AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252168
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0149	25	fatty acid/phospholipid synthesis protein
#1	TM0151	300	conserved hypothetical protein
#2	TM0524	209	conserved hypothetical protein
#3	TM0526	30	host factor I
#4	TM0770	60	conserved hypothetical protein
#5	TM0808	165	transcriptional regulator, XylR-related
#6	TM0811	49	sugar ABC transporter, permease protein
#7	TM1243	43	phosphoribosylaminoimidazole-succinocarboxamide synthase
#8	TM1507	46	phoH-related protein
#9	TM1666	104	succinyl-diaminopimelate desuccinylase, putative

Motif 1
TTACAGAAAACCTACCACCTAAAATCCAGT	1	81	1
TTCAGAGAAACCTACCACTTACCTACCACT	1	123	1
CTACCACTTACCTACCACTTACCTACCACC	1	134	1
CTACCACTTACCTACCACCCGGGTGGTAAG	1	145	1
ATGTCTGCAACTTACCACCCGGGTGGTAGG	1	155	0
ATACTCGAAACCTACCACCTGCGTCCCCTA	1	223	1
        TTTCTATCACCTCTTTTCAGGA	1	288	0
        TCTCTATCACCTCTAAGAGCTT	2	197	0
          CCTTTCACCTCAGTTCTGAT	4	50	0
          **********
MAP Score: 28.2959

Motif 2
CCTCCCTTTCGAAAGGAGAGAGAGA          	6	34	1
ATTGATCCTGAAAAGAGGTGATAGAAA        	1	283	1
GATCATAAAGAAAAGAAGCGTCAGAAGTCCCAGAT	2	45	0
GGAAAAACGAAAAGGTGGCTCCAGAAGGAGCCACC	5	33	0
ACGCTCATTAAAAGGACGTTGTAGAATCTTGAATC	1	47	0
GAATTTTCAAAAAGGGCGGGGAGGCGAGCGT    	7	22	1
GTTATAATTAGAAGGCGAGGTGAGATC        	4	2	0
TCTCCTTTCGAAAGGGAGGGGGACACACCCCTCCC	6	18	0
AGTGCCACCTGATAGTTGTGATAGCTCACGAGAAA	2	86	0
    TAGAGTGAAAATAGCGATCGATGTG      	0	6	1
ACCAGGAATTGAAGACAAAGATAGAGGAACAGAAA	2	150	1
          AAAAGATGGGGAGGGGTGTGTCCCC	6	0	1
  ACTGAGGCCAAGAAGGCGGAAGCATTTCAGAGT	2	8	1
TAGAGGAACAGAAAGCGCTGAACGAGAAGCTCTTA	2	171	1
ACGTCCTTTTAATGAGCGTTACAGAAAACCTACCA	1	63	1
AGTAGTAGTAAATAATAGGGGACGCAGGTGGTAGG	1	233	0
          *****  * *  ***
MAP Score: 14.827

Motif 3
TTACAGAAAACCTACCACCTAAAATCCAGTATCCAAGC	1	81	1
CTACCACTTACCTACCACCCGGGTGGTAAGTTGCAGAC	1	145	1
AAACCTACCACCTGCGTCCCCTATTATTTACTACTACT	1	230	1
     TTTCTATCACCTCTTTTCAGGATCAATTATACT	1	277	0
CTCTGAAATGCTTCCGCCTTCTTGGCCTCAGT      	2	4	0
          CTCCCCCCTCGATGTGATTTCAAAATAG	3	12	0
       GATCTCACCTCGCCTTCTAATTATAACAACC	4	3	1
CCTTTTCGTTTTTCCCTCCTTAAATTCTTCCATCAGTT	5	53	1
GAGGGGGACACACCCCTCCCCATCTTTT          	6	0	0
GAGGGGTGTGTCCCCCTCCCTTTCGAAAGGAGAGAGAG	6	20	1
  ACGCTCGCCTCCCCGCCCTTTTTGAAAATTCTATAC	7	17	0
        GGCTTCACGCTCCCTGTAGTATAATTTCCT	8	2	1
       GTAAACACCTCCCTAAATTTTTTCTATCAAT	9	3	1
      TGAAAACACCTCCCAGATTCAAGTATATCCTA	9	82	0
          * **** ***    *  *
MAP Score: 12.88

Motif 4
CCACTTACCTACCACCCGGGTGGTAAGTTGCAG	1	148	1
GTATAATTGATCCTGAAAAGAGGTGATAGAAA 	1	278	1
    ACTGAGGCCAAGAAGGCGGAAGCATTTCA	2	6	1
GAGCTATCACAACTATCAGGTGGCACTGGAGAA	2	94	1
TTTTGAAATCACATCGAGGGGGGAG        	3	15	1
GTTATAATTAGAAGGCGAGGTGAGATC      	4	4	0
AGAAAATAAAAACAAGAAAGCGGGTGGCTCCTT	5	11	1
AGGAGGGAAAAACGAAAAGGTGGCTCCAGAAGG	5	40	0
ACTGATGGAAGAATTTAAGGAGGGAAAAACGAA	5	57	0
         AAAAGATGGGGAGGGGTGTGTCCC	6	1	1
TCTCCTTTCGAAAGGGAGGGGGACACACCCCTC	6	20	0
CCTCCCTTTCGAAAGGAGAGAGAGA        	6	34	1
TATAGAATTTTCAAAAAGGGCGGGGAGGCGAGC	7	18	1
AAGGAAATTATACTACAGGGAGCGTGAAGCC  	8	8	0
TTGATAGAAAAAATTTAGGGAGGTGTTTAC   	9	7	0
          ****  **** **
MAP Score: 10.8194

Motif 5
TGTAGAATCTTGAATCTGAACGGTAATATTGTT	1	30	0
CTTGGATACTGGATTTTAGGTGGTAGGTTTTCT	1	85	0
CCACTTACCTACCACCCGGGTGGTAAGTTGCAG	1	148	1
TAAATAATAGGGGACGCAGGTGGTAGGTTTCGA	1	227	0
    ACTGAGGCCAAGAAGGCGGAAGCATTTCA	2	6	1
GAGCTATCACAACTATCAGGTGGCACTGGAGAA	2	94	1
GGAATTGAAGACAAAGATAGAGGAACAGAAAGC	2	154	1
TTTTGAAATCACATCGAGGGGGGAG        	3	15	1
TGTTATAATTAGAAGGCGAGGTGAGATC     	4	5	0
TGATAAAATCAGAACTGAGGTGAAAGG      	4	43	1
AATAAAAACAAGAAAGCGGGTGGCTCCTTCTGG	5	15	1
       AAAAGATGGGGAGGGGTGTGTCCCCC	6	3	1
CTCTCCTTTCGAAAGGGAGGGGGACACACCCCT	6	21	0
TATAGAATTTTCAAAAAGGGCGGGGAGGCGAGC	7	18	1
TTGATAGAAAAAATTTAGGGAGGTGTTTAC   	9	7	0
AGGATATACTTGAATCTGGGAGGTGTTTTCA  	9	83	1
          **** * *** **
MAP Score: 8.09147

Motif 6
CTACAACGTCCTTTTAATGAGCGTTACAGA	1	58	1
TCTGATGAGGCTTTTAATGATGTCTGCAAC	1	174	0
TTTGAACAGGCTTCTGATGAGGCTTTTAAT	1	186	0
TCTATCACCTCTTTTCAGGATCAATTATAC	1	278	0
TCTGACGCTTCTTTTCTTTATGATCTTTGT	2	55	1
GATCTTTGTTTTTCTCGTGAGCTATCACAA	2	76	1
CCTCTAAGAGCTTCTCGTTCAGCGCTTTCT	2	180	0
CTCACCTCGCCTTCTAATTATAACAACCAA	4	13	1
CGGGTGGCTCCTTCTGGAGCCACCTTTTCG	5	31	1
CTGGAGCCACCTTTTCGTTTTTCCCTCCTT	5	44	1
GTTACAGTTTCATTTCGTTAACTGATGGAA	5	80	0
          **********
MAP Score: 2.5618