AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242168
 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	recA	260	hypothetical protein
#6	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
GCATCTGCATTCTTTTTTTTGAAAAAAGAGGTCT	5	49	1
AAAAAGAGTGTGGTTTTTTTGAAATTCTAGCACT	5	128	1
AGCACTTGACTGTTGTCTTTGAAATATTGCAAAC	5	156	1
CCTCTTAAAGTAGAGTCTTCTAGACAGCGCAACA	5	225	1
TTTTATGCAATCTTCTTTTAGAGAAATTTTATTT	6	88	0
AGTAGACCGATATAGTACTGGAAGCAAGGATTTT	6	119	0
          * ** * ** ****
MAP Score: 15.1867

Motif 2
ATAAGCGAGGTTCTTTTTTTGGAGGGGGAG	0	114	1
ATAAGAAAAACTCTATTTTAAAGGATACAA	0	159	0
TACTACACGAATCGTTTTTTTCCGCACCAC	2	47	0
ATAGGGACGGCTCTTTGTTTTGTTGAGCGT	2	76	1
CCAGACTATACTCTACTTAAAACAGCTGCT	2	143	0
TCTTCTAAAAATCTATTTTAAGCATCAGCA	3	72	0
        CTCTCTATTATTTCTTTTATTT	4	2	1
GTCGTCAATACTCCTTTCATTTAGCTTAAT	4	128	0
CTTCTAAGACCTCGTTTTTTGCTATCAGTC	4	202	0
AAAAAGCTCCCTCCTCTTTTCTGCATCTGC	5	27	1
TGCATCTGCATTCTTTTTTTTGAAAAAAGA	5	48	1
AGAAAGAGACCTCTTTTTTCAAAAAAAAGA	5	59	0
GGAGGTTTCTCTCTATTCTTGAGTACAAGA	5	86	0
AGAGAGAAACCTCCATTCTAGATAAAAAAA	5	102	1
AAAAACCACACTCTTTTTTTTATCTAGAAT	5	116	0
GTCTAGAAGACTCTACTTTAAGAGGTTGCC	5	220	0
TTTTTATGCAATCTTCTTTTAGAGAAATTT	6	93	0
 GCTTTGTTCCTCTTTTTATGTGTTAACAA	6	281	0
          **********
MAP Score: 13.9689

Motif 3
AAGGAAAATCTAGCGCGTTTCTCATCTCGA	0	41	0
TGTGGCGATAGGCCGGGTCTAGCGCCGATA	0	196	1
TTGTCCTTAGGGGATCGTATACTTTTTCAA	0	246	1
ATTTTTAGAAGAACTGGTTTCTCTATTCAG	3	90	1
TAGCGATATGGGGATGGTTTCTTAGAAATG	3	208	1
GCTGGAGATTTGGCTGTTCTCTGAGAATTA	3	257	0
TATGATGCCCGGGCTGGTCTAGCCTAGACT	4	176	1
CAGCTTCTAAGACCTCGTTTTTTGCTATCA	4	205	0
         AGAGCTGTTTTACGTATAAAA	5	1	1
GAAAAGAGGAGGGAGCTTTTTATACGTAAA	5	18	0
ACAAGAAAGAGACCTCTTTTTTCAAAAAAA	5	62	0
TGCCATCTGCGACCTCTTATATTTCGTGGC	5	194	0
         TGGGCTCGGCTTCGGTCGGGT	6	1	1
GATTCTGATCGGGCGCTTTTACTCCTAATA	6	212	1
          **********
MAP Score: 9.6594

Motif 4
TTTAGAATTGTCTCTTCGAGATGAGAAACGCGCTAG	0	26	1
GCGCTAGATTTTCCTTTTGGTTGAGGATATAAATTC	0	55	1
AAAAAGAACCTCGCTTATCGCAAAGATACTTTTAAC	0	96	0
GATAAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCT	0	113	1
GAGTATAGTCTGGCTTAGAACAAAGATCATTCAGGT	2	160	1
TACCATCCCTGCTCTGAGTTCTAAGAACCCTCTACC	3	151	1
ATGGGGATGGTTTCTTAGAAATGAGGGGGATATGGA	3	215	1
GCTGGAGATTTGGCTGTTCTCTGAGAATTATAGGGA	3	251	0
CTCTCTATTATTTCTTTTATTTGACACACCTTACTC	4	10	1
GACAATACGTTTGCTGTGTAAAGAGAGGGAGTAGGG	4	81	0
TTTAGCTTAATAGCTTTTAGAAGACAATACGTTTGC	4	103	0
TCTGCATTCTTTTTTTTGAAAAAAGAGGTCTCTTTC	5	52	1
AAGAGGTCTCTTTCTTGTACTCAAGAATAGAGAGAA	5	74	1
ATTTTTATGCAATCTTCTTTTAGAGAAATTTTATTT	6	88	0
          * **** *    ****
MAP Score: 9.11083

Motif 5
TAGCGCGTTTCTCATCTCGAAGAGACAATTCTAAATAA	0	23	0
AAGAACCTCGCTTATCGCAAAGATACTTTTAACAGAAT	0	91	0
TAAGACGCTCAACAAAACAAAGAGCCGTCCCTATACTA	2	72	0
AGCCTCTATCAGGAAGCCTAAGATACTATAAGACGCTC	2	100	0
TATAGTCTGGCTTAGAACAAAGATCATTCAGGTATATA	2	163	1
ATCTATTTTAAGCATCAGCAAAATAAAAATTTTTATAT	3	54	0
CATCCCTGCTCTGAGTTCTAAGAACCCTCTACCAGAGT	3	154	1
CCATATCCCCCTCATTTCTAAGAAACCATCCCCATATC	3	212	0
TCTATTCTTGAGTACAAGAAAGAGACCTCTTTTTTCAA	5	67	0
TCTTGTACTCAAGAATAGAGAGAAACCTCCATTCTAGA	5	86	1
GTCAAGTGCTAGAATTTCAAAAAAACCACACTCTTTTT	5	128	0
GTCAGTTTGCAATATTTCAAAGACAACAGTCAAGTGCT	5	156	0
          *  *   * **** ** *
MAP Score: 8.69119

Motif 6
TTTTTGGAGGGGGAGCTCCTTACAGGAGGC	0	129	1
TCGATTATCTGGAGGCTCTT          	0	290	1
GTAGTATAGGGACGGCTCTTTGTTTTGTTG	2	71	1
GACTCTGGTAGAGGGTTCTTAGAACTCAGA	3	163	0
TACCAGAGTCGCCACCTCTTCCTACTAGCG	3	183	1
GAAAAGAGGAGGGAGCTTTTTATACGTAAA	5	18	0
GTACAAGAAAGAGACCTCTTTTTTCAAAAA	5	64	0
GTTGCCATCTGCGACCTCTTATATTTCGTG	5	196	0
GTCGCAGATGGCAACCTCTTAAAGTAGAGT	5	211	1
GATTCTGATCGGGCGCTTTTACTCCTAATA	6	212	1
          **********
MAP Score: 8.50455

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	5	81	0
TCCAGTACTATATCGGTCTACTTGAGCGCGCCCGTAGC	6	131	1
      GCTTTGTTCCTCTTTTTATGTGTTAACAAGGC	6	278	0
          * **  * *  * * ***
MAP Score: 7.37608

Motif 8
CCTGTAAGGAGCTCCCCCTCCAAAAAAAGAA	0	124	0
AAGGATACAAGCCTCCTGTAAGGAGCTCCCC	0	138	0
      AAGAGCCTCCAGATAATCGATACGG	0	285	0
AGTATCTTAGGCTTCCTGATAGAGGCTTGTA	2	111	1
TCTGAATAGAGAAACCAGTTCTTCTAAAAAT	3	90	0
TGAGTTCTAAGAACCCTCTACCAGAGTCGCC	3	165	1
TACCAGAGTCGCCACCTCTTCCTACTAGCGA	3	183	1
ACAATACGCCGCATCCTCACCCCTACTCCCT	4	61	1
CGTATAAAAAGCTCCCTCCTCTTTTCTGCAT	5	22	1
GTTGCCATCTGCGACCTCTTATATTTCGTGG	5	195	0
GTCGCAGATGGCAACCTCTTAAAGTAGAGTC	5	211	1
AAAAATCCTTGCTTCCAGTACTATATCGGTC	6	118	1
          ** ********
MAP Score: 7.08249

Motif 9
ATAAGCGAGGTTCTTTTTTTGGAGGGGGAG	0	114	1
AAGAACTGGTTTCTCTATTCAGAGGAGACT	3	98	1
TCTCTATTATTTCTTTTATTTGACACACCT	4	11	1
CACCCCTACTCCCTCTCTTTACACAGCAAA	4	78	1
AAAAGCTCCCTCCTCTTTTCTGCATCTGCA	5	28	1
TGCATCTGCATTCTTTTTTTTGAAAAAAGA	5	48	1
ATGGAGGTTTCTCTCTATTCTTGAGTACAA	5	88	0
AAAAACCACACTCTTTTTTTTATCTAGAAT	5	116	0
TTGACTTCCTTCCTATCTTTTTGCAAGCCA	6	58	1
   GCTTTGTTCCTCTTTTTATGTGTTAAC	6	283	0
          **********
MAP Score: 4.57718

Motif 10
TTATTTAGAATTGTCTCTTCGAGATGAGAAACGCGCTA	0	23	1
TCTGTTAAAAGTATCTTTGCGATAAGCGAGGTTCTTTT	0	93	1
CGATAAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCTT	0	112	1
AAATATCGGTTGGTTTTTGTCCTTAGGGGATCGTATAC	0	230	1
GGGACGGCTCTTTGTTTTGTTGAGCGTCTTATAGTATC	2	79	1
TATACCTGAATGATCTTTGTTCTAAGCCAGACTATACT	2	161	0
TATTTGAAGTTTTGTTTTGATGGTTGCGGTTTAGCAGC	3	19	0
TTAGAAGAACTGGTTTCTCTATTCAGAGGAGACTTGAT	3	94	1
TCTGGTAGAGGGTTCTTAGAACTCAGAGCAGGGATGGT	3	152	0
GATATGGGGATGGTTTCTTAGAAATGAGGGGGATATGG	3	212	1
AGACAATACGTTTGCTGTGTAAAGAGAGGGAGTAGGGG	4	80	0
TCTAAGACCTCGTTTTTTGCTATCAGTCTAGGCTAGAC	4	192	0
ATCTGCATTCTTTTTTTTGAAAAAAGAGGTCTCTTTCT	5	51	1
AAAGAGTGTGGTTTTTTTGAAATTCTAGCACTTGACTG	5	130	1
CACTTGACTGTTGTCTTTGAAATATTGCAAACTGACGC	5	158	1
          ** ******      * *
MAP Score: 0.690089

Motif 11
ATTTAGAATTGTCTCTTCGAGATGAGAAAC	0	25	1
TGGGATGTCAGTTTTTTCGATAGTGGTGCG	2	25	1
GTATAGGGACGGCTCTTTGTTTTGTTGAGC	2	74	1
TAGTATCTTAGGCTTCCTGATAGAGGCTTG	2	110	1
TCTGGTAGAGGGTTCTTAGAACTCAGAGCA	3	160	0
TATGGGGATGGTTTCTTAGAAATGAGGGGG	3	214	1
CAAACGTATTGTCTTCTAAAAGCTATTAAG	4	104	1
ATTTTTCTTAAGCTTCTAGAGCAAACACAC	4	261	1
AAAGAGTGTGGTTTTTTTGAAATTCTAGCA	5	130	1
TTAAAGTAGAGTCTTCTAGACAGCGCAACA	5	229	1
TACTATATCGGTCTACTTGAGCGCGCCCGT	6	136	1
          **********
MAP Score: 0.578517