AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241276
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
GCAAGCAGAAGCAGAGCGGCAGTTAATCCT	0	140	0
ACTGTTTGCAGCAGTGCAAGCAGAAGCAGA	0	155	0
ACTCTGAATTTGAGTGCAGCCAGTTATGGT	0	195	0
CGCTTCCTAATCTCTGCAGCTTTCTTGTAA	4	87	1
TGGGCTGAAAGCAGAGCAGGGGAGCAGAGT	4	154	1
GAGCAGGGGAGCAGAGTGGCAAGGTAACTG	4	167	1
CCACGATAAGGCTCTGCGGGGATGATGAGG	4	215	1
TGATTCCCTTGCTGAGCAAGCTGCTGGACA	4	257	1
 GACTTCTTGGAAGAGCAGCAACCTGTCCA	4	281	0
          **********
MAP Score: 10.3906

Motif 2
TGCTTCTGCTTGCACTGCTGCAAACAGTAAACG	0	157	1
TTTGTTGTTTTGGACTGCTGAACCTTTTTTTCG	3	38	1
GAGTTTTTACTCCATTGCAGTAAAAAAGTTATG	3	112	0
GCCCTTGAGATGCTTTGCTCGGATGACCTTGAA	4	50	1
GCCACTCTGCTCCCCTGCTCTGCTTTCAGCCCA	4	154	0
GCCACGATAAGGCTCTGCGGGGATGATGAGGTA	4	214	1
AGCTTCTGATTCCCTTGCTGAGCAAGCTGCTGG	4	251	1
GACAGGTTGCTGCTCTTCCAAGAAGTC      	4	283	1
       GTCTCCGCTTCGGGGAAATTGTATTT	5	3	1
          *** **** * **
MAP Score: 9.69451

Motif 3
CTGCTTTTGAAAAATAGTAAAAACCTCTAAA	0	25	0
CTATTTTTCAAAAGCAGGGAATTATTAAGTA	0	39	1
TGCACTGCTGCAAACAGTAAACGCAGCTACC	0	167	1
CCAACTTTAAAAAATAGGGAAAAAGAGTTTT	1	29	0
TATAATTGCGAAAAAATGAAATG        	2	2	0
ATTATTAACCAAAAAATTTAAATAGGAGCTA	2	36	1
GAGCTAATATCAAACATTAAAATA       	2	61	1
TCCAAAACAACAAAAATTAATAATTTGTAAA	3	21	0
AGTTATGTTTCAAAAATGAAAGTTGCTATAA	3	88	0
CCATTGCAGTAAAAAAGTTATGTTTCAAAAA	3	103	0
ATTGATGTGGAAAAAAGTGCAATTGAAGCCC	4	23	1
          **** ******
MAP Score: 8.09795

Motif 4
TCAAAAGCAGGGAATTATTAAGTATTAGGAATGTGCT	0	46	1
ATTAGGAATGTGCTTTTGTAATTAATCAGTTAAATTG	0	69	1
   CATTTCATTTTTTCGCAATTATACTGATTATTAA	2	7	1
  GTTCGAAATGGTTTACAAATTATTAATTTTTGTTG	3	8	1
TTTGCTCGGATGACCTTGAAAGTACGCTTCCTAATCT	4	63	1
TCTCTGCAGCTTTCTTGTAAATTATGCTAAGGTGAGT	4	97	1
GACAGGTTGCTGCTCTTCCAAGAAGTC          	4	283	1
TCGGGGAAATTGTATTTAAAATTACTCCCAAAACAAA	5	19	1
          **  **   *****  *
MAP Score: 3.15673

Motif 5
TTTGGGAAATTTCGGACTGTTTAGAGGATT	0	116	1
GCCGCTCTGCTTCTGCTTGCACTGCTGCAA	0	150	1
GAAAAAGAGTTTTTGATTGTGTTACAATCG	1	12	0
TTTTTGTTGTTTTGGACTGCTGAACCTTTT	3	36	1
AAACATAACTTTTTTACTGCAATGGAGTAA	3	109	1
    CGAGAGTTTTTACTCCATTGCAGTAA	3	122	0
GTAATAAAGCTTCTGATTCCCTTGCTGAGC	4	244	1
          **********
MAP Score: 3.04119

Motif 6
TAATCAGTTAAATTGGAGGTGAAAGTTTGGGAAATT	0	91	1
     GTTCGAAATGGTTTACAAATTATTAATTTTT	3	5	1
TTTTTTACTGCAATGGAGTAAAAACTCTCG      	3	118	1
AAACAACGAAAATTGATGTGGAAAAAAGTGCAATTG	4	12	1
GTGGCAAGGTAACTGAGGTAAAAACTGGAGATGCCA	4	182	1
GCTTCGGGGAAATTGTATTTAAAATTACTCCCAAAA	5	16	1
          ** **  **  *** *
MAP Score: 2.6891

Motif 7
AGAGGTTTTTACTATTTTTCAAAAGCAGGG	0	28	1
ACAATCAAAAACTCTTTTTCCCTATTTTTT	1	22	1
      CATTTCATTTTTTCGCAATTATAC	2	4	1
GACTGCTGAACCTTTTTTTCGAAAGGTGTT	3	50	1
TTGAAACATAACTTTTTTACTGCAATGGAG	3	106	1
          **********
MAP Score: 1.77394