AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_sum_all023_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245015
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ribC	300	Riboflavin Synthase
#1	zntA	23	Metal Transport P-type ATPase
#2	CT728	36	hypothetical protein
#3	serS_ribD	41	serS: Seryl tRNA Synthetase, ribD: Riboflavin Deaminase
#4	ribA/ribB	109	GTP Cyclohydratase and DHBP Synthase

Motif 1
ATTCTTGATTGTGATTTGTGGTGATTTTTTTTCAA	0	17	1
GTGATTTGTGGTGATTTTTTTTCAAAAGTCGCCTA	0	27	1
TCAAGATACCACGGTTTTTATTTTAATGGATAAAA	0	77	1
ATAAAATCCTGTGTCTTGTGTTGAAAAGAACCTCT	0	106	1
GATCCGGAGAGGGCTTTTTCGTGTATCTAGTTTTT	0	221	1
GCAGAAAGTAGAGGTTTGTGTTATACTCTGCGCAC	4	14	1
          * * ***** **  *
MAP Score: 4.63441

Motif 2
ACCTTTCTAAGAAGAGGTTCTTTTCAACACAA	0	121	0
GATCAGATCCGGAGAGGGCTTTTTCGTGTATC	0	216	1
TCACGACCTAGCAAAGGTATTTAATTGTCT  	0	280	1
GTCGCAGAAAGTAGAGGTTTGTGTTATACTCT	4	11	1
TTAGCCAGTGGGAAACGTTCTTTGTCTATAAT	4	58	0
          * ****** ***
MAP Score: 3.93902

Motif 3
TGTTGAAAAGAACCTCTTCTTAGAAAGGTTTTCTCTA	0	124	1
TCAAAAAATAATTATACTCCGAGACCGCCCGTAGAGA	0	155	0
GTTTGCCTTGATCAGATCCGGAGAGGGCTTTTTCGTG	0	207	1
AGACAATTAAATACCTTTGCTAGGTCGTGACAACAAT	0	273	0
       TTCATACTCTTAGTAGGTGGCCT       	1	3	1
AACCTGAAAAATCAGATAGCGAGAGAGATGCAAGG  	3	16	1
GGTTTGTGTTATACTCTGCGCACAGCGAGGGGATTAT	4	26	1
CAGCGAGGGGATTATAGACAAAGAACGTTTCCCACTG	4	48	1
AGTTTTCCTCAAAAACGGGGTAGATTGAGA       	4	89	1
          ** * ** *  ***  *
MAP Score: 2.86286

Motif 4
TTGTGGTGATTTTTTTTCAAAAGTCGCCTAAT	0	32	1
GAAGAGGTTCTTTTCAACACAAGACACAGGAT	0	111	0
CAGCGGTTACTTATAATCAAAAAATAATTATA	0	176	0
CTAAAAAGTATTGTTGTCACGACCTAGCAAAG	0	264	1
AGCGAGGGGATTATAGACAAAGAACGTTTCCC	4	49	1
ACTGGCTAAGTTTTCCTCAAAAACGGGGTAGA	4	81	1
          ****  ******
MAP Score: 2.00959