AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238210
 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	5	0
TTACGAGGGATTTTACGATGACCTGTGTATAG	0	61	0
GCAAGGATGTTTTTACGAGGGATTTTACGATG	0	73	0
TATTAGAAAGTTTTAATTGCAACAAAAACTTC	1	12	1
AACAAAAACTTCTTAGTTGAAAAATGTACTTT	1	32	1
AAAATGTACTTTGTTTTCGGAACTCACTTATT	1	52	1
CTCCAGCAACTCTTTCTCTGAATCAGAAAATA	1	80	0
TGCTGGAGATTTTTTATATAAAAATTTTTAAT	1	104	1
ATAGCCTTCTTCTTTCTAGAACGGATAAAAGA	1	204	1
GATCGGATTGTCTTTTCTGGAACACTCAGTGC	1	234	1
ATAGCAATTGTCTTAACAGGAAATTGAGATAG	1	275	1
          ***** * ****
MAP Score: 7.82217

Motif 2
          ACATTTTGCGCCTAAAACTCAGTTCATT	0	0	1
AACTCAGTTCATTCTCTAGGATTAAAACACTTGCCACT	0	25	1
 TCTATTAGAAAGTTTTAATTGCAACAAAAACTTCTTA	1	9	1
TTGCAACAAAAACTTCTTAGTTGAAAAATGTACTTTGT	1	28	1
GAACTCACTTATTTTCTGATTCAGAGAAAGAGTTGCTG	1	71	1
GAGTTGCTGGAGATTTTTTATATAAAAATTTTTAATTT	1	100	1
AAAAATTTTTAATTTCTAAAGACGACAAGGATAATTAT	1	123	1
ATTTCCGTTGCTTTTCTTTTCCTAATACCCTAAGATAG	1	170	1
GATCTTTTATCCGTTCTAGAAAGAAGAAGGCTATCTTA	1	200	0
AAAGCACTGAGTGTTCCAGAAAAGACAATCCGATCTTT	1	231	0
ACTCTATCTCAATTTCCTGTTAAGACAATTGCTATGGT	1	272	0
          *  *****     ** **
MAP Score: 7.16297

Motif 3
         TCTATTAGAAAGTTTTAATTGC	1	1	1
CAAAAACTTCTTAGTTGAAAAATGTACTTTG	1	34	1
TATTTTCTGATTCAGAGAAAGAGTTGCTGGA	1	80	1
TGCTGGAGATTTTTTATATAAAAATTTTTAA	1	104	1
ACAAGGATAATTATGAGAAAGGGATTTCCGT	1	147	1
CTATCTTAGGGTATTAGGAAAAGAAAAGCAA	1	177	0
TCTTTTATCCGTTCTAGAAAGAAGAAGGCTA	1	205	0
AGCACTGAGTGTTCCAGAAAAGACAATCCGA	1	236	0
AGCAATTGTCTTAACAGGAAATTGAGATAGA	1	277	1
          *** *******
MAP Score: 1.44115

Motif 4
TTTTGCGCCTAAAACTCAGTTCATTCTCTAGGATT	0	13	1
TCCCTCGTAAAAACATCCTTGCGTTTATCATCC  	0	83	1
TTTTAATTGCAACAAAAACTTCTTAGTTGAAAAAT	1	22	1
GTGAGTTCCGAAAACAAAGTACATTTTTCAACTAA	1	44	0
CTCTGAATCAGAAAATAAGTGAGTTCCGAAAACAA	1	62	0
TTTTTTATATAAAAATTTTTAATTTCTAAAGACGA	1	113	1
TTCCAGAAAAGACAATCCGATCTTTTATCCGTTCT	1	221	0
TCTTTTCTGGAACACTCAGTGCTTTCAGACCATAG	1	244	1
          ******   * * **
MAP Score: 0.899435