AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241643
 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
GCAGGTTAATATTCTTTGTGCAGACTTATTC	0	25	1
CTAAAAAAATATTTTAAATGCCGATTCTGGT	3	26	0
CATTTAAAATATTTTTTTAGCTTTCAAAACC	3	37	1
TTTTCCGTTAATTTTTTATTCTTTTAAGCAT	3	68	1
          ATTTTTATATCTGCTACCGTT	4	0	1
CCAAAACCTTATATTTTCTGCGTGTTAAGGC	5	11	1
          ******* ***
MAP Score: 8.07008

Motif 2
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