AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255565
 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	3	1
CCTTTTCTTTTCTTCACCTATTAGCCTTTCAA	1	19	1
CCTATTAGCCTTTCAACCCTTTATAAAAGACT	1	35	1
       CTTTTTTGCCCCCTTAAGCTTTCAA	1	210	0
       TTTTCTTAAACCTTTTTATATGGAG	2	3	1
        ATTTATTACCCTTTTTGAGAG   	3	2	1
          **** **** **
MAP Score: 7.26869

Motif 2
        GTTTATAGCTTAATCCTGAACAA	0	2	1
AGCTTAATCCTGAACAATTTTAAATATTTAG	0	16	1
       TCTTCATCACCTTTTCTTTTCTTC	1	3	1
CCTTTTCTTTTCTTCACCTATTAGCCTTTCA	1	19	1
TATTAGCCTTTCAACCCTTTATAAAAGACTT	1	37	1
CAACCCTTTATAAAAGACTTTCGGTAATAGT	1	48	1
TATTCGGCGATCAACGATTTTAGATTGTACT	1	76	0
ATGTAGGTAATGATAGCATTTGACAATTGTC	1	108	1
TCAGATTAATTGAAAGCTTAAGGGGGCAAAA	1	201	1
     TTTTCTTAAACCTTTTTATATGGAGG	2	5	1
       ATTTATTACCCTTTTTGAGAG   	3	3	1
          * *********
MAP Score: 5.47016

Motif 3
TTAATCCTGAACAATTTTAAATATTTAGAGG	0	19	1
TATTTAGAGGACACCTTAACACGGTGGTTGA	0	40	1
TTAGCCTTTCAACCCTTTATAAAAGACTTTC	1	39	1
   TTTTCTTAAACCTTTTTATATGGAGGGA	2	7	1
   ATTTATTACCCTTTTTGAGAG       	3	7	1
          ********* *
MAP Score: 0.52634

Motif 4
    GTTTATAGCTTAATCCTGAACAATTTTA	0	6	1
TTTAGAGGACACCTTAACACGGTGGTTGA   	0	42	1
TTGTACTATTACCGAAAGTCTTTTATAAAGGG	1	51	0
TAATAGTACAATCTAAAATCGTTGATCGCCGA	1	72	1
ATTAATTGAAAGCTTAAGGGGGCAAAAAAG  	1	205	1
        TTTTCTTAAACCTTTTTATATGGA	2	2	1
          *******  ***
MAP Score: 0.276278