AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241382
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ycdF	106	similar to glucose 1-dehydrogenase
#1	ycdG	24	similar to oligo-1,6-glucosidase
#2	treP	192	phosphotransferase system (PTS) trehalose-specific enzyme IIBC component
#3	treA	70	trehalose-6-phosphate hydrolase
#4	amyX	25	pullulanase
#5	ytlR	48	ytlR
#6	ytlQ	25	ytlQ
#7	ytlP	148	similar to ABC transporter (permease)
#8	glgB	300	1,4-alpha-glucan branching enzyme
#9	yugT	126	similar to exo-alpha-1,4-glucosidase
#10	yvdH	39	similar to maltodextrin transport system permease
#11	yvdG	95	similar to maltose/maltodextrin-binding protein
#12	yvdF	112	similar to glucan 1,4-alpha-maltohydrolase

Motif 1
ACTACAGGTTCTCTGCTTTTTTTGTGCTGTT	0	23	1
GTGGAAAATACCCTGTTTTTCCGAGTTGAAA	0	53	0
TGATATCCTCCTCTGTTTCTCACTATGCAGT	0	82	0
CCCGCAATCCCCCTGTTTTGTCTT       	1	3	0
 AGAGGCTCACCCTGCTTTTTAATGTCATAT	2	9	1
GGGTAACCTTGTCTGTTTCATATATTCCAGA	2	63	1
AGGTAGTCAACACTTTTTTATAGCGCTTTCA	2	100	0
          GTTTGTTTCTCCACTCCGCAA	6	14	0
TGTTTTCATACACTGTTCCTCTATCCGCACA	7	77	1
GATTTTTGTAGTCTGTTTTTAAAATAAAGAA	8	145	0
CCATATATTTCGTTTTTCTTCAGAAAATGAA	8	177	1
TTCAGGAAAGGGCTTTTTTTTATTTCTTCGA	8	234	1
TTTGTTCCCCGGCTGTTTTTTA         	9	1	0
GGGAACAAACGGCTGTTTTTTGTGTCATCAA	9	23	1
GTCTTTACAGCATTGCTTTTTAAGAAATGAC	9	54	0
 TTTTCCGCCCTCTATTCTTCCGGACGCTAT	10	19	0
          CTCTTTTCCTCCTTCTATTTA	11	84	0
          * *********
MAP Score: 22.1854

Motif 2
TCTGCTTTTTTTGTGCTGTTTTCAACTCGGAAAAACAGG	0	34	1
TATAATCATATTGTATTCCTGTATATACAGGTAGTCAAC	2	120	0
TCTCACCTGCTTATGTTATGAGAAAACCGCTCAAATCGT	5	16	0
TATATGACACTTGTTTTATTCAGAAAGGAATGACA    	7	6	0
TTGACAGCTATTATTTTATCAATAAAGAGGCTGTGCGGA	7	100	0
CTGCAAGGTTTTTTTGTTTTTATAAATCATGATATGTCT	8	97	1
GTCTTAGATTTTGTTCTTTATTTTAAAAACAGACTACAA	8	132	1
ATATATTTCGTTTTTCTTCAGAAAATGAAGTTAATTGTC	8	179	1
AAGGGCTTTTTTTTATTTCTTCGAATAAATACTATAAAT	8	241	1
AAACGGCTGTTTTTTGTGTCATCAAGTCATTTCTTAAAA	9	29	1
        CATTCTGTTATCGGTAACAAATCGAAAGTTG	11	2	1
ACTATAACAATTGTATTGTCCTATAGAAAGCGGTTACAA	11	41	0
AATACAATTGTTATAGTTTCGTAAATAGAAGGAGGAAAA	11	63	1
  GCGCCTTATTCTGTTATCGGTAACAGGGTGAAAAGGA	12	8	1
CCCCTTTGATTTCCGTTTTATTGAAGCCGGCTCATAGTT	12	78	0
          ** * ** *    **  **
MAP Score: 11.6657

Motif 3
TTTTCAACTCGGAAAAACAGGGTATTTTCCAC	0	52	1
CACTGCATAGTGAGAAACAGAGGAGGATATCA	0	81	1
AAGACAAAACAGGGGGATTGCGGG        	1	10	1
ATTCCAGACTAGGATGAAAGCGCTATAAAAAA	2	86	1
TAAATTGAAAACGGGAAAAGGGAACGTTCAAC	3	29	0
   ACGTGTTTGGAGGAGAGAGCTTCCG    	4	7	1
CTGTGCGGATAGAGGAACAGTGTATGAAAACA	7	77	0
CCGTGTTACCGCCGTGAAAGGGCGGTGTCTTA	8	25	0
AACGGTACACTGGGAAGGAGTGGCTGT     	9	109	1
       AACGGCGGGATAGCGTCCGGAAGAA	10	3	1
GATAGCGTCCGGAAGAATAGAGGGCGGAAAA 	10	18	1
GTAAATAGAAGGAGGAAAAGAG          	11	83	1
TATTCTGTTATCGGTAACAGGGTGAAAAGGAT	12	16	1
          ******* ** *
MAP Score: 11.143

Motif 4
          GAAATGGCAGAGAACTACAGGTTC	0	0	1
AAACAGCACAAAAAAAGCAGAGAACCTGTAGTTC	0	21	0
TGCATAGTGAGAAACAGAGGAGGATATCAAGT  	0	84	1
       AAGACAAAACAGGGGGATTGCGGG   	1	3	1
ATATGACATTAAAAAGCAGGGTGAGCCTCT    	2	6	0
TGGAATATATGAAACAGACAAGGTTACCCTAAAA	2	58	0
ACAAGTTATAAAAACGGATACGGAGGGGTTGGC 	2	169	1
TTTCAATTTAAATATGGTGGTGGAAACAG     	3	51	1
TTTTCTCATAACATAAGCAGGTGAGAAAG     	5	29	1
TTATTTTATCAATAAAGAGGCTGTGCGGATAGAG	7	95	0
CTTTATTGATAAAATAATAGCTGTCAAAGAAGGG	7	112	1
       TAAAAAACAGCCGGGGAACAAACGGCT	9	3	1
GCTTTTTAAGAAATGACTTGATGACACAAAAAAC	9	37	0
GCGTCCGGAAGAATAGAGGGCGGAAAA       	10	22	1
TATCGGTAACAAATCGAAAGTTGTTGTAACCGCT	11	18	1
ATAGTTTCGTAAATAGAAGGAGGAAAAGAG    	11	75	1
AATAAAACGGAAATCAAAGGGGGAAAC       	12	95	1
          **** **  * ***
MAP Score: 10.3909

Motif 5
TCTCTGCTTTTTTTGTGCTGTTTTCAACTCGGAAAAA	0	32	1
CCTCCGTATCCGTTTTTATAACTTGTATATACAACTT	2	158	0
CGTTCCCTTTTCCCGTTTTCAATTTAAATATGGTGGT	3	35	1
     TGTCATTCCTTTCTGAATAAAACAAGTGTCAT	7	5	1
ATCCGCACAGCCTCTTTATTGATAAAATAATAGCTGT	7	99	1
TGACACTCCCTTCTTTGACAGCTATTATTTTATCAAT	7	116	0
TCCTGCAAGGTTTTTTTGTTTTTATAAATCATGATAT	8	95	1
ATGTCTTAGATTTTGTTCTTTATTTTAAAAACAGACT	8	130	1
TCTCCATATATTTCGTTTTTCTTCAGAAAATGAAGTT	8	174	1
GGAAAGGGCTTTTTTTTATTTCTTCGAATAAATACTA	8	238	1
GCTGTAAAGACCTTTTTCTACATAGGATATATAAGAA	9	74	1
        CATTCTGTTATCGGTAACAAATCGAAAGT	11	2	1
          CTCTTTTCCTCCTTCTATTTACGAAAC	11	78	0
  GCGCCTTATTCTGTTATCGGTAACAGGGTGAAAAG	12	8	1
  GTTTCCCCCTTTGATTTCCGTTTTATTGAAGCCGG	12	87	0
          ******* *   *   *
MAP Score: 7.89631

Motif 6
CAGACTAGGATGAAAGCGCTATAAAAAAGT	2	90	1
ATATTTAAATTGAAAACGGGAAAAGGGAAC	3	36	0
TATGTTATGAGAAAACCGCTCAAATCGTTC	5	14	0
GAACAGTGTATGAAAACACTCTCGCACAAA	7	65	0
GTTACCGCCGTGAAAGGGCGGTGTCTTAAC	8	23	0
AGCCCTTTCCTGAAAGCGCTTATACTTATA	8	218	0
AGCGCTTTCAGGAAAGGGCTTTTTTTTATT	8	228	1
CGAAAGTTGTTGTAACCGCTTTCTATAGGA	11	32	1
GGTAACAGGGTGAAAAGGATTGTTCCCACA	12	28	1
          **********
MAP Score: 7.48235

Motif 7
CTCTGCTTTTTTTGTGCTGTTTTCAACTCGGAAAAACAGGGTAT	0	33	1
     AGAGGCTCACCCTGCTTTTTAATGTCATATTCAATAAGT	2	5	1
TTAGGGTAACCTTGTCTGTTTCATATATTCCAGACTAGGATGAA	2	60	1
TGAACGTTCCCTTTTCCCGTTTTCAATTTAAATATGGTGGTGGA	3	31	1
AAGAGAACGATTTGAGCGGTTTTCTCATAACATAAGCAGGTGAG	5	10	1
          TGTCATTCCTTTCTGAATAAAACAAGTGTCATAT	7	0	1
CCTCTATCCGCACAGCCTCTTTATTGATAAAATAATAGCTGTCA	7	94	1
AGAACAAAATCTAAGACATATCATGATTTATAAAAACAAAAAAA	8	105	0
TGGAGATTTTTGTAGTCTGTTTTTAAAATAAAGAACAAAATCTA	8	136	0
GGAAAGGGCTTTTTTTTATTTCTTCGAATAAATACTATAAATGA	8	238	1
CTGTTTTTTGTGTCATCAAGTCATTTCTTAAAAAGCAATGCTGT	9	35	1
CAGTGTACCGTTCTTATATATCCTATGTAGAAAAAGGTCTTTAC	9	77	0
TTACAACAACTTTCGATTTGTTACCGATAACAGAATG       	11	3	0
        CTCTTTTCCTCCTTCTATTTACGAAACTATAACAAT	11	69	0
GAACAATCCTTTTCACCCTGTTACCGATAACAGAATAAGGCGC 	12	9	0
          ***   *   ** *   *   * *
MAP Score: 5.75049