AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions006_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241192
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0252	251	CTP synthase (pyrG)
#1	AF1319	300	A. fulgidus predicted coding region AF1319
#2	AF1320	24	GMP synthase (guaA-2)
#3	AF1604	300	anthranilate synthase component II (trpD)

Motif 1
TAAATACCGCAAAAAAGCCTACCAGC          	0	0	0
GGTATGAGTAAATAACGATTTCCGCCTTAATTTTAA	0	33	0
AGAGAGGACACGCGAGGATTTCCAGAAGCTTCCTTT	0	86	0
TTCAACTTCCAATTCCGACTTGCAGAGAGGACACGC	0	109	0
CAACTGCTGCAAACGAGCTTTCCAGATATAATCTCC	0	165	0
TTTCCCATTGAGGATGGGATTCCAGATTTGCGCCCT	0	211	1
         TAATATGGAATTGCTGATACCTTTATC	1	1	1
GGTAAATATTAATATAGAATTCCTGAACTTCTTACA	1	59	1
GAGTCTTATTAAATTGCAATTCCAGCTAAGTTAAAA	1	209	1
AAAGCTTCTTCATCAGGTCTTCGGGAACGTAAACTG	3	32	0
GTAAAGCCTGAAGGAGGCATTCCGGGATTTGAGGTC	3	142	1
          **   **  **** **
MAP Score: 12.8586

Motif 2
GGCTTTTTTGCGGTATTTAAAATTAAGGCGGAAATCGTTAT	0	17	1
CTCTGCAAGTCGGAATTGGAAGTTGAAGTGGTTGAGGAGAA	0	118	1
AGATTATATCTGGAAAGCTCGTTTGCAGCAGTTGTCGTGCT	0	167	1
AGTTGTCGTGCTGAATTTCCCATTGAGGATGGGATTCCAGA	0	196	1
TATAGAATTCCTGAACTTCTTACATCTGGAGTGTTCACATT	1	71	1
TTTAACTTAGCTGGAATTGCAATTTAATAAGACTCCAGTCC	1	203	0
CTTGAAAACCCGGCAGTTTACGTTCCCGAAGACCTGATGAA	3	19	1
CCTCAAATCCCGGAATGCCTCCTTCAGGCTTTACTGTGCTG	3	135	0
ATACACTTCGCGGGATTAATCCCACATGGTGGGAGCAG   	3	272	1
          *** * *     ** * *  *
MAP Score: 7.83541

Motif 3
CAGCATTCATGAAAAGGAAGCTTCTGGAAATC	0	74	1
GTCGGAATTGGAAGTTGAAGTGGTTGAGGAGA	0	126	1
AGTGGTTGAGGAGAACGAAGAGGAGATTATAT	0	144	1
CCGAAGACCTGATGAAGAAGCTTTGGTTCACA	3	44	1
ACCTCAGCTGGATGAAGAAGCGAGGAGGAAGA	3	75	1
ATGAAGAAGCGAGGAGGAAGATAGAAAATCTC	3	86	1
          ** ** ******
MAP Score: 7.7793

Motif 4
ATTTAAAATTAAGGCGGAAATCGTTATTTACTC	0	31	1
GAAAAGGAAGCTTCTGGAAATCCTCGCGTGTCC	0	84	1
TCCTCTCTGCAAGTCGGAATTGGAAGTTGAAGT	0	114	1
ATCCCATCCTCAATGGGAAATTCAGCACGACAA	0	198	0
GGAGGGCGCAAATCTGGAATCCCATCCTCAATG	0	216	0
         TAATATGGAATTGCTGATACCTTT	1	1	1
GGTAAATATTAATATAGAATTCCTGAACTTCTT	1	59	1
AGGAGGAGTTATCATGGAAATACCACTCAGTTC	1	116	0
ATTTTTAACTTAGCTGGAATTGCAATTTAATAA	1	214	0
GTAAAGCCTGAAGGAGGCATTCCGGGATTTGAG	3	142	1
          **   ********
MAP Score: 6.00411

Motif 5
CAGCATTCATGAAAAGGAAGCTTCTGGAAAT	0	74	1
TGAATTTCCCATTGAGGATGGGATTCCAGAT	0	207	1
TTTCTGGATAGTTAACGATGGGGTAAATATT	1	38	1
TTCCAGCTAAGTTAAAAATGGTTATATTTAT	1	228	1
  GCCCTTAAGTTGGTGAAGGAAAAA     	2	5	0
CCGAAGACCTGATGAAGAAGCTTTGGTTCAC	3	44	1
ACCTCAGCTGGATGAAGAAGCGAGGAGGAAG	3	75	1
ACCGAGAGCCGTTAAGGCTGCACCGACCTCA	3	171	0
          ***** *****
MAP Score: 3.47082

Motif 6
TGGTAGGCTTTTTTGCGGTATTTAAAATTA	0	12	1
AAGAGGAGATTATATCTGGAAAGCTCGTTT	0	161	1
CCGGAGGGCGCAAATCTGGAATCCCATCCT	0	221	0
ATACCTTTATCGTTTCTGGATAGTTAACGA	1	26	1
CTGAACTTCTTACATCTGGAGTGTTCACAT	1	81	1
CCATTTTTAACTTAGCTGGAATTGCAATTT	1	219	0
TGGTTCACACCTCAGCTGGATGAAGAAGCG	3	67	1
CTGAAGGAGGCATTCCGGGATTTGAGGTCG	3	149	1
CTTAAATACACTTCGCGGGATTAATCCCAC	3	267	1
          **********
MAP Score: 3.27949

Motif 7
GGCTTTTTTGCGGTATTTAAAATTAAGGCGG	0	17	1
ACTTCCAATTCCGACTTGCAGAGAGGACACG	0	110	0
AAGTCGGAATTGGAAGTTGAAGTGGTTGAGG	0	124	1
CCATTGAGGATGGGATTCCAGATTTGCGCCC	0	215	1
TTTGCGCCCTCCGGAGTTGAGACA       	0	237	1
     TAATATGGAATTGCTGATACCTTTAT	1	5	1
CCGAACTGAGTGGTATTTCCATGATAACTCC	1	114	1
TTAACTTAGCTGGAATTGCAATTTAATAAGA	1	212	0
CGTAAACTGCCGGGTTTTCAAGCACCTCCTC	3	10	0
GGAGGCATTCCGGGATTTGAGGTCGGTGCAG	3	154	1
          *** *******
MAP Score: 1.16711