AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241291
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0274	300	sarcosine oxidase, subunit beta (soxB)
#1	AF0275	266	surface layer protein B (slgB-1)
#2	AF0276	53	conserved hypothetical protein
#3	AF0277	75	signal-transducing histidine kinase, putative
#4	AF0579	138	A. fulgidus predicted coding region AF0579
#5	AF0770	300	signal-transducing histidine kinase
#6	AF1621	78	conserved hypothetical protein

Motif 1
GCCAGTGGGGTGATAAGCGTGAAGGACAGGAAGGTT	0	17	1
CACGCCATCGAGCTTGGCTACGACGACCTTGAGAGC	0	92	1
ACATGGGCCAGTCGTTGCTCCGGTAAACCTCTTGAG	0	128	0
AGTATTCTTAGGATGTGCATCAGACAGCTCTTACCC	0	166	0
CTCAGCCAGAAGACTGGCAAGAGCGTTGATGAGATT	0	200	1
CCCGCTTTACATACTCGCTGCAGGGAAGGGTGATAA	0	271	1
TGCAAGCAGAAGCAGAGCGGCAGTTAATCCTCTAAA	1	135	0
TGCTTCTGCTTGCACTGCTGCAAACAGTAAACGCAG	1	157	1
GCTGCAAACAGTAAACGCAGCTACCATAACTGGCTG	1	173	1
CAAATTCAGAGTCCGGGCTACTACGAGCTTGCCAGC	1	213	1
TGCCAGCGACATAACAGCATCGGGAACGTGTATT  	1	242	1
GCCCTTGAGATGCTTTGCTCGGATGACCTTGAAAGT	5	50	1
GTGGGCTGAAAGCAGAGCAGGGGAGCAGAGTGGCAA	5	153	1
GGTAAAAACTGGAGATGCCACGATAAGGCTCTGCGG	5	198	1
GCCACGATAAGGCTCTGCGGGGATGATGAGGTAATA	5	214	1
TCCAGCAGCTTGCTCAGCAAGGGAATCAGAAGCTTT	5	249	0
  GACTTCTTGGAAGAGCAGCAACCTGTCCAGCAGC	5	276	0
          GTCTCCGCTTCGGGGAAATTGTATTT	6	0	1
          ***   **  *** **
MAP Score: 13.1758

Motif 2
GCTGCCTCTGCGTTGTTACGCCAATCTCATCAA	0	225	0
GAGGTTTTTACTATTTTTCAAAAGCAGGGAATT	1	29	1
TAGGAATGTGCTTTTGTAATTAATCAGTTAAAT	1	71	1
        TACGATTGTAACACAATCAAAAACT	2	2	1
     CATTTCATTTTTTCGCAATTATACTGAT	3	5	1
AAAAATTAATAATTTGTAAACCATTTCGAAC  	4	8	0
ACTGCTGAACCTTTTTTTCGAAAGGTGTTATAG	4	51	1
TAGCAACTTTCATTTTTGAAACATAACTTTTTT	4	91	1
TGAAACATAACTTTTTTACTGCAATGGAGTAAA	4	107	1
      CGAGAGTTTTTACTCCATTGCAGTAAA	4	121	0
CTTCAATTGCACTTTTTTCCACATCAATTTTCG	5	18	0
TGGCATCTCCAGTTTTTACCTCAGTTACCTTGC	5	185	0
GAATCAGAAGCTTTATTACCTCATCATCCCCGC	5	230	0
          * *******  **
MAP Score: 10.8342

Motif 3
   CTGTAAGGCCAGTGGGGTGATAAGCGTGAAGGACAGGAA	0	7	1
AAGGTTGTTTGCAGGTGTGAGGATCTGACCGAGGAGGAGATA	0	47	1
GCAACGACTGGCCCATGTCAGGGTAAGAGCTGTCTGATGCAC	0	146	1
CAGAAGACTGGCAAGAGCGTTGATGAGATTGGCGTAACAACG	0	206	1
ACCCTTCCCTGCAGCGAGTATGTAAAGCGGGACCGGATTCAC	0	260	0
TGCAATTGAAGCCCTTGAGATGCTTTGCTCGGATGACCTTGA	5	40	1
TGGGCTGAAAGCAGAGCAGGGGAGCAGAGTGGCAAGGTAACT	5	154	1
AACTGGAGATGCCACGATAAGGCTCTGCGGGGATGATGAGGT	5	204	1
CAGCAACCTGTCCAGCAGCTTGCTCAGCAAGGGAATCAGAAG	5	253	0
          ***       **   ***  **
MAP Score: 10.7967

Motif 4
TTTATCACCCTTCCCTGCAGCGAGTATGTAAAG	0	275	0
TGCTTCTGCTTGCACTGCTGCAAACAGTAAACG	1	157	1
TTTGTTGTTTTGGACTGCTGAACCTTTTTTTCG	4	38	1
GAGTTTTTACTCCATTGCAGTAAAAAAGTTATG	4	112	0
GCCCTTGAGATGCTTTGCTCGGATGACCTTGAA	5	50	1
GCCACTCTGCTCCCCTGCTCTGCTTTCAGCCCA	5	154	0
GCCACGATAAGGCTCTGCGGGGATGATGAGGTA	5	214	1
AGCTTCTGATTCCCTTGCTGAGCAAGCTGCTGG	5	251	1
GACAGGTTGCTGCTCTTCCAAGAAGTC      	5	283	1
       GTCTCCGCTTCGGGGAAATTGTATTT	6	3	1
          *** **** * **
MAP Score: 10.681

Motif 5
CGCCATCGAGCTTGGCTACGACGACCTTGAGAGCCTCAA	0	94	1
ATGGGCCAGTCGTTGCTCCGGTAAACCTCTTGAGGCTCT	0	123	0
CTTTATCACCCTTCCCTGCAGCGAGTATGTAAAGCGGGA	0	270	0
CTTAATAATTCCCTGCTTTTGAAAAATAGTAAAAACCTC	1	29	0
AAACAGTAAACGCAGCTACCATAACTGGCTGCACTCAAA	1	178	1
AATTCAGAGTCCGGGCTACTACGAGCTTGCCAGCGACAT	1	215	1
TACACGTTCCCGATGCTGTTATGTCGCTGGCAAGCTCGT	1	235	0
CCTTGAGATGCTTTGCTCGGATGACCTTGAAAGTACGCT	5	52	1
TAATTTACAAGAAAGCTGCAGAGATTAGGAAGCGTACTT	5	82	0
CACGATAAGGCTCTGCGGGGATGATGAGGTAATAAAGCT	5	216	1
        GTCTCCGCTTCGGGGAAATTGTATTTAAAAT	6	2	1
          *   *** * * **   **
MAP Score: 9.92819

Motif 6
CAGGAAGGTTGTTTGCAGGTGTGAGGATCTGAC	0	43	1
ATGGGCCAGTCGTTGCTCCGGTAAACCTCTTGA	0	129	0
CTGGCAAGAGCGTTGATGAGATTGGCGTAACAA	0	213	1
TTTACATACTCGCTGCAGGGAAGGGTGATAAAG	0	276	1
TTAGAGGATTAACTGCCGCTCTGCTTCTGCTTG	1	136	1
CTCTGCTTCTGCTTGCACTGCTGCAAACAGTAA	1	154	1
TACACGTTCCCGATGCTGTTATGTCGCTGGCAA	1	241	0
CCTTGAGATGCTTTGCTCGGATGACCTTGAAAG	5	52	1
TTTACAAGAAAGCTGCAGAGATTAGGAAGCGTA	5	85	0
CACTCTGCTCCCCTGCTCTGCTTTCAGCCCACC	5	152	0
ACCTCAGTTACCTTGCCACTCTGCTCCCCTGCT	5	168	0
CACGATAAGGCTCTGCGGGGATGATGAGGTAAT	5	216	1
CTTCTGATTCCCTTGCTGAGCAAGCTGCTGGAC	5	253	1
CTGCTGGACAGGTTGCTGCTCTTCCAAGAAGTC	5	277	1
          * **** * ****
MAP Score: 9.06984

Motif 7
      CTGTAAGGCCAGTGGGGTGATAAGCGTGAAGGACAGGA	0	4	1
GATAAGCGTGAAGGACAGGAAGGTTGTTTGCAGGTGTGAGGATC	0	28	1
TGTGAGGATCTGACCGAGGAGGAGATAATCCACGCCATCGAGCT	0	62	1
TCAAGAGGTTTACCGGAGCAACGACTGGCCCATGTCAGGGTAAG	0	129	1
CATCCTAAGAATACTCAGCCAGAAGACTGGCAAGAGCGTTGATG	0	187	1
TGGCGTAACAACGCAGAGGCAGCCCGTGAATCCGGTCCCGCTTT	0	235	1
GTGCAAGCAGAAGCAGAGCGGCAGTTAATCCTCTAAACAGTCCG	1	128	0
TGCAAACAGTAAACGCAGCTACCATAACTGGCTGCACTCAAATT	1	175	1
CTGCACTCAAATTCAGAGTCCGGGCTACTACGAGCTTGCCAGCG	1	206	1
  AATACACGTTCCCGATGCTGTTATGTCGCTGGCAAGCTCGTA	1	234	0
GGTGGGCTGAAAGCAGAGCAGGGGAGCAGAGTGGCAAGGTAACT	5	152	1
AGTGGCAAGGTAACTGAGGTAAAAACTGGAGATGCCACGATAAG	5	181	1
TCTGATTCCCTTGCTGAGCAAGCTGCTGGACAGGTTGCTGCTCT	5	255	1
          *  * ****  *       **  *
MAP Score: 4.73253

Motif 8
AATTTACAAGAAAGCTGCAGAGATTAGGAA	5	90	0
AAGCAGAAGCAGAGCGGCAGTTAATCCTCT	1	138	0
ATGAGGTAATAAAGCTTCTGATTCCCTTGC	5	239	1
CCTTGCTGAGCAAGCTGCTGGACAGGTTGC	5	263	1
ACTTCTTGGAAGAGCAGCAACCTGTCCAGC	5	279	0
GCAGGGGAGCAGAGTGGCAAGGTAACTGAG	5	169	1
TTCAAAAATGAAAGTTGCTATAAACATCTA	4	81	0
CTTTCGAAAAAAAGGTTCAGCAGTCCAAAA	4	45	0
AAGCATCTCAAGGGCTTCAATTGCACTTTT	5	35	0
ATAGGGAAAAAGAGTTTTTGATTGTGTTAC	2	17	0
GACGACCTTGAGAGCCTCAAGAGGTTTACC	0	113	1
        CGAGAGTTTTTACTCCATTGCA	4	126	0
CTTTTTTTCGAAAGGTGTTATAGATGTTTA	4	61	1
          **********
MAP Score: 3.68595

Motif 9
TGATAAGCGTGAAGGACAGGAAGGTTGTTTGCAGGT	0	27	1
ACGACCTTGAGAGCCTCAAGAGGTTTACCGGAGCAA	0	114	1
TTTTTCATAGGTAGTTTTAGAGGTTTTTACTATTTT	1	10	1
GGAAATTTCGGACTGTTTAGAGGATTAACTGCCGCT	1	120	1
TTTAAAAAATAGGGAAAAAGAGTTTTTGATTGTGTT	2	19	0
TTTTTCGAAAGGTGTTATAGATGTTTATAGCAACTT	4	64	1
GTGCAATTGAAGCCCTTGAGATGCTTTGCTCGGATG	5	39	1
AGAAAGCTGCAGAGATTAGGAAGCGTACTTTCAAGG	5	76	0
TTGCTCAGCAAGGGAATCAGAAGCTTTATTACCTCA	5	240	0
TTTTATATATGTTGGTACAGACTATTTAGCAG    	6	56	1
          ** * *  *** * **
MAP Score: 2.45345