AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241204
 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
          GCTGGTAGGCTTTTTTGCGGTATTTA	0	0	1
TTAAAATTAAGGCGGAAATCGTTATTTACTCATACC	0	33	1
AAAGGAAGCTTCTGGAAATCCTCGCGTGTCCTCTCT	0	86	1
GCGTGTCCTCTCTGCAAGTCGGAATTGGAAGTTGAA	0	109	1
GGAGATTATATCTGGAAAGCTCGTTTGCAGCAGTTG	0	165	1
AGGGCGCAAATCTGGAATCCCATCCTCAATGGGAAA	0	211	0
GATAAAGGTATCAGCAATTCCATATTA         	1	1	0
TGTAAGAAGTTCAGGAATTCTATATTAATATTTACC	1	59	0
TTTTAACTTAGCTGGAATTGCAATTTAATAAGACTC	1	209	0
CAGTTTACGTTCCCGAAGACCTGATGAAGAAGCTTT	3	32	1
GACCTCAAATCCCGGAATGCCTCCTTCAGGCTTTAC	3	142	0
          ** ****  **   **
MAP Score: 12.8586

Motif 2
ATGAAGAAGCGAGGAGGAAGATAGAAAATC	3	86	1
TGGCAAAAAAGAGGTAAAAGTCACCTAAAC	3	222	0
CCGAAGACCTGATGAAGAAGCTTTGGTTCA	3	44	1
ACCTCAGCTGGATGAAGAAGCGAGGAGGAA	3	75	1
AATGCTGTTGGAGGTATGAGTAAATAACGA	0	51	0
TCTCATGATTGAGGTTAAGGCCAGCACAGT	3	114	1
GTAATTTTTTGAGGATAAAAAATAAATATA	1	250	0
TGAAGTGGTTGAGGAGAACGAAGAGGAGAT	0	141	1
ATTTCCCATTGAGGATGGGATTCCAGATTT	0	210	1
GTCGGAATTGGAAGTTGAAGTGGTTGAGGA	0	126	1
TCATCCAGCTGAGGTGTGAACCAAAGCTTC	3	60	0
GAACACTCCAGATGTAAGAAGTTCAGGAAT	1	77	0
AAGTTGATGTGATGAAAACAAGTTTTAGGA	1	145	0
          **********
MAP Score: 9.49725

Motif 3
ATTCCGACTTGCAGAGAGGACACGCGAGGATTTCCAGAA	0	95	0
AGTTGAAGTGGTTGAGGAGAACGAAGAGGAGATTATATC	0	138	1
CAGTTGTCGTGCTGAATTTCCCATTGAGGATGGGATTCC	0	195	1
GGATGGGATTCCAGATTTGCGCCCTCCGGAGTTGAGACA	0	222	1
GGAGTGTTCACATTACCCGAACTGAGTGGTATTTCCATG	1	98	1
TTCCCGAAGACCTGATGAAGAAGCTTTGGTTCACACCTC	3	41	1
TCACACCTCAGCTGGATGAAGAAGCGAGGAGGAAGATAG	3	71	1
CACAGTAAAGCCTGAAGGAGGCATTCCGGGATTTGAGGT	3	138	1
GTCGGTGCAGCCTTAACGGCTCTCGGTGGATCATCTCTT	3	175	1
ATAGCAAAAAGCTTAAATACACTTCGCGGGATTAATCCC	3	256	1
CACTTCGCGGGATTAATCCCACATGGTGGGAGCAG    	3	275	1
          *****    * *   * **
MAP Score: 9.33282

Motif 4
GTATTTAAAATTAAGGCGGAAATCGTTATT	0	29	1
GTTGAAGTGGTTGAGGAGAACGAAGAGGAG	0	139	1
GAATTTCCCATTGAGGATGGGATTCCAGAT	0	208	1
TTCTGGATAGTTAACGATGGGGTAAATATT	1	39	1
GAAAACAAGTTTTAGGAGGAGTTATCATGG	1	132	0
AGGTAATTTTTTGAGGATAAAAAATAAATA	1	252	0
AATCTCATGATTGAGGTTAAGGCCAGCACA	3	112	1
CAGTAAAGCCTGAAGGAGGCATTCCGGGAT	3	140	1
ATTCCGGGATTTGAGGTCGGTGCAGCCTTA	3	160	1
CCGAGAGCCGTTAAGGCTGCACCGACCTCA	3	171	0
TATCAGAAAGTTTAGGTGACTTTTACCTCT	3	213	1
          **********
MAP Score: 7.64569

Motif 5
TAGGCTTTTTTGCGGTATTTAAAATTAAGGCGGAA	0	15	1
TTAAAATTAAGGCGGAAATCGTTATTTACTCATAC	0	33	1
AAAGGAAGCTTCTGGAAATCCTCGCGTGTCCTCTC	0	86	1
CTCTCTGCAAGTCGGAATTGGAAGTTGAAGTGGTT	0	116	1
AGGGCGCAAATCTGGAATCCCATCCTCAATGGGAA	0	212	0
       TAATATGGAATTGCTGATACCTTTATCG	1	3	1
TGTAAGAAGTTCAGGAATTCTATATTAATATTTAC	1	60	0
TTTTAACTTAGCTGGAATTGCAATTTAATAAGACT	1	210	0
AACGTAAACTGCCGGGTTTTCAAGCACCTCCTC  	3	8	0
TCATCAGGTCTTCGGGAACGTAAACTGCCGGGTTT	3	24	0
AAGGAGGCATTCCGGGATTTGAGGTCGGTGCAGCC	3	152	1
GCTCCCACCATGTGGGATTAATCCCGCGAAGTGTA	3	273	0
          * *******  *  *
MAP Score: 5.26068

Motif 6
       GCTGGTAGGCTTTTTTGCGGTATTTAAAATTAAGGCG	0	3	1
GGAGGTATGAGTAAATAACGATTTCCGCCTTAATTTTAAATACC	0	28	0
CAGCATTCATGAAAAGGAAGCTTCTGGAAATCCTCGCGTGTCCT	0	74	1
TCTGCAAGTCGGAATTGGAAGTTGAAGTGGTTGAGGAGAACGAA	0	119	1
GACAACTGCTGCAAACGAGCTTTCCAGATATAATCTCCTCTTCG	0	159	0
GGGGTAAATATTAATATAGAATTCCTGAACTTCTTACATCTGGA	1	57	1
TTTATTTAGCCAAACCCTAAGTTGATGTGATGAAAACAAGTTTT	1	149	0
         GGTTAAAACTTGTTGGTGAATTAAATAAAGGTAAT	1	275	0
CAGGTCTTCGGGAACGTAAACTGCCGGGTTTTCAAGCACCTCCT	3	11	0
CTCAAATCCCGGAATGCCTCCTTCAGGCTTTACTGTGCTGGCCT	3	131	0
TAGCAAAAAGCTTAAATACACTTCGCGGGATTAATCCCACATGG	3	257	1
          * **       ***  *   * **
MAP Score: 4.75532