AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241092
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0448	104	signal-transducing histidine kinase, putative
#1	AF0451	52	A. fulgidus predicted coding region AF0451
#2	AF0454	32	A. fulgidus predicted coding region AF0454
#3	AF1045	86	methyl-accepting chemotaxis protein (tlpC-2)
#4	AF1049	102	type II secretion system protein (gspE-4)
#5	AF1178	195	A. fulgidus predicted coding region AF1178
#6	AF1179	62	conserved hypothetical protein
#7	AF1181	35	GTP-binding protein
#8	AF1184	37	signal-transducing histidine kinase
#9	AF1452	117	signal-transducing histidine kinase
#10	AF1473	98	response regulator
#11	AF1475	109	mitochondrial benzodiazepine receptor/sensory transduction protein

Motif 1
TAACCAAAACAAAAATTAAAAA        	9	2	0
TTTTTTAGGATAAATTTAAACAAGTTACCC	0	66	1
AAAGCACTCGTAAATTTAAAACCTCGCCAA	11	59	1
 GGGTATAGTTAAATTTAAAGTATAAAAGA	11	90	0
GTGTAATCCCAAAAATGAAAGCAAAGGTTA	4	29	1
CTATCCCATTCAAAATTAAATATTTTTCGT	10	47	0
TTGCGAAAATAAAAAATAAAATTTTCTCTA	3	48	0
GCTTTTCCCGTAAAATCAAAAATTCGACAA	6	11	1
ATTGGTTCAAAAAAATTAAGCCTTACTCCT	5	167	0
AGTGCTTTTTAAAAAAGAAAAATCGCTTTC	11	37	0
TTTAGAACTTAATATTTAAAACTTT     	2	5	0
         TTAATTTTAAATAATCATTTG	8	1	1
GCTCCGCCAACATAATCAAAAACTT     	10	5	0
TAATAGTTATTATAATGAAGGGGGGAGGAT	4	82	1
          **********
MAP Score: 12.2594