AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons023_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242854
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
GTTGAAAAGAACCTCTTCTTAGAAAGGTTT	0	125	1
CTTCTTAGAAAGGTTTTCTCTACGGGCGGT	0	139	1
ATACACGAAAAAGCCCTCTCCGGATCTGAT	0	217	0
TATTTTAATGAAGATCTCTTCAAGAAGTTG	1	26	1
TAAAAGAGGTAAGATCTCTTCACAACTTCT	1	48	0
TCCAACTTTAAACTCTTCTTTTTCAAAGAG	2	16	1
TGGTAACATGATCTTCTCTTAGGGATCAAT	2	106	1
AATTCGCTTTTACCTCTCTTCTTGCTGAAG	2	172	1
AAGAGCCCTAAACTTTTCTTATCATCTTCT	2	263	1
AAACCCAGAGAACCCCTCTCCCAAAGCAGC	4	56	1
  GATAAGCAACCTTTTCTCCTTAGTCTAT	4	236	0
TATTGCAATATCGATTTCTCTTATAAACAG	5	10	0
AACTTAGCACTAGTTCTCTCTATTGCAATA	5	30	0
CTCACTTTCTTAGTTCTCTCATTCTTAGCA	5	129	0
TCTATCCGGCTCCTTCTCTCCTCCTCTCTG	5	189	0
GAATTCAAAAAAGATTTCTTGGGGAACAG 	5	281	1
          **********
MAP Score: 15.9904

Motif 2
TGTTGAAAAGAACCTCTTCTTAGAAAGGTT	0	124	1
CCCGTAGAGAAAACCTTTCTAAGAAGAGGT	0	135	0
TCGTGACAACAATACTTTTTAGCAATCTTG	0	256	0
TTTTAATGAAGATCTCTTCAAGAAGTTGTG	1	28	1
AAAGAGGTAAGATCTCTTCACAACTTCTTG	1	46	0
ATCCAACTTTAAACTCTTCTTTTTCAAAGA	2	15	1
ATGGTAACATGATCTTCTCTTAGGGATCAA	2	105	1
GAAGAGCCCTAAACTTTTCTTATCATCTTC	2	262	1
AAAACCCAGAGAACCCCTCTCCCAAAGCAG	4	55	1
TCAAGAGTAGAATCTTTGTTTGCTTTTAAT	4	120	0
CTGATTTTGGAATATTTTCTATTCCTTTAA	4	169	1
AGGAATGCTGAATCCCCGCTCTGTGGAAAA	4	201	1
   GATAAGCAACCTTTTCTCCTTAGTCTA	4	237	0
ATACATTCTAAATCCTTTTTCAAAAACTTA	5	54	0
CTTTACACCAGATATTTTCTTTTTGAAAAA	5	239	0
TTCCCCAAGAAATCTTTTTTGAATTCCCAA	5	277	0
          **********
MAP Score: 12.6951

Motif 3
ACAAAGATTCTACTCTTGAAAACGACATAGCTAT	4	131	1
TTTAATGAAGATCTCTTCAAGAAGTTGTGAAGAG	1	29	1
AAGAGATCTTACCTCTTTTAGAGGGCATATAATT	1	58	1
GAAAAGAACCTCTTCTTAGAAAGGTTTTCTCTAC	0	128	1
CAATATCGATTTCTCTTATAAACAG         	5	1	0
CACGTGTTCCTCGTCTTTAAGATGAGGAACTAGT	3	24	1
TTTGTGGTGATTTTTTTTCAAAAGTCGCCTAATA	0	31	1
CCAGATATTTTCTTTTTGAAAAAGTCAGCGCCAC	5	228	0
ACATTCTAAATCCTTTTTCAAAAACTTAGCACTA	5	48	0
CTTTAAACTCTTCTTTTTCAAAGAGCTATTTTCC	2	21	1
TTCGAAAAGCTGCTTTGGGAGAGGGGTTCTCTGG	4	60	0
CTTTTACCTCTCTTCTTGCTGAAGACTTGGCTAT	2	178	1
AATCTTTGTTTGCTTTTAATGAAAAAAAGAATAT	4	106	0
TAAGAAGAGGTTCTTTTCAACACAAGACACAGGA	0	112	0
          * *****  *** *
MAP Score: 12.0465

Motif 4
     TAACACAATTCTTGATTGTGATTTGTGGTGATTT	0	5	1
TGAAAAGAACCTCTTCTTAGAAAGGTTTTCTCTACGGGC	0	127	1
ATCTCTTCACAACTTCTTGAAGAGATCTTCATTAAAATA	1	26	0
TCAAAGAGCTATTTTCCTTGCCAGTTATTTCCACTATTA	2	38	1
GTAACATGATCTTCTCTTAGGGATCAATTTCTTGCGTAA	2	108	1
GCTTTTACCTCTCTTCTTGCTGAAGACTTGGCTATGTTT	2	177	1
AAGTTTAGGGCTCTTCCTTCGCAACTCTTTTATGCCTTA	2	239	0
GAGCCCTAAACTTTTCTTATCATCTTCTTTAACTAGGAG	2	265	1
ACCCAGAGAACCCCTCTCCCAAAGCAGCTTTTCGAACAC	4	58	1
AACAAAGATTCTACTCTTGAAAACGACATAGCTATGCTT	4	130	1
GATAAGCAACCTTTTCTCCTTAGTCTATAGAATTTTTCC	4	225	0
TCCTTCTCTCCTCCTCTCTGTAAAAACGGCAAAAATCCC	5	170	0
TACACCAGATATTTTCTTTTTGAAAAAGTCAGCGCCACA	5	227	0
          CTGTTCCCCAAGAAATCTTTTTTGAATTC	5	281	0
          ** *****    *  *  *
MAP Score: 1.96734

Motif 5
ATTTGTGGTGATTTTTTTTCAAAAGTCGCCTAA	0	30	1
AGACACAGGATTTTATCCATTAAAATAAAAACC	0	89	0
GTTGAAAAGAACCTCTTCTTAGAAAGGTTTTCT	0	125	1
TCTCTTCACAACTTCTTGAAGAGATCTTCATTA	1	31	0
AAGAGATCTTACCTCTTTTAGAGGGCATATAAT	1	58	1
ATAATTCCTGTCCCCTTTGCAAGCAC       	1	86	1
AACTTTAAACTCTTCTTTTTCAAAGAGCTATTT	2	19	1
CAAAGAGCTATTTTCCTTGCCAGTTATTTCCAC	2	39	1
TTAGGGATCAATTTCTTGCGTAATAGTCCGAGG	2	124	1
CTTTTACCTCTCTTCTTGCTGAAGACTTGGCTA	2	178	1
AGTTTAGGGCTCTTCCTTCGCAACTCTTTTATG	2	244	0
ACTTTTCTTATCATCTTCTTTAACTAGGAGTCA	2	274	1
ACTCACGTGTTCCTCGTCTTTAAGATGAGGAAC	3	21	1
AACCCAGAGAACCCCTCTCCCAAAGCAGCTTTT	4	57	1
GTGTATATTCTTTTTTTCATTAAAAGCAAACAA	4	102	1
AAACAAAGATTCTACTCTTGAAAACGACATAGC	4	129	1
AATATTTTCTATTCCTTTAACAAGGAATGCTGA	4	179	1
TGCAATATCGATTTCTCTTATAAACAG      	5	4	0
ACATTCTAAATCCTTTTTCAAAAACTTAGCACT	5	49	0
CCTTCTCTCCTCCTCTCTGTAAAAACGGCAAAA	5	175	0
CCAGATATTTTCTTTTTGAAAAAGTCAGCGCCA	5	229	0
TTCAAAAAAGATTTCTTGGGGAACAG       	5	284	1
          ********   **
MAP Score: 1.15513

Motif 6
TAGGCGACTTTTGAAAAAAAATCACCACAA	0	32	0
TCTATTTATTTTAATGAAGATCTCTTCAAG	1	20	1
AAATAGCTCTTTGAAAAAGAAGAGTTTAAA	2	22	0
AAAAGCGAATTAGAAAACGATTTATTCCTC	2	153	0
AAGAAGAGAGGTAAAAGCGAATTAGAAAAC	2	165	0
TGACTCCTAGTTAAAGAAGATGATAAGAAA	2	277	0
GTTCCTCATCTTAAAGACGAGGAACACGTG	3	24	0
TGCTTTTAATGAAAAAAAGAATATACACGA	4	100	0
GATTCTACTCTTGAAAACGACATAGCTATG	4	136	1
ATAGACTAAGGAGAAAAGGTTGCTTATC  	4	236	1
TATTGCAATAGAGAGAACTAGTGCTAAGTT	5	30	1
TGCTAAGTTTTTGAAAAAGGATTTAGAATG	5	51	1
CCTCCTCTCTGTAAAAACGGCAAAAATCCC	5	170	0
TATTTTCTTTTTGAAAAAGTCAGCGCCACA	5	227	0
          **********
MAP Score: 0.642348