AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242346
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pepA	300	Leucyl Aminopeptidase A
#1	folD	117	Methylene Tetrahydrofolate Dehydrogenase
#2	ychF	256	GTP Binding Protein
#3	phnP	28	predicted metal dependent hydrolase (histidinic triad)
#4	artJ	68	Arginine Binding Protein
#5	aroG	136	phospho-2-dehydro-3-deoxyheptonate aldolase
#6	yhbZ	89	GTP Binding Protein
#7	rl27	30	L27 Ribosomal Protein
#8	rl21	300	L21 Ribosomal Protein
#9	trxA	300	Thioredoxin
#10	rsbV_2	153	Sigma Regulatory Factor

Motif 1
TCCTATAGTCCTTTTTTTCATCTCGGAATA	0	131	1
AGACTTGTCCCTTTTTTTCTTATTTGGGAC	8	135	0
GGGTTTCTCACTTTTTTTCTATTTAAAAAA	10	53	0
ATTAAAACAGCTTTCTCTCTATACTGGCCT	9	18	1
TTCTAGTGAGCTTTTGCTCATGGAAGTTCA	9	91	1
AGTTGTACAGCTTTTTCTTAAGGCTAACAC	2	227	0
GTATATAAATGTTTTTCTCAAGAAAGAAGG	2	57	1
ACTAATCTTGCTTTTTCTTTAGAATTTCTT	2	175	1
TAGCTGCAAACTTCTTTTCAACAAACGCCC	9	129	1
GAAGTCTCTACCTTTTATCTTCCAATAAGG	10	81	0
AAAGAGTAGTCTTTTTAGCAAATAAGCTCT	0	102	0
AAAAAAACGCCCTCTTCTCTTGAAGAGAAG	5	26	0
AGAAGAGGGCGTTTTTTTCATTGAAAAATC	5	38	1
TCTTCTAACTCTTTTGCGCAAATGTGAAAT	8	73	0
GGTCTAGACTCTTTCCCTCTAAACAACCTA	1	68	1
CTAACACAGCCTTTTTATTATTAAGGAAAA	2	204	0
TCTGTCTTGACTTTTTCGTAGAGGTTATGG	9	171	1
GCATCTGCCACCTTCTTTCTTGAGAAAAAC	2	67	0
CGCTTGTGTTGTTTTGCTCATGTCCCAAAT	8	114	1
TAAACGTTCTCTTCTCTTCAAGAGAAGAGG	5	16	1
AAGTTCAAGTCTTCTTAGCTGCAAACTTCT	9	114	1
        AACCTTTTATTAAAACAGCTTT	9	2	1
ATTGAAAAATCTTTCTATTTCTTTTCTCTT	5	57	1
AAACAACATAGTTTTCATCTCTACATTATT	0	157	0
AGTAGAACGCGTTTTGCTTATTTCCGTCTC	0	237	0
CAAGTCAGGCGCTTTCTTCTAGAATGGAGA	8	246	1
          **********
MAP Score: 24.0237

Motif 2
TTGAGACGGAAATAAGCAAAACGCGTTCTACTGGTGTTT	0	235	1
CCATTTATAAACAAAGAGTAAGGGGTTCTTTAGAGAACG	2	102	1
CATTTGCGCAAAAGAGTTAGAAGATTTCTACAAGCCGCT	8	79	1
CAAATAAGAAAAAAAGGGACAAGTCTTTTCGAATATAGT	8	139	1
GCTTTTGCTCATGGAAGTTCAAGTCTTCTTAGCTGCAAA	9	100	1
TGATCAGTTTACAAAAGCTGATGAATTTTTAAAACTAGA	1	24	0
GGGAAGAGAAAAGAAATAGAAAGATTTTTCAATGAAAAA	5	51	0
ATCTGTCACAAAAAAATTTAGAGAGTTCTCCGTCAAAAC	8	36	0
TTATTGGAAGATAAAAGGTAGAGACTTCTTCCGTCAAGA	10	83	1
     ATTGTAGGGAACATAAAGGGTTTTTGAGTC    	7	5	1
CTTCTCTTCAAGAGAAGAGGGCGTTTTTTTCATTGAAAA	5	26	1
TAGCCTTAAGAAAAAGCTGTACAACTTCTTAGGTA    	2	231	1
GGGCTCTCCGGCCAAGTCAGGCGCTTTCTTCTAGAATGG	8	234	1
AGAGGCCAGTATAGAGAGAAAGCTGTTTTAATAAAAGGT	9	11	0
GGGGTTCTTTAGAGAACGGAATATTTTTTTTAAAGAGCG	2	123	1
TTTGCCTACGTGTAAGAATAGGGCTTTTTTTGTTTGTTC	6	49	1
AAAGGACTATAGGAAAGAGTAGTCTTTTTAGCAAATAAG	0	106	0
ATGTCCGCTAATGGCGTTTAGAGAGTTTTGACGGAGAAC	8	12	1
          *  ***    * *  ****
MAP Score: 19.8309

Motif 3
AAAAAAGGACTATAGGAAAGAGTAGTCTTTT	0	117	0
TATTCCGAGATGAAAAAAAGGACTATAGGAA	0	130	0
CATTCTCTGCAGTAGAAAAGGCCAGAACAAG	0	189	0
ATAGGTTGTTTAGAGGGAAAGAGTCTAGACC	1	68	0
TGTTTTTCTCAAGAAAGAAGGTGGCAGATGC	2	66	1
TAAGGGGTTCTTTAGAGAACGGAATATTTTT	2	120	1
AAAGAAATTCTAAAGAAAAAGCAAGATTAGT	2	175	0
CTTTTTATTATTAAGGAAAAAGAAATTCTAA	2	193	0
TGTGTTAGCCTTAAGAAAAAGCTGTACAACT	2	226	1
         TTTTAGAAAACGATTAAGGGGC	3	1	1
TCTCTTGAAGAGAAGAGAACGTTTAATGATG	5	10	0
TCTCTTCTCTTCAAGAGAAGAGGGCGTTTTT	5	23	1
GATTTTTCAATGAAAAAAACGCCCTCTTCTC	5	37	0
ACACACAGGGAAGAGAAAAGAAATAGAAAGA	5	66	0
TGTTCATGAGTTAAGAGAAGAAACAAGGAAA	5	106	1
        ATTGTAGGGAACATAAAGGGTTT	7	2	1
CATGTCCCAAATAAGAAAAAAAGGGACAAGT	8	132	1
AAGTAAAGTTTATAGGGAAAGAATTG     	8	284	1
GAGGCCAGTATAGAGAGAAAGCTGTTTTAAT	9	18	0
TGCTTTTTTAAATAGAAAAAAAGTGAGAAAC	10	50	1
          * *********
MAP Score: 16.4274

Motif 4
CAAGTAAAGTTTATAGGGAAAGAATTG      	8	283	1
GAAAAAGAAATTCTAAAGAAAAAGCAAGATTAG	2	176	0
ACAAACTGAATTATAAATAAAAATGAA      	6	4	0
CATAGGTTGTTTAGAGGGAAAGAGTCTAGACCT	1	67	0
CTCATCCCATTTATAAACAAAGAGTAAGGGGTT	2	96	1
CCCAACATGATTCTTAAAAAAAATAAGAAT   	4	7	0
GCCACCTTCTTTCTTGAGAAAAACATTTATATA	2	58	0
GTCCCGGGCGTTTGTTGAAAAGAAGTTTGCAGC	9	131	0
AGAAAGATTTTTCAATGAAAAAAACGCCCTCTT	5	40	0
GTAACAGAGCTTATTTGCTAAAAAGACTACTCT	0	97	1
AATTGCTTTTTTAAATAGAAAAAAAGTGAGAAA	10	47	1
GAAACCCTTATTGGAAGATAAAAGGTAGAGACT	10	76	1
TTCTTTTTCCTTAATAATAAAAAGGCTGTGTTA	2	200	1
GAACGGAATATTTTTTTTAAAGAGCGTTTTTCA	2	136	1
TACTTCCACTATATTCGAAAAGACTTGTCCCTT	8	152	0
          TTTTAGAAAACGATTAAGGGGCC	3	0	1
          ** ** * *****
MAP Score: 9.3426

Motif 5
CTTCTTGTCTATGGAGTAACAGAGCTTATTTGCT	0	82	1
TAACAGAGCTTATTTGCTAAAAAGACTACTCTTT	0	98	1
ATTGACTCAATCGATTCAACAAAGAGGTTATT  	0	278	1
GCTTTTGTAAACTGATCAAGAGAGGTCTAGACTC	1	45	1
ATATAAATGTTTTTCTCAAGAAAGAAGGTGGCAG	2	59	1
TGCTCATCCCATTTATAAACAAAGAGTAAGGGGT	2	94	1
GAACGGAATATTTTTTTTAAAGAGCGTTTTTCAT	2	136	1
AGGAAAAAGAAATTCTAAAGAAAAAGCAAGATTA	2	177	0
AAGGCTGTGTTAGCCTTAAGAAAAAGCTGTACAA	2	221	1
ACCCAACATGATTCTTAAAAAAAATAAGAAT   	4	7	0
AACGTTCTCTTCTCTTCAAGAGAAGAGGGCGTTT	5	18	1
TTTGCTGTTCATGAGTTAAGAGAAGAAACAAGGA	5	101	1
TCTTACACGTAGGCAAAAACAGAGCTTGAACAAA	6	32	0
TGTCCGCTAATGGCGTTTAGAGAGTTTTGACGGA	8	13	1
AGATTTCACATTTGCGCAAAAGAGTTAGAAGATT	8	71	1
TCATGTCCCAAATAAGAAAAAAAGGGACAAGTCT	8	131	1
GAAACTCTCCATTCTAGAAGAAAGCGCCTGACTT	8	247	0
GTCCCGGGCGTTTGTTGAAAAGAAGTTTGCAGCT	9	130	0
GTGCATCTAGAAGAATCTAAAAAGAATTGCTTTT	10	23	1
TCACTTTTTTTCTATTTAAAAAAGCAATTCTTTT	10	42	0
          * *  * *******
MAP Score: 9.13166

Motif 6
TTGTTCTGGCCTTTTCTACTGCAGAGAATGGGT	0	190	1
     AATAACCTCTTTGTTGAATCGATTGAGT	0	282	0
CATCTGCCACCTTCTTTCTTGAGAAAAACATTT	2	63	0
TTTTAAAGAGCGTTTTTCATGAAGCACTAATCT	2	150	1
AAAAAACGCCCTCTTCTCTTGAAGAGAAGAGAA	5	22	0
CTTTCTATTTCTTTTCTCTTCCCTGTGTGTATG	5	67	1
ACTCAAAAACCCTTTATGTTCCCTACAAT    	7	6	0
AAGTTCAAGTCTTCTTAGCTGCAAACTTCTTTT	9	114	1
GGGACAGGGGCATCTGTCTTGACTTTTTCGTAG	9	159	1
     AATAACCTCTAACGTGCATCTAGAAGAA	10	5	1
AAGTCTCTACCTTTTATCTTCCAATAAGGGTTT	10	77	0
AAGGTAGAGACTTCTTCCGTCAAGAATTTCATC	10	97	1
          * *** ** ****
MAP Score: 5.31638

Motif 7
AAAAGGCCAGAACAAGCAAAACAACATAGTT	0	174	0
TTGAGACGGAAATAAGCAAAACGCGTTCTAC	0	235	1
GCTTAAGCGCTATAAGGAATACTTCGCAAGT	2	22	1
ATTATTAAGGAAAAAGAAATTCTAAAGAAAA	2	187	0
CTTTTTCCTTAATAATAAAAAGGCTGTGTTA	2	202	1
TAAGAGAAGAAACAAGGAAAACAAATCTA  	5	117	1
CTCGTCCTGGAACAAACAAAAAAAGCCCTAT	6	66	0
TCATGTCCCAAATAAGAAAAAAAGGGACAAG	8	131	1
GGAGAGTTTCAACAAGTAAAGTTTATAGGGA	8	271	1
TTTCTATTTAAAAAAGCAATTCTTTTTAGAT	10	37	0
          ****** ****
MAP Score: 4.4708

Motif 8
ACGGAAATAAGCAAAACGCGTTCTACTGGTGT	0	240	1
AACAACCTATGTGAAACCATTTAACTAAGTAT	1	89	1
AGTGCTTCATGAAAAACGCTCTTTAAAAAAAA	2	146	0
AGTCCCTGCCGTTAGACCATTGAGTCGGAGTG	4	43	1
      GACTCAAAAACCCTTTATGTTCCCTA	7	14	0
GACTTGGCCGGAGAGCCCCTGTTAGCGCTTAA	8	220	0
CTCCGGCCAAGTCAGGCGCTTTCTTCTAGAAT	8	239	1
ATAGCTGCATGAGAGGCCAGTATAGAGAGAAA	9	29	0
TGGCGGAACCGGTAGACGCGCTAGATTCAGGT	9	60	1
GCCGTGTTCTGAAAGGCCAGTTAGCCATAACC	9	193	0
TCAGAACACGGCTAGCCCCGTTTGCTTGCGGT	9	213	1
GCGGTTCTTAGGGAAGCCCTGAAACCTCCTAG	9	240	1
GAAAAAAAGTGAGAAACCCTTATTGGAAGATA	10	64	1
          *  *********
MAP Score: 4.40863