AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252247
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0013	161	conserved hypothetical protein
#1	TM0015	90	pyruvate ferredoxin oxidoreductase, gamma subunit
#2	TM0019	41	oxidoreductase, short chain dehydrogenase/reductase family
#3	TM0132	300	flagellin, putative
#4	TM0297	108	oxidoreductase, short chain dehydrogenase/reductase family
#5	TM0324	300	conserved hypothetical protein
#6	TM0402	300	ammonium transporter
#7	TM0404	47	deoxycytidylate deaminase, putative
#8	TM0411	161	transcriptional regulator, XylR-related
#9	TM0433	246	pectate lyase
#10	TM0434	89	alpha-glucosidase, putative
#11	TM0436	55	alcohol dehydrogenase, zinc-containing
#12	TM0475	73	pyrazinamidase/nicotinamidase-related protein
#13	TM0476	34	hypothetical protein
#14	TM0477	82	outer membrane protein alpha
#15	TM0478	30	tyrosyl-tRNA synthetase
#16	TM0481	300	conserved hypothetical protein
#17	TM0662	33	acyl carrier protein
#18	TM0666	163	serine acetyltransferase
#19	TM0802	141	3-oxoacyl-(acyl carrier protein) synthase II
#20	TM1171	89	transcriptional regulator, crp family
#21	TM1551	76	conserved hypothetical protein
#22	TM1554	35	hypothetical protein
#23	TM1724	300	3-oxoacyl-(acyl carrier protein) reductase

Motif 1
   TGAAATATCCCTCCTCCTGTGTTAATAT	18	7	1
        AATACCACCTCCTGACAAAAAAA	19	128	0
TGGGTTCAAGTCCCACCTCTCGCACCAAGAT	16	134	1
     TTTTCCACCTCCTCTTAGAAGTGTCG	17	17	0
     CCTATTCCCTCCTTCTCCTCAATATG	19	5	1
       AACTCTCCCCTCCTAACATAAGAT	9	3	1
AGAGGGGGTCTCCCCCCTCCAAATGTTAACG	10	26	0
     ACTTTTCCCTCCTTTTTCTGGGCTTT	20	5	1
GCGGGGGTTACCCCGCCTTTTCTGTGGGGTG	2	15	1
    CCTAAATCCCCCCTTTCCATAATGAAT	3	283	0
ATACCATATCCACCACCTCCAGATCGTTTGA	18	138	0
     GAACGCACCTCCTCGCGTTTTTTTAA	23	284	0
     AAAAACACCTCCTTTTGGTAAATATG	6	284	0
        GTTCCCACCACCTGTAACAATTA	21	63	0
     GTGTGCACCTCCTCTAAATTCCGGGT	10	73	0
   GTCATCTTTCCTCCTTCTTGTTGCCTCT	5	282	0
GAGCGCGTTGTTTCACCTCCTTATGAGAGGA	23	197	1
TGAAGAAGCTCCTCACCTTTT          	22	0	0
GGAGAAACCTCCTCCCCTTTTTTCGGCCTCC	7	25	1
        CCCATCACCTCGTTAGAACGAAA	15	17	0
   CCGATTGCACCTCCTCGACAACATGGAT	1	72	0
GGGGAGGAGGTTTCTCCTCCCGAAAGGAAAC	7	11	0
   GTTCTATCCTCTCCTTTCTCGATCTCTC	21	7	1
GGAGGGGGGAGACCCCCTCTTTGTATTTGAA	10	37	1
   AACATCTTACCTCCCCTCAGAATAAATT	13	16	0
GAAGGGGAAATTTCCCCTTCTTCTTTTTCTT	16	256	1
GAAGGGGAAATTTCCCCTTCTTTTTTGTCTG	16	245	0
        TCTCTCACCCCGTAACAATTGTT	20	76	0
CGTCTGCCAGTTCCGCCACTCTCGCACCGCT	16	68	0
TCAGTGATGTTACCACATCTTTTCGATTCAA	9	186	0
  GGCTCTTCTACCTCCACGACATAAAGAAA	16	281	0
TATTAACACACTTCGCCTTGAAGTATAATGA	4	51	0
          **** ******
MAP Score: 49.3259

Motif 2
ATACAATAACGTGGGTTAAATCCATGTTGTCGAG	1	53	1
   AACGGGCGGGGGTTACCCCGCCTTTTCTGTG	2	7	1
TAATCCAACATGGGGTTTGTGCCCTCTAAAAAAA	6	160	1
AAAAGGGGAGGAGGTTTCTCCTCCCGAAAGGAAA	7	12	0
AATACAAAGAGGGGGTCTCCCCCCTCCAAATGTT	10	30	0
GGCAAGTGCCGGGGGTTGATTTGCGGTGGTGTGG	12	11	0
TCAGGGGGTCGTGGGTTCGAATCCCACCCGGGTC	16	31	1
TTAGAATCCAGTGGGCTGAAGCCCGTGTGGGTTC	16	107	1
TGAAGCCCGTGTGGGTTCAAGTCCCACCTCTCGC	16	123	1
GCTGGGGGTCGCGGGTTCGAATCCCGTCGCCCGC	16	209	1
TAATCTCACATTGGGTTACAATCCCGATGTTCTC	19	76	0
CTCCTTATGAGAGGATTATACTCCTTCCGGGGTA	23	213	1
          * *****  * ***
MAP Score: 17.3621

Motif 3
TGAAGCCCGTGTGGGTTCAAGTCCCACCTCTCGCA	16	123	1
GTTAACATTTGGAGGGGGGAGACCCCCTCTTTGTA	10	27	1
TCAGGGGGTCGTGGGTTCGAATCCCACCCGGGTCA	16	31	1
GCTGGGGGTCGCGGGTTCGAATCCCGTCGCCCGCT	16	209	1
CCACAGAAAAGGCGGGGTAACCCCCGCCCGTT   	2	7	0
CTTTTTTTTAGAGGGCACAAACCCCATGTTGGATT	6	161	0
AGACAAAAAAGAAGGGGAAATTTCCCCTTCTTCTT	16	246	1
TTTCCTTTCGGGAGGAGAAACCTCCTCCCCTTTTT	7	12	1
TTAGAATCCAGTGGGCTGAAGCCCGTGTGGGTTCA	16	107	1
TGTTTTATAGGAAAGATAAAAGCCCCACACAATGA	5	130	0
TTTATGTCGTGGAGGTAGAAGAGCC          	16	285	1
AGTTACCCCGGAAGGAGTATAATCCTCTCATAAGG	23	215	0
CCTCTCATAAGGAGGTGAAACAACGCGCTCCTTTT	23	192	0
GGCAAGTGCCGGGGGTTGATTTGCGGTGGTGTGGA	12	10	0
          * *** * **  ***
MAP Score: 16.178

Motif 4
CGGGGTAACCCCCGCCCGTT          	2	0	0
CGGGGGTTACCCCGCCTTTTCTGTGGGGTG	2	16	1
GATCTTTCACCACGATCTTTCCAGTTTGGC	3	165	1
     AAAAACACCTCCTTTTGGTAAATAT	6	285	0
GGAGAAACCTCCTCCCCTTTTTTCGGCCTC	7	25	1
ACTTTTGTTTCCTCTTTTTTTCTAATTTTT	8	73	1
AGTGATGTTACCACATCTTTTCGATTCAAG	9	185	0
AGGGGGGAGACCCCCTCTTTGTATTTGAAC	10	39	1
 GGCAGAGCACCTGACTTTTAATCAGGGGG	16	9	1
GCTACACCCGCCTGCTCTATCTTGGTGCGA	16	153	0
GGGGAAATTTCCCCTTCTTTTTTGTCTGGA	16	243	0
GGGGAAATTTCCCCTTCTTCTTTTTCTTTA	16	259	1
   TTTTCCACCTCCTCTTAGAAGTGTCGA	17	16	0
AGGTGAACCTCTTCACTTTTTTCACAAAAG	18	50	0
TCCACCACCTCCAGATCGTTTGATTCAATG	18	131	0
TATAATCATGCCAGATTTTTTTGTCAGGAG	19	113	1
   ACTTTTCCCTCCTTTTTCTGGGCTTTC	20	7	1
   GTTCTATCCTCTCCTTTCTCGATCTCT	21	7	1
TGAAGAAGCTCCTCACCTTTT         	22	1	0
CTCTAGCACACCAGATCTTTCTCCGGTAAA	23	95	1
TGGATACTTACCTGTTCGTTTTACCGGAGA	23	114	0
AGGTAAGTATCCAGAACTTTCAAAACGGAC	23	131	1
CGCGTTGTTTCACCTCCTTATGAGAGGATT	23	200	1
          **********
MAP Score: 13.3367

Motif 5
        AACGGGCGGGGGTTACCCCGCCTTTTCTGT	2	2	1
GCATAGCTGACTTGAGGGATAGTATCTGCTTGCTTTTA	3	90	1
AAATCGTTTTCCGGCGGAGGTGTATTCTT         	4	1	0
ACTTTAGCTACACGTGGGTTACACTTAGTGTTCCTGTT	5	193	1
ACTTAGTGTTCCTGTTGGTGCGATTCTGCTCTTCAGAA	5	215	1
TCTAATCCAACATGGGGTTTGTGCCCTCTAAAAAAAAG	6	158	1
AAAAGAACCCCATGGTGTTTGTTTTTTGTTTTTCAAGA	6	191	1
GAAAAAAGGGGAGGAGGTTTCTCCTCCCGAAAGGAAAC	7	11	0
TTAACATTTGGAGGGGGGAGACCCCCTCTTTGTATTTG	10	28	1
CCGGCAAGTGCCGGGGGTTGATTTGCGGTGGTGTGGA 	12	9	0
CCGGCACTTGCCGGGGGTTTTGTTTTGTTGTATAATTT	12	33	1
GACTTTTAATCAGGGGGTCGTGGGTTCGAATCCCACCC	16	22	1
GGCTGAAGCCCGTGTGGGTTCAAGTCCCACCTCTCGCA	16	120	1
CAAGATAGAGCAGGCGGGTGTAGCTCAGTGGTAGAGCA	16	159	1
GCTTGCCAAGCTGGGGGTCGCGGGTTCGAATCCCGTCG	16	200	1
TATATTAACACAGGAGGAGGGATATTTCA         	18	1	0
ATCAAACGATCTGGAGGTGGTGGATATGGTATCGGG  	18	137	1
          * ** *** *    ** *
MAP Score: 12.701

Motif 6
GAAAAAAATATCAGATAAAAATT       	0	3	0
CTATGGTGAATGTGAAAAAAATATCAGATA	0	16	0
CTCACTGTCATATGATGAAAAGAAAAGAAA	0	61	1
GCATTATGTATCTGATACAATAACGTGGGT	1	39	1
GTGGGGTCAAAGTGATAAAAGCAAGCAGAT	3	113	0
CTTTGCACGTTCTGATAAAATTCATTATGG	3	264	1
TGGATATACTTGTGAAGAAATTCTCCGAAA	5	51	1
TCTCTATCAATATGATACAAATAAACAATA	6	230	0
ATGAAAATTCGGTGATAAAATCCCTTTGAA	9	56	0
CAAAGGCTTTTGTGAAAAAAGTGAAGAGGT	18	44	1
TTCACCTTTCTGTGATGAAAAGGTTTCTTT	18	73	1
TCTCAAATTCTATGATACAACAGGTGCTAT	21	34	1
AGGAGCTTCTTCAGAAAAAAAGATGTG   	22	18	1
TATCTCAGATTGAGATGAAAATA       	23	3	0
CTCATAAGGAGGTGAAACAACGCGCTCCTT	23	194	0
AAATAGAACACGTGATACAATTTAAAAAAA	23	263	1
          **********
MAP Score: 12.407

Motif 7
ATCATATGACAGTGAGAGGTGTTATAATCGACTATGGTG	0	38	0
TAAATCCATGTTGTCGAGGAGGTGCAATCGG        	1	69	1
          AACGGGCGGGGGTTACCCCGCCTTTTCTG	2	0	1
GAAAATCGTTTTCCGGCGGAGGTGTATTCTT        	4	2	0
GGGAATAAATTTCTGGAGGATTTTATATGTCTCAATACT	6	101	0
GGGTTCTTTTTTTTAGAGGGCACAAACCCCATGTTGGAT	6	162	0
  GGTTTCCTTTCGGGAGGAGAAACCTCCTCCCCTTTTT	7	8	1
ATCCGTTAACATTTGGAGGGGGGAGACCCCCTCTTTGTA	10	23	1
ATTACCCGGAATTTAGAGGAGGTGCACAC          	10	70	1
CCCCGGCAAGTGCCGGGGGTTGATTTGCGGTGGTGTGGA	12	10	0
CTGACTTTTAATCAGGGGGTCGTGGGTTCGAATCCCACC	16	20	1
TGGACTTAGAATCCAGTGGGCTGAAGCCCGTGTGGGTTC	16	102	1
ACCAAGATAGAGCAGGCGGGTGTAGCTCAGTGGTAGAGC	16	157	1
CCCCCAGCTTGGCAAGCTGGTGCTCTACCACTGAGCTAC	16	178	0
CAGCTTGCCAAGCTGGGGGTCGCGGGTTCGAATCCCGTC	16	198	1
CCAGACAAAAAAGAAGGGGAAATTTCCCCTTCTTCTTTT	16	244	1
TTTCTTTATGTCGTGGAGGTAGAAGAGCC          	16	281	1
GGTTTTAACAATTAGGTTGATATAATTCCATTGAATCAA	18	103	1
AACGATCTGGAGGTGGTGGATATGGTATCGGG       	18	141	1
TTCACCTCCTTATGAGAGGATTATACTCCTTCCGGGGTA	23	208	1
AATTTAAAAAAACGCGAGGAGGTGCGTTC          	23	281	1
          * * ** *** *     **
MAP Score: 4.79354

Motif 8
TCCATGTTGTCGAGGAGGTGCAATCGG   	1	73	1
         AACGGGCGGGGGTTACCCCGC	2	1	1
ACCCCACAGAAAAGGCGGGGTAACCCCCGC	2	15	0
ACATTTAAGGCAAAGCGCTGTGGGGTCAAA	3	132	0
TTCATTATGGAAAGGGGGGATTTAGG    	3	284	1
ATATCTAATCCAACATGGGGTTTGTGCCCT	6	155	1
CAAAAAACAAACACCATGGGGTTCTTTTTT	6	189	0
ATATTTACCAAAAGGAGGTGTTTTT     	6	285	1
GGCCGAAAAAAGGGGAGGAGGTTTCTCCTC	7	23	0
ACTTGAATCGAAAAGATGTGGTAACATCAC	9	184	1
GGTTCAAATACAAAGAGGGGGTCTCCCCCC	10	40	0
CCCGGAATTTAGAGGAGGTGCACAC     	10	74	1
GCTTTCGTTCTAACGAGGTGATGGG     	15	15	1
TCTTGGTGCGAGAGGTGGGACTTGAACCCA	16	134	0
CCCAGCTTGGCAAGCTGGTGCTCTACCACT	16	185	0
TCCAGACAAAAAAGAAGGGGAAATTTCCCC	16	243	1
GACACTTCTAAGAGGAGGTGGAAAA     	17	18	1
AAGCCCAGAAAAAGGAGGGAAAAGT     	20	5	0
TATAATTGTTACAGGTGGTGGGAAC     	21	61	1
         AAAAGGTGAGGAGCTTCTTCA	22	1	1
TCTTCAGAAAAAAAGATGTG          	22	25	1
AATCCTCTCATAAGGAGGTGAAACAACGCG	23	200	0
CAATTTAAAAAAACGCGAGGAGGTGCGTTC	23	280	1
          **********
MAP Score: 2.01184

Motif 9
GTGACTGTTTCTTTTCTTTTCATCATATGA	0	68	0
GCGCTCCACTCTTTGGCTTCTTTATTTATG	3	46	1
GATCTTTCCAGTTTGGCTTTCGCTGACAAG	3	178	1
CACCGACATCATTTTGTTTTCACGCCAGGC	5	23	0
ACCCCATGGTGTTTGTTTTTTGTTTTTCAA	6	197	1
CCCGAGGAAACTTTTGTTTCCTCTTTTTTT	8	64	1
TCAAGTCAATATTTGGTTTCATAAGAACAC	9	160	0
CTTGCCGGGGGTTTTGTTTTGTTGTATAAT	12	39	1
TCCCCTTCTTCTTTTTCTTTATGTCGTGGA	16	268	1
GAAAAGGTTTCTTTGGTTTTAACAATTAGG	18	89	1
          **********
MAP Score: 1.56244

Motif 10
TCGTTTGAAATCTGGAGGTGACAAT         	0	146	1
TCCATGTTGTCGAGGAGGTGCAATCGG       	1	73	1
AAATTCTCCGAAAGAACTCAGAATAGTGAATTAC	5	68	1
TTCAGAGGCAACAAGAAGGAGGAAAGATGAC   	5	279	1
GAAAAATTAGAAAAAAAGAGGAAACAAAAGTTTC	8	70	0
ATAACAAACGAAAGGAATGGAAAA          	8	147	1
ACTTGAATCGAAAAGATGTGGTAACATCACTGAC	9	184	1
CTCCAGACAAAAAAGAAGGGGAAATTTCCCCTTC	16	242	1
ATAAAGAAAAAGAAGAAGGGGAAATTTCCCCTTC	16	256	0
GACACTTCTAAGAGGAGGTGGAAAA         	17	18	1
GTATATTAACACAGGAGGAGGGATATTTCA    	18	6	0
GATTTTTTTGTCAGGAGGTGGTATT         	19	126	1
TGAAGTATAATTAGGTTGGAATAATCCTGTCTGT	20	42	1
TATAATTGTTACAGGTGGTGGGAAC         	21	61	1
          * **** * ** **
MAP Score: 0.944969

Motif 11
TATCTGATACAATAACGTGGGTTAAATCCATGTTGTCGAGG	1	47	1
          AACGGGCGGGGGTTACCCCGCCTTTTCTGTG	2	0	1
CTTTGCCTTAAATGTTGAGATCTTTCACCACGATCTTTCCA	3	147	1
GCCGAAAAAAGGGGAGGAGGTTTCTCCTCCCGAAAGGAAAC	7	11	0
GTTCAAATACAAAGAGGGGGTCTCCCCCCTCCAAATGTTAA	10	28	0
TTTTAATCAGGGGGTCGTGGGTTCGAATCCCACCCGGGTCA	16	25	1
CTGGACTTAGAATCCAGTGGGCTGAAGCCCGTGTGGGTTCA	16	101	1
AGGCGGGTGTAGCTCAGTGGTAGAGCACCAGCTTGCCAAGC	16	170	1
TGCCAAGCTGGGGGTCGCGGGTTCGAATCCCGTCGCCCGCT	16	203	1
CCAGACAAAAAAGAAGGGGAAATTTCCCCTTCTTCTTTTTC	16	244	1
         AAAAGGTGAGGAGCTTCTTCAGAAAAAAAGAT	22	1	1
CCTATCAAAAAGGAGCGCGTTGTTTCACCTCCTTATGAGAG	23	185	1
          **    * **  *  * ** *
MAP Score: 0.22768