AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions036_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241925
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yjbQ	234	similar to Na+/H+ antiporter
#1	tenA	248	transcriptional regulator
#2	yqhI	300	similar to aminomethyltransferase
#3	yurR	300	similar to opine catabolism

Motif 1
TAAAACAATCGGTAAGGAGGAGACCGC     	0	5	0
TTTATTATGAAGCAAAGTGTTGTGAGTCATCA	0	37	1
ACGCGATTTTAACAAGGGTGATGATGAAAAAT	0	136	0
TATGTTTTTTAAAAATGAGGTTTTGTTCTCTG	0	168	1
ACCCTGACTTAAAAAGGAGGTTCTGATT    	0	216	1
GATTCGTGTTAATATAGAGGTGCAGAACAATT	1	26	1
AGACCTGCGTAGGGAAGTGGAGCGGTATTTGT	1	148	1
TTTCCCGCAAGGAAAAGTGGTTTGGAATTGGC	1	193	0
TTTTCCTTGCGGGAAAGTGGTTTTTTTATTTT	1	209	1
CTGCGCCGTTGATAAAGGGGAGGAATTAG   	2	281	1
CTATCAATAGAGAAAGGATGATACCATGAGCG	3	145	0
TCGATAGGAGAGTAAAGAGATTGGACGAACTT	3	188	1
ACATTATAATAGAAAAGGTGTTTGCAT     	3	283	1
          ** **** ****
MAP Score: 11.3141

Motif 2
GTTTTGTTCTCTGAGTGAGAACTAGCATAAC	0	187	1
TAGCATAACCCTGACTTAAAAAGGAGGTTCT	0	209	1
TTCATAAGGGCTGAGATAAAAGTGTGACTTT	1	91	1
TTTTTATTTTCAGAGGGGGAATGATTT    	1	231	1
GGGGAGAGACCTGACCGAAAACCTCGGGATA	2	47	1
TTCAGGTGCCAGGACAGAGAACCTTCATTTT	2	210	1
CATACAAAAAAGGACAGAGAAACACCTCATG	2	242	0
GCGCAGTCACAAGACGGAGAAG         	3	1	0
GGATGATACCATGAGCGAAAATCGTCATGAA	3	131	0
GATATTCGATAGGAGAGTAAAGAGATTGGAC	3	183	1
          ***** *****
MAP Score: 11.2914

Motif 3
          GCGGTCTCCTCCTTACCGATTGT	0	0	1
ATAAAGTGATAAGGTCTTAATCCTGTTTAGAAA	0	105	0
TTTTAAAAATGAGGTTTTGTTCTCTGAGTGAGA	0	174	1
CTTCCCTACGCAGGTCTGAACCTGTTCAAGTTA	1	132	0
GGGAAGTGGAGCGGTATTTGTGTTATTTTACTA	1	159	1
TTGCGGGAAAGTGGTTTTTTTATTTTCAGAGGG	1	215	1
GGTTTTCGGTCAGGTCTCTCCCCTTGCTGTCAT	2	37	0
GATTCACTCCGCAGTTTGCTCCTTCGGCGCCTG	2	78	0
GTCCCCAAAGGTGGTTTGCGCATCCGCACAAAC	2	153	0
CATTTTACATGAGGTGTTTCTCTGTCCTTTTTT	2	235	1
ATTTTCGCTCATGGTATCATCCTTTCTCTATTG	3	140	1
GACGAACTTCGCGGTTTTTCCACATTAGGGCAA	3	211	1
TATAATAGAAAAGGTGTTTGCAT          	3	287	1
          ***** **  ***
MAP Score: 9.28025

Motif 4
ATTTTCTAAACAGGATTAAGACCTTATCACT	0	103	1
TGTCCTTCATAAGGGCTGAGATAAAAGTGTG	1	86	1
CAGACCTGCGTAGGGAAGTGGAGCGGTATTT	1	147	1
CTTTCCCGCAAGGAAAAGTGGTTTGGAATTG	1	195	0
CTTTTCCTTGCGGGAAAGTGGTTTTTTTATT	1	208	1
TTATTTTCAGAGGGGGAATGATTT       	1	234	1
GAATGACAGCAAGGGGAGAGACCTGACCGAA	2	35	1
CCGAAAACCTCGGGATACAGGCGCCGAAGGA	2	61	1
GTGAATCTCTCAGGCAAAAGAACTCTTGCTC	2	104	1
TTTCAGGTGCCAGGACAGAGAACCTTCATTT	2	209	1
ACATACAAAAAAGGACAGAGAAACACCTCAT	2	243	0
CATGAAAATGAAGAAAACAGACGCGATGCGG	3	106	0
TTTCCACATTAGGGCAAAAGGTCGAAGGAAA	3	227	1
          ***** *****
MAP Score: 8.87393

Motif 5
GTCATCACAAGCTTTTATGTGCAAATTATAGAAGAAG	0	62	1
ATAACAGCATGAAAATATGAGCGAATGACAGCAAGGG	2	13	1
CAACTCTGGAGAGTGTTTGTGCGGATGCGCAAACCAC	2	139	1
CCACCTTTGGGGACGTCTTTGCGTATGCAAAGTAAAC	2	172	1
TACATGAGGTGTTTCTCTGTCCTTTTTTGTATGTTTT	2	240	1
TTGCATTACCGCTGTTTTGGACTTTTGCCACTGCCGC	3	73	1
TCATTTTCATGACGATTTTCGCTCATGGTATCATCCT	3	126	1
GCTTTCCTTCGACCTTTTGCCCTAATGTGGAAAAACC	3	223	0
          *    * ** *** ***
MAP Score: 5.51626

Motif 6
TCCTTACCGATTGTTTTATTTATTATGAAGC	0	19	1
TAAAATCGCGTTATGTTTTTTAAAAATGAGG	0	157	1
AAAAATGAGGTTTTGTTCTCTGAGTGAGAAC	0	178	1
GGAGCGGTATTTGTGTTATTTTACTATGCCA	1	166	1
GGGAAAGTGGTTTTTTTATTTTCAGAGGGGG	1	219	1
GTCCTTTTTTGTATGTTTTTTAGCTGCGCCG	2	258	1
GCCGCATCGCGTCTGTTTTCTTCATTTTCAT	3	105	1
          ** ********
MAP Score: 3.95006