AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242193
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ytgA	300	Solute Protein Binding Family
#1	yaeM	26	hypothetical protein
#2	yaeL	195	Metalloprotease
#3	yaeS	300	YaeS family
#4	uhpC	300	Hexosphosphate Transport
#5	CT646	100	hypothetical protein
#6	recA	260	hypothetical protein
#7	rs2	300	S2 Ribosomal Protein

Motif 1
TTATTTAGAATTGTCTCTTCGAGATGAGAAACGC	0	23	1
TAAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCT	0	115	1
TACAGGAGGCTTGTATCCTTTAAAATAGAGTTTT	0	149	1
   AAGAACCTCGTATTCTCTACATTGCC     	1	5	0
AAATAAAAATTTTTATATTTGAAGTTTTGTTTTG	3	38	0
ATGCTTAAAATAGATTTTTAGAAGAACTGGTTTC	3	77	1
GATATGGGGATGGTTTCTTAGAAATGAGGGGGAT	3	212	1
CTCTATTATTTCTTTTATTTGACACACCTTACTC	4	12	1
ACAGCAAACGTATTGTCTTCTAAAAGCTATTAAG	4	100	1
TTATAATTAATGTTTTTCTTGAAAAAGATGTTTT	5	24	1
AAAAAGATGTTTTTATTTTTTAAAATGAGCGCTC	5	45	1
GCATCTGCATTCTTTTTTTTGAAAAAAGAGGTCT	6	49	1
AAAAAGAGTGTGGTTTTTTTGAAATTCTAGCACT	6	128	1
AGCACTTGACTGTTGTCTTTGAAATATTGCAAAC	6	156	1
CCTCTTAAAGTAGAGTCTTCTAGACAGCGCAACA	6	225	1
TTTTATGCAATCTTCTTTTAGAGAAATTTTATTT	7	88	0
AGTAGACCGATATAGTACTGGAAGCAAGGATTTT	7	119	0
          * ** * ** ****
MAP Score: 21.2807

Motif 2
ATTCTTTTTTTTGAAAAAAGAGGTCTCTTTCT	6	57	1
ATCAAGTCTCCTCTGAATAGAGAAACCAGTTC	3	100	0
GCTTGTATCCTTTAAAATAGAGTTTTTCTTAT	0	157	1
TAATGTTTTTCTTGAAAAAGATGTTTTTATTT	5	31	1
ATGGCAACCTCTTAAAGTAGAGTCTTCTAGAC	6	218	1
GCGCTCTTCATTTTAAAAAGATAAAGAAAAAC	5	73	1
TTATTTTGGCTTGCAAAAAGATAGGAAGGAAG	7	62	0
GGGATGGTTTCTTAGAAATGAGGGGGATATGG	3	218	1
TGTTTTTATTTTTTAAAATGAGCGCTCTTCAT	5	52	1
ATAGCAGCTGTTTTAAGTAGAGTATAGTCTGG	2	141	1
TAAAATTTCTCTAAAAGAAGATTGCATAAAAA	7	91	1
TTTGCTGATGCTTAAAATAGATTTTTAGAAGA	3	70	1
AAAACATTAATTATAAACAGAGTTTTTTAA  	5	8	0
AGAATTGTCTCTTCGAGATGAGAAACGCGCTA	0	29	1
CCATTCTAGATAAAAAAAAGAGTGTGGTTTTT	6	114	1
AATACGTTTGCTGTGTAAAGAGAGGGAGTAGG	4	82	0
AGAATGCAGATGCAGAAAAGAGGAGGGAGCTT	6	30	0
GGAGCTCCCCCTCCAAAAAAAGAACCTCGCTT	0	116	0
TATAGTCTGGCTTAGAACAAAGATCATTCAGG	2	163	1
          **  ********
MAP Score: 19.1765

Motif 3
TCCCCCTCCAAAAAAAGAACCTCGCTTATCGCA	0	110	0
ACATGGGATCATAAGAAAAACTCTATTTTAAAG	0	166	0
CGCAACCATCAAAACAAAACTTCAAATATAAAA	3	29	1
AAGCATCAGCAAAATAAAAATTTTTATATTTGA	3	50	0
GACTGATAGCAAAAAACGAGGTCTTAGAAGCTG	4	202	1
AAGCTTAAGAAAAATACAAATGCATACTGAGAC	4	243	0
TCATTTTAAAAAATAAAAACATCTTTTTCAAGA	5	40	0
TATCTTTTTAAAATGAAGAGCGCTCATTTTAAA	5	63	0
TTTAAAAAGATAAAGAAAAACGCTAA       	5	84	1
TCTTTTTTCAAAAAAAAGAATGCAGATGCAGAA	6	45	0
TCTTTTTTTTGAAAAAAGAGGTCTCTTTCTTGT	6	59	1
ATTCTAGATAAAAAAAAGAGTGTGGTTTTTTTG	6	116	1
GACGCCACGAAATATAAGAGGTCGCAGATGGCA	6	191	1
TTTGCAAGCCAAAATAAAATTTCTCTAAAAGAA	7	77	1
AAATTTCTCTAAAAGAAGATTGCATAAAAATCC	7	93	1
          **** ****  **
MAP Score: 15.5791

Motif 4
TAAAAGTATCTTTGCGATAAGCGAGGTTCTTTTTTTGGAGGGGGA	0	98	1
AAACGATTCGTGTAGTATAGGGACGGCTCTTTGTTTTGTTGAGCG	2	60	1
ATAGCAGCTGTTTTAAGTAGAGTATAGTCTGGCTTAGAACAAAGA	2	141	1
TAAAATAGATTTTTAGAAGAACTGGTTTCTCTATTCAGAGGAGAC	3	82	1
TTATTTCTTTTATTTGACACACCTTACTCTCCGCTTATCCATCCA	4	17	1
AATTGTCCAATATGATGCCCGGGCTGGTCTAGCCTAGACTGATAG	4	166	1
GATGTTTTTATTTTTTAAAATGAGCGCTCTTCATTTTAAAAAGAT	5	50	1
CTGTTTTACGTATAAAAAGCTCCCTCCTCTTTTCTGCATCTGCAT	6	14	1
GCATTCTTTTTTTTGAAAAAAGAGGTCTCTTTCTTGTACTCAAGA	6	55	1
CTTTTTTTTATCTAGAATGGAGGTTTCTCTCTATTCTTGAGTACA	6	89	0
AGTGCTAGAATTTCAAAAAAACCACACTCTTTTTTTTATCTAGAA	6	117	0
ACTCCCTTGTTGCGCTGTCTAGAAGACTCTACTTTAAGAGGTTGC	6	221	0
          * *   *    *    ****   **
MAP Score: 15.2506

Motif 5
TTTTTGGAGGGGGAGCTCCTTACAGGAGGC	0	129	1
TCGATTATCTGGAGGCTCTT          	0	290	1
GTAGTATAGGGACGGCTCTTTGTTTTGTTG	2	71	1
GACTCTGGTAGAGGGTTCTTAGAACTCAGA	3	163	0
TACCAGAGTCGCCACCTCTTCCTACTAGCG	3	183	1
TTTTTAAAATGAGCGCTCTTCATTTTAAAA	5	61	1
GAAAAGAGGAGGGAGCTTTTTATACGTAAA	6	18	0
GTACAAGAAAGAGACCTCTTTTTTCAAAAA	6	64	0
GTTGCCATCTGCGACCTCTTATATTTCGTG	6	196	0
GTCGCAGATGGCAACCTCTTAAAGTAGAGT	6	211	1
GATTCTGATCGGGCGCTTTTACTCCTAATA	7	212	1
          **********
MAP Score: 12.046

Motif 6
TAAAAGTATCTTTGCGATAAGCGAGGTTCTTTTTTTGGAG	0	98	1
GCGAGGTTCTTTTTTTGGAGGGGGAGCTCCTTACAGGAGG	0	118	1
AAAACTCTATTTTAAAGGATACAAGCCTCCTGTAAGGAGC	0	143	0
TATGATCCCATGTGGCGATAGGCCGGGTCTAGCGCCGATA	0	186	1
GGGGACATACTTTGAAAAAGTATACGATCCCCTAAGGACA	0	247	0
     GGCAATGTAGAGAATACGAGGTTCTT         	1	5	1
AAACGATTCGTGTAGTATAGGGACGGCTCTTTGTTTTGTT	2	60	1
ATAGCAGCTGTTTTAAGTAGAGTATAGTCTGGCTTAGAAC	2	141	1
TTTGAAGTTTTGTTTTGATGGTTGCGGTTTAGCAGCTTAG	3	15	0
TTAAAATAGATTTTTAGAAGAACTGGTTTCTCTATTCAGA	3	81	1
AATTAATGTTTTTCTTGAAAAAGATGTTTTTATTTTTTAA	5	28	1
GATGTTTTTATTTTTTAAAATGAGCGCTCTTCATTTTAAA	5	50	1
   AGAGCTGTTTTACGTATAAAAAGCTCCCTCCTCTTTT	6	7	1
CTGCATTCTTTTTTTTGAAAAAAGAGGTCTCTTTCTTGTA	6	53	1
AGTGCTAGAATTTCAAAAAAACCACACTCTTTTTTTTATC	6	122	0
CTTGTTGCGCTGTCTAGAAGACTCTACTTTAAGAGGTTGC	6	221	0
TGCAATCTTCTTTTAGAGAAATTTTATTTTGGCTTGCAAA	7	77	0
          ***   * * *    * ***
MAP Score: 11.2755

Motif 7
CGCGCTAGATTTTCCTTTTGGTTGAGGATATAAATTCA	0	54	1
CGATAAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCTT	0	112	1
AATATCGGTTGGTTTTTGTCCTTAGGGGATCGTATACT	0	231	1
         CTATTTCTATGTTCGTGGGATGTCAGTTT	2	1	1
GGATGTCAGTTTTTTCGATAGTGGTGCGGAAAAAAACG	2	27	1
GGAAAAAAACGATTCGTGTAGTATAGGGACGGCTCTTT	2	54	1
TAGGGACGGCTCTTTGTTTTGTTGAGCGTCTTATAGTA	2	77	1
TTTGAAGTTTTGTTTTGATGGTTGCGGTTTAGCAGCTT	3	17	0
ATATAAAAATTTTTATTTTGCTGATGCTTAAAATAGAT	3	54	1
TTTGTATTTTTCTTAAGCTTCTAGAGCAAACACACTTG	4	256	1
AATGGAGGTTTCTCTCTATTCTTGAGTACAAGAAAGAG	6	81	0
TCCAGTACTATATCGGTCTACTTGAGCGCGCCCGTAGC	7	131	1
      GCTTTGTTCCTCTTTTTATGTGTTAACAAGGC	7	278	0
          * **  * *  * * ***
MAP Score: 6.69906

Motif 8
CCTGTAAGGAGCTCCCCCTCCAAAAAAAGAA	0	124	0
TGAGTTCTAAGAACCCTCTACCAGAGTCGCC	3	165	1
TACCAGAGTCGCCACCTCTTCCTACTAGCGA	3	183	1
CCTCACCCCTACTCCCTCTCTTTACACAGCA	4	75	1
TTTTTAAAATGAGCGCTCTTCATTTTAAAAA	5	61	1
CGTATAAAAAGCTCCCTCCTCTTTTCTGCAT	6	22	1
GTACAAGAAAGAGACCTCTTTTTTCAAAAAA	6	63	0
AGAATAGAGAGAAACCTCCATTCTAGATAAA	6	97	1
GTCGCAGATGGCAACCTCTTAAAGTAGAGTC	6	211	1
          ** ********
MAP Score: 3.43279

Motif 9
CTCCTTACAGGAGGCTTGTATCCTTTAAAA	0	144	1
TATAGTATCTTAGGCTTCCTGATAGAGGCT	2	108	1
CTTCCTGATAGAGGCTTGTATAGCAGCTGT	2	122	1
    CCAAACTAAGCTGCTAAACCGCAACC	3	6	1
AGCAAACGTATTGTCTTCTAAAAGCTATTA	4	102	1
GACGAAAGTATCAGCTTCTAAGACCTCGTT	4	216	0
GTATTTTTCTTAAGCTTCTAGAGCAAACAC	4	259	1
TCTTAAAGTAGAGTCTTCTAGACAGCGCAA	6	227	1
AAATTTTATTTTGGCTTGCAAAAAGATAGG	7	69	0
GGTAGAGCTGTAGCCTTCCAAGCTACCGGT	7	174	1
          **********
MAP Score: 3.37009

Motif 10
TTAGAATTGTCTCTTCGAGATGAGAAACGCGCTAG	0	27	1
AAAAGTATCTTTGCGATAAGCGAGGTTCTTTTTTT	0	99	1
ATAAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCT	0	114	1
AAGAAAAACTCTATTTTAAAGGATACAAGCCTCCT	0	152	0
GGATCGTATACTTTTTCAAAGTATGTCCCCGTATC	0	257	1
AAAATAAAAATTTTTATATTTGAAGTTTTGTTTTG	3	38	0
TGGGGATGGTTTCTTAGAAATGAGGGGGATATGGA	3	216	1
AATACGTTTGCTGTGTAAAGAGAGGGAGTAGGGGT	4	79	0
ATTACTACAATTGTCCAATATGATGCCCGGGCTGG	4	158	1
CCTAGACTGATAGCAAAAAACGAGGTCTTAGAAGC	4	198	1
ATTAATGTTTTTCTTGAAAAAGATGTTTTTATTTT	5	29	1
GATGTTTTTATTTTTTAAAATGAGCGCTCTTCATT	5	50	1
TTTTCTTTATCTTTTTAAAATGAAGAGCGCTCATT	5	68	0
GCATTCTTTTTTTTGAAAAAAGAGGTCTCTTTCTT	6	55	1
GTCTAGAAGACTCTACTTTAAGAGGTTGCCATCTG	6	215	0
CAAAATAAAATTTCTCTAAAAGAAGATTGCATAAA	7	86	1
          ** *   *** ****
MAP Score: 2.02498