AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242369
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pepA	300	Leucyl Aminopeptidase A
#1	folD	117	Methylene Tetrahydrofolate Dehydrogenase
#2	CT079	276	hypothetical protein
#3	ychF	256	GTP Binding Protein
#4	phnP	28	predicted metal dependent hydrolase (histidinic triad)
#5	artJ	68	Arginine Binding Protein
#6	aroG	136	phospho-2-dehydro-3-deoxyheptonate aldolase
#7	CT382.1	182	hypothetical protein
#8	yhbZ	89	GTP Binding Protein
#9	rl27	30	L27 Ribosomal Protein
#10	rl21	300	L21 Ribosomal Protein
#11	trxA	300	Thioredoxin
#12	rsbV_2	153	Sigma Regulatory Factor

Motif 1
AAAGAGTAGTCTTTTTAGCAAATAAGCTCT	0	102	0
TCCTATAGTCCTTTTTTTCATCTCGGAATA	0	131	1
AGTAGAACGCGTTTTGCTTATTTCCGTCTC	0	237	0
GTATATAAATGTTTTTCTCAAGAAAGAAGG	3	57	1
ACTAATCTTGCTTTTTCTTTAGAATTTCTT	3	175	1
CTAACACAGCCTTTTTATTATTAAGGAAAA	3	204	0
AGTTGTACAGCTTTTTCTTAAGGCTAACAC	3	227	0
AGAAGAGGGCGTTTTTTTCATTGAAAAATC	6	38	1
TTTAACAAAAGTTTTTCTTTGTCTTCAATG	7	55	1
TCTTCTAACTCTTTTGCGCAAATGTGAAAT	10	73	0
CGCTTGTGTTGTTTTGCTCATGTCCCAAAT	10	114	1
AGACTTGTCCCTTTTTTTCTTATTTGGGAC	10	135	0
ATTAAAACAGCTTTCTCTCTATACTGGCCT	11	18	1
TTCTAGTGAGCTTTTGCTCATGGAAGTTCA	11	91	1
TAGCTGCAAACTTCTTTTCAACAAACGCCC	11	129	1
TCTGTCTTGACTTTTTCGTAGAGGTTATGG	11	171	1
GGGTTTCTCACTTTTTTTCTATTTAAAAAA	12	53	0
          **********
MAP Score: 19.7618

Motif 2
        AGATTTCTTTTCGGTAACAGGG	0	2	1
TACTTAGTTAAATGGTTTCACATAGGTTGT	1	90	0
TAAATTAAAAAATTGTTTTTCATAAACCAT	2	53	1
TGTTCCTATCAATTGTTTTATGGTTTATGA	2	72	0
TCTCCGCAATATTCCTTTCCCAACGCTCAT	2	207	1
ACCGTATATAAATGTTTTTCTCAAGAAAGA	3	54	1
AGAACGGAATATTTTTTTTAAAGAGCGTTT	3	135	1
TTTCTTTAGAATTTCTTTTTCCTTAATAAT	3	188	1
AAGGCCCCTTAATCGTTTTCTAAAA     	4	5	0
    ATTCTTATTTTTTTTAAGAATCATGT	5	6	1
AAATCTTTCTATTTCTTTTCTCTTCCCTGT	6	63	1
       TAGATTTGTTTTCCTTGTTTCTT	6	123	0
CAATGAATTTAATGGTTTTAAATTAAATTG	7	80	1
TTTTAAATTAAATTGTTTTCATTTGAATTT	7	95	1
TTTAAGATCTATTTGTTTTAGTTTTATAAT	7	135	1
AAAAAGGGACAAGTCTTTTCGAATATAGTG	10	149	1
         CAATTCTTTCCCTATAAACTT	10	289	0
TTAGCTGCAAACTTCTTTTCAACAAACGCC	11	128	1
TTAAAAAAGCAATTCTTTTTAGATTCTTCT	12	31	0
AGGGTTTCTCACTTTTTTTCTATTTAAAAA	12	54	0
          **********
MAP Score: 19.0909

Motif 3
ACCAGAATAATTTATTTCAAAATCTATTCTAATTTTAA	2	18	1
GAACGGAATATTTTTTTTAAAGAGCGTTTTTCATGAAG	3	136	1
    TTCATTTTTATTTATAATTCAGTTTGTTCAAGCT	8	6	1
AATCTTGCTTTTTCTTTAGAATTTCTTTTTCCTTAATA	3	178	1
AGGGCGTTTTTTTCATTGAAAAATCTTTCTATTTCTTT	6	43	1
ATTAAATTGTTTTCATTTGAATTTAATTTTATTTTTTA	7	101	1
      AACCTTTTATTAAAACAGCTTTCTCTCTATAC	11	4	1
ACTCTCTAAATTTTTTTGTGACAGATTTCACATTTGCG	10	49	1
TATTCTAATTTTAAATTAAAAAATTGTTTTTCATAAAC	2	42	1
TGCCACCTTCTTTCTTGAGAAAAACATTTATATACGGT	3	54	0
GTCCCGGGCGTTTGTTGAAAAGAAGTTTGCAGCTAAGA	11	126	0
CCCCTTACTCTTTGTTTATAAATGGGATGAGCATCTGC	3	89	0
AAAGTTTTTCTTTGTCTTCAATGAATTTAATGGTTTTA	7	62	1
TACATAGATTTTAAATTAGGAACAAGTTTT        	11	280	1
GAATTTAATTTTATTTTTTAAGATCTATTTGTTTTAGT	7	119	1
 ATTCTTATTTTTTTTAAGAATCATGTTGGGTATAGTC	5	9	1
AATTTCATCATTAGATTACAAGCTGAATTAGAAGGCGA	12	121	1
ACTACTTCCACTATATTCGAAAAGACTTGTCCCTTTTT	10	149	0
TTTCAGTCTTCTAGTTTTAAAAATTCATCAGCTTTTGT	1	15	1
          *** ***  **     **
MAP Score: 18.6805

Motif 4
CCCATATCTTAAGAAGCTCTTGAATCTTCT	0	57	1
CTTTTTAGCAAATAAGCTCTGTTACTCCAT	0	92	0
          AATAACCTCTTTGTTGAATC	0	290	0
CCGTTCTCTAAAGAACCCCTTACTCTTTGT	3	112	0
TGCTTCATGAAAAACGCTCTTTAAAAAAAA	3	146	0
CTTAATAATAAAAAGGCTGTGTTAGCCTTA	3	209	1
TAGCCTTAAGAAAAAGCTGTACAACTTCTT	3	231	1
TTCAATGAAAAAAACGCCCTCTTCTCTTGA	6	33	0
TTTTTCATTGAAAAATCTTTCTATTTCTTT	6	51	1
GAACAAACAAAAAAAGCCCTATTCTTACAC	8	58	0
    GACTCAAAAACCCTTTATGTTCCCTA	9	14	0
GTTCTCCGTCAAAACTCTCTAAACGCCATT	10	21	0
GTTTTGACGGAGAACTCTCTAAATTTTTTT	10	36	1
CAGTATAGAGAGAAAGCTGTTTTAATAAAA	11	14	0
          AATAACCTCTAACGTGCATC	12	0	1
AAAAAAAGTGAGAAACCCTTATTGGAAGAT	12	65	1
TCTTGACGGAAGAAGTCTCTACCTTTTATC	12	92	0
          **********
MAP Score: 15.6379

Motif 5
CTCTTTCCTATAGTCCTTTTTTTCATCTCGGA	0	126	1
AACTATGTTGTTTTGCTTGTTCTGGCCTTTTC	0	174	1
GTAGAACGCGTTTTGCTTATTTCCGTCTCAAG	0	234	0
GAAGCACTAATCTTGCTTTTTCTTTAGAATTT	3	170	1
TTTTCTTTAGAATTTCTTTTTCCTTAATAATA	3	187	1
        ATTCTTATTTTTTTTAAGAATCAT	5	2	1
CATTGAAAAATCTTTCTATTTCTTTTCTCTTC	6	56	1
  TAGATTTGTTTTCCTTGTTTCTTCTCTTAA	6	116	0
TTAACAAAAGTTTTTCTTTGTCTTCAATGAAT	7	56	1
ATAGGGCTTTTTTTGTTTGTTCCAGGACGAGT	8	66	1
CTTGTCCCTTTTTTTCTTATTTGGGACATGAG	10	130	0
GAAGTAGTTATATTTGTTGTTCGCTTCGGGAT	10	179	1
    AAAACTTGTTCCTAATTTAAAATCTATG	11	282	0
ATCTAAAAAGAATTGCTTTTTTAAATAGAAAA	12	37	1
AATAAGGGTTTCTCACTTTTTTTCTATTTAAA	12	56	0
          * ** *******
MAP Score: 10.2629

Motif 6
       AGATTTCTTTTCGGTAACAGGGG	0	3	1
TAGTCCTTTTTTTCATCTCGGAATAATGTA	0	136	1
ACAACATAGTTTTCATCTCTACATTATTCC	0	155	0
 TTCTCTTTCAGTCTTCTAGTTTTAAAAAT	1	9	1
GTTCCTATCAATTGTTTTATGGTTTATGAA	2	71	0
CATTAAACGTTCTCTTCTCTTCAAGAGAAG	6	13	1
AATCTTTCTATTTCTTTTCTCTTCCCTGTG	6	64	1
GTTTTCCTTGTTTCTTCTCTTAACTCATGA	6	109	0
TTAAGATCTATTTGTTTTAGTTTTATAATA	7	136	1
     TTCATTTTTATTTATAATTCAGTTT	8	5	1
AAAAGGGACAAGTCTTTTCGAATATAGTGG	10	150	1
AGTCAGGCGCTTTCTTCTAGAATGGAGAGT	10	248	1
TTCTTTTTAGATTCTTCTAGATGCACGTTA	12	19	0
GTTTCTCACTTTTTTTCTATTTAAAAAAGC	12	51	0
          **********
MAP Score: 4.79522

Motif 7
AAGAGTAGTCTTTTTAGCAAATAAGCTCTGT	0	100	0
ACATAGGTTGTTTAGAGGGAAAGAGTCTAGA	1	70	0
TGTTTTATGGTTTATGAAAAACAATTTTTTA	2	58	0
CCACCTTCTTTCTTGAGAAAAACATTTATAT	3	59	0
AGTAAGGGGTTCTTTAGAGAACGGAATATTT	3	118	1
AAAAACGCTCTTTAAAAAAAATATTCCGTTC	3	136	0
AAAAAGAAATTCTAAAGAAAAAGCAAGATTA	3	177	0
GCCTTTTTATTATTAAGGAAAAAGAAATTCT	3	195	0
GCTGTGTTAGCCTTAAGAAAAAGCTGTACAA	3	224	1
CCAACATGATTCTTAAAAAAAATAAGAAT  	5	8	0
CAAACTGAATTATAAATAAAAATGAA     	8	5	0
AACTCTCCATTCTAGAAGAAAGCGCCTGACT	10	248	0
ACAAGTAAAGTTTATAGGGAAAGAATTG   	10	282	1
TGCAAACTTCTTTTCAACAAACGCCCGGGAC	11	133	1
AGCCATAACCTCTACGAAAAAGTCAAGACAG	11	172	0
TCTAGAAGAATCTAAAAAGAATTGCTTTTTT	12	28	1
ACTTTTTTTCTATTTAAAAAAGCAATTCTTT	12	43	0
          **** ******
MAP Score: 3.36957

Motif 8
CTTTTCGGTAACAGGGGCCTATTCTATTCA	0	16	1
TTTTGCTTGTTCTGGCCTTTTCTACTGCAG	0	184	1
AACGCGTTCTACTGGTGTTTAATTATTGAC	0	254	1
CGCTTAAGCAACTGGCCATCT         	3	1	0
AAACAAAGAGTAAGGGGTTCTTTAGAGAAC	3	110	1
AGAAAACGATTAAGGGGCCTTATT      	4	14	1
ACGTGTAAGAATAGGGCTTTTTTTGTTTGT	8	56	1
TATGTCCGCTAATGGCGTTTAGAGAGTTTT	10	11	1
TTAAGCGCTAACAGGGGCTCTCCGGCCAAG	10	220	1
TCCGGCCAAGTCAGGCGCTTTCTTCTAGAA	10	240	1
TTCTCTCTATACTGGCCTCTCATGCAGCTA	11	30	1
AACGCCCGGGACAGGGGCATCTGTCTTGAC	11	152	1
GTTATGGCTAACTGGCCTTTCAGAACACGG	11	194	1
CTAGGAGGTTTCAGGGCTTCCCTAAGAACC	11	242	0
          **********
MAP Score: 3.16352

Motif 9
GTTTTTCTCAAGAAAGAAGGTGGCAGATGCTC	3	67	1
CATCCCATTTATAAACAAAGAGTAAGGGGTTC	3	98	1
AGTTAAGAGAAGAAACAAGGAAAACAAATCTA	6	114	1
GTCCCAAATAAGAAAAAAAGGGACAAGTCTTT	10	135	1
TTTTTTAAATAGAAAAAAAGTGAGAAACCCTT	12	53	1
CCTTATTGGAAGATAAAAGGTAGAGACTTCTT	12	81	1
          ***** **** *
MAP Score: 2.25406