAATTTCTCATTT	6	29	1
   AATACCACCTCCTGACAAAAAAATCTGGCATGA	6	118	0
        CGCCTCCTGATAGAATTATATCAGGGCC	7	2	1
GATTTCTACTCCTCCTTCTCGTTCAAGGCCCTGATA	7	28	0
GTTGTGTCTCCTTCCGGAGGGATTCAATATGTATTG	9	34	0
TGAAAGCTGGCCCCCTTGCGGGGCATTTCTGATTTT	11	25	1
     TGAAAACACCTCCCAGATTCAAGTATATCCT	13	83	0
     GGACACCTCCTTTAGATTACAAAGAGTTTAC	14	5	1
          *******   *   **
MAP Score: 6.28675

Motif 6
CTTTATTTAAAGCTTTTCCAGACAGGAGGTAAGAAAA  	1	40	1
GCCTTTGTGTAGTATATTAACACAGGAGGAGGGATATTT	4	12	0
AAATCTTTCCAGATAATCCGAGAGGGAGGCTGGATT   	5	133	1
TAATCATGCCAGATTTTTTTGTCAGGAGGTGGTATT   	6	115	1
CAAGGCCCTGATATAATTCTATCAGGAGGCG        	7	2	0
    ATTTCTTGCTGTTTTTGAAAGCTGGCCCCCTTGCG	11	6	1
ATATTTTTTTAGGATATACTTGAATCTGGGAGGTGTTTT	13	73	1
ATGAATTGGGTGTTAATATAAACAGACGGATTTGTGTTA	14	187	1
          ** *  *     **** **
MAP Score: 3.13323

Motif 7
ATCCACCACCTCCAGATCGTTTGATTCAATGGAATTATATCAA	4	119	0
GTAAAATCTTTCCAGATAATCCGAGAGGGAGGCTGGATT    	5	130	1
AAATTTACTCTCCAGGTGATAACATATTGAGGAGAAGGAGGGA	6	15	0
      CGCCTCCTGATAGAATTATATCAGGGCCTTGAACGAG	7	4	1
AGGGATAGAGTCACGATAGAAGTGAAGAAGGGAGGTTTGATCT	8	24	1
       ATTTCTTGCTGTTTTTGAAAGCTGGCCCCCTTGCGG	11	3	1
AAATATTTTTTTAGGATATACTTGAATCTGGGAGGTGTTTTCA	13	71	1
          **  * *  *   * *    ***
MAP Score: 2.6711

Motif 8
CAAAGCGTGTTAAAATCACCATGAGAGGTGA	0	58	1
   CGTTTCATTATATCACCGGGAAAGGGGT	3	7	1
TTGTGTAGTATATTAACACAGGAGGAGGGAT	4	16	0
CTGTGTTAATATACTACACAAAGGCTTTTGT	4	26	1
AAAGAAACCTTTTCATCACAGAAAGGTGAAC	4	72	0
CTCATTTCCTTAACATGAGAGAACATCGGGA	6	58	1
TCCCTCCCTTTAAAATCAGAAATGCCCCGCA	11	41	0
AAGGCTGTTATAAGATCAGCGAAAGGAGGAT	12	47	1
TTACCGTCAGAAAATTCACAAAATGTTTCAC	14	37	1
TCACTAAGGATTTTAACACCGAATTTTCGTG	14	64	1
ATGAGTAATTTAAAAACACCGATTCGAATCC	14	105	0
CGTCTGTTTATATTAACACCCAATTCATAAC	14	184	0
TGGGTGTTAATATAAACAGACGGATTTGTGT	14	193	1
ACGATCAATAAATTAACACAAATCCGTCTGT	14	208	0
          *** *******
MAP Score: 1.32715