AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254988
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0678	225	185aa long hypothetical ferredoxin oxidoreductase gamma subunit
#1	PH0679	33	105aa long hypothetical ferredoxin oxidoreductase delta subunit

Motif 1
ACCGAAAGTCTTTTATAAAGGGTTGAAAGGCT	0	41	0
TGATCGCCGAATATATGTAGGTAATGATAGCA	0	94	1
TTATGTAGTTTTCGGTGGAGGTACTAAGACAT	0	142	0
TTTAAGTTAGATTTATGTAGTTTTCGGTGGAG	0	154	0
TTAAACCTTTTTATATGGAGGGATACCT    	1	15	1
          ** **** ****
MAP Score: 3.37723

Motif 2
TGAAGAAAAGAAAAGGTGATGAAGA       	0	3	0
TTGAAAGGCTAATAGGTGAAGAAAAGAAAAGG	0	19	0
GTCTTTTATAAAGGGTTGAAAGGCTAATAGGT	0	34	0
TACAATCTAAAATCGTTGATCGCCGAATATAT	0	78	1
CTCCATATAAAAAGGTTTAAGAAAA       	1	3	0
          **  ********
MAP Score: 2.65515

Motif 3
GATCGCCGAATATATGTAGGTAATGATAGC	0	95	1
TTAAGTTAGATTTATGTAGTTTTCGGTGGA	0	155	0
TAAACCTTTTTATATGGAGGGATACCT   	1	16	1
          **********
MAP Score: 2.58312

Motif 4
TCGCCGAATATATGTAGGTAATGATAGCAT	0	97	1
TGTAGTTTTCGGTGGAGGTACTAAGACATT	0	141	0
ATTGAAAGCTTAAGGGGGCAAAAAAG    	0	209	1
AACCTTTTTATATGGAGGGATACCT     	1	18	1
          **********
MAP Score: 1.54178