AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions032_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241750
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yclJ	212	similar to two-component response regulator [YclK]
#1	ydbF	69	similar to two-component sensor histidine kinase [YdbG]
#2	citS	126	two-component sensor histidine kinase
#3	kinA	163	two-component sensor histidine kinase
#4	fliL	251	flagellar protein
#5	fliM	33	flagellar motor switch protein
#6	cheY	25	two-component response regulator
#7	flhA	32	flagella-associated protein

Motif 1
TAATTTATCAGCAAGGGGACGCGCCCCAGA	0	51	0
TTATCCTTAACATAGGGGAGGGCTTTTC  	1	8	0
GTAAAGACCTGAAAGGAGAAGCTG      	1	55	1
      AAAGAAAAAGGCAGACGCGGTCTG	2	4	1
GTGAAAATAAAAAAAGGCAGACCGCGTCTG	2	21	0
CATTTTCTTACGAAGGAGTGAAAATAAAAA	2	38	0
GATCTAGGTAGAAAGGACGGCTGGTGCT  	2	108	1
TTGAATAAAAGAAAGGGCACACAATCTTTT	3	28	0
CCATAAGAATAGAAGGAGAATACTCATTTT	3	71	1
GATGATCATGCAAAGGAGGGATTCT     	3	148	1
       GGAGGGAGGGGAGGCGAGTAATC	4	3	1
TAACCCGTTTGAACGGGCAGCCCTTTACAC	4	59	1
    CGAAACACAAGGAGAGAGATAGATT 	6	6	1
TTTTCGATTTAAAAGGAGAGAAAAAACAGC	7	12	1
          **********
MAP Score: 13.8295

Motif 2
TTAATTTATCAGCAAGGGGACGCGCCCCAGAGG	0	49	0
TTAATAGTAGTCCAAAGGTATGAAAAAAATATG	0	78	1
CGTAAAGACCTGAAAGGAGAAGCTG        	1	54	1
        AAAGAAAAAGGCAGACGCGGTCTGC	2	2	1
GAGTGAAAATAAAAAAAGGCAGACCGCGTCTGC	2	20	0
TCCATTTTCTTACGAAGGAGTGAAAATAAAAAA	2	37	0
AAAATGGATTTTGAAAAATGAGAAAATTCCCTG	2	62	1
ATTCCCTGTGAAAAATGGTATGATCTAGGTAGA	2	87	1
ATGATCTAGGTAGAAAGGACGGCTGGTGCT   	2	106	1
AATTTTTGAATAAAAGAAAGGGCACACAATCTT	3	30	0
CGTTCACCATAAGAATAGAAGGAGAATACTCAT	3	65	1
ACGATGATCATGCAAAGGAGGGATTCT      	3	146	1
        GGAGGGAGGGGAGGCGAGTAATCGC	4	2	1
AGTAACCCGTTTGAACGGGCAGCCCTTTACACT	4	57	1
GCGCTATTTATTGAACAGATTGAATGTTTTCCG	4	94	1
AATTACTCTGTCAAATGGTAAGAAGTTTGTAGT	4	135	1
AAGTTTGTAGTAAAAGAAGATGAAGAAGCTGTT	4	157	1
GAAGCTGTTCTGGAAAAGATCGCAGCTTTCTAC	4	181	1
TTTGCAATGGATCAAGGAATAGAGGAACCGGA 	4	229	1
      CGAAACACAAGGAGAGAGATAGATT  	6	4	1
ATTTTTCGATTTAAAAGGAGAGAAAAAACAGC 	7	10	1
          * *******  **
MAP Score: 13.7765

Motif 3
ATAGCACCATTTTAAACAGAAGGTTTTGCGTTT	0	154	0
AAAGCATCAAAACAACCGGAGGATATA      	0	195	1
        AAAGAAAAAGGCAGACGCGGTCTGC	2	2	1
GAGTGAAAATAAAAAAAGGCAGACCGCGTCTGC	2	20	0
TTTTGAATAAAAGAAAGGGCACACAATCTTTTA	3	27	0
ACGTTCACCATAAGAATAGAAGGAGAATACTCA	3	64	1
CACGATGATCATGCAAAGGAGGGATTCT     	3	145	1
TACTTTAATCATAAAACAGCGGAGAAGCGATTA	4	28	0
CAATCTGTTCAATAAATAGCGCATTCAGTGTAA	4	83	0
AAGAAGTTTGTAGTAAAAGAAGATGAAGAAGCT	4	154	1
GCAATGGATCAAGGAATAGAGGAACCGGA    	4	232	1
        CGAAACACAAGGAGAGAGATAGATT	6	2	1
  ATTTTTCGATTTAAAAGGAGAGAAAAAACAG	7	8	1
          **  ** ******
MAP Score: 8.1342

Motif 4
AAAAATACCTATACGGAGGAACATAA    	0	6	0
GCACCATTTTAAACAGAAGGTTTTGCGTTT	0	154	0
GCATCAAAACAACCGGAGGATATA      	0	198	1
ATCCTTAACATAGGGGAGGGCTTTTC    	1	6	0
GTAAAGACCTGAAAGGAGAAGCTG      	1	55	1
     AAAGAAAAAGGCAGACGCGGTCTGC	2	5	1
TGAAAATAAAAAAAGGCAGACCGCGTCTGC	2	20	0
CATTTTCTTACGAAGGAGTGAAAATAAAAA	2	38	0
TGGATTTTGAAAAATGAGAAAATTCCCTGT	2	66	1
GATCTAGGTAGAAAGGACGGCTGGTGCT  	2	108	1
CCATAAGAATAGAAGGAGAATACTCATTTT	3	71	1
GATGATCATGCAAAGGAGGGATTCT     	3	148	1
          GGAGGGAGGGGAGGCGAGTA	4	0	1
AATCATAAAACAGCGGAGAAGCGATTACTC	4	25	0
ACAGAATACGGAGGTGAGGAAA        	5	21	1
    CGAAACACAAGGAGAGAGATAGATT 	6	6	1
TTTTCGATTTAAAAGGAGAGAAAAAACAGC	7	12	1
          **********
MAP Score: 4.71968

Motif 5
TCCTTAACATAGGGGAGGGCTTTTC     	1	5	0
TTTCTTACGAAGGAGTGAAAATAAAAAAAG	2	35	0
TTTTGAATAAAAGAAAGGGCACACAATCTT	3	30	0
        GGAGGGAGGGGAGGCGAGTAAT	4	2	1
TGGATCAAGGAATAGAGGAACCGGA     	4	236	1
CAGAATACGGAGGTGAGGAAA         	5	22	1
 CGAAACACAAGGAGAGAGATAGATT    	6	9	1
TCGATTTAAAAGGAGAGAAAAAACAGC   	7	15	1
          **********
MAP Score: 3.69009