AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255569
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0227	61	316aa long hypothetical protein
#1	PH0678	225	185aa long hypothetical ferredoxin oxidoreductase gamma subunit
#2	PH0679	33	105aa long hypothetical ferredoxin oxidoreductase delta subunit
#3	PH0682	21	108aa long hypothetical ferredoxin oxidoreductase delta subunit

Motif 1
        TCTTCATCACCTTTTCTTTTCTTCA	1	2	1
ACCTTTTCTTTTCTTCACCTATTAGCCTTTCAA	1	18	1
ACCTATTAGCCTTTCAACCCTTTATAAAAGACT	1	34	1
        CTTTTTTGCCCCCTTAAGCTTTCAA	1	210	0
        TTTTCTTAAACCTTTTTATATGGAG	2	2	1
         ATTTATTACCCTTTTTGAGAG   	3	1	1
          *** * **** **
MAP Score: 7.24444

Motif 2
TATAGCTTAATCCTGAACAATTTTAAATATTTAG	0	13	1
       TCTTCATCACCTTTTCTTTTCTTCACC	1	3	1
TTTTCTTCACCTATTAGCCTTTCAACCCTTTATA	1	26	1
ATATATTCGGCGATCAACGATTTTAGATTGTACT	1	76	0
CTTTTTTGCCCCCTTAAGCTTTCAATTAATCTGA	1	201	0
       TTTTCTTAAACCTTTTTATATGGAGGG	2	3	1
        ATTTATTACCCTTTTTGAGAG     	3	2	1
          ** * * * *****
MAP Score: 3.40966

Motif 3
TTAATCCTGAACAATTTTAAATATTTAGAGG	0	19	1
TATTTAGAGGACACCTTAACACGGTGGTTGA	0	40	1
TTAGCCTTTCAACCCTTTATAAAAGACTTTC	1	39	1
CGGTAATAGTACAATCTAAAATCGTTGATCG	1	69	1
ATCTAACTTAAAAACTCTAGATTGAACTCAG	1	174	1
   TTTTCTTAAACCTTTTTATATGGAGGGA	2	7	1
   ATTTATTACCCTTTTTGAGAG       	3	7	1
          ********* *
MAP Score: 0.793066