AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions027_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241674
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF1695	50	thiamine biosynthesis protein (apbA)
#1	AF1696	28	small multidrug export protein (qacE)
#2	AF1697	49	conserved hypothetical protein
#3	AF1699	102	pyruvate ferredoxin oxidoreductase, subunit gamma (porG)
#4	AF2055	32	2-ketoisovalerate ferredoxin oxidoreductase, subunit gamma (vorG)
#5	AF2056	35	conserved hypothetical protein

Motif 1
GCAGCAGGTTAATATTCTTTGTGCAGACTTATTC	0	22	1
 CCTGCTGAGCGTTCTTCTTGTGTCAGCG     	1	9	1
TTCCCAATAAACTTTTGGTTTCGTAATAAA    	2	6	0
         GCTTTAAGGTTCTGCAGTTTTCCCA	2	34	0
ATTCTGGTTGAATTCTGATTCAAC          	3	0	0
CGGCATTTAAAATATTTTTTTAGCTTTCAAAACC	3	34	1
TTTTCCGTTAATTTTTTATTCTTTTAAGCATCCT	3	68	1
          ATTTTTATATCTGCTACCGTTCTG	4	0	1
TATCTGCTACCGTTCTGTATCCGCT         	4	17	1
  ACCAAAACCTTATATTTTCTGCGTGTTAAGGC	5	8	1
          * ****  *** **
MAP Score: 6.83784

Motif 2
AGCAGGTTAATATTCTTTGTGCAGACTTATTC	0	24	1
GCTAAAAAAATATTTTAAATGCCGATTCTGGT	3	26	0
GCATTTAAAATATTTTTTTAGCTTTCAAAACC	3	36	1
CTTTTCCGTTAATTTTTTATTCTTTTAAGCAT	3	67	1
        ATTTTTATATCTGCTACCGTTCTG	4	2	1
ACCAAAACCTTATATTTTCTGCGTGTTAAGGC	5	10	1
          **** *** ***
MAP Score: 6.62351

Motif 3
CAGGTTAATATTCTTTGTGCAGACTTATTC	0	26	1
TTGTGCAGACTTATTCCTGA          	0	40	1
CTGCTGAGCGTTCTTCTTGTGTCAGCG   	1	11	1
GGCATTTAAAATATTTTTTTAGCTTTCAAA	3	35	1
CGTTAATTTTTTATTCTTTTAAGCATCCTC	3	73	1
      ATTTTTATATCTGCTACCGTTCTG	4	4	1
 ACCAAAACCTTATATTTTCTGCGTGTTAA	5	9	1
          **********
MAP Score: 2.04639