AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons035_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243174
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT142	300	hypothetical protein
#1	CT145	185	Serine/threonine Protein Kinase
#2	sohB	102	Protease
#3	CT495	211	ADP/ATP Translocase
#4	pgsA_1	300	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
#5	uvrD	80	DNA Helicase

Motif 1
CGACACCCCCAAAAAAAGATGCTGGAGAAAGGAATT	0	35	0
AAAAGAGCATAAAAAAAGCCTGGGAGAACCCAAGCT	0	184	0
AGTTTTATTTAAAAAAAGAATTAGTTTTGACTTCTA	0	227	1
TTTATTTTGAATAAAAAGCAAACTATTAATTAGAAG	0	257	0
GGAACCGCTTAACTAAAGCAAGCTAAGCGGTGTAAA	1	25	0
TTTTGTTTTGATAAAAAGGAACCGCTTAACTAAAGC	1	42	0
ATCCGTCTACAACAAAAGATCTCTTATTTTGTTTTG	1	68	0
TAATAGGTTCAAGTAAAGAAACTTCGCAATAAGGTT	1	144	1
   TCTTGAGAAGAAAAGGACCTGGAGTATAGTATT	2	7	1
TTAAATAAAAATTAAAAGACCTGGAATACTATACTC	2	31	0
CAGGGGGATTATAAAAAGAATTTTTAAATAAAAATT	2	54	0
   GTGCCCAAAGAAAAGAGGAGGCGGAGTGATCAA	3	7	1
GCAATGCATAATTACAAGATTTTTATGAAATCCAGG	3	81	0
AGAAAACACAATGTAAAGAAACGGAAAGAGAGGGAT	4	114	0
AAGAATTTTCAAGACAAGCTTCCGAATCAACGTT  	4	276	1
          ** ******    * *
MAP Score: 14.8655

Motif 2
AATTCCTTTCTCCAGCATCTTTTTTTGGGGGTGTCG	0	35	1
GCTTGGGTTCTCCCAGGCTTTTTTTATGCTCTTTTT	0	185	1
CTCTTTTTCATCCAAGTTTTATTTAAAAAAAGAATT	0	213	1
 TTAATTGTTTCCAAGTTTTTATTTTGAATAAAAAG	0	275	0
GATTTGCTCTTCCCAGTACTATACTTGTAGCTTTCC	1	105	0
AATACTATACTCCAGGTCCTTTTCTTCTCAAGA   	2	7	0
AGTATAGTATTCCAGGTCTTTTAATTTTTATTTAAA	2	32	1
CTTTTTATAATCCCCCTGTTTTAGTACCGTTTTGTT	2	72	1
GTATTCTAGTTCCCTGGATTTCATAAAAATCTTGTA	3	69	1
CAAAAATTTTTCCCAAAGTCTTCAATATTTATTAAA	3	171	1
AGGGTTCGAATCCCTCTCTTTCCGTTTCTTTACATT	4	105	1
TCCCGCCATTTCCCCCAGCTTATCAACAAAAAACAT	4	169	0
          **** *  ***   **
MAP Score: 12.0522

Motif 3
GAAGCTTGGGTTCTCCCAGGCTTTTTTTATGCTCTTTT	0	182	1
ACCTCTAACCTTATTGCGAAGTTTCTTTACTTGAACCT	1	148	0
AATAATCGATTTCTGATAGGATTTTTATGAGGTCCTGG	0	141	0
      TTAATTGTTTCCAAGTTTTTATTTTGAATAAA	0	278	0
AATCCCCCTGTTTTAGTACCGTTTTGTTGCTA      	2	80	1
TTACATTGTGTTTTCTGAAATTTTTGTTTGTTTGAATG	4	134	1
CTTTTAATTTTTATTTAAAAATTCTTTTTATAATCCCC	2	49	1
GTTCGAATCCCTCTCTTTCCGTTTCTTTACATTGTGTT	4	108	1
TTTATGCTCTTTTTCATCCAAGTTTTATTTAAAAAAAG	0	207	1
TGGCAATGCATAATTACAAGATTTTTATGAAATCCAGG	3	81	0
GACTTCTAATTAATAGTTTGCTTTTTATTCAAAATAAA	0	255	1
TTCAATTCCTTTCTCCAGCATCTTTTTTTGGGGGTGTC	0	32	1
AACAAAAGATCTCTTATTTTGTTTTGATAAAAAGGAAC	1	56	0
TAGCTTGCTTTAGTTAAGCGGTTCCTTTTTATCAAAAC	1	36	1
AGTATATGCATTCTCGAAAATTTTCTTCGAACCCGAAA	5	35	1
ATTTTTGTTTGTTTGAATGTTTTTTGTTGATAAGCTGG	4	153	1
  TTCGGAGCTTTTTGGGCCGGTTGTTTCGTTGGAAAG	4	8	1
ACCTGGAGTATAGTATTCCAGGTCTTTTAATTTTTATT	2	26	1
CCCAGTACTATACTTGTAGCTTTCCGATCCGTCTACAA	1	92	0
          ** *       *******
MAP Score: 10.759

Motif 4
CCCCCAAAAAAAGATGCTGGAGAAAGGAATTG	0	34	0
GGATTTTTATGAGGTCCTGGGGGTGGCTGGAT	0	129	0
AGAGCATAAAAAAAGCCTGGGAGAACCCAAGC	0	185	0
AGCTACAAGTATAGTACTGGGAAGAGCAAATC	1	109	1
AATAAGGTTAGAGGTCCCGAGGAG        	1	171	1
TTGAGAAGAAAAGGACCTGGAGTATAGTATTC	2	12	1
ATAAAAATTAAAAGACCTGGAATACTATACTC	2	31	0
CCAAAGAAAAGAGGAGGCGGAGTGATCAAGAA	3	14	1
AGATTTTTATGAAATCCAGGGAACTAGAATAC	3	69	0
GTTTTTTGTTGATAAGCTGGGGGAAATGGCGG	4	171	1
TAAGCTGGGGGAAATGGCGGGAAACATAGCTA	4	183	1
AATATGTGTCATTGCGCTGGAGGCTAAGAATT	4	251	1
          ** * *******
MAP Score: 9.50587

Motif 5
CCCCAAAAAAAGATGCTGGAGAAAGGAATTGAACC	0	30	0
CCGCTTAACTAAAGCAAGCTAAGCGGTGTAAATAG	1	22	0
CCCAAAGAAAAGAGGAGGCGGAGTGATCAAGAACT	3	13	1
AATTATCCCAAATTTCAACAGAGTGCGAGGTTCCT	3	129	1
GTTTCGTTGGAAAGATGACTGAGTGGTCGAAAGTA	4	32	1
CGTACCCCTTAAAGGGTACCGAGGGTTCGAATCCC	4	84	1
AATGTAAAGAAACGGAAAGAGAGGGATTCGAACCC	4	106	0
AGACACTCCAAAAGCAAGCAGAGAGTTTAGCTATG	4	207	0
TCTATGCCTTAGATTAAGGAGAGTGT         	5	1	0
          ****   ** *** *
MAP Score: 9.21492

Motif 6
TTCAATTCCTTTCTCCAGCATCTTTTTTTGGGGGTGTCGC	0	32	1
AAATCCGACTCCTTACGGATACGTTGGTTCAAATCCAGCC	0	97	1
TTTTATGAGGTCCTGGGGGTGGCTGGATTTGAACCAACGT	0	117	0
AGAAATCGATTATTTGCGAAGCTTGGGTTCTCCCAGGCTT	0	165	1
TCCCAGGCTTTTTTTATGCTCTTTTTCATCCAAGTTTTAT	0	195	1
     TTAATTGTTTCCAAGTTTTTATTTTGAATAAAAAG	0	275	0
GGACCTCTAACCTTATTGCGAAGTTTCTTTACTTGAACCT	1	148	0
TGGAATACTATACTCCAGGTCCTTTTCTTCTCAAGA    	2	6	0
TGGAGTATAGTATTCCAGGTCTTTTAATTTTTATTTAAAA	2	29	1
ATAATCCCCCTGTTTTAGTACCGTTTTGTTGCTA      	2	78	1
GCAAGTGCGGTATTCTAGTTCCCTGGATTTCATAAAAATC	3	60	1
   TTCGGAGCTTTTTGGGCCGGTTGTTTCGTTGGAAAGA	4	7	1
CGAATCCCTCTCTTTCCGTTTCTTTACATTGTGTTTTCTG	4	111	1
TTTACATTGTGTTTTCTGAAATTTTTGTTTGTTTGAATGT	4	133	1
CTCTGCTTGCTTTTGGAGTGTCTATGTTTCATAATATGTG	4	219	1
AGAGTATATGCATTCTCGAAAATTTTCTTCGAACCCGAAA	5	33	1
          * **   *    ***  ***
MAP Score: 8.70488

Motif 7
TTTATGCTCTTTTTCATCCAAGTTTTATTTA	0	207	1
TTTCATCCAAGTTTTATTTAAAAAAAGAATT	0	218	1
AATAGTTTGCTTTTTATTCAAAATAAAAACT	0	266	1
AAGCGGTTCCTTTTTATCAAAACAAAATAAG	1	51	1
GGTCTTTTAATTTTTATTTAAAAATTCTTTT	2	46	1
AATTACAAGATTTTTATGAAATCCAGGGAAC	3	77	0
AAGTCTTCAATATTTATTAAATTAGGAAGGA	3	186	1
TTCTCGAAAATTTTCTTCGAACCCGAAAATA	5	45	1
          ******** **
MAP Score: 6.41823

Motif 8
AGGACCTCATAAAAATCCTATCAGAAATCGATTATTTGC	0	143	1
AAGAGCATAAAAAAAGCCTGGGAGAACCCAAGCTTCGCA	0	179	0
GGTTCAAGTAAAGAAACTTCGCAATAAGGTTAGAGGTCC	1	149	1
ATTTTTATTTAAAAATTCTTTTTATAATCCCCCTGTTTT	2	55	1
TGGATTTCATAAAAATCTTGTAATTATGCATTGCCAAGC	3	83	1
CTCGCATCACAAAAATTTTTCCCAAAGTCTTCAATATTT	3	162	1
TTCAAACAAACAAAAATTTCAGAAAACACAATGTAAAGA	4	131	0
GCTGGAGGCTAAGAATTTTCAAGACAAGCTTCCGAATCA	4	266	1
TCGGGTTCGAAGAAAATTTTCGAGAATGCATATACTCTA	5	32	0
          ***** ***      *  *
MAP Score: 4.55532