AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242135
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	clpB	300	Clp Protease ATPase
#1	clpC	264	ClpC Protease ATPase
#2	lon	300	Lon ATP-dependent protease
#3	glyA	300	Serine Hydroxymethyltransferase
#4	hisS	300	Histidyl tRNA Synthetase
#5	clpP_2	166	CLP Protease
#6	tig	300	Trigger Factor-peptidyl prolyl isomerase
#7	alaS	300	Alanyl tRNA Synthetase
#8	CT779	155	hypothetical protein
#9	lysS	231	Lysyl tRNA Synthetase

Motif 1
AACAAAATTTTCCTCTCTTTTTTTCTTTTT	7	187	1
      AATTTTCTCTCTTTGTTTAATTGT	8	4	1
AAGCTGCATATCCTCTCTCTTCAAAATTTC	9	116	1
ACGCGCGTAATTCTCTTTTTTAATAAGAGA	9	12	1
TTAAAATAAATCCTCTTTCTCCTAGAAAGT	3	168	1
CTGGGTCGTTTTCTCTTTCTTGGAAATCCG	9	60	0
CGACCCAGTTTTCTCTTTCTATTTTGGAGA	9	82	1
CACCCCTACTCCCTCTCTTTACACAGCAAA	4	77	0
CCGGAACAATGTCTCTCTTTACAACCTGTG	8	119	1
ATCCTACCCTTCCTCTCTTCGATTTTTTTG	7	224	1
CTTTTTAAAGTTCTTTTTTTGCGCAAAGAA	4	234	0
AGTCCAATTTTTCTTTTTTTACCACCTCTT	6	76	1
CTCTCTTTTTTTCTTTTTTTTGCTCATCCT	7	199	1
TTTGTCGAAATTCTTTTTTTTAGCGCTCCA	7	250	1
CCTCTATTTTTCCCCTTTTTAAAGCTGTTT	6	44	1
GGAGAAGTTGTTCTCTGTCTGTTTATTTAG	1	35	0
GAACACGTTTTTCTCTTATTAAAAAAGAGA	9	23	0
GAAGCATCGTTTCTTTTTCTTATAGTTATA	3	137	1
CCTCTCTTCTTCCTCTATTTTTCCCCTTTT	6	33	1
TGATCGAAACTACTCTCTTTGATCAAGAAA	0	101	0
AACCTGCTCCTTTTCTCTCTATTATTTCTT	4	159	0
TCGTCAATACTCCTTTCATTTAGCTTAATA	4	28	1
ATTAGATGGGGTCTTTCTTTTCTAGGGTCA	5	89	1
CATCACCCGCTTCTCTTTCCCGGATAACTT	6	265	1
AAAATTTTGACCCTCTCTTCTTCCTCTATT	6	22	1
ACGGTTATAATCCTTTGTCTAAATCAATCT	2	14	0
CCCCAAAAAACCCTTTTTCTTAACCTCTCA	7	118	1
TCTCTATTATTTCTTTTATTTGACACACCT	4	144	0
CTAACTCTCTTCCCCTTACTGGCTATCCTA	0	68	0
TCTTATGCTATCCCCTATTTTTTATGCACC	7	73	1
  CTATCGCGCCCTCTCATCCACGTAAGAG	7	8	1
ATGATCTTAGCTCTTTTATTGACTGTAAGA	0	178	1
          **********
MAP Score: 41.5225

Motif 2
CAAATGATCTTAGCTCTTTTATTGACTGTAAGA	0	175	1
AAATTTTTAGAAGCTTTTTTAGAGTCAGGCATT	1	118	0
TGGGAGATTAAAGCACTTTTTATAGCAGACTTT	1	155	0
ATAACCGTTAAAACCGTTTTAATTCAAAAATTA	2	36	1
AATTATAAATGAGCTTTTTTAGTAAAGTCGGTT	2	89	0
ATTCGATAAATAACAGTTTTTCTATTCAACTTC	2	119	1
          AAGCTTTTTTCCTAGTAGGAAGC	3	0	1
GTAGTCCTGAAAACTCTTTTGGTGTAACATGGT	4	194	1
CACCTTTTTAAAGTTCTTTTTTTGCGCAAAGAA	4	234	0
TGAGATCACGAAACATTTTTCGTGAGAATAGTC	4	265	1
CCTTCTCAAAAAACCTTTTTCCAAAGTTTTTTT	6	108	1
CCTTTTTCCAAAGTTTTTTTGTAAAACCTACAA	6	121	1
ACTCCCCAAAAAACCCTTTTTCTTAACCTCTCA	7	115	1
ACACTATCCTTAACACTTTTTATAAAACAAAAT	7	162	1
TTTTTTGTCGAAATTCTTTTTTTTAGCGCTCCA	7	247	1
          **** *****  *
MAP Score: 14.9614

Motif 3
GATAGCCAGTAAGGGGAAGAGAGTTAGCTGTT	0	71	1
ACAGTCAATAAAAGAGCTAAGATCATTTGATC	0	172	0
AACTTTTCGTAAAGGGAAAGGAATTGGGAGAT	1	180	0
AAAATCCTTGGAAGAGCAAGGGTTGTGTGCAC	2	255	0
TAACTATAAGAAAAAGAAACGATGCTTCCAAG	3	133	0
AAACTTTCTAGGAGAAAGAGGATTTATTTTAA	3	168	0
AGATTCCCATAAAGGATAAGGGAGAGTGGGTA	3	221	1
GAGAGTGGGTAGAGGATAAAGAGTGCCTCTGC	3	242	1
TTTGCTGTGTAAAGAGAGGGAGTAGGGGTGAG	4	77	1
AAGAAATAATAGAGAGAAAAGGAGCAGGTTTT	4	159	1
AAAGAACTTTAAAAAGGTGAGATCACGAAACA	4	248	1
TCTTGACCCTAGAAAAGAAAGACCCCATCTAA	5	90	0
GAGGAAGAAGAGAGGGTCAAAATTTTCATTGA	6	16	0
ACAGCTTTAAAAAGGGGAAAAATAGAGGAAGA	6	40	0
AGGTTTTTTGAGAAGGTGAAGAGGTGGTAAAA	6	92	0
AAAAAAAGAAAAAAAGAGAGGAAAATTTTGTT	7	187	0
ATCGAAGAGAGGAAGGGTAGGATGAGCAAAAA	7	215	0
ACATTGTTCCGGAGGGATAAGGTTATCAGCCC	8	99	0
GAGAAATTTTGAAGAGAGAGGATATGCAGCTT	9	116	0
          ******  ****
MAP Score: 5.39363

Motif 4
AAGAAACAGCTAACTCTCTTCCCCTTACTGG	0	76	0
TTTTTGCCTGTAGTTTTCTGTGATCAAATGA	0	151	1
CAAATGATCTTAGCTCTTTTATTGACTGTAA	0	175	1
CCATACAGCTTAATTCTCTTACAGTCAATAA	0	193	0
ACGGGAGAAGTTGTTCTCTGTCTGTTTATTT	1	37	0
TTAACGGTTATAATCCTTTGTCTAAATCAAT	2	16	0
ATTCAAAAATTAATTCGCTGTCGCCAAATCA	2	57	1
TTTTCTATTCAACTTCTCTTTGCTGCAATTG	2	136	1
TCACCCCTACTCCCTCTCTTTACACAGCAAA	4	77	0
ACCTGCTCCTTTTCTCTCTATTATTTCTTTT	4	157	0
CATGGTGGTCTCGTTCTTTGCGCAAAAAAAG	4	221	1
CTTTTTAAAGTTCTTTTTTTGCGCAAAGAAC	4	233	0
TTAGATGGGGTCTTTCTTTTCTAGGGTCAAG	5	90	1
CCCTCTCTTCTTCCTCTATTTTTCCCCTTTT	6	32	1
TCCTCTATTTTTCCCCTTTTTAAAGCTGTTT	6	43	1
AGTCCAATTTTTCTTTTTTTACCACCTCTTC	6	76	1
GCATAAGATGTAGCTTTCTTTCGAACGAGGG	7	50	0
ACACTATCCTTAACACTTTTTATAAAACAAA	7	162	1
AAACAAAATTTTCCTCTCTTTTTTTCTTTTT	7	186	1
TTCCTCTCTTTTTTTCTTTTTTTTGCTCATC	7	196	1
CATCCTACCCTTCCTCTCTTCGATTTTTTTG	7	223	1
TTTGTCGAAATTCTTTTTTTTAGCGCTCCAA	7	250	1
       AATTTTCTCTCTTTGTTTAATTGT	8	3	1
 GTACGCGCGTAATTCTCTTTTTTAATAAGA	9	9	1
TGGGAACACGTTTTTCTCTTATTAAAAAAGA	9	25	0
ATAGTAGCAATATTTTTCTTCTTACGACAAT	9	189	0
          ** ********
MAP Score: 5.36054

Motif 5
ATCCATACAGCTTAATTCTCTTACAGTCAATAA	0	193	0
GCTTTAATCTCCCAATTCCTTTCCCTTTACGAA	1	174	1
TTTCATTTAGCTTAATAGCTTTTAGAAGACAAT	4	41	1
TCGAGTAGTCCTGAAAACTCTTTTGGTGTAACA	4	190	1
GGTGAGATCACGAAACATTTTTCGTGAGAATAG	4	263	1
TTCACCTTCTCAAAAAACCTTTTTCCAAAGTTT	6	104	1
AAACCTTTTTCCAAAGTTTTTTTGTAAAACCTA	6	118	1
ATCAACTCCCCAAAAAACCCTTTTTCTTAACCT	7	111	1
ACACACTATCCTTAACACTTTTTATAAAACAAA	7	160	1
ATTTTTTTGTCGAAATTCTTTTTTTTAGCGCTC	7	245	1
   GTACGCGCGTAATTCTCTTTTTTAATAAGA	9	7	1
          *  ** *******
MAP Score: 4.79511

Motif 6
GGATAGCCAGTAAGGGGAAGAGAGTTAGCTGT	0	70	1
AATTAAGCTGTATGGATATGAGGTCTGCTTTA	0	209	1
AAAATCCTTGGAAGAGCAAGGGTTGTGTGCAC	2	255	0
TTCTTACAGCAAAAGTCAAGAAGCTTCCTACT	3	23	0
CTAAACTTTCTAGGAGAAAGAGGATTTATTTT	3	170	0
AGATTCCCATAAAGGATAAGGGAGAGTGGGTA	3	221	1
GGATAAGGGAGAGTGGGTAGAGGATAAAGAGT	3	234	1
TGTGTAAAGAGAGGGAGTAGGGGTGAGGATGC	4	82	1
GCGTATTGTGGATGGATAAGCGGAGAGTAAGG	4	115	1
AGAAATAATAGAGAGAAAAGGAGCAGGTTTTC	4	160	1
CTTTCTTTTCTAGGGTCAAGAGTAGCCATAAC	5	101	1
GGGAAAAATAGAGGAAGAAGAGAGGGTCAAAA	6	26	0
GGTTTTTTGAGAAGGTGAAGAGGTGGTAAAAA	6	91	0
GGAAAGAGAAGCGGGTGATGAGGCTTGAACTC	6	253	0
ATTGAGAGGTTAAGAAAAAGGGTTTTTTGGGG	7	118	0
CATTGTTCCGGAGGGATAAGGTTATCAGCCCA	8	98	0
          *****  *****
MAP Score: 4.33587

Motif 7
GATTTCTAATCAAGTTTTTTGCCTGTAGTTTT	0	136	1
TTTTTAGAAGCTTTTTTAGAGTCAGGCATTAT	1	116	0
TATACTTTCTCGTGTTAGATGCACTAATTGTT	2	180	1
CTAATTGTTGCGATTTTGTAGTATATCGGTAA	2	203	1
GAAGCTTCTTGACTTTTGCTGTAAGAATATGA	3	28	1
TAGAAGACAATACGTTTGCTGTGTAAAGAGAG	4	63	1
GTCCTGAAAACTCTTTTGGTGTAACATGGTGG	4	197	1
TTTTAAAGTTCTTTTTTTGCGCAAAGAACGAG	4	230	0
ATAGAATTCATCATTTTGATGCGTAGGTGTAT	5	52	1
CTATTTTTCCCCTTTTTAAAGCTGTTTGCAGT	6	47	1
GTTTGCAGTCCAATTTTTCTTTTTTTACCACC	6	70	1
GATAATCTGGGGAGTTTTTCGCAATCCTTTGC	6	154	0
TGCTATCCCCTATTTTTTATGCACCTATTTTT	7	78	1
TTTTATGCACCTATTTTTTATCAACTCCCCAA	7	92	1
TCTCTTTTTTTCTTTTTTTTGCTCATCCTACC	7	200	1
TTCCTCTCTTCGATTTTTTTGTCGAAATTCTT	7	233	1
TGTCGAAATTCTTTTTTTTAGCGCTCCAAACA	7	252	1
AAGATGTAAGCTTGTTTGGAGCGCTAAAAAAA	7	264	0
TTTTCTCTTTCTATTTTGGAGAAAGCAAGCTG	9	90	1
CAAAATTTCTCAAGTTTGATGTAGCATGATGA	9	137	1
AATATTGCTACTATTTTTGAGCCAAAGGACGG	9	206	1
          * ****** ***
MAP Score: 0.264625