AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions033_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241777
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yhcV	136	similar to hypothetical proteins
#1	spoIVFA	150	inhibitor of SpoIVFB
#2	ytoI	175	ytoI
#3	acuA	160	acetoin dehydrogenase
#4	acuB	26	acetoin dehydrogenase
#5	yumD	278	similar to GMP reductase

Motif 1
AGAGCTTTTCTAAAAATAGAAAAGCCCTTGCCGCATGA	0	10	0
GTATCAGAGAAATCATATCATAAAACCTTTCCTCTAAC	0	52	1
AATCAAAGAGAAGAATCTGACAAAGCATATGCTGTGTC	1	18	1
AAAGCAGGCAAAAACAAAAAAAAACCTGACACAGCATA	1	45	0
ATATTCGGTTTAGTCAAGAACAAAGCAGGCAAAAACAA	1	66	0
AACCGAATATTTGCCATGGACAAGACATATGATGTACA	1	94	1
GAACGAAATCAACGCTGTAAGAAGCCGGTCGGGCTTCT	2	64	1
TGAGGCTGGAAAATAAAAAAGAAGCCCGACCGGCTTCT	2	83	0
AAACCTTATAATAAAAACAAGAAGACTGTCCTTAGAGG	2	139	1
TCTTCTCAATTTTTAAAATATAAACCATGTTGAAAACG	3	66	1
TCTTTAAGAATACCAAATTATAAAGCGTTTTCAACATG	3	91	0
ATCAATTCTTATCAAAAATACATGCCTTCTTTAAGAAT	3	118	0
TCCCATGTCCATGCCATAAAGAAAGCCTGGTGCTGAAC	5	24	1
          **  **   * *** * *
MAP Score: 10.8698

Motif 2
TGCGGCAAGGGCTTTTCTATTTTTAGAAAAG	0	13	1
TACAAAAAGAGCTTTTCTAAAAATAGAAAAG	0	24	0
TATCATAAAACCTTTCCTCTAACTCCCTTTT	0	67	1
TCCTCTAACTCCCTTTTTAAACGGCTCGTGT	0	81	1
TGCTGTGTCAGGTTTTTTTTTGTTTTTGCCT	1	47	1
GTTTTTGCCTGCTTTGTTCTTGACTAAACCG	1	68	1
AAGCCGGTCGGGCTTCTTTTTTATTTTCCAG	2	85	1
CAAACATCCCCCTTTGCTGAAGTTGTCACAA	3	13	1
AAAAATACATGCCTTCTTTAAGAATACCAAA	3	112	0
TCAGCACCAGGCTTTCTTTATGGCATGGACA	5	29	0
GAACGACCAAGCTTTGCTGAACGTATATCAT	5	58	1
          ******** **
MAP Score: 6.64829

Motif 3
TTTGTATCAGAGAAATCATATCATAAAACCTTTC	0	49	1
GAAGAATCTGACAAAGCATATGCTGTGTCAGGTT	1	27	1
TTTGCCATGGACAAGACATATGATGTACAAACCC	1	103	1
ATAAATCCTTTGAAACCTTATAATAAAAACAAGA	2	127	1
TGAAGTTGTCACAATTATTATAGTATATATTCAT	3	30	1
AGCGTTTTCAACATGGTTTATATTTTAAAAATTG	3	72	0
GTATTCTTAAAGAAGGCATGTATTTTTGATAAGA	3	116	1
CACCGTCCCATCAATTCTTATCAAAAATACATGC	3	131	0
CAAGCTTTGCTGAACGTATATCATTCGCGTTTTG	5	65	1
ATTTAGGATGTCAAACATTATGATTTGCTGGCAG	5	179	0
TATAAGGCGAACATTTCATATATTATACTTTTAA	5	229	1
          ****  *****  *
MAP Score: 6.17385

Motif 4
ACAAAAAGAGCTTTTCTAAAAATAGAAAAG	0	24	0
TTAAACGGCTCGTGTCTGAACATACTAATG	0	97	1
CTGCTTTGTTCTTGACTAAACCGAATATTT	1	76	1
AAACATCCCCCTTTGCTGAAGTTGTCACAA	3	14	1
AACGACCAAGCTTTGCTGAACGTATATCAT	5	59	1
          **********
MAP Score: 3.2499

Motif 5
  TCATGCGGCAAGGGCTTTTCTATTTTTAGAAAAGCTCT	0	8	1
CATAAAACCTTTCCTCTAACTCCCTTTTTAAACGGCTCGT	0	70	1
TATGCTGTGTCAGGTTTTTTTTTGTTTTTGCCTGCTTTGT	1	45	1
TAAAAGGAATCACGTGGTCCTTGCGTTTGACTGGAACGAA	2	31	1
CTGTAAGAAGCCGGTCGGGCTTCTTTTTTATTTTCCAGCC	2	78	1
AGTATATATTCATATTCTTCTCAATTTTTAAAATATAAAC	3	51	1
     TAATTCACCGTCCCATCAATTCTTATCAAAAATAC	3	135	0
CTTTGCTGAACGTATATCATTCGCGTTTTGATCCGCTCTC	5	69	1
ATATATTATACTTTTAAATATTCGTTTTTAGGAGTGAAAA	5	246	1
          *   *     **  ******
MAP Score: 2.90187

Motif 6
ATGATTGAAAGGGGTGCTGACA         	0	124	1
CAAACATCCCCCTTTGCTGAAGTTGTCACAA	3	13	1
TAAAGAAAGCCTGGTGCTGAACGACCAAGCT	5	40	1
GAACGACCAAGCTTTGCTGAACGTATATCAT	5	58	1
AGGTGTGGTGCAAGTGCCGAAGCTTGTCATG	5	150	0
CAAACATTATGATTTGCTGGCAGGTGTGGTG	5	171	0
          * *********
MAP Score: 2.24781