AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241400
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rapJ	122	response regulator aspartate phosphatase
#1	ycdF	106	similar to glucose 1-dehydrogenase
#2	ycdG	24	similar to oligo-1,6-glucosidase
#3	treP	192	phosphotransferase system (PTS) trehalose-specific enzyme IIBC component
#4	treA	70	trehalose-6-phosphate hydrolase
#5	amyX	25	pullulanase
#6	ytlR	48	ytlR
#7	ytlQ	25	ytlQ
#8	ytlP	148	similar to ABC transporter (permease)
#9	glgB	300	1,4-alpha-glucan branching enzyme
#10	yugT	126	similar to exo-alpha-1,4-glucosidase
#11	yugS	27	similar to hypothetical proteins from B. subtilis
#12	yugP	300	yugP
#13	yvdH	39	similar to maltodextrin transport system permease
#14	yvdG	95	similar to maltose/maltodextrin-binding protein
#15	yvdF	112	similar to glucan 1,4-alpha-maltohydrolase
#16	yvdE	205	similar to transcriptional regulator (LacI family)
#17	yvdD	116	similar to hypothetical proteins

Motif 1
AACAGCACAAAAAAAGCAGAGAACCTGTAGT	1	23	0
TTTCAACTCGGAAAAACAGGGTATTTTCCAC	1	53	1
ACTGCATAGTGAGAAACAGAGGAGGATATCA	1	82	1
       AAGACAAAACAGGGGGATTGCGGG	2	3	1
ATATGACATTAAAAAGCAGGGTGAGCCTCT 	3	9	0
TCTGGAATATATGAAACAGACAAGGTTACCC	3	63	0
TGAAAGCGCTATAAAAAAGTGTTGACTACCT	3	100	1
TTGCGGAGTGGAGAAACAAAC          	7	14	1
TGTGCGGATAGAGGAACAGTGTATGAAAACA	8	77	0
TTCTTTATTTTAAAAACAGACTACAAAAATC	9	145	1
TTCATTTTCTGAAGAAAAACGAAATATATGG	9	177	0
TCGAAGAAATAAAAAAAAGCCCTTTCCTGAA	9	234	0
         TAAAAAACAGCCGGGGAACAAA	10	1	1
TTGATGACACAAAAAACAGCCGTTTGTTCCC	10	23	0
GTCATTTCTTAAAAAGCAATGCTGTAAAGAC	10	54	1
CAATCAGCAAAAAGAACAGGCCTGCTGAAAA	12	170	0
TCCAAGCCGGAAGAAAAAGCGCATTTCTGTA	12	211	1
ATAGCGTCCGGAAGAATAGAGGGCGGAAAA 	13	19	1
TAAATAGAAGGAGGAAAAGAG          	14	84	1
CCAAAGAGAAATAAAAAAGAGATTTCCCTTA	16	106	0
          ********* *
MAP Score: 22.784

Motif 2
GTAAATAGAAGGAGGAAAAGAG          	14	83	1
GATAGCGTCCGGAAGAATAGAGGGCGGAAAA 	13	18	1
CGGTACACTGGGAAGGAGTGGCTGT       	10	111	1
AAACGGATACGGAGGGGTTGGC          	3	180	1
TTTTCAACTCGGAAAAACAGGGTATTTTCCAC	1	52	1
AATAGTAGCAGGAGGAAGGAGGCAGACCG   	0	103	1
TGATGGAAGTGGAGAGAATGAGTCTGCCACCT	16	23	1
GCTCCAAGCCGGAAGAAAAAGCGCATTTCTGT	12	209	1
  ACGTGTTTGGAGGAGAGAGCTTCCG     	5	8	1
ATTGCGGAGTGGAGAAACAAAC          	7	13	1
AAACAGCCGGGGAACAAACGGCTGTTTTTTGT	10	14	1
TTCATTTTCTGAAAGAACTGGCCGGCAGTTTC	12	126	1
CACTGCATAGTGAGAAACAGAGGAGGATATCA	1	81	1
CAGCACATCTTGAGAAAGTGAGACCGAT    	0	6	0
GTTTTATTCAGAAAGGAATGACA         	8	1	0
TATGAATCCATGAAAAATCGAGTGTTTTTAAC	16	59	1
ATTGAAAACGGGAAAAGGGAACGTTCAACACG	4	26	0
GCACAGATAAGGAGGGGATGAAA         	16	192	1
       CGTTAAGGAGGTGGCCCCTTACCAT	11	3	1
          *******  ***
MAP Score: 17.0165

Motif 3
CAATCACTTAAAAGCGTTAACATTCAGCACA	0	31	0
ACACTTTTTTATAGCGCTTTCATCCTAGTCT	3	91	0
TGTTTGGAGGAGAGAGCTTCCG         	5	13	1
GAGAACGATTTGAGCGGTTTTCTCATAACAT	6	12	1
CGTTTGTGCGAGAGTGTTTTCATACACTGTT	8	63	1
CCCTTTCCTGAAAGCGCTTATACTTATAGAC	9	215	0
GAAATAAAAAAAAGCCCTTTCCTGAAAGCGC	9	229	0
GCAATGCTGTAAAGACCTTTTTCTACATAGG	10	69	1
AGCTTCCGGAAAAGTGATTATATGAATTCAA	12	86	0
CGTGTACAGAAATGCGCTTTTTCTTCCGGCT	12	215	0
CGATTATTTTAATGAGTTTTCTTTCTCGTGT	12	241	0
TGTCCTATAGAAAGCGGTTACAACAACTTTC	14	33	0
         AAAAGAGATTTTCTGATGGAAG	16	1	1
TTTTTAACAAAGTGAGGTTTCCTTAAGGGAA	16	83	1
GAGAAATAAAAAAGAGATTTCCCTTAAGGAA	16	101	0
GACAATATATAGTGTGTTTTTGAATGTTTAA	17	67	1
          ****** ****
MAP Score: 13.0869

Motif 4
        TTTTCCGCCCTCTATTCTTCCGG	13	26	0
GTCTGCCTCCTTCCTCCTGCTACTATTTATG	0	99	0
     CTCTTTTCCTCCTTCTATTTACGAAA	14	79	0
ACCTGTAGTTCTCTGCCATTTC         	1	1	0
AATGCGCTTTTTCTTCCGGCTTGGAGCACAC	12	205	0
     AGAGGCTCACCCTGCTTTTTAATGTC	3	5	1
TCACCGCGGATGCCGCCAGCTGCGTACCGAT	12	38	0
AACAATCCTTTTCACCCTGTTACCGATAACA	15	21	0
GCGGTTAAGACACCGCCCTTTCACGGCGGTA	9	20	1
    CCCGCAATCCCCCTGTTTTGTCTT   	2	7	0
TGGCCGGCAGTTTCGCCTTTTATTTGTTTTC	12	144	1
         GTTTCCCCCTTTGATTTCCGTT	15	100	0
TTCCGGAAGCTTCTCCTGGCTTCATTTTCTG	12	106	1
  CCGTCTGACACTCCCTTCTTTGACAGCTA	8	129	0
ACTTGATATCCTCCTCTGTTTCTCACTATGC	1	85	0
ACTACAGGTTCTCTGCTTTTTTTGTGCTGTT	1	23	1
GAACGTTCCCTTTTCCCGTTTTCAATTTAAA	4	32	1
ACAGCCGTTTGTTCCCCGGCTGTTTTTTA  	10	8	0
ACACTATATATTGTCCCATCTTCATGTGATA	17	51	0
          ******* ***
MAP Score: 11.1578

Motif 5
ACACTTGTTTTATTCAGAAAGGAATGACA  	8	8	0
AAGCCTTGCATATCCTGCAAGGTTTTTTTGT	9	83	1
ATTAACTTCATTTTCTGAAGAAAAACGAAAT	9	183	0
AAAAAAGCCCTTTCCTGAAAGCGCTTATACT	9	222	0
CCTGGCTTCATTTTCTGAAAGAACTGGCCGG	12	120	1
CTTTTATTTGTTTTCAGCAGGCCTGTTCTTT	12	160	1
GAAATGCGCTTTTTCTTCCGGCTTGGAGCAC	12	207	0
TTCCGCCCTCTATTCTTCCGGACGCTATCCC	13	16	0
  AAAAGAGATTTTCTGATGGAAGTGGAGAG	16	8	1
CAAAGTGAGGTTTCCTTAAGGGAAATCTCTT	16	90	1
          ******** **
MAP Score: 7.48937

Motif 6
CTACAGGTTCTCTGCTTTTTTTGTGCTGTTT	1	24	1
CTGCTTTTTTTGTGCTGTTTTCAACTCGGAA	1	35	1
AGTGGAAAATACCCTGTTTTTCCGAGTTGAA	1	54	0
TTGATATCCTCCTCTGTTTCTCACTATGCAG	1	83	0
  CCCGCAATCCCCCTGTTTTGTCTT     	2	5	0
AGAGGCTCACCCTGCTTTTTAATGTCATATT	3	10	1
ACGTTCCCTTTTCCCGTTTTCAATTTAAATA	4	34	1
GAGAACGATTTGAGCGGTTTTCTCATAACAT	6	12	1
ATATTATATGACACTTGTTTTATTCAGAAAG	8	18	0
CGTTTGTGCGAGAGTGTTTTCATACACTGTT	8	63	1
CCGCCGTGAAAGGGCGGTGTCTTAACCGCTT	9	18	0
AGATTTTTGTAGTCTGTTTTTAAAATAAAGA	9	146	0
CTTTCAGGAAAGGGCTTTTTTTTATTTCTTC	9	232	1
GTTTGTTCCCCGGCTGTTTTTTA        	10	2	0
CGGGGAACAAACGGCTGTTTTTTGTGTCATC	10	21	1
AATGCTGTAAAGACCTTTTTCTACATAGGAT	10	71	1
TCAAAGAACGATCGTGGTTTTAATCGGTACG	12	16	1
TGTTTTCAGCAGGCCTGTTCTTTTTGCTGAT	12	168	1
TGTACAGAAATGCGCTTTTTCTTCCGGCTTG	12	213	0
       AAAAGAGATTTTCTGATGGAAGTG	16	3	1
CATGAAAAATCGAGTGTTTTTAACAAAGTGA	16	67	1
TTTTTAACAAAGTGAGGTTTCCTTAAGGGAA	16	83	1
GACAATATATAGTGTGTTTTTGAATGTTTAA	17	67	1
          ** ********
MAP Score: 6.02572

Motif 7
ATGTGCTGAATGTTAACGCTTTTAAGTGATT	0	30	1
CAGACTAGGATGAAAGCGCTATAAAAAAGTG	3	90	1
ATATTTAAATTGAAAACGGGAAAAGGGAACG	4	35	0
AAGAGAACGATTTGAGCGGTTTTCTCATAAC	6	10	1
AGCCCTTTCCTGAAAGCGCTTATACTTATAG	9	217	0
ATAGGATATATAAGAACGGTACACTGGGAAG	10	95	1
CGATCGTGGTTTTAATCGGTACGCAGCTGGC	12	24	1
     CATTCTGTTATCGGTAACAAATCGAA	14	5	1
CGAAAGTTGTTGTAACCGCTTTCTATAGGAC	14	32	1
CGCCTTATTCTGTTATCGGTAACAGGGTGAA	15	11	1
          ***** *****
MAP Score: 5.71295

Motif 8
ACTACAGGTTCTCTGCTTTTTTTGTGCTGTTTT	1	23	1
TATCCTGCAAGGTTTTTTTGTTTTTATAAATCA	9	93	1
GTCTTAGATTTTGTTCTTTATTTTAAAAACAGA	9	132	1
CAGGAAAGGGCTTTTTTTTATTTCTTCGAATAA	9	236	1
GAACAAACGGCTGTTTTTTGTGTCATCAAGTCA	10	25	1
ATCCGCGGTGATTTTGTTTATTTTCGATTTGAA	12	58	1
GCAGTTTCGCCTTTTATTTGTTTTCAGCAGGCC	12	150	1
TTCAGCAGGCCTGTTCTTTTTGCTGATTGGATT	12	172	1
TAAGGGAAATCTCTTTTTTATTTCTCTTTGGCC	16	106	1
          ** ** *** ***
MAP Score: 4.50039

Motif 9
CGGTCTGCCTCCTTCCTCCTGCTACTATTTATGTTATATT	0	92	0
TTGAACGTTCCCTTTTCCCGTTTTCAATTTAAATATGGTG	4	30	1
GTCTGACACTCCCTTCTTTGACAGCTATTATTTTATCAAT	8	116	0
CAGAAGCCTTGCATATCCTGCAAGGTTTTTTTGTTTTTAT	9	80	1
TAAAAAAAAGCCCTTTCCTGAAAGCGCTTATACTTATAGA	9	216	0
GCTGTAAAGACCTTTTTCTACATAGGATATATAAGAACGG	10	74	1
TTTTCCGGAAGCTTCTCCTGGCTTCATTTTCTGAAAGAAC	12	104	1
CAGGCCTGTTCTTTTTGCTGATTGGATTGTGTGCTCCAAG	12	177	1
          CTCTTTTCCTCCTTCTATTTACGAAACTAT	14	75	0
       GCGCCTTATTCTGTTATCGGTAACAGGGTGAAA	15	3	1
TACTTTCAAACTATGAGCCGGCTTCAATAAAACGGAAATC	15	70	1
TTTTATTTCTCTTTGGCCTGCATCGTATATTTAGCAGTAA	16	121	1
          ** *   ***  * *  * *
MAP Score: 2.40112

Motif 10
TTTTTTGTGCTGTTTTCAACTCGGAAAAACAGGGTATTTTCCACT	1	40	1
AGGCTCACCCTGCTTTTTAATGTCATATTCAATAAGTGCTTGTGA	3	12	1
GAATACAATATGATTATAAGTTGTATATACAAGTTATAAAAACGG	3	141	1
TCTTTGACAGCTATTATTTTATCAATAAAGAGGCTGTGCGGATAG	8	97	0
TCCTGCAAGGTTTTTTTGTTTTTATAAATCATGATATGTCTTAGA	9	95	1
GTCTTAGATTTTGTTCTTTATTTTAAAAACAGACTACAAAAATCT	9	132	1
TCCATATATTTCGTTTTTCTTCAGAAAATGAAGTTAATTGTCTAT	9	176	1
TGTTTATTTTCGATTTGAATTCATATAATCACTTTTCCGGAAGCT	12	72	1
GATCATTTCTCTATTACGATTATTTTAATGAGTTTTCTTTCTCGT	12	243	0
      CATTCTGTTATCGGTAACAAATCGAAAGTTGTTGTAACC	14	4	1
CATGAAAAATCGAGTGTTTTTAACAAAGTGAGGTTTCCTTAAGGG	16	67	1
ACTCCTGCATTCTTTATGTATTTCATATTGATATTATCACATGAA	17	17	1
CTATATATCGTGTTAAACATTCAAAAACACACTATATATTGTCCC	17	65	0
          *  **     *   ***  **   *
MAP Score: 1.70234