AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254991
 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
       TCTTCATCACCTTTTCTTTTCTTCA	0	3	1
CCTTTTCTTTTCTTCACCTATTAGCCTTTCAA	0	19	1
CCTATTAGCCTTTCAACCCTTTATAAAAGACT	0	35	1
       CTTTTTTGCCCCCTTAAGCTTTCAA	0	210	0
       TTTTCTTAAACCTTTTTATATGGAG	1	3	1
          **** **** **
MAP Score: 3.36081

Motif 2
        TCTTCATCACCTTTTCTTTTCTTC	0	2	1
ACCTTTTCTTTTCTTCACCTATTAGCCTTTCA	0	18	1
CCTATTAGCCTTTCAACCCTTTATAAAAGACT	0	35	1
      CTTTTTTGCCCCCTTAAGCTTTCAAT	0	209	0
       TTTTCTTAAACCTTTTTATATGGAG	1	3	1
          ***  *******
MAP Score: 2.85247

Motif 3
CCGAAAGTCTTTTATAAAGGGTTGAAAGGC	0	42	0
GATCGCCGAATATATGTAGGTAATGATAGC	0	95	1
TTAAGTTAGATTTATGTAGTTTTCGGTGGA	0	155	0
TATCCCTCCATATAAAAAGGTTTAAGAAAA	1	10	0
          **********
MAP Score: 2.04556