AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions029_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241603
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	aroI	275	shikimate kinase
#1	tyrA	48	prephenate dehydrogenase
#2	trpE	215	anthranilate synthase
#3	aroB	61	3-dehydroquinate synthase
#4	aroF	69	chorismate synthase
#5	cheR	236	methyl-accepting chemotaxis proteins (MCPs) methyltransferase
#6	aroC	111	3-dehydroquinate dehydratase
#7	yqeG	300	similar to hypothetical proteins

Motif 1
TCTAATTGCTTTATACACACTCTTGTGTAT	2	31	0
ATATAGTATTTTATCCTCTCATGCCATCTT	2	164	1
TTTTCTCATATTCTCCACATTTTCTCTAAT	3	24	0
ATTCAACCCTTTATTCACTTTAATGTAAAC	5	78	0
CCTTGTTTTATTATACACGTACAACTTTTT	6	66	0
AATCGTTCTGTTATCCACACCAAAAAGTGG	7	84	1
TACTCACAAGTTATCCACTTTTTGGTGTGG	7	98	0
TTTAGACAAATTATAAACACGATACTCACA	7	120	0
TTTACACACACTATCCACTCTTATTACATC	7	154	0
GTGTGTAAATTTATCCACACCTGGTGAAGA	7	175	1
          **********
MAP Score: 13.3652

Motif 2
ATTTATCATACAGAAAAAGACCCTTCCATCG	0	28	1
ATACTTCGACGCAAAAAAGCGTTAAAACCTT	0	89	0
TGTCATTCAGGCAAAAATGGCTACAACAAAG	0	151	1
AATAGGGTAGCAGAGAATGAGTTTAGTTGAG	2	77	1
TTATTCTACCCAAAAGAAGTCTTTCTTTTGG	2	122	1
CAAGGAGAATGAGAAGATGGCATGAGAGGAT	2	176	0
GACCGCATTAGAGAAAATGTGGAGAATATGA	3	18	1
AGAAAATGTGGAGAATATGAGAAAACTGTCG	3	29	1
GCGATGAAGGGAGAAGAAGTC          	4	58	1
AGATCGTTGGGAAAGGCAGAGGTCTGATGCA	5	115	0
GCTATACTAGGACAAAAAGACAGCGAGACTG	5	204	1
CAAAAAGACAGCGAGACTGGGAGAGTAGAG 	5	216	1
GGTAAAGATTGAAAGGATTTGAGACGA    	6	94	1
TGTTATCCACACCAAAAAGTGGATAACTTGT	7	92	1
AAAAAATTTCGACAAAAATTGGGTTTCTTCA	7	199	0
TGCGCCTAAAGAAAAACTGAGCAAAAAAATT	7	222	0
AATGATTGTCGAAAAAAATCGAACTTGCGCC	7	247	0
TTTTGAAAGAAAGAAAAAGGGAAGGGTGCGG	7	276	1
          ********* *
MAP Score: 10.2422

Motif 3
CTGGAAAAACAATAAAGGCGGAAGGTTTTAACG	0	68	1
CTTCGACGCAAAAAAGCGTTAAAACCTTCCGCC	0	84	0
GAAGTATTAAAATACCTGCAGAAATGTTGTACA	0	113	1
TCATTCAGGCAAAAATGGCTACAACAAAGCGCA	0	153	1
TATCTATATAAATATTCGCTAAATAAGCATATA	0	211	1
CGCATTAGAGAAAATGTGGAGAATATGAGAAAA	3	21	1
TTTTTGCTGAAAAATATGTTATAGTAGTCTTAC	4	11	1
  TCATTGTGAAAATAAGCAACAGAGCCGGCAA	5	8	1
ATTAAAGTGAATAAAGGGTTGAATGGCAGTGTG	5	84	1
CCAACGATCTAAAATCAGCTGAAAAGCTGATTT	5	136	1
ATTTCCTGATAAAACAAGCTATACTAGGACAAA	5	187	1
GAAATTTTCAAAAAAAAGTTGTACGTGTATAAT	6	54	1
CGTGTATAATAAAACAAGGTAAAGATTGAAAGG	6	77	1
GCCTAAAGAAAAACTGAGCAAAAAAATTTCGAC	7	217	0
          ****   ******
MAP Score: 9.7227

Motif 4
TATGATAAATAGGAAGGGAGGAATGGCG    	0	6	0
CTGGAAAAACAATAAAGGCGGAAGGTTTTAAC	0	68	1
GGTTTATAGACTAAAGAGGTGATATTTGATCA	1	14	0
TAAAGCAATTAGAATGAGTTGAGTTAGAGAAT	2	48	1
ACCGCATTAGAGAAAATGTGGAGAATATGAGA	3	19	1
CGTTAATGCGATGAAGGGAGAAGAAGTC    	4	51	1
ATTAAAGTGAATAAAGGGTTGAATGGCAGTGT	5	84	1
CTAAAATCAGCTGAAAAGCTGATTTTTTTATT	5	144	1
GAAATTTTCAAAAAAAAGTTGTACGTGTATAA	6	54	1
GTTATCCACACCAAAAAGTGGATAACTTGTGA	7	93	1
TATAATTTGTCTAAAGAGTGATGTAATAAGAG	7	135	1
AGAGTGATGTAATAAGAGTGGATAGTGTGTGT	7	149	1
TTTGAAAGAAAGAAAAAGGGAAGGGTGCGGGT	7	277	1
          * ****** ***
MAP Score: 7.54899

Motif 5
CTTCGACGCAAAAAAGCGTTAAAACCTTCCGC	0	85	0
CATTCAGGCAAAAATGGCTACAACAAAGCGCA	0	154	1
TTTATAGACTAAAGAGGTGATATTTGATCACC	1	12	0
GAAATACACAAGAGTGTGTATAAAGCAATTAG	2	28	1
TAAAGCAATTAGAATGAGTTGAGTTAGAGAAT	2	48	1
AGGGTAGCAGAGAATGAGTTTAGTTGAGCTGA	2	80	1
GAAGATGGCATGAGAGGATAAAATACTATATA	2	163	0
TATGGCAAGGAGAATGAGAAGATGGCATGAGA	2	180	0
CGCATTAGAGAAAATGTGGAGAATATGAGAAA	3	21	1
TAGTCTTACTTAAAAGCGTTAATGCGATGAAG	4	35	1
GGTTTACATTAAAGTGAATAAAGGGTTGAATG	5	77	1
AGCAACTAAAAAAGAGCCTTAAAGGGCTCTTT	6	10	0
TATCCACACCAAAAAGTGGATAACTTGTGAGT	7	95	1
ATTTGTCTAAAGAGTGATGTAATAAGAGTGGA	7	139	1
AGTGATGTAATAAGAGTGGATAGTGTGTGTAA	7	151	1
          ****** *** *
MAP Score: 5.54011

Motif 6
  AAAGAGCCCTTTAAGGCTCTTTTTTAGTTGCTA	6	8	1
AAAAAATCAGCTTTTCAGCTGATTTTAGATCGTTG	5	137	0
AGGCGGAAGGTTTTAACGCTTTTTTGCGTCGAAGT	0	83	1
ATGTTGCCGGCTCTGTTGCTTATTTTCACAATGA 	5	9	0
GAAACCCAATTTTTGTCGAAATTTTTTTGCTCAGT	7	203	1
TGTACAACATTTCTGCAGGTATTTTAATACTTCGA	0	111	0
GTATTTTATCCTCTCATGCCATCTTCTCATTCTCC	2	169	1
TAGTGCGCTTTGTTGTAGCCATTTTTGCCTGAATG	0	154	0
ACGTACAACTTTTTTTTGAAAATTTCTATTATATG	6	45	0
AGAAGTCTTTCTTTTGGGTTTATTTGTTATATAGT	2	136	1
TATGAGAAAACTGTCGAGGGAATTTTA        	3	44	1
ACGCCGCCGGTTTTTGTTCTGTTTTGTAAAGGTTT	5	47	1
TTATATGCTTATTTAGCGAATATTTATATAGATAC	0	210	0
          ****   **  ****
MAP Score: 5.35651

Motif 7
AAAAGACCCTTCCATCGAAGAGTCAGCTGGAA	0	42	1
AATACTTCGACGCAAAAAAGCGTTAAAACCTT	0	89	0
CAAAAATGGCTACAACAAAGCGCACTATAAGC	0	162	1
AGCTTAGAAATACACAAGAGTGTGTATAAAGC	2	22	1
AACAAATAAACCCAAAAGAAAGACTTCTTTTG	2	132	0
TAACATATTTTTCAGCAAAAAG          	4	0	0
ATAGTAGTCTTACTTAAAAGCGTTAATGCGAT	4	31	1
TGTAAAGGTTTACATTAAAGTGAATAAAGGGT	5	71	1
AATAGAAATTTTCAAAAAAAAGTTGTACGTGT	6	50	1
TTCTGTTATCCACACCAAAAAGTGGATAACTT	7	89	1
          * ** *******
MAP Score: 5.04404

Motif 8
GGTGATCAAATATCACCTCTTTAGTCTATAA	1	12	1
TATAGTATTTTATCCTCTCATGCCATCTTCT	2	165	1
ATCGTTCTGTTATCCACACCAAAAAGTGGAT	7	85	1
ACTCACAAGTTATCCACTTTTTGGTGTGGAT	7	96	0
TTACACACACTATCCACTCTTATTACATCAC	7	152	0
TGTGTAAATTTATCCACACCTGGTGAAGAAA	7	176	1
          ********* *
MAP Score: 4.96285

Motif 9
TCGATGGAAGGGTCTTTTTCTGTATGATAA	0	30	0
CGGCTCTGTTGCTTATTTTCACAATGA   	5	7	0
TAACGCCGCCGGTTTTTGTTCTGTTTTGTA	5	45	1
CTGAAAAGCTGATTTTTTTATTGAAACAAT	5	154	1
AGTCTCGCTGTCTTTTTGTCCTAGTATAGC	5	204	0
GCCCTTTAAGGCTCTTTTTTAGTTGCTATT	6	15	1
TACACGTACAACTTTTTTTTGAAAATTTCT	6	53	0
GAAGAAACCCAATTTTTGTCGAAATTTTTT	7	200	1
GCGCAAGTTCGATTTTTTTCGACAATCATT	7	248	1
          **********
MAP Score: 0.631803