AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241256
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF1045	86	methyl-accepting chemotaxis protein (tlpC-2)
#1	AF1049	102	type II secretion system protein (gspE-4)
#2	AF1473	98	response regulator
#3	AF1475	109	mitochondrial benzodiazepine receptor/sensory transduction protein
#4	AF1484	87	A. fulgidus predicted coding region AF1484
#5	AF1898	74	response regulator
#6	AF2249	66	response regulator
#7	AF2251	30	competence-damage protein, putative
#8	AF2252	78	argininosuccinate synthetase (argG)

Motif 1
GAAAGGGAATAATCTTTTAAGTTTTCTGTCAAT	4	19	0
CGGAATGACTAAGTTTTTAAATTGCCAAGTCTA	5	31	1
TGCAAGAAAAGATTTTTTAACTTGTAAATTACA	6	34	1
AAGATTTGGCGAGGTTTTAAATTTACGAGTGCT	3	61	0
CTTTATAGAGAAAATTTTATTTTTTATTTTCGC	0	43	1
GACCTCACAAAATCTTTTATTTTCAAATAGCAA	4	55	1
AAACCCAGGAAGTTTTTTAACTTTTGTTTAATC	8	19	1
AACCTCGCCAAATCTTTTATACTTTAAATTTAA	3	78	1
TCACACGAAAAATATTTAATTTTGAATGGGATA	2	43	1
   TATTTTTAAATTTTTAAAATAACTTGGAAC	7	7	1
TTAATCTCAAAAGATTTAAACCTCTCCGCATGA	8	46	1
TTTCTTATTCGAAATTTTACTTTATAGAGAAAA	0	24	1
 TAAGCAAAGTGGCTTTTAAGCTCGATTGAAAG	3	9	1
          **  ****** **
MAP Score: 21.3811

Motif 2
TCTTATTCGAAATTTTACTTTATAGAGAAAATTT	0	26	1
TTATAGAGAAAATTTTATTTTTTATTTTCGCAAT	0	45	1
       AAGTTTTTGATTATGTTGGCGGAGCAG	2	3	1
ACACGAAAAATATTTAATTTTGAATGGGATAGTG	2	45	1
TTGAAAGCGATTTTTCTTTTTTAAAAAGCACTCG	3	35	1
TTTGGCGAGGTTTTAAATTTACGAGTGCTTTTTA	3	56	0
TCGCCAAATCTTTTATACTTTAAATTTAACTATA	3	82	1
CCTCACAAAATCTTTTATTTTCAAATAGCAACAA	4	57	1
AATGACTAAGTTTTTAAATTGCCAAGTCTAATTT	5	34	1
AAGAAAAGATTTTTTAACTTGTAAATTACAATTG	6	37	1
        TATTTTTAAATTTTTAAAATAACTTG	7	2	1
CCCAGGAAGTTTTTTAACTTTTGTTTAATCTCAA	8	22	1
          ***** * ***  *
MAP Score: 12.9311