AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254993
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0285	108	112aa long hypothetical methionyl-tRNA synthetase
#1	PH0636	128	476aa long hypothetical cysteinyl-tRNA synthetase

Motif 1
ACGTCGTCAAGATATTTAAGGGTTTCCTTA	0	47	1
TATATTTGTGGATAAGGAAACCCTTAAATA	0	59	0
  CCTAGAAAGATTATTAAATCTTAAGTTT	0	90	0
AATTCTTTTTGGTGATGAAGA         	1	1	0
ACCTTCTTTAGGTATTTAAAGCTTGCTTTT	1	32	1
ATTCCTGGATGGAGATTAAGGAGGTGAAGG	1	104	1
          **********
MAP Score: 3.6162

Motif 2
     TTCTTATCTATGGTTTTATTAACTTCATGATACT	0	5	1
TTTGTGGATAAGGAAACCCTTAAATATCTTGACGACGTT	0	46	0
GGGTTTCCTTATCCACAAATATAAAAACTTAAGATTTAA	0	66	1
AAATATAAAAACTTAAGATTTAATAATCTTTCTAGG   	0	82	1
CTCAAGCCAAAAGCAAGCTTTAAATACCTAAAGAAGGTA	1	31	0
GCCAAAACCGACATCCTAATAAAATTCCTGGATGGAGAT	1	81	1
          *   *    ***** * **
MAP Score: 2.76171

Motif 3
TATGGTTTTATTAACTTCATGATACTATAAC	0	18	1
AAGGAAACCCTTAAATATCTTGACGACGTTA	0	45	0
TCTTAAGTTTTTATATTTGTGGATAAGGAAA	0	69	0
ACTTAAGATTTAATAATCTTTCTAGG     	0	92	1
CCTAAAGAAGGTAAATTCTTTTTGGTGATGA	1	13	0
AAAGCAAGCTTTAAATACCTAAAGAAGGTAA	1	30	0
GACATCCTAATAAAATTCCTGGATGGAGATT	1	90	1
          ******** **
MAP Score: 1.78709