AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons028_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252643
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0711	51	hypothetical protein
#1	TM0713	44	hypothetical protein
#2	TM0826	127	hypothetical protein
#3	TM0828	29	sugar kinase, pfkB family
#4	TM0934	27	conserved hypothetical protein
#5	TM1132	155	moxR protein, putative
#6	TM1135	83	branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
#7	TM1136	78	branched chain amino acid ABC transporter, permease protein
#8	TM1161	207	Mg2+ transporter MgtE, putative
#9	TM1344	300	ribosomal protein S15
#10	TM1345	73	polynucleotide phosphorylase
#11	TM1357	50	conserved hypothetical protein

Motif 1
ACATCCTTGAAAACACCCCGTGAACGGCCG	0	12	0
        CCAATCACCTCCAGGATAGATT	2	2	1
      GAGGCATCACCTCGTTTTTGATTC	2	113	0
        ACGATCACCTCGAAGTCAAAAG	3	17	0
        AATATCTCCCCCGGAGGTAAGA	4	15	0
        GTTACCACCTCCCATTTTAGAT	8	2	1
ACTATTCTAACATCACACCGGAAGAAACAC	8	100	0
TCCACTTAGAAATCACCTCCCGAAAAAGCA	8	140	0
     TTTCACACCTCCTCGGACCGCTTTT	8	192	0
      ACTGCTCCACCCCGCACCGTCTAA	9	4	1
TATAATATAGCATCACCCCGTTAGGTTGTC	9	43	1
         CGAACACCTCCATTTTATCAG	9	289	0
     ATTCCTATCACCTCTACCCAATCAA	10	58	0
          **********
MAP Score: 27.2307

Motif 2
     ACCGGCCGTTCACGGGGTGTTTTCAA	0	5	1
TTAAAATCTATCCTGGAGGTGATTGG     	2	5	0
TAGATTTTAACCCTGGAGACGTTTTATTACA	2	26	1
AGAATCAAAAACGAGGTGATGCCTC      	2	112	1
  AATATCTCCCCCGGAGGTAAGAGATCG  	4	8	0
AAATACTTCTATCTGGAGGGATCCTCGG   	5	137	1
AAAAATCATTCTCATGAGGGGAGGGAAGAGA	6	61	1
GAAAGCGAAGCCCCTGAGGGGCCTCGCTTTT	7	30	0
ATTTTTCTTTCTGTACTGGTGTTTCTTCCGG	8	82	1
GGTGTTTCTTCCGGTGTGATGTTAGAATAGT	8	99	1
TAGAATAGTTCTACGCAGATGCTTTTTCGGG	8	121	1
CAGATGCTTTTTCGGGAGGTGATTTCTAAGT	8	136	1
AAAAAGCGGTCCGAGGAGGTGTGAAA     	8	191	1
TGACAACCTAACGGGGTGATGCTATATTATA	9	43	0
TAATCAACGAACGAGCGGGTGTAGCTCAGCT	9	117	1
GCGGGTGTAGCTCAGCTGGTAGAGCACCAGC	9	131	1
CACCAGCTTCCCAAGCTGGGGGTCGCGGGTT	9	155	1
CGCTCCACAACCCGGCACATGCCGGGGTATG	9	200	1
ATCCTTGACCCCAGTCTGGGGAAGAACCTGG	9	247	1
GGGGAAGAACCTGGGCTGGCGGAGACTGATA	9	264	1
      AATTCTAAGGAGGGGGAAGCGGGCT	10	4	1
          *** *******
MAP Score: 22.1873

Motif 3
         TTTCGTTCGGTGGAGACAGCGGTGCTTAT	1	1	1
GGGTTAAAATCTATCCTGGAGGTGATTGG         	2	1	0
CCAGGATAGATTTTAACCCTGGAGACGTTTTATTACAT	2	20	1
GATCATTACAATTAAAACCCGGAGAATGTAATAAAACG	2	45	0
CTCCTCACTTTTGACTTCGAGGTGATCGT         	3	10	1
     AATATCTCCCCCGGAGGTAAGAGATCG      	4	4	0
TATAAAAATCATTCTCATGAGGGGAGGGAAGAGAT   	6	58	1
ACGCAGATGCTTTTTCGGGAGGTGATTTCTAAGTGGAA	8	133	1
TCGGACCGCTTTTTTACGGAGGAAGACTGGTGCTTTCC	8	167	0
TAAAAACGGGATTAGACGGTGCGGGGTGGAGCAGT   	9	7	0
GAGCACCAGCTTCCCAAGCTGGGGGTCGCGGGTTCGAA	9	152	1
ATGTGCCGGGTTGTGGAGCGGGCGACGGGATTCGAACC	9	182	0
GGGGAAGAACCTGGGCTGGCGGAGACTGATAAAATGGA	9	264	1
GCGGAGACTGATAAAATGGAGGTGTTCG          	9	282	1
         AATTCTAAGGAGGGGGAAGCGGGCTTGTT	10	1	1
TACCCAATCAATTTAAATCAGGAAGCGGGCAACAAGCC	10	31	0
ATTTAAATTGATTGGGTAGAGGTGATAGGAAT      	10	51	1
          **     ***** **  *
MAP Score: 21.2724

Motif 4
   CCAATCACCTCCAGGATAGATTTTAACCCTGGA	2	7	1
   TTTCACACCTCCTCGGACCGCTTTTTTACGGAG	8	184	0
         ACCTCCTGGAATATCTTTTCTTCTGAA	5	1	1
  AATTTATCCCTCCCACTTTTAGTTTATCATTAAA	11	26	0
   GTTACCACCTCCCATTTTAGATTATACTCTTTT	8	7	1
TTGTTGCCCGCTTCCTGATTTAAATTGATTGGGTAG	10	34	1
TTAGAAATCACCTCCCGAAAAAGCATCTGCGTAGAA	8	129	0
 CCGAGGATCCCTCCAGATAGAAGTATTTGCATACT	5	130	0
TTTATTACATTCTCCGGGTTTTAATTGTAATGATCC	2	48	1
   AATCTATCCTCCACTATTTAATGATAAACTAAA	11	7	1
AAGCCCGCTTCCCCCTCCTTAGAATT          	10	0	0
CGATCTCTTACCTCCGGGGGAGATATT         	4	10	1
ACTGGTGTTTCTTCCGGTGTGATGTTAGAATAGTTC	8	96	1
TCTTCCCTCCCCTCATGAGAATGATTTTTATAAGTA	6	54	0
GAACCCGCGACCCCCAGCTTGGGAAGCTGGTGCTCT	9	151	0
TTGATTCTAACCCCAAACCTTTAATTGGACTTGTAT	2	84	0
          ***** *  *  * **
MAP Score: 20.2857

Motif 5
      ACCGGCCGTTCACGGGGTGTTTTCAAG	0	4	1
ATGTTTTAAGGTTGAAGAGGGAG          	0	38	1
          TTTCGTTCGGTGGAGACAGCGGT	1	0	1
CCTCACTTTTGACTTCGAGGTGATCGT      	3	12	1
   CGATCTCTTACCTCCGGGGGAGATATT   	4	7	1
CAAATACTTCTATCTGGAGGGATCCTCGG    	5	136	1
AGGATTTCTTGACCGTTTCGTGGTGAGCCTGTA	6	18	1
TAAAAATCATTCTCATGAGGGGAGGGAAGAGAT	6	60	1
GCAAAAGCGAGGCCCCTCAGGGGCTTCGCTTTC	7	28	1
TGTACTGGTGTTTCTTCCGGTGTGATGTTAGAA	8	93	1
GCAGATGCTTTTTCGGGAGGTGATTTCTAAGTG	8	135	1
AAAAAAGCGGTCCGAGGAGGTGTGAAA      	8	190	1
AACGGGATTAGACGGTGCGGGGTGGAGCAGT  	9	8	0
CCCGTTAGGTTGTCAAGAGGGAGAAACTCTTGA	9	59	1
AATAATCAACGAACGAGCGGGTGTAGCTCAGCT	9	115	1
AGCACCAGCTTCCCAAGCTGGGGGTCGCGGGTT	9	153	1
CCACAACCCGGCACATGCCGGGGTATGTTTTTG	9	204	1
CCCAGGTTCTTCCCCAGACTGGGGTCAAGGATG	9	246	0
       AATTCTAAGGAGGGGGAAGCGGGCTT	10	3	1
          * **  *******
MAP Score: 2.36317

Motif 6
CAACCTTAAAACATCCTTGAAAACACCCCGTGA	0	19	0
CACCGCTGTCTCCACCGAACGAAA         	1	1	0
    CCAATCACCTCCAGGATAGATTTTAACCC	2	6	1
CATTACAATTAAAACCCGGAGAATGTAATAAAA	2	47	0
 CGATCTCTTACCTCCGGGGGAGATATT     	4	9	1
          ACCTCCTGGAATATCTTTTCTTC	5	0	1
  CCGAGGATCCCTCCAGATAGAAGTATTTGCA	5	134	0
ATTCTAACATCACACCGGAAGAAACACCAGTAC	8	94	0
CTTAGAAATCACCTCCCGAAAAAGCATCTGCGT	8	133	0
GCACCAGTCTTCCTCCGTAAAAAAGCGGTCCGA	8	172	1
TAATCAACGAACGAGCGGGTGTAGCTCAGCTGG	9	117	1
CGCCCGCTCCACAACCCGGCACATGCCGGGGTA	9	196	1
          ****** ** * *
MAP Score: 2.33005

Motif 7
AGCACCGCTGTCTCCACCGAACGAAA      	1	4	0
    GAGGCATCACCTCGTTTTTGATTCTAAC	2	109	0
      ACGATCACCTCGAAGTCAAAAGTGAG	3	13	0
     AATATCTCCCCCGGAGGTAAGAGATCG	4	10	0
  CCGAGGATCCCTCCAGATAGAAGTATTTGC	5	135	0
  ATCTCTTCCCTCCCCTCATGAGAATGATTT	6	63	0
      GTTACCACCTCCCATTTTAGATTATA	8	4	1
AAGCACCAGTCTTCCTCCGTAAAAAAGCGGTC	8	170	1
   TTTCACACCTCCTCGGACCGCTTTTTTAC	8	188	0
    ACTGCTCCACCCCGCACCGTCTAATCCC	9	6	1
TAATATAGCATCACCCCGTTAGGTTGTCAAGA	9	45	1
CTGAGCTACACCCGCTCGTTCGTTGATTATTT	9	114	0
AAGCCCGCTTCCCCCTCCTTAGAATT      	10	4	0
   AATCTATCCTCCACTATTTAATGATAAAC	11	7	1
 AATTTATCCCTCCCACTTTTAGTTTATCATT	11	29	0
          ******** * *
MAP Score: 1.02075