AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241272
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	acoA	231	acetoin dehydrogenase E1 component (TPP-dependent alpha subunit)
#1	pdhA	300	pyruvate dehydrogenase (E1 alpha subunit)
#2	bfmBAA	73	branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit)
#3	yqiS	124	similar to phosphate butyryltransferase

Motif 1
CCGGATATCACCCGGCCTTTGACAATGATCGA	0	35	0
CGGGTGATATCCGGTCTTTTTTTTGCATGCTG	0	53	1
TGTCTCAAACTGATTCATTTGTCTCGTTTTAC	0	84	0
GCCCGTAAAATCAGTCTTCTCATCTTCACTTT	0	145	0
AAGAAGTGTGCCAGTCTTTTGAGCCCGTAAAA	0	167	0
CTGGCACACTTCTTGCATTTATAATGGTGAAC	0	185	1
   TTTGTGCGCCTCCTTCTATTTAGGGTTCA	0	212	0
AAACGATTGACGGTTCTTCTTTATTTGGTGTA	1	56	1
CATTAGACGTGCATTCCTTTTATACATACAAA	1	246	0
GTCACCTCTTCCTTTCTTTTAAACAGTCATTA	1	273	0
GATGGCAAAGCCATTCATTTTTAAAAGCATAA	2	38	1
     TCAAGCCCCTCCTTTATGCTTTTAAAA	2	56	0
TTGTTTCGACTCCGCCTTTTATTATGCAAGTT	3	87	0
 CTGTTACCACCTTTCTTGTTTCGACTCCGCC	3	103	0
          ** ******* *
MAP Score: 11.1055

Motif 2
GTTTCGACTCCGCCTTTTATTATGCAAGTTC	3	86	0
GACTGGCACACTTCTTGCATTTATAATGGTG	0	183	1
 TTTGTGCGCCTCCTTCTATTTAGGGTTCAC	0	211	0
TTGAGACGTGTGTCTCGTTTTGTCTCAAACT	0	105	0
CTGATTCATTTGTCTCGTTTTACAGCATGCA	0	76	0
AAGTCACCTCTTCCTTTCTTTTAAACAGTCA	1	276	0
TAAAATCAGTCTTCTCATCTTCACTTTGGAG	0	141	0
AGCAGTAAGTCGTATTATATTTTAGCCGATC	1	194	0
ATTGACGGTTCTTCTTTATTTGGTGTAAACT	1	61	1
GGTGATATCCGGTCTTTTTTTTGCATGCTGT	0	55	1
GCAAGCGCAGCTTCTCCAATTGCT       	2	3	0
TCATTAGACGTGCATTCCTTTTATACATACA	1	248	0
TAAATGTATTCGCTTTACATTTTCATCAA  	1	8	0
CAATGATCGACGTATTTATTTCCTTGGAAAT	0	14	0
TGTTACCACCTTTCTTGTTTCGACTCCGCCT	3	102	0
          ****** ****
MAP Score: 7.64213

Motif 3
TCTTTTTTTTGCATGCTGTAAAACGAGACAAATGAATCAG	0	67	1
AAATGAATCAGTTTGAGACAAAACGAGACACACGTCTCAA	0	96	1
GACTGATTTTACGGGCTCAAAAGACTGGCACACTTCTTGC	0	161	1
GTTCTTCTTTATTTGGTGTAAACTAATCCATGTTAAGCGG	1	68	1
ATTATTTCGAAGTTGTAAAAAACTAATACAACACCGCTTA	1	101	0
CCCTAAGTTTGTATGTATAAAAGGAATGCACGTCTAATGA	1	239	1
CACGTCTAATGACTGTTTAAAAGAAAGGAAGAGGTGACTT	1	267	1
TGCGCTTGCCGCAGATGGCAAAGCCATTCATTTTTAAAAG	2	25	1
CATAATAAAAGGCGGAGTCGAAACAAGAAAGGTGGTAACA	3	93	1
          *  **    ***   ** **
MAP Score: 7.42097

Motif 4
TAGGGTTCACCATTATAAATGCAAGAAGTGTG	0	189	0
ATGGTGAACCCTAAATAGAAGGAGGCGCACAA	0	208	1
TAAACTAATCCATGTTAAGCGGTGTTGTATTA	1	86	1
TGTAACTATCCTACATAAAAGGTTTTGGCAAA	1	157	1
CTAAGTTTGTATGTATAAAAGGAATGCACGTC	1	241	1
CGTCTAATGACTGTTTAAAAGAAAGGAAGAGG	1	269	1
AAAGCCATTCATTTTTAAAAGCATAAAGGAGG	2	44	1
      TTTGCAGAATAAACGCAAACATCTGC	3	4	1
ATGGAACTTGCATAATAAAAGGCGGAGTCGAA	3	83	1
          **  ********
MAP Score: 4.94849

Motif 5
AAATACGTCGATCATTGTCAAAGGCCGGGTGATA	0	28	1
CTCGTTTTACAGCATGCAAAAAAAAGACCGGATA	0	60	0
GCACACTTCTTGCATTTATAATGGTGAACCCTAA	0	188	1
TTTATAATGGTGAACCCTAAATAGAAGGAGGCGC	0	202	1
GAGTGTAACTATCCTACATAAAAGGTTTTGGCAA	1	154	1
ACCCTAAGTTTGTATGTATAAAAGGAATGCACGT	1	238	1
GCACGTCTAATGACTGTTTAAAAGAAAGGAAGAG	1	266	1
GGCAAAGCCATTCATTTTTAAAAGCATAAAGGAG	2	41	1
CTGGTATGACAGCACCCTTAAGAGCTGGCATGGA	3	54	1
GCATGGAACTTGCATAATAAAAGGCGGAGTCGAA	3	81	1
          *****  * ** **
MAP Score: 2.51537

Motif 6
TCGATCATTGTCAAAGGCCGGGTGATATCCG	0	35	1
AGCATGCAAAAAAAAGACCGGATATCACCCG	0	53	0
TTTTACGGGCTCAAAAGACTGGCACACTTCT	0	167	1
TGGTGAACCCTAAATAGAAGGAGGCGCACAA	0	209	1
AATAATACAGTTCAAAGCAGAGTGTAACTAT	1	135	1
GTAACTATCCTACATAAAAGGTTTTGGCAAA	1	158	1
TTTGTATGTATAAAAGGAATGCACGTCTAAT	1	246	1
TAATGACTGTTTAAAAGAAAGGAAGAGGTGA	1	273	1
TATGCTTTTAAAAATGAATGGCTTTGCCATC	2	38	0
TTTTAAAAGCATAAAGGAGGGGCTTGA    	2	56	1
GACAGCACCCTTAAGAGCTGGCATGGAACTT	3	61	1
ACTTGCATAATAAAAGGCGGAGTCGAAACAA	3	88	1
GCGGAGTCGAAACAAGAAAGGTGGTAACAG 	3	104	1
          ******** **
MAP Score: 1.94815