AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons001_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241581
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	lepA	185	GTPase
#1	CT065	300	ADP/ATP Translocase
#2	truB	37	tRNA Pseudouridine Synthase
#3	nusA	117	Transcription antitermination factor
#4	rs1	244	S1 Ribosomal Protein
#5	adk	206	adenylate kinase
#6	rpoC	24	RNA Polymerase Beta'
#7	rpoB	300	RNA Polymerase Beta
#8	rl7	31	L7/L12 Ribosomal Protein
#9	rl10	21	L10 Ribosomal Protein
#10	rl1	22	L1 Ribosomal Protein
#11	rl11	105	L11 Ribosomal Protein
#12	secE	142	Preprotein translocase subunit
#13	tufA	300	Elongation Factor Tu
#14	infA	300	Initiation Factor IF-1
#15	fusA	41	Elongation Factor G
#16	rs7	49	S7 Ribosomal Protein
#17	rs12	259	S12 Ribosomal Protein
#18	CT460	300	SWIB (YM74) complex protein
#19	yaeI	57	phosphohydrolase
#20	rs11	21	S11 Ribosomal Protein
#21	rs13	55	S13 Ribosomal Protein
#22	secY	22	Translocase
#23	rl18	21	L18 Ribosomal Protein
#24	rl6	27	L6 Ribosomal Protein
#25	rl16	32	L16 Ribosomal Protein
#26	rl2	23	L2 Ribosomal Protein
#27	rl3	300	L3 Ribosomal Protein
#28	mutL	294	DNA Mismatch Repair
#29	rs4	300	S4 Ribosomal Protein
#30	rl36	300	L36 Ribosomal Protein
#31	rs14	23	S14 Ribosomal Protein
#32	pnp	28	Polyribonucleotide Nucleotidyltransferase
#33	rs15	156	S15 Ribosomal Protein
#34	map	57	Methionine Aminopeptidase
#35	CT853	194	hypothetical protein
#36	CT854	52	ABC transporter permease fused to pyrimidine biosynthesis enzyme

Motif 1
GACGGGGCTTTTCTTTTGTCTTTAAAAATCCCC	0	56	1
AATCAAAATTTTTTCACGACTTTTTAAAGAAAT	1	205	1
TTAGCATTATTTTTTTTGCTTTTTTTCCCTTAC	3	77	1
GGACTGTCAATCCTTGAGATTTTCAAGGATATC	4	18	0
TTTACACTACTCTTTTTGACTTTGTAGTTTTTA	4	206	1
TGTACACGAGTTTTTATTTTTTTTCGAAACAGA	5	128	0
CTCTCCTAAGACTTTAAGACTTTTGGCGATATC	7	272	0
TATAATTTAACTTTTTCGTTTTTCCCCCTCGTT	11	48	1
TTGACATTCTCTCTTGAGTTTTTGCGGGAATAA	14	98	0
AAGATACTTTTCCTTCTGTTTTTTGACAAGTTG	14	131	1
AGATAGAATGTTTTTTAGGTTTTTTTAGGA   	14	280	1
ACAAGTCTTGTTTTCAAGTTTTTGAACTAACAG	17	13	1
 GTTATTCTTCTCTTCCTTCTTTA         	26	1	0
CCTAGAACGATTTTTCAGGCTTTGTTTTTGCGA	27	51	1
TCAGGCTTTGTTTTTGCGATTTTTGGTGTGGGA	27	65	1
TAATTTGTTATTTTTATTTTTTTAGGAATTATC	28	13	0
AATAAAAACGTTTTTAATATTTTGCTTTTAATA	28	92	1
CTCCGCTATGATTTTAAGACTTTACTATTCAGT	28	264	0
AAATCGACCTTTTTTGAGATTTTTTAAATAAGA	29	110	1
ACTAGAATGCTCTTTTGTATTTTGTCAAGCGCG	29	199	1
TGTAAGAAAACTTTTATGGTTTTTAGTTGTGCT	30	138	1
AAGAAGGGATCTTTCAGTCCTTTGTAACTGAGG	35	135	0
CATGAAGTCGTTTTTTCTATTTTT         	36	38	1
          *****  * ****
MAP Score: 24.9308

Motif 2
GTTTATTGTTAAGTTTTCTTTGTTGATCAA	1	257	0
AAACTAGTGAAACTTTTTTTAATAAAGAGA	4	123	1
TTAATTAGGAAAGGCTTTTTTTATAAGAAC	5	68	0
TTCTGTTGCAATGGTTTTTTCTTAATGGAA	7	100	1
     AAGCGAATTCTTCTTTCAGTTACCT	12	127	0
CAAGAGATAGAATGTTTTTTAGGTTTTTTT	14	276	1
AATGTTTTTTAGGTTTTTTTAGGA      	14	286	1
     GATACAAGTCTTGTTTTCAAGTTTT	17	5	1
TGCTGATAAAATGTTTTCTTCGAATACTGT	17	42	0
GCAAGGATTTAACTCTTTTTTTATTAATTA	17	69	1
ATTTTTAGGGAAGGCTTGTTTTAAGAAAAT	17	98	1
TTTTGGAGGAAATGTTTTTTAATAAAATTG	17	129	1
TCCAACTTTAAACTCTTCTTTTTCAAAGAG	18	16	1
AAGAGCCCTAAACTTTTCTTATCATCTTCT	18	263	1
  AGCGTTATAAGTTTTCTTCCAAGGAAGC	27	8	1
AAACATAATTAATTCTTTTTGCGTAAGTTA	28	125	1
GTTGCCTTGCAATTTTTTTTAACAGGAGGT	28	177	1
GATACTGAAAAAGGTTTCTTTTTATTTCTT	29	59	0
GTGCTAAAAAAACTCTTCTTATTTAAAAAA	29	129	0
AAAACCATAAAAGTTTTCTTACAGTGATCT	30	131	0
CCGATAAAAAAGGTTTTCTTGAATTAAGAA	33	25	1
CTAGAGTAAGAAGTTTTTTTTCTCTGTGCA	33	130	0
          **********
MAP Score: 21.7763

Motif 3
          TCCTAAAAAAACCTAAAAAA	14	290	0
 CGCGATAATTCCTAAAAAAATAAAAATAA	28	9	1
TTACTTGGGCTCTTAAAAAAGAGACTGATT	30	272	0
CTTATTTTATTCCTTAAAAAACATCGCCTC	29	272	0
TTTTCTTTTGTCTTTAAAAATCCCCTCGCC	0	64	1
TTAAAGTATTTCTTTAAAAAGTCGTGAAAA	1	215	0
ATTTAAAAAATCTCAAAAAAGGTCGATTTA	29	109	0
AAACAAGCCTTCCCTAAAAATAATTAATAA	17	89	0
AATGATGTTCTCCTAAAAACTACAAAGTCA	4	222	0
   GGAGTTGTCCTAAAAACGAAATGGGGT	32	11	0
TTCTAAAAATTCTCTAAAAAGAAGCCCCGT	0	17	1
AGATTCTCAGTGCTAAAAAAACTCTTCTTA	29	138	0
CGGTACCTCCTGTTAAAAAAAATTGCAAGG	28	181	0
CAAAAGATTTTCTTAAAACAAGCCTTCCCT	17	104	0
TGCATCTCTTTATTAAAAAAAGTTTCACTA	4	127	0
ATAACAATTTTATTAAAAAACATTTCCTCC	17	133	0
TCCTAAAAAAACCTAAAAAACATTCTATCT	14	280	0
CCCTCCGATATCCTTGAAAATCTCAAGGAT	4	12	1
GGAAAATAGCTCTTTGAAAAAGAAGAGTTT	18	25	0
AAACTCTTCTTATTTAAAAAATCTCAAAAA	29	120	0
GTAAATATTCACCTTAAAAAAGGCAAGATT	4	181	0
 AACACTCTCTCCTAAAAATTA        	20	2	0
      ATCATCCTAATAAACTATCTTGTA	5	192	0
TCAAACAACTTGTCAAAAAACAGAAGGAAA	14	139	0
          **********
MAP Score: 20.4195

Motif 4
GAGTCGTGAAATCAAAATTTTTTCACGACTTT	1	196	1
CTTAACAATAAACACAAGCTTTTCAGAGGGTG	1	274	1
      CAAAAAGACAATCCTTCTGAACTCCA	2	4	1
GGCTTTTTTTATAAGAACCTTTCGTTCAATAT	5	54	0
AGGTTCTTATAAAAAAAGCCTTTCCTAATTAA	5	66	1
GCCTTTCCTAATTAAAATCTTTTATCGAAAAA	5	83	1
TGGCATCGCAAACAGAATATTTCTGTTGCAAT	7	80	1
TAAACAAATTAAAAAAATATTTGTTATTCCCG	14	75	1
CAAAAACTTGAAAACAAGACTTGTATC     	17	5	0
ACAGTATTCGAAGAAAACATTTTATCAGCAAG	17	42	1
AATAATTAATAAAAAAAGAGTTAAATCCTTGC	17	69	0
AGATTTTCTTAAAACAAGCCTTCCCTAAAAAT	17	98	0
GGCTTGTTTTAAGAAAATCTTTTGGAGGAAAT	17	110	1
AATGTTTTTTAATAAAATTGTTATAGAGATCG	17	139	1
AGCTCTTTGAAAAAGAAGAGTTTAAAGTTGGA	18	16	0
AAAGAAGATGATAAGAAAAGTTTAGGGCTCTT	18	263	0
       AAAATAACAATTTTTGACCTAAGAT	21	3	1
CAAGTTAATTAATAAAAACGTTTTTAATATTT	28	82	1
TTATTTCTTCATCAAAACTCTTTGATCTATTC	29	36	0
TGAAGAAATAAAAAGAAACCTTTTTCAGTATC	29	57	1
TCTCAGTGCTAAAAAAACTCTTCTTATTTAAA	29	132	0
AGATCACTGTAAGAAAACTTTTATGGTTTTTA	30	131	1
TTCTTAATTCAAGAAAACCTTTTTTATCGGGT	33	23	0
TTCGTTAGTCAAAAAAAATGTTACTCTTTCTC	35	38	1
          ** **** ****
MAP Score: 19.6777

Motif 5
TAGCCAAGTCTTCAGCAAGAAGAGAGGTAAAAGC	18	177	0
TTGAGATTTTTTAAATAAGAAGAGTTTTTTTAGC	29	123	1
          TAAAGAAGGAAGAGAAGAATAAC 	26	0	1
AATCTTCGATTACGTGAGGAGGAGATGCCCTCCA	1	149	0
GTACTTCTTGTCCGGTAGGAGGAGGCTGTTTTGC	30	191	1
TTTTTCCCTTACCCATAAGAGGAGTATTA     	3	98	1
AAATAGCTCTTTGAAAAAGAAGAGTTTAAAGTTG	18	18	0
TGGTTCCCTAAACCTAAAGAAAAGAAATACGAAG	16	12	1
CATAAAAGAGTTGCGAAGGAAGAGCCCTAAACTT	18	244	1
CTTGTCAAAAAACAGAAGGAAAAGTATCTTTTGA	14	127	0
CAGAAATCCAACCTTTAGGAAAAGAGTATACCAC	1	81	0
CGTATTAGGTAACTGAAAGAAGAATTCGCTT   	12	121	1
AAAAACGACTTCATGAAGGAAGAATCATAGGGGA	36	19	0
GGATTTTTAAAGACAAAAGAAAAGCCCCGTCCGA	0	53	0
TAAAAATAATTAATAAAAAAAGAGTTAAATCCTT	17	71	0
TAAGAGAGGTTGAATCGAGAAGAGTAC       	17	242	1
AACCTAATAATCAACGAGAAAGAGTAACATTTTT	35	51	0
GAAGGAAGAATCATAGGGGAAGAGAGCAT     	36	5	0
CTAGTTCCTCATCTTAAAGACGAGGAACACGTGA	19	23	0
CAAGAAATTGATCCCTAAGAGAAGATCATGTTAC	18	108	0
TAAAAACTACAAAGTCAAAAAGAGTAGTGTAAAT	4	205	0
TCACCTTGATTCCATTAAGAAAAAACCATTGCAA	7	105	0
GGGATTTCTTAGCGTCAAGAAAAATCTCTTGTGT	27	94	1
TTTCTAAAAATTCTCTAAAAAGAAGCCCCGTTCT	0	16	1
CGATGTTAACTTACGCAAAAAGAATTAATTATGT	28	127	0
GTTTTGATGAAGAAATAAAAAGAAACCTTTTTCA	29	50	1
          * *   ********
MAP Score: 16.013

Motif 6
TCCGGCTGAATCTTCGATTACGTGAGGAGGAGATGCC	1	154	0
GCAAGGGAAATCTTGCCTTTTTTAAGGTGAATATTTA	4	173	1
GGTAGCAAACTAATTTTTAATTTGAGGATTTTTGAG 	13	274	1
TACTGTGAAGTATTGAGTCTAAGGAGGACAAGTTTAA	14	19	1
ATAATCGCTCTCTCGAGTTTCCGGAGGACAACAGGTG	14	188	1
ATAGAATGTTTTTTAGGTTTTTTTAGGA         	14	282	1
AACCTCTTCGTATTTCTTTTCTTTAGGTTTAGGGAAC	16	14	0
ACTCTTTTTTTATTAATTATTTTTAGGGAAGGCTTGT	17	80	1
GACTTGGCTATGTTTTTTATTTTGACGATAAACCTAG	18	201	1
CACGTGTTCCTCGTCTTTAAGATGAGGAACTAGTTCA	19	24	1
AAGATGCTTATATTACTTTAAGGGAGGCCCTTCGT  	21	30	1
TCGCCGCCTTTGTTTGCTTTAAGGAGCCGCGTTTTCT	27	158	1
TGCCTTGCAATTTTTTTTAACAGGAGGTACCGTTACC	28	179	1
CTTTTATGGTTTTTAGTTGTGCTGCGGATTTTATAGC	30	148	1
CATTTCTAAGTATTTTATGTGGTGAGGGTGTAGTAAG	30	235	1
TTAGGTGCTTTGTAGTATGTTATGAGGGGTTTTTGAT	33	74	0
          * **   * *  *****
MAP Score: 11.0163

Motif 7
AGATAGAACGGGGCTTCTTTTTAGAGAATTTTT	0	21	0
ATCTCGGACGGGGCTTTTCTTTTGTCTTTAAAA	0	50	1
GGAGTTCAGAAGGATTGTCTTTTTG        	2	2	0
CTGCTCCGTTAGCATTATTTTTTTTGCTTTTTT	3	69	1
TAATTAGGAAAGGCTTTTTTTATAAGAACCTTT	5	64	0
TATTTCTGTTGCAATGGTTTTTTCTTAATGGAA	7	97	1
    TTTGTCACCCTTATTTTTTAGAATGTTAA	8	12	0
TTAGTTTGCTACCAATATCTTTTGCCCAGAATA	13	254	0
TGCGGGAATAACAAATATTTTTTTAATTTGTTT	14	76	0
TGGGTGCCCAAGCCTGTTTTTTTGTTTGAATGC	14	237	1
ATCAAGAGATAGAATGTTTTTTAGGTTTTTTTA	14	274	1
CAAGGATTTAACTCTTTTTTTATTAATTATTTT	17	70	1
TTTTTAGGGAAGGCTTGTTTTAAGAAAATCTTT	17	99	1
ATCTTTTGGAGGAAATGTTTTTTAATAAAATTG	17	126	1
CTGAAGACTTGGCTATGTTTTTTATTTTGACGA	18	196	1
ACGATTTTTCAGGCTTTGTTTTTGCGATTTTTG	27	57	1
GTAATTTGTTATTTTTATTTTTTTAGGAATTAT	28	14	0
TCGTTGCCTTGCAATTTTTTTTAACAGGAGGTA	28	175	1
ATACTGAAAAAGGTTTCTTTTTATTTCTTCATC	29	55	0
AAATAGAACTAGAATGCTCTTTTGTATTTTGTC	29	192	1
AAGTTAGCGAGGCGATGTTTTTTAAGGAATAAA	29	264	1
ATTAAGAATTAGTTTGATTTTTTCTAAATCAAA	33	47	1
          **  ** ******
MAP Score: 8.52938

Motif 8
GAGGGGATTTTTAAAGACAAAAGAAAAGCCCCGTCCG	0	54	0
CTTCGTTGATTTGATCAACAAAGAAAACTTAACAATA	1	247	1
CTCCTAAAAACTACAAAGTCAAAAAGAGTAGTGTAAA	4	206	0
CGACTTCTGTTTCGAAAAAAAATAAAAACTCGTGTAC	5	123	1
GGGTTTTTGCTTGTAAACAAATTAAAAAAATATTTGT	14	62	1
CAAGAGCGATTTCCACGACAAAGAAAACGCGGCTCCT	27	179	0
  CGCGATAATTCCTAAAAAAATAAAAATAACAAATT	28	8	1
TCAAAGAGTTTTGATGAAGAAATAAAAAGAAACCTTT	29	43	1
TTTTTTGAGATTTTTTAAATAAGAAGAGTTTTTTTAG	29	119	1
CGAGGCGATGTTTTTTAAGGAATAAAATAAGGACTGA	29	271	1
ATCAAACTAATTCTTAATTCAAGAAAACCTTTTTTAT	33	28	0
TTATGAGGGGTTTTTGATTTAGAAAAAATCAAACTAA	33	55	0
TTATATTTCTCTGCACAGAGAAAAAAAACTTCTTACT	33	119	1
ACACTACGAGTTCGTTAGTCAAAAAAAATGTTACTCT	35	28	1
          **  * *   ** ****
MAP Score: 7.83638

Motif 9
AAAGACAAAAGAAAAGCCCCGTCCGAGATAG	0	48	0
CTCCTTGAGTGGAGGGCATCTCCTCCTCACG	1	140	1
TTCACCCTCTGAAAAGCTTGTGTTTATTGTT	1	277	0
CATCCCCATGGAAAGGACTGTCAATCCTTGA	4	34	0
TTTTAATTAGGAAAGGCTTTTTTTATAAGAA	5	69	0
TGTCCTAGCTGGAAAGCATCTGTCGTATTCC	7	206	1
TAAAGTCTTAGGAGAGCTCGC          	7	289	1
TGGCGAGGCTGAAAAGCCTTGCCTTTGGGTG	12	24	1
ATACGAGTGCGGAGGGATTCGAACCCCCGAC	12	95	0
TTATTTTTAGGGAAGGCTTGTTTTAAGAAAA	17	96	1
 TAATTTTTAGGAGAGAGTGTT         	20	9	1
        ACGAAGGGCCTCCCTTAAAGTAA	21	42	0
CTTGCAGGATGGAGGGCATGGCCGTTTGCTA	27	212	1
CCTCCTGCGCGAAAGGCTTGGACTTCACGCT	28	214	1
CCTTTATCCGGGAAGGCTCTTGTTTGCAATT	30	53	1
TATCTTGAAAGAAGGGATCTTTCAGTCCTTT	35	145	0
          ******* ***
MAP Score: 7.10915

Motif 10
CGAGATAGAACGGGGCTTCTTTTTAGAGAA	0	26	0
CTATCTCGGACGGGGCTTTTCTTTTGTCTT	0	48	1
AAAAAAGGCGAGGGGATTTTTAAAGACAAA	0	70	0
TTCCGCCCTCCTGGGCTCCTTGAGTGGAGG	1	125	1
CCTTGAGTGGAGGGCATCTCCTCCTCACGT	1	142	1
CTGGGCACAGAGGGGTTCCCGGTACGTCTT	7	18	1
      ACGAAGGGCCTCCCTTAAAGTAAT	21	41	0
ACAAAGAAAACGCGGCTCCTTAAAGCAAAC	27	169	0
TTGTCAAGCGCGGGGAACTCGCGTTCAACA	29	220	1
CTGTTTTGCTAGGGGCTCTCATTTCTAAGT	30	216	1
GTATGTTATGAGGGGTTTTTGATTTAGAAA	33	67	0
GTGACGATTTCGGGGATCCCTCAGTTACAA	35	117	1
          **********
MAP Score: 5.50899

Motif 11
CTTATGGGTAAGGGAAAAAAAGCAAAAAAAATAA	3	83	0
GAGATTTTCAAGGATATCGGAGGGGG        	4	2	0
TGTGATACTAATGACAGGATAGGGGATA      	5	4	0
CTTTCCAGCTAGGACAAAACAGAGCCTATCCAAT	7	188	0
GAGGAATACTAAGGTAGAGTAGGGTTGAAT    	11	85	1
TGTAGCTTAGATGGTAGAGCAGTGGCCTCCAAAG	12	55	1
TCTTACAAACAGGGAAATATAGAATAAGAATATC	17	213	0
AAACCTAGTTAAGGCATAAAAGAGTTGCGAAGGA	18	230	1
          AGGGTAAAGTAGAGTCGAACT   	23	0	1
     TAAAGAAGGAAGAGAAGAATAAC      	26	5	1
CTAGTGCCTTAGGAATGCGTAGAGAGCAGAGATC	30	102	1
GAAGAATCATAGGGGAAGAGAGCAT         	36	1	0
          **** ** * ** *
MAP Score: 2.00016