AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252178
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0149	25	fatty acid/phospholipid synthesis protein
#1	TM0151	300	conserved hypothetical protein
#2	TM0521	81	heat shock protein HslV
#3	TM0524	209	conserved hypothetical protein
#4	TM0526	30	host factor I
#5	TM0770	60	conserved hypothetical protein
#6	TM0803	141	CTP synthetase
#7	TM0807	161	alkyl hydroperoxide reductase, putative
#8	TM0808	165	transcriptional regulator, XylR-related
#9	TM0811	49	sugar ABC transporter, permease protein
#10	TM1243	43	phosphoribosylaminoimidazole-succinocarboxamide synthase
#11	TM1507	46	phoH-related protein
#12	TM1666	104	succinyl-diaminopimelate desuccinylase, putative

Motif 1
TACTGGATTTTAGGTGGTAGGTTTTCTGTA	1	82	0
ACTTACCACCCGGGTGGTAGGTAAGTGGTA	1	146	0
ATAGGGGACGCAGGTGGTAGGTTTCGAGTA	1	224	0
ATCCTGAAAAGAGGTGATAGAAA       	1	287	1
CATCTTAAATGAGGAGGTGCGAAC      	2	4	0
AAAATAACTTGAGGAGGTGTTGAACC    	2	65	1
TCACAACTATCAGGTGGCACTGGAGAAGCA	3	100	1
GAAGCTCTTAGAGGTGATAGAGA       	3	196	1
AAATCACATCGAGGGGGGAG          	4	20	1
ATTAGAAGGCGAGGTGAGATC         	5	1	0
AATCAGAACTGAGGTGAAAGG         	5	49	1
TTTTTGTCAGGAGGTGGTATT         	6	1	0
ATTTACTCTCCAGGTGATAACATATTGAGG	6	105	1
TATTGAGGAGAAGGAGGGAATAGG      	6	127	1
      AGACGGGGAGAGATTCTCCCCGTT	7	4	1
AAAAATTTACGAGGAGGTGTTTTGT     	7	146	1
GGAAGAATTTAAGGAGGGAAAAACGAAAAG	8	54	0
   AAAAGATGGGGAGGGGTGTGTCCCCCT	9	7	1
TCCTTTCGAAAGGGAGGGGGACACACCCCT	9	21	0
TCCCTTTCGAAAGGAGAGAGAGA       	9	36	1
CAAAAAGGGCGGGGAGGCGAGCGT      	10	29	1
GAAAAAATTTAGGGAGGTGTTTAC      	12	4	0
TACTTGAATCTGGGAGGTGTTTTCA     	12	89	1
          **********
MAP Score: 35.7324

Motif 2
   TAGAGTGAAAATAGCGATCGATGTG          	0	7	1
GCAGTATAATTGATCCTGAAAAGAGGTGATAGAAA   	1	275	1
AAATGGTATCATCTTAAATGAGGAGGTGCGAAC     	2	5	0
AGAAATTGAGTTAAAATAACTTGAGGAGGTGTTGAACC	2	53	1
CTATTTTGAAATCACATCGAGGGGGGAG          	4	12	1
TTGGTTGTTATAATTAGAAGGCGAGGTGAGATC     	5	5	0
AACCAATGATAAAATCAGAACTGAGGTGAAAGG     	5	37	1
ACTCTCCAGGTGATAACATATTGAGGAGAAGGAGGGAA	6	109	1
TTACACATAGAGAACAAAAAACGGGGAGAATCTCTCCC	7	15	0
TAGAATCATTTTAAAAATTTACGAGGAGGTGTTTTGT 	7	134	1
 CAGAAAATAAAAACAAGAAAGCGGGTGGCTCCTTCTG	8	9	1
          AAAAGATGGGGAGGGGTGTGTCCCCCTC	9	0	1
GTATAGAATTTTCAAAAAGGGCGGGGAGGCGAGCGT  	10	17	1
CTTTCTAAGGAAATTATACTACAGGGAGCGTGAAGCC 	11	9	0
TGATTGATAGAAAAAATTTAGGGAGGTGTTTAC     	12	5	0
TCAATCAATTATATAAAATCTTGGGGTATCATTTCAAA	12	36	1
TTTAGGATATACTTGAATCTGGGAGGTGTTTTCA    	12	80	1
          * ** *      ******
MAP Score: 27.8687

Motif 3
       GTAAACACCTCCCTAAATTTTTT	12	3	1
      TGAAAACACCTCCCAGATTCAAGT	12	90	0
     GGTTCAACACCTCCTCAAGTTATTT	2	66	0
      ACAAAACACCTCCTCGTAAATTTT	7	147	0
       AATACCACCTCCTGACAAAAAAA	6	3	1
GAGGGGGACACACCCCTCCCCATCTTTT  	9	8	0
AGCGTTACAGAAAACCTACCACCTAAAATC	1	77	1
GAGGGGTGTGTCCCCCTCCCTTTCGAAAGG	9	20	1
       GTTCGCACCTCCTCATTTAAGAT	2	3	1
TTCAATACTCGAAACCTACCACCTGCGTCC	1	219	1
CGATTTCAGAGAAACCTACCACTTACCTAC	1	119	1
CCACTTACCTACCACTTACCTACCACCCGG	1	137	1
AATGATGTCTGCAACTTACCACCCGGGTGG	1	159	0
          **********
MAP Score: 23.723

Motif 4
ATAATTGATCCTGAAAAGAGGTGATAGAAA 	1	280	1
ATGGTATCATCTTAAATGAGGAGGTGCGAAC	2	10	0
AAAGATCATAAAGAAAAGAAGCGTCAGAAGT	3	52	0
TCGAAATACCAGGAATTGAAGACAAAGATAG	3	143	1
ACAAAGATAGAGGAACAGAAAGCGCTGAACG	3	164	1
ATGATAAAATCAGAACTGAGGTGAAAGG   	5	42	1
TCTCATGTTAAGGAAATGAGAAATTTACTCT	6	83	1
AAATTTGATACAGAACAGAAAAATTCACGAA	7	67	1
          CAGAAAATAAAAACAAGAAAG	8	0	1
TAACTGATGGAAGAATTTAAGGAGGGAAAAA	8	61	0
CCATCAGTTAACGAAATGAAACTGTAACTTG	8	82	1
          * *********
MAP Score: 6.91907

Motif 5
          GTTCGCACCTCCTCATTTAAG	2	0	1
TAAAGGAAATGGTATCATCTTAAATGAGGAG	2	18	0
     GGTTCAACACCTCCTCAAGTTATTTT	2	65	0
CCAAGAAGGCGGAAGCATTTCAGAGTTAATC	3	17	1
GTGCTTCTCCAGTGCCACCTGATAGTTGTGA	3	100	0
          GATCTCACCTCGCCTTCTAAT	5	0	1
          AATACCACCTCCTGACAAAAA	6	0	1
TCCTCAATATGTTATCACCTGGAGAGTAAAT	6	105	0
ATATCAAATTAGAATCATTTTAAAAATTTAC	7	125	1
         ACAAAACACCTCCTCGTAAATT	7	149	0
GGCTCCAGAAGGAGCCACCCGCTTTCTTGTT	8	21	0
GGCTCCTTCTGGAGCCACCTTTTCGTTTTTC	8	36	1
GTCAAGTTACAGTTTCATTTCGTTAACTGAT	8	84	0
TCAACCAATAGGTCACACTTTGTCAAGTTAC	8	105	0
AAAGGGAGGGGGACACACCCCTCCCCATCTT	9	12	0
CGCTCCCTGTAGTATAATTTCCTTAGAAAGT	11	17	1
          GTAAACACCTCCCTAAATTTT	12	0	1
AAAATCTTGGGGTATCATTTCAAATATTTTT	12	50	1
         TGAAAACACCTCCCAGATTCAA	12	92	0
          **** ******
MAP Score: 3.17434

Motif 6
ATTGATCCTGAAAAGAGGTGATAGAAA    	1	283	1
TTTCTCAAATAAAGGAAATGGTATCATCTTA	2	27	0
ACTGAGGCCAAGAAGGCGGAAGCATTTCAGA	3	10	1
TTTTGAAATCACATCGAGGGGGGAG      	4	15	1
TGTTATAATTAGAAGGCGAGGTGAGATC   	5	7	0
TTAACATGAGAGAACATCGGGATTGTAACCC	6	63	0
CATATTGAGGAGAAGGAGGGAATAGG     	6	125	1
          AGACGGGGAGAGATTCTCCCC	7	0	1
AGAGAACAAAAAACGGGGAGAATCTCTCCCC	7	14	0
TTTTAAAAATTTACGAGGAGGTGTTTTGT  	7	142	1
TAAAAACAAGAAAGCGGGTGGCTCCTTCTGG	8	17	1
AAGGAGGGAAAAACGAAAAGGTGGCTCCAGA	8	43	0
          AAAAGATGGGGAGGGGTGTGT	9	0	1
TCTCCTTTCGAAAGGGAGGGGGACACACCCC	9	22	0
CCTCCCTTTCGAAAGGAGAGAGAGA      	9	34	1
AGAATTTTCAAAAAGGGCGGGGAGGCGAGCG	10	21	1
          ****** ****
MAP Score: 1.75823

Motif 7
GTGGTAAGTTGCAGACATCATTAAAAGCCTCA	1	167	1
          GTTCGCACCTCCTCATTTAAGA	2	0	1
         ACAAAACACCTCCTCGTAAATTT	7	148	0
GGCTCCAGAAGGAGCCACCCGCTTTCTTGTTT	8	20	0
GTTGCATGCCGCAAACAACTTCATAAATTATT	8	137	0
AAAGGGAGGGGGACACACCCCTCCCCATCTTT	9	11	0
        ACGCTCGCCTCCCCGCCCTTTTTG	10	29	0
          GTAAACACCTCCCTAAATTTTT	12	0	1
         TGAAAACACCTCCCAGATTCAAG	12	91	0
          * * ********
MAP Score: 0.224029