AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240886
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yirY	300	similar to DNA exonuclease
#1	mcpC	134	methyl-accepting chemotaxis protein
#2	yknT	136	alternate gene name: cse15; similar to sporulation protein sigma-E-controlled
#3	yomK	300	yomK
#4	yomJ	81	similar to phage-related immunity protein
#5	yomI	53	yomI
#6	ytwP	196	ytwP
#7	yttA	194	yttA
#8	yukB	27	yukB
#9	yukD	143	yukD

Motif 1
GTCTTTGTTCTGTTCTTCAAAAACCGGCCT	0	134	0
TTTTCATAAAATTTCTTAAAGCGGTCCTCG	0	196	0
ACCGCCAGTTTGTTTTTCATAAAATTTCTT	0	209	0
CAGCCTCACCATTTCTTCATCCGGCACCGC	0	239	0
CTTATAATTTATTTTTTGATTATTCATTTT	1	73	1
TTGATTATTCATTTTTCAAACGAAAGGGCC	1	88	1
ATACTTACAATTTTGTCCAACCCGAACTCT	3	28	1
TTGCAAAATAATTTTTTGAATTATTTCAGC	3	81	1
TAACATGATTCTTTTTTGATTTACATAAAA	3	121	1
AAATGACTCAATTTTTCGATTTTTTATGTA	3	142	0
AAATTGAGTCATTTTTCCTTGGAGAATGAC	3	158	1
TCCTTTGCGTATTTGTCGATAATATGGAGA	3	270	1
CCATTTATACAGTTCTCCATGACTGGAAAC	4	22	1
GGATTTGACTATTTTTTCATGGGGTGACAT	6	12	0
TTGCACAAAAAGTTTTTGATTTCTGGTCAA	6	50	1
TGTAACAAACATTTTTTGACCAGAAATCAA	6	65	0
AAACGACAGTTTTTCTCAATACATATCCTG	6	115	1
TTAGGTTTCGTTTTTTTCATGAGCTTTTTT	7	31	0
TCTCTCTCACATTTTTCAACTGATGAGCGT	7	108	1
TATTTGTTAGATTTTTTCACGCTCATCAGT	7	126	0
TTTATTTTACATTTTTCAAACAATATTTGT	7	149	0
          **********
MAP Score: 15.8604

Motif 2
TGATATGGATAAAGCCCGGGTGCGCCTTCCGCAGCC	0	99	0
TATGAAAAACAAACTGGCGGTGCGGTGCCGGATGAA	0	218	1
CCGGATGAAGAAATGGTGAGGCTGTTTTTAGAGCTT	0	245	1
TTCATTTTTCAAACGAAAGGGCCGATATAGAAATTA	1	95	1
GCCGATATAGAAATTAGGAGGGGATTGGT       	1	115	1
GCTTTTAACGAAACTAGAGGTGAGATGAT       	2	3	0
TGTAGTGTTAACATCATGAGGGAGATGGTTCGA   	2	113	1
GATTAAAGTAATATTGCCAGAGAGTTCGGGTTGGAC	3	42	0
ATTTGTCGATAATATGGAGAGGTGATGAAA      	3	280	1
AGAACTGTATAAATGGAAAGTGAAATCA        	4	2	0
TGTTTACCTTAATCTGTCAGGGTGTTTTATTTATTC	6	155	0
AGATTAAGGTAAACAGCAAGGGGGCTCATT      	6	176	1
CATCAGTTGAAAAATGTGAGAGAGACAGATAGAATG	7	97	0
AATGTAAAATAAATAGAAAAAGGGGTCATATTATGG	7	166	1
TAACAGTATGAAAGGGAAGGAGCGCCTGATTCAAAA	9	81	1
GATCACCCTTACATAGAAAGAGCGCCGTCTTCTTTT	9	113	0
          ***  * *** * * *
MAP Score: 13.491

Motif 3
AATCGAGGACCGCTTTAAGAAATTTTATGAAA	0	193	1
GGTGCGGTGCCGGATGAAGAAATGGTGAGGCT	0	236	1
TCCTCTTCAACGCCTGATGCAAGCTCTAAAAA	0	269	0
ACAGCTATTCCTCTTTAATAAACAGACAAGCA	2	66	0
 TGATGTCACCCCATGAAAAAATAGTCAAATC	6	9	1
CCTAAAAAAGCTCATGAAAAAAACGAAACCTA	7	28	1
TCAACTGATGAGCGTGAAAAAATCTAACAAAT	7	123	1
    ATCAGCAGCTTGATCAAACAGCAAATAC	9	6	1
AGGGAAGGAGCGCCTGATTCAAAAGAAGACGG	9	93	1
          *** **** ***
MAP Score: 8.55262

Motif 4
TGTTCTGTTCTTCAAAAACCGGCCTGATATGGATAAAGCCCG	0	117	0
CAGTTTGTTTTTCATAAAATTTCTTAAAGCGGTCCTCGATTG	0	192	0
TGATGCAAGCTCTAAAAACAGCCTCACCATTTCTTCATCCGG	0	245	0
GAATAATCAAAAAATAAATTATAAGAAAATCGGAATATATTT	1	56	0
AAAGGGCCGATATAGAAATTAGGAGGGGATTGGT        	1	110	1
CTATTCCTCTTTAATAAACAGACAAGCAGTAGCGTTGAGCCT	2	52	0
CTGAAATAATTCAAAAAATTATTTTGCAATATGATTAAAGTA	3	68	0
TTTTTTGATTTACATAAAAAATCGAAAAATTGAGTCATTTTT	3	132	1
CTCCATATTATCGACAAATACGCAAAGGATTTTAATGGAAAT	3	257	0
TCTCCATGACTGGAAACAATGGTATAATGTAGGAAAATGATA	4	35	1
TGATTTCTGGTCAAAAAATGTTTGTTACATGGTATCATAATA	6	66	1
CGCTCATCAGTTGAAAAATGTGAGAGAGACAGATAGAATGAA	7	95	0
CTGATGAGCGTGAAAAAATCTAACAAATATTGTTTGAAAAAT	7	127	1
CAAATATTGTTTGAAAAATGTAAAATAAATAGAAAAAGGGGT	7	150	1
          *  * ***       ** ** *
MAP Score: 6.15609

Motif 5
CCGGATGAAGAAATGGTGAGGCTGTTTTTAG	0	245	1
ATGAAACAACATAAGGAGAGTG         	1	1	0
TTCATTTTTCAAACGAAAGGGCCGATATAGA	1	95	1
CGATATAGAAATTAGGAGGGGATTGGT    	1	117	1
AAAGCATAGCAAAAGCAAAGGCTCAACGCTA	2	34	1
TTATCGACAAATACGCAAAGGATTTTAATGG	3	261	0
TTTGTCGATAATATGGAGAGGTGATGAAA  	3	281	1
AGAACTGTATAAATGGAAAGTGAAATCA   	4	7	0
ATGGTATAATGTAGGAAAATGATACCGGCGG	4	53	1
CTCCCCTACTGAAAGGAAGTGATTCTTAC  	5	34	1
GATTAAGGTAAACAGCAAGGGGGCTCATT  	6	177	1
GCTTTTTTAGGTAAGAAAGGGGGATGAGT  	7	8	0
GCGGATAACAGTATGAAAGGGAAGGAGCGCC	9	76	1
          *** *******
MAP Score: 5.8828

Motif 6
CTTGAAGAGATTCACAGGCTGCGGAAGGCGCACCCGG	0	83	1
TGAAGAACAGAACAAAGACCGGGAACGGATCGAGGTT	0	145	1
AATTTTATGAAAAACAAACTGGCGGTGCGGTGCCGGA	0	213	1
GTGCCGGATGAAGAAATGGTGAGGCTGTTTTTAGAGC	0	242	1
TTATAATGAAACAACATAAGGAGAGTG          	1	0	0
AGGGCCGATATAGAAATTAGGAGGGGATTGGT     	1	112	1
TATTGTAGTGTTAACATCATGAGGGAGATGGTTCGA 	2	110	1
TTGTAAGTATTTAATACACTGGGGCTGC         	3	1	0
CTGAATAAATAAAACACCCTGACAGATTAAGGTAAAC	6	153	1
CAGATTAAGGTAAACAGCAAGGGGGCTCATT      	6	175	1
GCTCATCAGTTGAAAAATGTGAGAGAGACAGATAGAA	7	99	0
AAATCCGCGGATAACAGTATGAAAGGGAAGGAGCGCC	9	70	1
GAGCGCCTGATTCAAAAGAAGACGGCGCTCTTTCTAT	9	100	1
          *  ***    ***** *
MAP Score: 1.42846