AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241282
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yfjN	300	similar to hypothetical proteins
#1	yfjM	195	yfjM
#2	yfjL	29	alternate gene name: yztA
#3	acoA	231	acetoin dehydrogenase E1 component (TPP-dependent alpha subunit)
#4	pdhA	300	pyruvate dehydrogenase (E1 alpha subunit)
#5	bfmBAA	73	branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit)
#6	yqiS	124	similar to phosphate butyryltransferase
#7	yqiR	152	similar to transcriptional regulator (sigma-L-dependent)

Motif 1
CAAAAAGTTCAAAAGCAAGGCCACTAAGAA	0	86	1
TAAGTGTAAAAGAAGCATGGTCAGTTTTTA	0	227	1
AAAGGCTAACAAAATAAAGGGATTTTTACA	1	29	1
GGATTTACCGAAAATCCAGGTTTATTTTAG	1	69	0
CTGCGTACAAAAAAGACCCGGATTTACCGA	1	88	0
TAAATTAGAGAAAAGACAGGCTGAGTAAAA	1	119	0
TTATTGTAAGAAAATAATGGTATATTTAGT	1	146	1
ACATATGAGGAAAAGAGTGGGAAC      	2	15	1
GCATGCAAAAAAAAGACCGGATATCACCCG	3	53	0
TTACGGGCTCAAAAGACTGGCACACTTCTT	3	169	1
CACCAAATAAAGAAGAACCGTCAATCGTTT	4	56	0
ATGACTGTTTAAAAGAAAGGAAGAGGTGAC	4	275	1
ATGCTTTTAAAAATGAATGGCTTTGCCATC	5	38	0
     TTTGCAGAATAAACGCAAACATCTG	6	5	1
CGGAGTCGAAACAAGAAAGGTGGTAACAG 	6	105	1
AGGAAATGAAAAGATAAAGGGGTTTTCTGA	7	12	0
TTTCCGCTGGACAATAAAGGAAATGAAAAG	7	29	0
          **********
MAP Score: 26.4572

Motif 2
GCTTTTGAACTTTTTGGATAAAAAGGATTCCAACC	0	67	0
AGTTAACCAGAATATAAAAAATAGGGTAGATAATC	0	133	1
TTCAGCCGTATCCCATAATGAAAGGATTTGATTTT	0	271	1
 CAGCAGTGCTTGATTCAAAAAAGGCTAACAAAAT	1	9	1
CAAAAAAGGCTAACAAAATAAAGGGATTTTTACAC	1	25	1
GAGTAAAAGCTGCGTACAAAAAAGACCCGGATTTA	1	92	0
TACAATAAATTAGAGAAAAGACAGGCTGAGTAAAA	1	119	0
TTTAGTGGAGATATCATATAAAGGGGGAGAGGAAA	1	170	1
TTCACCATTATAAATGCAAGAAGTGTGCCAGTCTT	3	181	0
ATAATGGTGAACCCTAAATAGAAGGAGGCGCACAA	3	205	1
GAGTGTAACTATCCTACATAAAAGGTTTTGGCAAA	4	154	1
ACCCTAAGTTTGTATGTATAAAAGGAATGCACGTC	4	238	1
GTCTAATGACTGTTTAAAAGAAAGGAAGAGGTGAC	4	270	1
CCTTTATGCTTTTAAAAATGAATGGCTTTGCCATC	5	38	0
GGCATGGAACTTGCATAATAAAAGGCGGAGTCGAA	6	80	1
AAAGGCGGAGTCGAAACAAGAAAGGTGGTAACAG 	6	100	1
ATAAAGGAAATGAAAAGATAAAGGGGTTTTCTGAA	7	11	0
TGTGCAAATTTTTTCATACAAAGGGGTATCGGG  	7	129	1
          *    * ********
MAP Score: 11.5465

Motif 3
AACCAGAATATAAAAAATAGGGTAGATAATCATCCC	0	137	1
TTAATTTGGGATAAAGGTTCAGCCGTATCCCATAAT	0	254	1
AATAAATTAGAGAAAAGACAGGCTGAGTAAAAGCTG	1	115	0
ATTTATTGTAAGAAAATAATGGTATATTTAGTGGAG	1	144	1
GAGATATCATATAAAGGGGGAGAGGAAA        	1	177	1
GTCGATCATTGTCAAAGGCCGGGTGATATCCGGTCT	3	34	1
TCAAACTGTCTCCAAAGTGAAGATGAGAAGACTGAT	3	132	1
TTTTACGGGCTCAAAAGACTGGCACACTTCTTGCAT	3	167	1
      TTGATGAAAATGTAAAGCGAATACATTTAT	4	4	1
AATAATACAGTTCAAAGCAGAGTGTAACTATCCTAC	4	135	1
TAATGACTGTTTAAAAGAAAGGAAGAGGTGACTTAG	4	273	1
CCATTCATTTTTAAAAGCATAAAGGAGGGGCTTGA 	5	48	1
ACTTGCATAATAAAAGGCGGAGTCGAAACAAGAAAG	6	88	1
ATAAAGGAAATGAAAAGATAAAGGGGTTTTCTGAAG	7	10	0
          * *****   **  **
MAP Score: 4.26961

Motif 4
TATTACCAACGCAAAATAATTGCCCTGTTA  	0	8	0
AAAAGCAAGGCCACTAAGAAAGACGAAGGTCA	0	96	1
CGCCAGTTAACCAGAATATAAAAAATAGGGTA	0	129	1
CAGCCGTATCCCATAATGAAAGGATTTGATTT	0	273	1
AAAAAGGCTAACAAAATAAAGGGATTTTTACA	1	27	1
TAAAAGCTGCGTACAAAAAAGACCCGGATTTA	1	92	0
GAAAAGACAGGCTGAGTAAAAGCTGCGTACAA	1	108	0
TTTACAGCATGCAAAAAAAAGACCGGATATCA	3	57	0
CAAACTGTCTCCAAAGTGAAGATGAGAAGACT	3	133	1
TTAGGGTTCACCATTATAAATGCAAGAAGTGT	3	190	0
AATGGTGAACCCTAAATAGAAGGAGGCGCACA	3	207	1
GTGTAACTATCCTACATAAAAGGTTTTGGCAA	4	156	1
       TTTGCAGAATAAACGCAAACATCTG	6	3	1
CATGGAACTTGCATAATAAAAGGCGGAGTCGA	6	82	1
TTTTTCCGCTGGACAATAAAGGAAATGAAAAG	7	29	0
TTATTGTCCAGCGGAAAAAATATTTTGTCAAG	7	42	1
          *** ****** *
MAP Score: 2.77269

Motif 5
TATTTAGGTTGGAATCCTTTTTATCCAAAAAGTT	0	61	1
TCGGTAAATCCGGGTCTTTTTTGTACGCAGCTTT	1	88	1
TTTTACTCAGCCTGTCTTTTCTCTAATTTATTGT	1	119	1
CGGGTGATATCCGGTCTTTTTTTTGCATGCTGTA	3	53	1
AAACGATTGACGGTTCTTCTTTATTTGGTGTAAA	4	56	1
ACTAAGTCACCTCTTCCTTTCTTTTAAACAGTCA	4	276	0
ATGTTACCACGTTTTCTTCTCTTGACAAAATATT	7	60	0
          *   ******** *
MAP Score: 1.64096

Motif 6
CAGAATATAAAAAATAGGGTAGATAATCATC	0	140	1
AAGTGTAAAAGAAGCATGGTCAGTTTTTAAT	0	228	1
TGCTTGATTCAAAAAAGGCTAACAAAATAAA	1	16	1
GAGATATCATATAAAGGGGGAGAGGAAA   	1	177	1
CATATGAGGAAAAGAGTGGGAAC        	2	16	1
ACCCTAAATAGAAGGAGGCGCACAAA     	3	215	1
TTAAAAGCATAAAGGAGGGGCTTGA      	5	58	1
GTCGAAACAAGAAAGGTGGTAACAG      	6	109	1
TCAAGAGAAGAAAACGTGGTAACATAGGGTT	7	69	1
ATTTTTTCATACAAAGGGGTATCGGG     	7	136	1
          **** ******
MAP Score: 1.02633