AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID067_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391848
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	leuA	92	2-isopropylmalate synthase
#1	leuL_leuO	482	leuL: leu operon leader peptide, leuO: probable transcriptional activator for leuABCD operon
#2	ilvI	227	acetolactate synthase III, valine sensitive, large subunit
#3	acnB	300	aconitate hydrase B
#4	yeaU	81	putative tartrate dehydrogenase
#5	ilvB	105	acetolactate synthase I,valine-sensitive, large subunit
#6	ivbL	300	ilvB operon leader peptide
#7	ilvM	300	acetolactate synthase II, valine insensitive, small subunit
#8	ilvD	95	dihydroxyacid dehydratase
#9	ilvC	149	ketol-acid reductoisomerase

Motif 1
AGGCGACTGACGAAACCTCGCTCCGGCGGGG	6	144	1
CACACGATTCCAAAACCCCGCCGGCGCAAAC	5	22	1
AACGATACAGCGAAACCACCCTTACTGATAA	7	78	1
AGTCAAACAAAAAACCCGCGCCATTGCGCGG	0	20	1
CGGGCATAAAAAAACCCGCGCAATGGCGCGG	0	35	0
GCAGATAACAAAAAACCCCGCCGGAGCGAGG	6	159	0
TGCTTAAACGAAAAACCCCGCCCGGTTTGCG	5	46	0
TTACGGATGCAGAACTCACGCTGGCGGGACG	1	381	1
AAGCGGCACTCGACACCATGCTGAACAGTGA	7	180	1
CTGCCATTGTCGAACCATCCCTAACCGTTGG	7	31	0
CTGACGCAATAAAAACGTCCCGCCAGCGTGA	1	396	0
AACACCTCGTCAAAATCCTGCTATTCTGCCC	3	181	1
AAATTCGTGCCGAAATTGCGCGTTCTGCGCG	6	56	1
CACGCGTTGCAAAACCTATCCTGATGATTTG	1	217	0
          ******* ***
MAP Score: 18.4989

Motif 2
GCCCGGTTTGCGCCGGCGGGGTTTTGGAAT	5	28	0
TTTCGTCAGTCGCCTGCGGCTGGTAACCGC	6	129	0
TGAAGAGAATCGCCTGCCGCACTATGACAA	3	260	1
AAACGAAAAACCCCGCCCGGTTTGCGCCGG	5	42	0
CGCCAGGCGGCACCAGCGGCCAGACGTTCT	7	249	0
TTCGTTTAAGCACCTCCCGGAAAGTCGGCC	5	65	1
GCAGAACTCACGCTGGCGGGACGTTTTTAT	1	389	1
CGAAACCTCGCTCCGGCGGGGTTTTTTGTT	6	154	1
CCGCTGGTGCCGCCTGGCGCCAGTAATTCA	7	260	1
TGTTAGCCAGCGCCTTCGGCATCCATGGCC	7	123	1
TAGAGCGCCTCGCTTCGGGCATAAAAAAAC	0	51	0
ATGGCCAACACATCACCCGGAAAGACCAGG	7	147	1
TGCCCAGTACCGCAACGGGCAGAATAGCAG	3	198	0
          **********
MAP Score: 18.1722

Motif 3
GTCAAACAAAAAACCCGCGCCATTGCGCGGGTTT	0	21	1
CTGACGCAATAAAAACGTCCCGCCAGCGTGAGTT	1	393	0
GCGTGAAGAGAATCGCCTGCCGCACTATGACAAT	3	257	1
ACACGATTCCAAAACCCCGCCGGCGCAAACCGGG	5	23	1
TTAAACGAAAAACCCCGCCCGGTTTGCGCCGGCG	5	40	0
TTTTTCGTTTAAGCACCTCCCGGAAAGTCGGCCC	5	62	1
AAATACGTCAAAATTCGTGCCGAAATTGCGCGTT	6	46	1
AGGTTTCGTCAGTCGCCTGCGGCTGGTAACCGCA	6	128	0
CGACTGACGAAACCTCGCTCCGGCGGGGTTTTTT	6	147	1
TCATGTTAGCCAGCGCCTTCGGCATCCATGGCCA	7	120	1
TGGCGCCAGGCGGCACCAGCGGCCAGACGTTCTC	7	248	0
AAAAATGGGACGGCACGCACCGTCCCATTTACGA	8	15	1
AGTATGCCTAAGTACCGTTCCGCCACCACCACTC	8	71	1
TCAATCTCGCAAACGCGAACCGAACAATAAGAAG	9	103	1
          ** * *** *** *
MAP Score: 12.3406

Motif 4
      TTACCACAGCATAATAATCCATAATGTT	1	4	1
CAATAATATTCACCAAATCAATATCAAAAAAAAT	1	162	1
TAATTCAATACAAATCATCAGGATAGGTTTTGCA	1	207	1
TTACTTTAACCACCGCAGCACAATTAGCTAATTT	1	348	1
ATAGAGAGCCCACACATTCAGAATAAAATTCTAC	2	68	0
AATCTGTTTACAAAAAAGCAACATAAAAAAGTGG	3	147	0
AACAGATTAACACCTCGTCAAAATCCTGCTATTC	3	173	1
CATCAAAATTGACAACATCACCATCCTATAATTG	4	38	0
AAAACGTGATCAACCCCTCAATTTTCCCTTGCTG	6	200	1
TTGATATATTCACAACGTCACATTGCAATTTTTG	9	36	0
CAATAAGAAGCACAACATCACGAGGAATCACC  	9	127	1
          **** * ***  **
MAP Score: 9.66694

Motif 5
CAGTCAAACAAAAAACCCGCGCCATTGCGC	0	19	1
TCGGGCATAAAAAAACCCGCGCAATGGCGC	0	37	0
ACACGATTCCAAAACCCCGCCGGCGCAAAC	5	23	1
CAGATAACAAAAAACCCCGCCGGAGCGAGG	6	159	0
ACCCTTACTGATAACCCCGATTTCCTCATG	7	95	1
TGGCCAACACATCACCCGGAAAGACCAGGT	7	148	1
          **********
MAP Score: 7.41066

Motif 6
CGCGCAATGGCGCGGGTTTTTTGTTTGACTGC	0	18	0
CCCGCGCCATTGCGCGGGTTTTTTTATGCCCG	0	34	1
GGTTTTGCAACGCGTGCATTTTGTCCCCTTTT	1	232	1
CTCACGCTGGCGGGACGTTTTTATTGCGTCAG	1	395	1
ACGGGCAGAATAGCAGGATTTTGACGAGGTGT	3	182	0
TGTCATAGTGCGGCAGGCGATTCTCTTCACGC	3	257	0
CGGTTTGCGCCGGCGGGGTTTTGGAATCGTGT	5	23	0
CGGCGCAAACCGGGCGGGGTTTTTCGTTTAAG	5	43	1
GCCGACTTTCCGGGAGGTGCTTAAACGAAAAA	5	62	0
AACCTCGCTCCGGCGGGGTTTTTTGTTATCTG	6	157	1
AGCATGGTGTCGAGTGCCGCTTCAACCTGGTC	7	170	0
ACGGTGCGTGCCGTCCCATTTTTTGTAT    	8	6	0
TCTTATTGTTCGGTTCGCGTTTGCGAGATTGA	9	103	0
          **** ** ****
MAP Score: 5.42966

Motif 7
CATCTACAAAATGGATTAAATGTGCTTATTT	1	83	1
TATATATTTAATGCATTAATTCTTAACATTA	1	125	1
CGTTGATTAGATGCAAAAATTTATGCTGAAA	1	268	1
GTCGGTAGTTAAGCAGAAATTAATATCGCTT	1	319	1
CTCTCTATTTTAGGATTAATTAAAAAAATAG	2	94	1
AATTAAAAAAATAGAGAAATTGCTGTAAGTT	2	111	1
ATACTCAACTATGCACTAAATACGTCAAAAT	6	29	1
ATTTTTCAGCAAGGGAAAATTGAGGGGTTGA	6	209	0
AGGGGAGACAATGGAAAATTTTTCAGCAAGG	6	226	0
TTCAGAAATGTTGGAGAAATTATC       	7	286	1
          ATACAAAAAATGGGACGGCAC	8	0	1
GATGTTGACGTTGCAAAAATTGCAATGTGAC	9	23	1
AGGAAATTTATTGCGGAAATTGATATATTCA	9	58	0
          ***** *****
MAP Score: 5.28421

Motif 8
GGGTAAATGCCCAGTACCGCAACGGGCAGA	3	205	0
TGAAGAGAATCGCCTGCCGCACTATGACAA	3	260	1
GCAGAACGCGCAATTTCGGCACGAATTTTG	6	54	0
GCCGAAATTGCGCGTTCTGCGCGGAACACG	6	64	1
TTTCGTCAGTCGCCTGCGGCTGGTAACCGC	6	129	0
CCTGAAAAAACAGTTGCTGCCATTGTCGAA	7	48	0
TGTTAGCCAGCGCCTTCGGCATCCATGGCC	7	123	1
AGCATGGTGTCGAGTGCCGCTTCAACCTGG	7	172	0
CAGACGTTCTCAAGTTCGTCGATTGAGACA	7	229	0
CGTCTGGCCGCTGGTGCCGCCTGGCGCCAG	7	253	1
AATGGGACGGTGCGTGCCGTCCCATTTTTT	8	14	0
GTGAATATATCAATTTCCGCAATAAATTTC	9	57	1
          **********
MAP Score: 4.51573

Motif 9
ACAAAAAACCCGCGCCATTGCGCGGGTTTT	0	26	1
ATGCAGAACTCACGCTGGCGGGACGTTTTT	1	387	1
ATTCTCTTCACGCTCCTGTGAGACAGCAGT	3	240	0
ATTCCAAAACCCCGCCGGCGCAAACCGGGC	5	28	1
GCGGTTACCAGCCGCAGGCGACTGACGAAA	6	129	1
GACGAAACCTCGCTCCGGCGGGGTTTTTTG	6	152	1
GGATGCCGAAGGCGCTGGCTAACATGAGGA	7	117	0
AGAACGTCTGGCCGCTGGTGCCGCCTGGCG	7	249	1
GCCGCTGGTGCCGCCTGGCGCCAGTAATTC	7	259	1
TTGTTCGGTTCGCGTTTGCGAGATTGAATT	9	100	0
          **********
MAP Score: 3.54845

Motif 10
TCAAACAAAAAACCCGCGCCATTGCGCGGG	0	22	1
GGCATAAAAAAACCCGCGCAATGGCGCGGG	0	34	0
ATCTAATCATAACTACCGCGAATACTCAAT	1	53	1
ATTTCTGCTTAACTACCGACGCTTTTCATC	1	309	0
CGCTTACTTTAACCACCGCAGCACAATTAG	1	345	1
CGCAATAAAAACGTCCCGCCAGCGTGAGTT	1	393	0
CGGATGTCAACCCTGACGCAATAAAAACGT	1	409	0
TCAAAATTTAAACTACCGCCTCTTTATACT	3	19	0
GGTAAATGCCCAGTACCGCAACGGGCAGAA	3	204	0
CACGATTCCAAAACCCCGCCGGCGCAAACC	5	24	1
CTTAAACGAAAAACCCCGCCCGGTTTGCGC	5	45	0
TCGTTTAAGCACCTCCCGGAAAGTCGGCCC	5	66	1
CTTTGCGGTTACCAGCCGCAGGCGACTGAC	6	125	1
GACTGACGAAACCTCGCTCCGGCGGGGTTT	6	148	1
TCCTCATGTTAGCCAGCGCCTTCGGCATCC	7	117	1
GCCAGGCGGCACCAGCGGCCAGACGTTCTC	7	248	0
ATTTCTGAATTACTGGCGCCAGGCGGCACC	7	265	0
ATGGGACGGCACGCACCGTCCCATTTACGA	8	19	1
TGCCTAAGTACCGTTCCGCCACCACCACTC	8	75	1
          **********
MAP Score: 3.13713

Motif 11
AATACAAATCATCAGGATAGGTTTTGCAACGC	1	213	1
     CTGATTGCAGAATAGGTCAGACATGAA	2	5	1
AAGAATAAACAGGAGGAAAGGTGAAAAGAAAC	2	197	0
TTGGGATTCGTTGAGAAAGGTGATTATCACCA	3	55	1
TAGTGCATAGTTGAGTATCGATCACAGTTTGC	6	15	0
TGGAAAATTTTTCAGCAAGGGAAAATTGAGGG	6	214	0
CAACTGTTTTTTCAGGAACGATACAGCGAAAC	7	62	1
AATCGGGGTTATCAGTAAGGGTGGTTTCGCTG	7	85	0
CCCATCACTGTTCAGCATGGTGTCGAGTGCCG	7	183	0
GCGCCAGTAATTCAGAAATGTTGGAGAAATTA	7	276	1
 GAGTGGTGGTGGCGGAACGGTACTTAGGCAT	8	74	0
          ***** ** ***
MAP Score: 2.49329

Motif 12
TGAAAAGAAACGATAAAATCCTCCATTACAG	2	177	0
ATTAACACCTCGTCAAAATCCTGCTATTCTG	3	178	1
AAATTGACAACATCACCATCCTATAATTGAC	4	36	0
CACACGATTCCAAAACCCCGCCGGCGCAAAC	5	22	1
GGTGCTTAAACGAAAAACCCCGCCCGGTTTG	5	48	0
AGGCGACTGACGAAACCTCGCTCCGGCGGGG	6	144	1
TTGCAGATAACAAAAAACCCCGCCGGAGCGA	6	161	0
AACGATACAGCGAAACCACCCTTACTGATAA	7	78	1
AAGCGGCACTCGACACCATGCTGAACAGTGA	7	180	1
TGGCGCCAGGCGGCACCAGCGGCCAGACGTT	7	251	0
AGTACCGTTCCGCCACCACCACTC       	8	81	1
ATTTTTGCAACGTCAACATCGAGGGCTGTCC	9	12	0
ATATTCACAACGTCACATTGCAATTTTTGCA	9	34	0
          ** ********
MAP Score: 2.3882

Motif 13
TTCAATACAAATCATCAGGATAGGTTTTGC	1	210	1
GGTGATTATCACCATGCGAATTAACGAAGT	3	73	1
CAATCTCTAGACCATCCTTAACGATTCAGC	3	118	1
TCGTTTAAGCACCTCCCGGAAAGTCGGCCC	5	66	1
ATACAGCGAAACCACCCTTACTGATAACCC	7	82	1
TGGCCAACACATCACCCGGAAAGACCAGGT	7	148	1
GGCACTCGACACCATGCTGAACAGTGATGG	7	184	1
GAAGCACAACATCACGAGGAATCACC    	9	133	1
          **********
MAP Score: 1.41953

Motif 14
CACGCAGTCAAACAAAAAACCCGCGCCATT	0	15	1
CATATAATTCAATACAAATCATCAGGATAG	1	203	1
TTCTACATTCAATAAAAAATGCAGAATAAA	2	44	0
AATTGCAGATAACAAAAAACCCCGCCGGAG	6	164	0
TCTGCAATTCAGTACAAAACGTGATCAACC	6	185	1
AATATTGTTAAACACAAAACCAACAAGGTC	6	276	1
          **********
MAP Score: 0.346033