AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238217
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pheT	106	phenylalanyl tRNA Synthetase Beta
#1	infC	300	Initiation Factor 3

Motif 1
ATGAACTGAGTTTTAGGCGCAAAATGT       	0	3	0
TATTAGAAAGTTTTAATTGCAACAAAAACTTCTT	1	12	1
AACAAAAACTTCTTAGTTGAAAAATGTACTTTGT	1	32	1
CAACTCTTTCTCTGAATCAGAAAATAAGTGAGTT	1	72	0
AATTAAAAATTTTTATATAAAAAATCTCCAGCAA	1	103	0
GATCGGATTGTCTTTTCTGGAACACTCAGTGCTT	1	234	1
ATAGCAATTGTCTTAACAGGAAATTGAGATAGAG	1	275	1
          *****   * ****
MAP Score: 5.73834

Motif 2
    TCTATTAGAAAGTTTTAATTGCAACA	1	6	1
TGTGTATAGTGGCAAGTGTTTTAATCCTAG	0	40	0
TTTTCAACTAAGAAGTTTTTGTTGCAATTA	1	25	0
TCTGATTCAGAGAAAGAGTTGCTGGAGATT	1	85	1
TTCAGACCATAGCAATTGTCTTAACAGGAA	1	267	1
AAGAGTTGCTGGAGATTTTTTATATAAAAA	1	98	1
TTTTTTATATAAAAATTTTTAATTTCTAAA	1	113	1
ATAAACGCAAGGATGTTTTTACGAGGGATT	0	81	0
          **********
MAP Score: 2.53305

Motif 3
       TCTATTAGAAAGTTTTAATTGCAACA	1	3	1
TTTTCTGATTCAGAGAAAGAGTTGCTGGAGATT	1	82	1
AAGGATAATTATGAGAAAGGGATTTCCGTTGCT	1	149	1
TCCTAATACCCTAAGATAGCCTTCTTCTTTCTA	1	189	1
TAGAACGGATAAAAGATCGGATTGTCTTTTCTG	1	220	1
          ** ******  **
MAP Score: 0.48246