AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241328
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yhaR	164	similar to 3-hydroxbutyryl-CoA dehydratase
#1	yngG	250	similar to hydroxymethylglutaryl-CoA lyase
#2	mmgB	149	3-hydroxybutyryl-CoA dehydrogenase
#3	ysiA	104	similar to transcriptional regulator (TetR/AcrR family)
#4	menB	34	dihydroxynapthoic acid synthetase
#5	menF	288	menaquinone-specific isochorismate synthase
#6	yusL	267	similar to 3-hydroxyacyl-CoA dehydrogenase

Motif 1
CAAGATATCCCTTCTTTTTCACTATATAAA	0	10	1
AATAAACCTTTTTATTTTTCAAGGTCAATA	0	81	0
CGCTTACTTTTTTCTTTCTCCTATACATTC	0	124	0
CGATCGGGATTTCCATTTTCATCGATTCCA	1	115	0
TTTTTTTTGACTTCTTTTACGATTCCGCTT	1	155	0
CAAAGTCGCCTTCCTTTTTTTTGACTTCTT	1	169	0
AGTACGTCTCCTTCATTTACAAAGTCGCCT	1	188	0
CCATTCAAATCCCCTTTTTCATCATGTT  	2	8	0
  ATGATGACCTCCTTTTATTCTCTATGTG	4	16	0
 TGTGATCGCCTCGTTTCTCTGTGATGCAT	5	9	1
ATAGGAGGTTTTCCTTTTATGGTAAGCGGA	5	94	1
CAAGCTTAAATTTCTTTCTCCACTGATAGC	5	134	0
TTTAAGCTTGTTTCTTTTTCATTTCTGAAA	5	154	1
GGACCGGCATCTCCCTTTACGCTCGCCGCG	6	110	1
TCTCGTACCATTCCCTTCACCTCCGGGCTT	6	170	1
          **********
MAP Score: 19.5274

Motif 2
TTTATATAGTGAAAAAGAAGGGATATCTTG 	0	9	0
AGGTTTATTTGGGGATGGCGGGGAATGTATA	0	102	1
TTTTGGAATCGATGAAAATGGAAATCCCGAT	1	112	1
GATCGTTGCAGATAGAAGCGGAATCGTAAAA	1	140	1
     AACATGATGAAAAAGGGGATTTGAAT	2	5	1
AATCATGGTAGCTGGCGCAGGTCAGATGGGG	2	48	1
TCCAGAGGCCGCGGAGGCAGGA         	2	137	1
TTCATAAATGGCGGGTGGAGGAATATAGGAG	5	70	1
TTTCTCCACTGATAGCAAAGGTTGTATCCGC	5	119	0
GTTTATAATAGGTAAGGCAGGCCATTTGGAC	5	188	1
TTGACACAAAGGAGACACAGGTGTATGGTAT	5	233	1
GCATTTTAAGGATTATGGAGGAATGTCTC  	5	269	1
CATTACGGCGGCGGAAAACGGACAAGTCAAA	6	72	0
GAGCGTAAAGGGAGATGCCGGTCCGACTCAG	6	103	0
GCTGACTGCCGCTGAAGACGGATTTTTTTTC	6	139	1
ACTTAAGCCCGGAGGTGAAGGGAATGGTACG	6	173	0
          ***** *****
MAP Score: 17.6217

Motif 3
TATAGTGAAAAAGAAGGGATATCTTG        	0	2	0
TTATTTGGGGATGGCGGGGAATGTATAGGAGAAA	0	106	1
AAGCGCATACATGGAGGTGCTTTTA         	0	149	1
GGCAGTTGTCATGACGGTTAGCATACAAATGGCA	1	14	1
TAGCATACAAATGGCAGGAAACCTGTGGAAAGTC	1	32	1
CGAAAAGGGCCAGGAGGTAGCCATTTTGGAATCG	1	89	1
AGTCAAAAAAAAGGAAGGCGACTTTGTAAATGAA	1	173	1
CGACTTTGTAAATGAAGGAGACGTACTGCTCGAA	1	191	1
TAGAGAATAAAAGGAGGTCATCAT          	4	20	1
TGGAGGAATATAGGAGGTTTTCCTTTTATGGTAA	5	85	1
TATAATAGGTAAGGCAGGCCATTTGGACTGCATG	5	191	1
TTTAAGGATTATGGAGGAATGTCTC         	5	273	1
ACTGCCGCTGAAGACGGATTTTTTTTCTCTCGTA	6	143	1
AAGCCTATAAAAGTCGGGCAACTTAAGCCCGGAG	6	190	0
          ********   * *
MAP Score: 14.2138

Motif 4
TTTATTTGGGGATGGCGGGGAATGTATAGGA	0	105	1
TAAGCGCATACATGGAGGTGCTTTTA     	0	148	1
AGTCCACGTCAAAGCCGGCGACCAAATCGAA	1	62	1
AGTCAAAAAAAAGGAAGGCGACTTTGTAAAT	1	173	1
AATTGCTCAAACAGCCGCCGACGCGGCTTTT	2	84	1
TGTGAATCCAGAGGCCGCGGAGGCAGGA   	2	131	1
ATAGAGAATAAAAGGAGGTCATCAT      	4	19	1
CATCACAGAGAAACGAGGCGATCACA     	5	5	0
TATAATAGGTAAGGCAGGCCATTTGGACTGC	5	191	1
GGACAATCATAATGCAGCTGCTTCCCACGGC	6	15	0
CGTAAAGGGAGATGCCGGTCCGACTCAGCAT	6	100	0
CAGCGGCAGTCAGCGCGGCGAGCGTAAAGGG	6	122	0
CGCCGCGCTGACTGCCGCTGAAGACGGATTT	6	133	1
GCAACTTAAGCCCGGAGGTGAAGGGAATGGT	6	176	0
GAAGCCTATAAAAGTCGGGCAACTTAAGCCC	6	194	0
          ** ********
MAP Score: 11.1988

Motif 5
TTTGGGGATGGCGGGGAATGTATAGGAGAAAG	0	109	1
GAGAAAGAAAAAAGTAAGCGCATACATGGAGG	0	134	1
        AGGAGGCAGTTGTCATGACGGTTA	1	2	1
AGTTGTCATGACGGTTAGCATACAAATGGCAG	1	17	1
CGGAATCGTAAAAGAAGTCAAAAAAAAGGAAG	1	158	1
AGTCAAAAAAAAGGAAGGCGACTTTGTAAATG	1	173	1
CTTTGTAAATGAAGGAGACGTACTGCTCGAAC	1	194	1
GGGGATTTGAATGGAAATCAAACAAATCATGG	2	24	1
ACAAATCATGGTAGCTGGCGCAGGTCAGATGG	2	45	1
CGCAGGTCAGATGGGGAGCGGAATTGCTCAAA	2	63	1
        AAAAAGAGAACGCCTATGAATAAA	3	2	1
TAGAGAATAAAAGGAGGTCATCAT        	4	20	1
ACAGAGAAACGAGGCGATCACA          	5	0	0
GTTCATACTAAAGGTATGCATCACAGAGAAAC	5	22	0
ACTTTCATAAATGGCGGGTGGAGGAATATAGG	5	67	1
TTTTCCTTTTATGGTAAGCGGATACAACCTTT	5	102	1
TGTTTGACACAAAGGAGACACAGGTGTATGGT	5	230	1
  AAGCAGCCGTGGGAAGCAGCTGCATTATGA	6	8	1
CATTACGGCGGCGGAAAACGGACAAGTCAAAA	6	71	0
GGCGAGCGTAAAGGGAGATGCCGGTCCGACTC	6	105	0
GGCAGTCAGCGCGGCGAGCGTAAAGGGAGATG	6	117	0
TCCGTCTTCAGCGGCAGTCAGCGCGGCGAGCG	6	129	0
          **** ***** *
MAP Score: 9.72874

Motif 6
TTTCGATTTGGTCGCCGGCTTTGACGTGGACTT	1	61	0
GTTGCAGATAGAAGCGGAATCGTAAAAGAAGTC	1	144	1
CAAAAAAAAGGAAGGCGACTTTGTAAATGAAGG	1	176	1
TGTAAATGAAGGAGACGTACTGCTCGAACTGAG	1	197	1
TCCAAATTATTGAGTGGAATTGCTCAGTTCGAG	1	219	0
GGTCAGATGGGGAGCGGAATTGCTCAAACAGCC	2	67	1
TGCTCAAACAGCCGCCGACGCGGCTTTTATGTG	2	87	1
CACAGATCATGCAGTCCAAATGGCCTGCCTTAC	5	199	0
TCCGTTTTCCGCCGCCGTAATGCTGAGTCGGAC	6	81	1
GCCGTAATGCTGAGTCGGACCGGCATCTCCCTT	6	94	1
GTCTTCAGCGGCAGTCAGCGCGGCGAGCGTAAA	6	125	0
GACTGCCGCTGAAGACGGATTTTTTTTCTCTCG	6	142	1
ATTAGCTATTGAAGTCGAACCGGAAATCTTTTA	6	242	1
          * ** **** ***
MAP Score: 9.39269

Motif 7
       CAAGATATCCCTTCTTTTTCACTATATAAA	0	3	1
TTTTCTTTCTCCTATACATTCCCCGCCATCCCCAAAT	0	108	0
CAACGATCGGGATTTCCATTTTCATCGATTCCAAAAT	1	111	0
TTTACGATTCCGCTTCTATCTGCAACGATCGGGATTT	1	133	0
TGATTTGTTTGATTTCCATTCAAATCCCCTTTTTCAT	2	16	0
GCTGTTTGAGCAATTCCGCTCCCCATCTGACCTGCGC	2	62	0
     ATGATGACCTCCTTTTATTCTCTATGTGAATG	4	12	0
    TGTGATCGCCTCGTTTCTCTGTGATGCATACCT	5	6	1
CTGATTTTGACTTGTCCGTTTTCCGCCGCCGTAATGC	6	67	1
GTCGGACCGGCATCTCCCTTTACGCTCGCCGCGCTGA	6	107	1
CGAGAGAAAAAAAATCCGTCTTCAGCGGCAGTCAGCG	6	138	0
TTCTCTCGTACCATTCCCTTCACCTCCGGGCTTAAGT	6	167	1
          *   *** *** *  **
MAP Score: 6.6747

Motif 8
TTTGGGGATGGCGGGGAATGTATAGGAGAAA	0	109	1
TTGCAGATAGAAGCGGAATCGTAAAAGAAGT	1	145	1
CCAAATTATTGAGTGGAATTGCTCAGTTCGA	1	220	0
CATGATGAAAAAGGGGATTTGAATGGAAATC	2	12	1
GTCAGATGGGGAGCGGAATTGCTCAAACAGC	2	68	1
TCAGCGCGGCGAGCGTAAAGGGAGATGCCGG	6	113	0
GCCCGGAGGTGAAGGGAATGGTACGAGAGAA	6	167	0
          ********* *
MAP Score: 3.96652

Motif 9
TTATATAGTGAAAAAGAAGGGATATCTTG  	0	8	0
CATATTGTTTGAATGGAAACATAAAGTTTTA	0	36	0
AATGTATAGGAGAAAGAAAAAAGTAAGCGCA	0	125	1
GTTAGCATACAAATGGCAGGAAACCTGTGGA	1	30	1
GCCGGCGACCAAATCGAAAAGGGCCAGGAGG	1	75	1
GAATCGATGAAAATGGAAATCCCGATCGTTG	1	117	1
AGCGGAATCGTAAAAGAAGTCAAAAAAAAGG	1	156	1
GAAGTCAAAAAAAAGGAAGGCGACTTTGTAA	1	171	1
GGCGACTTTGTAAATGAAGGAGACGTACTGC	1	189	1
AAGGGGATTTGAATGGAAATCAAACAAATCA	2	22	1
          AAAAAGAGAACGCCTATGAAT	3	0	1
CATAGAGAATAAAAGGAGGTCATCAT     	4	18	1
CGCTTACCATAAAAGGAAAACCTCCTATATT	5	91	0
TTCAGAAATGAAAAAGAAACAAGCTTAAATT	5	152	0
ATTTTAAGGATTATGGAGGAATGTCTC    	5	271	1
          ********* *
MAP Score: 2.14885

Motif 10
AAACAAATCATGGTAGCTGGCGCAGGTCAGATGGG	2	43	1
AGCGGAATTGCTCAAACAGCCGCCGACGCGGCTTT	2	79	1
TATGATGTGAATCCAGAGGCCGCGGAGGCAGGA  	2	126	1
ATGCAGCTGCTTCCCACGGCTGCTT          	6	0	0
ACATGGGACAATCATAATGCAGCTGCTTCCCACGG	6	16	0
TTGACTTGTCCGTTTTCCGCCGCCGTAATGCTGAG	6	73	1
ACGCTCGCCGCGCTGACTGCCGCTGAAGACGGATT	6	128	1
          ***   * ***** *
MAP Score: 0.551688