AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242873
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ribC	300	Riboflavin Synthase
#1	CT433	300	hypothetical protein
#2	ygbB	102	YgbB family
#3	CT460	300	SWIB (YM74) complex protein
#4	yaeI	57	phosphohydrolase
#5	cysS	254	Cysteinyl tRNA Synthetase
#6	pgsA_2	300	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase

Motif 1
ATATTAGGCGACTTTTGAAAAAAAATCACCACAA	0	32	0
AAGAAGAGGTTCTTTTCAACACAAGACACAGGAT	0	111	0
AGTATAATTATTTTTTGATTATAAGTAACCGCTG	0	174	1
GGGAATCTAATCTTTTGATGAGAAAGTCTAAACT	1	28	1
GAAAGTCTAAACTTTCTAGGAGAAAGAGGATTTA	1	49	1
AAAGAGGATTTATTTTAACTATAACTATAAGAAA	1	71	1
GTTGATCATATTCTTACAGCAAAAGTCAAGAAGC	1	192	1
TGTTAGAGTTTTTTTTAAATAGAAGAGAAGCTTT	1	240	0
TCTTTCTATTTATTTTAATGAAGATCTCTTCAAG	2	16	1
GGAAAATAGCTCTTTGAAAAAGAAGAGTTTAAAG	3	21	0
CTATGTTTTTTATTTTGACGATAAACCTAGTTAA	3	208	1
TCTTATCATCTTCTTTAACTAGGAGTCATCC   	3	279	1
TGTATATTCTTTTTTTCATTAAAAGCAAACAAAG	5	103	1
TATTTTCTATTCCTTTAACAAGGAATGCTGAATC	5	181	1
         CTGTTTATAAGAGAAATCGATATTG	6	1	1
TAGTGCTAAGTTTTTGAAAAAGGATTTAGAATGT	6	48	1
TGGCGCTGACTTTTTCAAAAAGAAAATATCTGGT	6	229	1
          * **** *  ****
MAP Score: 20.0115

Motif 2
GAAAAGAACCTCTTCTTAGAAAGGTTTTCTCTAC	0	128	1
AAGAGATCTTACCTCTTTTAGAGGGCATATAATT	2	58	1
CAATATCGATTTCTCTTATAAACAG         	6	1	0
CCAGATATTTTCTTTTTGAAAAAGTCAGCGCCAC	6	228	0
ACATTCTAAATCCTTTTTCAAAAACTTAGCACTA	6	48	0
TTTCTTATCATCTTCTTTAACTAGGAGTCATCC 	3	277	1
CACGTGTTCCTCGTCTTTAAGATGAGGAACTAGT	4	24	1
CTTTTACCTCTCTTCTTGCTGAAGACTTGGCTAT	3	178	1
TCTCTTCACAACTTCTTGAAGAGATCTTCATTAA	2	30	0
ACAAAGATTCTACTCTTGAAAACGACATAGCTAT	5	131	1
AACTTTAAACTCTTCTTTTTCAAAGAGCTATTTT	3	19	1
CTTGAAGAGATCTTCATTAAAATAAATAGAAAGA	2	16	0
TTTGTGGTGATTTTTTTTCAAAAGTCGCCTAATA	0	31	1
CTAACATGAAACCTTTTACACAAGAGATCTCCCT	1	268	1
TAAGAAGAGGTTCTTTTCAACACAAGACACAGGA	0	112	0
GGAAAAAAGCTTCTCTTCTATTTAAAAAAAACTC	1	235	1
CATCGTTTCTTTTTCTTATAGTTATAGTTAAAAT	1	82	0
AGTTTAGACTTTCTCATCAAAAGATTAGATTCCC	1	28	0
GTGTATATTCTTTTTTTCATTAAAAGCAAACAAA	5	102	1
          *******  * * *
MAP Score: 14.6257

Motif 3
GATTTGTGGTGATTTTTTTTCAAAAGTCGCC	0	29	1
TGTTGAAAAGAACCTCTTCTTAGAAAGGTTT	0	124	1
TCTTCTTAGAAAGGTTTTCTCTACGGGCGGT	0	138	1
GATACACGAAAAAGCCCTCTCCGGATCTGAT	0	217	0
AGTTAAAATAAATCCTCTTTCTCCTAGAAAG	1	60	0
AATAGAAGAGAAGCTTTTTTCCTAGTAGGAA	1	226	0
TTTCATGTTAGAGTTTTTTTTAAATAGAAGA	1	248	0
CTCTAACATGAAACCTTTTACACAAGAGATC	1	266	1
AAAGAGGTAAGATCTCTTCACAACTTCTTGA	2	45	0
ATCCAACTTTAAACTCTTCTTTTTCAAAGAG	3	15	1
ATGGTAACATGATCTTCTCTTAGGGATCAAT	3	105	1
GAAGAGCCCTAAACTTTTCTTATCATCTTCT	3	262	1
AAAACCCAGAGAACCCCTCTCCCAAAGCAGC	5	55	1
TCAAGAGTAGAATCTTTGTTTGCTTTTAATG	5	119	0
AGGAATGCTGAATCCCCGCTCTGTGGAAAAA	5	201	1
   GATAAGCAACCTTTTCTCCTTAGTCTAT	5	236	0
ATACATTCTAAATCCTTTTTCAAAAACTTAG	6	53	0
AAAACGGCAAAAATCCCTCTCGTGACTGCTC	6	156	0
GTTCCCCAAGAAATCTTTTTTGAATTCCCAA	6	277	0
          ** ********
MAP Score: 13.1501

Motif 4
CCTTTCTAAGAAGAGGTTCTTTTCAACACAAGA	0	119	0
CCTCTTCTTAGAAAGGTTTTCTCTACGGGCGGT	0	136	1
ATCAGATCCGGAGAGGGCTTTTTCGTGTATCTA	0	217	1
CAAGATTGCTAAAAAGTATTGTTGTCACGACCT	0	256	1
TTCTAGGAGAAAGAGGATTTATTTTAACTATAA	1	62	1
TTAAATAGAAGAGAAGCTTTTTTCCTAGTAGGA	1	227	0
TTCTTTTTCAAAGAGCTATTTTCCTTGCCAGTT	3	31	1
AGCGAATTAGAAAACGATTTATTCCTCGGACTA	3	147	0
GCTGCTTTGGGAGAGGGGTTCTCTGGGTTTTCG	5	53	0
AGACTAAGGAGAAAAGGTTGCTTATC       	5	238	1
GAGCAGTCACGAGAGGGATTTTTGCCGTTTTTA	6	156	1
TGGGAATTCAAAAAAGATTTCTTGGGGAACAG 	6	278	1
          ******  ** **
MAP Score: 12.9636

Motif 5
GTGATTTGTGGTGATTTTTTTTCAAAAGTCGCCTAATA	0	27	1
TTATGGGAATCTAATCTTTTGATGAGAAAGTCTAAACT	1	24	1
ATGAGAAAGTCTAAACTTTCTAGGAGAAAGAGGATTTA	1	45	1
ACGATGCTTCCAAGACCATTACCAAGCGCCCCATTTTC	1	110	1
TAGGAAGCTTCTTGACTTTTGCTGTAAGAATATGATCA	1	194	0
AAAAAAGCTTCTCTTCTATTTAAAAAAAACTCTAACAT	1	237	1
GTGAAGAGATCTTACCTCTTTTAGAGGGCATATAATTC	2	55	1
CATATAATTCCTGTCCCCTTTGCAAGCAC         	2	83	1
CAACTTTAAACTCTTCTTTTTCAAAGAGCTATTTTCCT	3	18	1
TCGCTTTTACCTCTCTTCTTGCTGAAGACTTGGCTATG	3	175	1
ATTCCTACTCCTTACTTGTTCGTTAGAAATAACGACAC	5	12	1
TAGAATCTTTGTTTGCTTTTAATGAAAAAAAGAATATA	5	105	0
AGAAGCATAGCTATGTCGTTTTCAAGAGTAGAATCTTT	5	133	0
GGAATATTTTCTATTCCTTTAACAAGGAATGCTGAATC	5	177	1
AGAACTAGTGCTAAGTTTTTGAAAAAGGATTTAGAATG	6	43	1
TCCTTCTCTCCTCCTCTCTGTAAAAACGGCAAAAATCC	6	171	0
ACATGTGGCGCTGACTTTTTCAAAAAGAAAATATCTGG	6	224	1
          **   ** **   *** *
MAP Score: 12.7972

Motif 6
TAAACTTTCTAGGAGAAAGAGGATTTATTTT	1	56	1
TAATCTTTTGATGAGAAAGTCTAAACTTTCT	1	35	1
TATTTTCTTTTTGAAAAAGTCAGCGCCACAT	6	226	0
CTATAGACTAAGGAGAAAAGGTTGCTTATC 	5	234	1
CCAAATATAGATGGGAAAGACTGGCGATAAA	6	89	1
TTTGCTTTTAATGAAAAAAAGAATATACACG	5	101	0
GCTTCCTACTAGGAAAAAAGCTTCTCTTCTA	1	224	1
CTATAACTATAAGAAAAAGAAACGATGCTTC	1	89	1
GTAAGCGACTAGGGAAAATGGGGCGCTTGGT	1	130	0
  CTGTTTATAAGAGAAATCGATATTGCAAT	6	8	1
AAGAGTTGCGAAGGAAGAGCCCTAAACTTTT	3	249	1
AACTAGATACACGAAAAAGCCCTCTCCGGAT	0	222	0
TACAGAGAGGAGGAGAGAAGGAGCCGGATAG	6	187	1
AATAACTGGCAAGGAAAATAGCTCTTTGAAA	3	36	0
CCCCGCTCTGTGGAAAAATTCTATAGACTAA	5	214	1
TGCTAAGTTTTTGAAAAAGGATTTAGAATGT	6	51	1
AAATAGCTCTTTGAAAAAGAAGAGTTTAAAG	3	21	0
GCAAGAAGAGAGGTAAAAGCGAATTAGAAAA	3	166	0
AAAAGCTGCTTTGGGAGAGGGGTTCTCTGGG	5	59	0
AGACCGCCCGTAGAGAAAACCTTTCTAAGAA	0	140	0
GATTCCCATAAAGGATAAGGGAGAG      	1	4	0
TTAAAATAAATAGAAAGATTGTTA       	2	3	0
TAGAAATGCTAAGAATGAGAGAACTAAGAAA	6	123	1
TAGGCGACTTTTGAAAAAAAATCACCACAAA	0	31	0
TAATAGTCCGAGGAATAAATCGTTTTCTAAT	3	144	1
          ********* *
MAP Score: 11.421

Motif 7
TGACTCACGTGTTCCTCGTCTTTAAGATGAGG	4	19	1
GAATGAACTAGTTCCTCATCTTAAAGACGAGG	4	32	0
AGCAAACAAAGATTCTACTCTTGAAAACGACA	5	126	1
GTGTTGAAAAGAACCTCTTCTTAGAAAGGTTT	0	123	1
TCCTTTATGGGAATCTAATCTTTTGATGAGAA	1	20	1
ACATAGCTATGCTTCTGATTTTGGAATATTTT	5	155	1
GATCTATCCGGCTCCTTCTCTCCTCCTCTCTG	6	189	0
TAGGAAAAAAGCTTCTCTTCTATTTAAAAAAA	1	233	1
CTAGTAGGAAGCTTCTTGACTTTTGCTGTAAG	1	204	0
GGTCTTGGAAGCATCGTTTCTTTTTCTTATAG	1	95	0
AGCTTCAGTTGATCATATTCTTACAGCAAAAG	1	185	1
GCTTTTTCGTGTATCTAGTTTTTCAAGATTGC	0	233	1
CACTTTTCGTGTATATTCTTTTTTTCATTAAA	5	94	1
TCTGATTTTGGAATATTTTCTATTCCTTTAAC	5	168	1
          ******  ****
MAP Score: 10.7603

Motif 8
TTTACACCAGATATTTTCTTTTTGAAAAAGTCA	6	235	0
TGATTTTGGAATATTTTCTATTCCTTTAACAAG	5	170	1
TCTTGGAAGCATCGTTTCTTTTTCTTATAGTTA	1	92	0
AAGAGCCCTAAACTTTTCTTATCATCTTCTTTA	3	263	1
TCCAACTTTAAACTCTTCTTTTTCAAAGAGCTA	3	16	1
      TAACAATCTTTCTATTTATTTTAATGA	2	4	1
TACTAGGAAAAAAGCTTCTCTTCTATTTAAAAA	1	230	1
AGACTTGGCTATGTTTTTTATTTTGACGATAAA	3	200	1
GAGGAATAAATCGTTTTCTAATTCGCTTTTACC	3	153	1
  GATAAGCAACCTTTTCTCCTTAGTCTATAGA	5	233	0
TAGAAAGTTTAGACTTTCTCATCAAAAGATTAG	1	34	0
TCAAGATACCACGGTTTTTATTTTAATGGATAA	0	77	1
CTTCTTAGAAAGGTTTTCTCTACGGGCGGTCTC	0	139	1
ACGACATAGCTATGCTTCTGATTTTGGAATATT	5	152	1
TCGTGTATATTCTTTTTTTCATTAAAAGCAAAC	5	100	1
CGGAGTATAATTATTTTTTGATTATAAGTAACC	0	171	1
TCCCCAAGAAATCTTTTTTGAATTCCCAAGTCT	6	273	0
          *  ****** ***
MAP Score: 10.4145

Motif 9
ACCTTTCTAAGAAGAGGTTCTTTTCAACACA	0	122	0
ACCTCTTCTTAGAAAGGTTTTCTCTACGGGC	0	135	1
TCAGATCCGGAGAGGGCTTTTTCGTGTATCT	0	218	1
TTTCTAGGAGAAAGAGGATTTATTTTAACTA	1	61	1
TTTTCCTAGTAGGAAGCTTCTTGACTTTTGC	1	210	0
CCTACTAGGAAAAAAGCTTCTCTTCTATTTA	1	228	1
TAAAATAAATAGAAAGATTGTTA        	2	2	0
TACCTCTTTTAGAGGGCATATAATTCCTGTC	2	67	1
CTTCTTTTTCAAAGAGCTATTTTCCTTGCCA	3	30	1
CTGCTTTGGGAGAGGGGTTCTCTGGGTTTTC	5	54	0
TTTTAATGAAAAAAAGAATATACACGAAAAG	5	96	0
TAAGTTTTTGAAAAAGGATTTAGAATGTATT	6	54	1
AGCAGTCACGAGAGGGATTTTTGCCGTTTTT	6	157	1
CTGTTCCCCAAGAAATCTTTTTTGAATTCCC	6	279	0
          ********* *
MAP Score: 9.92528