AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240841
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yknW	109	yknW
#1	ytsC	101	similar to ABC transporter (ATP-binding protein)
#2	ytrD	29	similar to cytochrome c oxidase subunit
#3	ytrA	300	similar to transcriptional regulator (GntR family)
#4	yvrM	32	similar to hypothetical proteins
#5	yvrN	104	alternate gene name: yziB; similar to hypothetical proteins from B. subtilis
#6	yvrP	170	similar to hypothetical proteins from B. subtilis
#7	opuBA	274	choline ABC transporter (ATP-binding protein)

Motif 1
ATCCTTCCCGTACTATTTGTTAGATATTCTC	0	74	1
CACATGCTTTTCTTTTTTGTTCGCCGTATCG	1	19	1
AGCCCGGCATTCCTTTTTATAATGAGATTAT	1	57	1
TTACGCAGTCTCCTTTATATTGGATAATCTC	1	80	0
         CGTTTTTTTGTAAAAAAAGGAT	3	1	1
AGTCAAAGTATTTATTGTATTAAGTGTACTA	3	42	1
ATATATAAATGATTTTATATTAGTGTCTATA	3	88	0
ATATAAAATCATTTATATATTGACATTAAGG	3	99	1
GTTTGTTTCGTTTTTTATGTTTCATAACTGC	3	133	0
AATTGATCATTTTTATCTATAAAAGGTTCAG	3	255	1
 TTACTTCCCTACTTTCTATACGATCTGAAC	3	280	0
GAAGCCGGGATTTTTTTTATTCGGCTTTGAA	6	24	1
TGAAAATACAATTTTTCTATTTGATTCCGTC	6	51	1
TTCTAACCAATATTATCTATTAATTCAAAAA	6	106	0
AATTTGTTCATATTATTTATAAAGTATGTGT	7	142	0
ATAAAAAGTTTACAATTTGTTCATATTATTT	7	155	0
ACAAATTGTAAACTTTTTATTTTATAAACTT	7	166	1
TTTTATAAACTTTATTCTATAATGGGAAGCA	7	185	1
ATTAAGTTTATTCAATTTGTTCAGTTTAAAT	7	237	0
          ****** ****
MAP Score: 11.4753

Motif 2
TTTTTGGAAATTTATTAGAAAAACATGAAACTTTTTGA	0	35	1
       CGTTTTTTTGTAAAAAAAGGATTGACTTTGT	3	3	1
AGTCAAAGTATTTATTGTATTAAGTGTACTAATTGAAG	3	42	1
GAGGCAGTTATGAAACATAAAAAACGAAACAAACGTAA	3	130	1
ATGATCGGTTTTGAATGGCAAAAAAGTATAATTGATCA	3	226	1
GATCTGAACCTTTTATAGATAAAAATGATCAATTATAC	3	251	0
AATGACGGAATCAAATAGAAAAATTGTATTTTCAAAGC	6	47	0
TTGCAATCCTTTTATTGAAATGACGGAATCAAATAGAA	6	65	0
AAATATTACATAGTTTACAGAAAGAGGAGATCGTT   	6	145	1
ACTTTATAAATAATATGAACAAATTGTAAACTTTTTAT	7	148	1
TTGTAAACTTTTTATTTTATAAACTTTATTCTATAATG	7	171	1
AAATTAAATTTAAACTGAACAAATTGAATAAACTTAAT	7	230	1
          *  * ** * ***  * *
MAP Score: 9.96582

Motif 3
GAAAAACATGAAACTTTTTGATATCCTTCCCG	0	52	1
AAAGCCCGGCATTCCTTTTTATAATGAGATTA	1	55	1
TCACAAAGTCAATCCTTTTTTTACAAAAAAAC	3	11	0
ACTAATATAAAATCATTTATATATTGACATTA	3	95	1
AAGTATAATTGATCATTTTTATCTATAAAAGG	3	249	1
GGGAAGGCAAGACCATTATTATGATAACCCAC	5	18	1
AAGCTGACAGAACCGTTTTTATCAGAGACGGA	5	69	1
TTGAAGCCGGGATTTTTTTTATTCGGCTTTGA	6	22	1
AAAGACTTGCAATCCTTTTATTGAAATGACGG	6	77	0
GAAACATTCTAACCAATATTATCTATTAATTC	6	111	0
AACAAATTGTAAACTTTTTATTTTATAAACTT	7	165	1
TTTATTTTATAAACTTTATTCTATAATGGGAA	7	181	1
          ** * *******
MAP Score: 9.71303

Motif 4
     TATGAAAAGCCTTCAATATTGAAGGTTTTTGGA	0	5	1
TTCCTTCGATACGGCGAACAAAAAAGAAAAGCATGTGA	1	18	0
GTAATACACTATAGACACTAATATAAAATCATTTATAT	3	79	1
GATCATCACAAGAACAAGAAAAAAAGAACAAGCGATCA	3	194	0
ATCGGTTTTGAATGGCAAAAAAGTATAATTGATCATTT	3	229	1
TGAACCTTTTATAGATAAAAATGATCAATTATACTTTT	3	247	0
TTTTTTTTATTCGGCTTTGAAAATACAATTTTTCTATT	6	34	1
TATTGAAATGACGGAATCAAATAGAAAAATTGTATTTT	6	53	0
TATTGGTTAGAATGTTTCGAAAATATTACATAGTTTAC	6	125	1
ATACGGCGAAAATGCTGTCAAAAGAGAATTTGGCAGGA	7	52	1
ATTATAGAATAAAGTTTATAAAATAAAAAGTTTACAAT	7	170	0
GAAGCATTCAATTGTCTGAAAAATTAAATTTAAACTGA	7	210	1
          *  *     ****** **
MAP Score: 8.95116

Motif 5
AAAGTTTCATGTTTTTCTAATAAATTTCCAA	0	38	0
AAACATGAAACTTTTTGATATCCTTCCCGTA	0	55	1
ATGTCACATGCTTTTCTTTTTTGTTCGCCGT	1	15	1
CCCGGCATTCCTTTTTATAATGAGATTATCC	1	59	1
          CGTTTTTTTGTAAAAAAAGGA	3	0	1
CGTTTGTTTCGTTTTTTATGTTTCATAACTG	3	134	0
TCTGTGATCGCTTGTTCTTTTTTTCTTGTTC	3	190	1
TTCTTTTTTTCTTGTTCTTGTGATGATCGGT	3	204	1
TGAAGCCGGGATTTTTTTTATTCGGCTTTGA	6	23	1
TGAAAATACAATTTTTCTATTTGATTCCGTC	6	51	1
GATTGCAAGTCTTTTTGAATTAATAGATAAT	6	95	1
AAATTGTAAACTTTTTATTTTATAAACTTTA	7	168	1
          ****** ****
MAP Score: 6.15549

Motif 6
ATTCTCAAGGAGGTTTTGAA          	0	99	1
TTTTTGTTCGCCGTATCGAAGGAAAAGCCC	1	32	1
TTGTGATGATCGGTTTTGAATGGCAAAAAA	3	221	1
    CGGAAAACGATTTAAACAGCACACAC	4	6	1
AAAAAAATCCCGGCTTCAAACCGGGATTTT	6	11	0
TTTTTTTATTCGGCTTTGAAAATACAATTT	6	35	1
ATTGAAATGACGGAATCAAATAGAAAAATT	6	60	0
ATTGGTTAGAATGTTTCGAAAATATTACAT	6	126	1
AGCATTTTCGCCGTATCAAAAATGTGGTAT	7	38	0
GCTGATTTACCCGCATTGACGTGTGTTGAT	7	108	0
          **********
MAP Score: 5.63902

Motif 7
AAAACCTTCAATATTGAAGGCTTTTCATA 	0	9	0
TTTGTTCGCCGTATCGAAGGAAAAGCCCGG	1	34	1
AAATGCCTTAGGTTTGGAGGGAAGTGAG  	2	11	1
GTGATGATCGGTTTTGAATGGCAAAAAAGT	3	223	1
GGTTCAGATCGTATAGAAAGTAGGGAAGTA	3	279	1
 AAAAATCCCGGTTTGAAGCCGGGATTTTT	6	9	1
TTCAATAAAAGGATTGCAAGTCTTTTTGAA	6	84	1
AGATAATATTGGTTAGAATGTTTCGAAAAT	6	119	1
AATAAACTTAATTTTGGAGGTGCGATGT  	7	256	1
          **********
MAP Score: 2.71597