AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons018_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243004
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0167	123	flavoprotein (fprA-1)
#1	AF0270	158	alkyl hydroperoxide reductase
#2	AF0342	137	nigerythrin, putative
#3	AF0344	239	desulfoferrodoxin, putative
#4	AF0880	62	rubredoxin (rd-1)
#5	AF1348	67	A. fulgidus predicted coding region AF1348
#6	AF1520	27	flavoprotein (fprA-2)
#7	AF1638	31	ribulose bisphosphate carboxylase, large subunit (rbcL-2)
#8	AF1639	30	signal-transducing histidine kinase
#9	AF1640	49	rubrerythrin (rr3)
#10	AF2311	108	conserved hypothetical protein

Motif 1
      GTTTTTCCATTTTTGTTATCTCAAG	1	4	1
TTATCTCAAGTTCGAATTCCGTAATAAAAGG	1	25	1
TATTGTCTGATTAGAATTTAGAATATCTCTT	1	59	1
TTGTAACGACTTCAATTTCCGGGAATTATCC	1	126	0
AGGCAAATGGTTCGAATTTCGTAAATTTGGA	2	57	1
ACTTAAGTCTTTCGAAATTTTTCTGGATTTT	2	94	0
AAGACTTAAGTTAGAGTTTGGCCAAGTTAAG	2	114	1
CCTTTCTATGTTCGAATTTCGTATTTACGAA	3	177	0
TCCCTTACCTTTAAAATTTCTTCCCTAATAA	3	209	0
TAAGCTTTCCCTCGATTTCCTAACCT     	5	5	0
AAAAGAAAAATTCGATTGCTGGAGGTGTTTT	5	45	1
    AATTTTTTAAATTTTTTGAGTACTTTT	8	6	1
AAAACATTCTCTAAAATTTTTTCCGAATATC	10	15	1
AAAGCTTAGGTTCGATATTCGGAAAAAATTT	10	28	0
AACCTAAGCTTTAAATATCGGAAATAATATT	10	47	1
GCTCATAGCGTTAAATATTATTTCCGATATT	10	60	0
          ********* *
MAP Score: 14.5176

Motif 2
GGAGATTGCTGAAAAAGTTTACTGGGTTGG	0	16	1
ATGAGCGAGTCAAAAATTCTGCGATTCCAG	0	55	0
      TCATCAACAATCAGGTAGCTGTTG	0	109	0
TAAGGAAAAGGTAAAAATTGCAAACGGTAA	2	13	0
TACGAAATTCGAACCATTTGCCTGTCTGAC	2	50	0
TCAAAATCCAGAAAAATTTCGAAAGACTTA	2	92	1
CCATGCCTTCGAAAAAGGTGTTAATCTGGT	3	50	0
TTTCTGAGTCCAACAAGCTGAGCTTCCATG	3	75	0
TTAGAAAAAAGAAAAATTCGATTGCTGGAG	5	39	1
          CAAAAAGGTCTTTCGCTAAC	6	0	1
AGGTCTTTCGCTAACAGTTGTA        	6	15	1
         GCAACAAGTTGCTAAGGAGGT	7	20	0
TAAAAGTACTCAAAAAATTTAAAAAATT  	8	8	0
         GGTAAAAGTACTCAAAAAATT	8	19	0
TCATGGTTGTGAAAAAGCAG          	9	39	1
TCGATATTCGGAAAAAATTTTAGAGAATGT	10	18	0
  CGCCTCAAGAACAAGTTGCTTTGGGTCG	10	90	0
          **********
MAP Score: 9.79748

Motif 3
GGGTTGGTGCGAAGGACTGGAATCGCAGAATTTTTGACTC	0	39	1
TTAGAATTTAGAATATCTCTTTAACGAGGAGGTGATTGAT	1	69	1
GAAAAATTTCGAAAGACTTAAGTTAGAGTTTGGCCAAGTT	2	102	1
GTTGGAGATGGAAAGGCTGCTCGAAGAAAAAGCAATGATC	3	12	0
CACCTTTTTCGAAGGCATGGAAGCTCAGCTTGTTGGACTC	3	60	1
TTCGAACATAGAAAGGTTTATTAGGGAAGAAATTTTAAAG	3	192	1
ATATTTAAGCGAAAGGATTATAACTGAGAAGAAACATGAT	4	27	1
GAAATCGAGGGAAAGCTTAATATTAGAAAAAAGAAAAATT	5	17	1
          *** *  *  *    *** *
MAP Score: 8.02671

Motif 4
    GAGTGTGGAGATTGCTGAAAAAGTTTA	0	6	1
GGTAGCTGTTGTAGCTCGTTCCCTGCGGGAG	0	89	0
GGTCAGACAGGCAAATGGTTCGAATTTCGTA	2	49	1
AAAAAGGTGTTAATCTGGTTGGAGATGGAAA	3	38	0
GCATGGAAGCTCAGCTTGTTGGACTCAGAAA	3	74	1
GGAAGAGTTTGTAGCGGGCTGATGGAAAGTA	3	111	0
TTAATATCGCTAAACTGGCTGTAAATCACCA	3	146	0
TACCTCCTTAGCAACTTGTTGC         	7	19	1
GCGACCCAAAGCAACTTGTTCTTGAGGCG  	10	89	1
          * *********
MAP Score: 5.91559

Motif 5
GATTGCTGAAAAAGTTTACTGGGTTGGTGCGAAGGACTGGAA	0	19	1
AACGAGCTACAACAGCTACCTGATTGTTGATGA         	0	100	1
ATATCTCTTTAACGAGGAGGTGATTGATTTGGCGCCGCTTTT	1	81	1
CTTCGAAAAAGGTGTTAATCTGGTTGGAGATGGAAAGGCTGC	3	32	0
GTAAATCACCAAAGAGGAAGAGTTTGTAGCGGGCTGATGGAA	3	115	0
TATTAGAAAAAAGAAAAATTCGATTGCTGGAGGTGTTTTT  	5	37	1
    CGCCTCAAGAACAAGTTGCTTTGGGTCGCTCATAGCGT	10	80	0
          ** *   *   * ***  *  *
MAP Score: 4.87502

Motif 6
GGAGATTGCTGAAAAAGTTTACTGGGTTGGTGCGA	0	16	1
GGGTTGGTGCGAAGGACTGGAATCGCAGAATTTTT	0	39	1
AATTCCGTAATAAAAGGTTATATTGTCTGATTAGA	1	39	1
TCAGGCTAAGGAAAAGGTAAAAATTGCAAACGGTA	2	14	0
TCAAAATCCAGAAAAATTTCGAAAGACTTAAGTTA	2	92	1
CCATGCCTTCGAAAAAGGTGTTAATCTGGTTGGAG	3	45	0
CACCAAAGAGGAAGAGTTTGTAGCGGGCTGATGGA	3	116	0
TTCGAACATAGAAAGGTTTATTAGGGAAGAAATTT	3	192	1
GTTTATTAGGGAAGAAATTTTAAAGGTAAGGGAGG	3	207	1
ATATTTAAGCGAAAGGATTATAACTGAGAAGAAAC	4	27	1
TCGATATTCGGAAAAAATTTTAGAGAATGTTTTTA	10	13	0
          ****** **  *  *
MAP Score: 3.9666

Motif 7
 GAGTGTGGAGATTGCTGAAAAAGTTTACT	0	9	1
ACAGCTACCTGATTGTTGATGA        	0	111	1
TGGAAGCTCAGCTTGTTGGACTCAGAAACC	3	77	1
AGAAAAATTCGATTGCTGGAGGTGTTTTT 	5	48	1
          **********
MAP Score: 1.57494

Motif 8
       GTTTTTCCATTTTTGTTATCTCAAGT	1	3	1
 ACTTTACCGTTTGCAATTTTTACCTTTTCCTT	2	9	1
ATTTCGTAAATTTGGATTTTTCAAAATCCAGAA	2	72	1
AACTTAAGTCTTTCGAAATTTTTCTGGATTTTG	2	93	0
CCTCCCTTACCTTTAAAATTTCTTCCCTAATAA	3	209	0
       AATTTTTTAAATTTTTTGAGTACTTT	8	3	1
        ATTTTTTATTCTTTTAAACATTGTG	9	2	1
AAAAACATTCTCTAAAATTTTTTCCGAATATCG	10	14	1
          ***  ****** *
MAP Score: 1.11337