AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238003
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	lon	300	Lon ATP-dependent Protease
#1	clpB	300	Clp Protease ATPase
#2	clpC	197	ClpC Protease
#3	glyA	189	Serine Hydroxymethyltransferase
#4	clpP_2	178	CLP Protease Subunit
#5	tigA	285	Trigger Factor-peptidyl-prolyl isomerase

Motif 1
TTTAAAATTGCTCAGAGATAAGGGATTAAG	0	36	0
CTCTTTTTACCCTAGAGAAAAAGAGCCGTA	0	236	1
TGTATTTTTAGAAAGGGGAAAGAGATCCTC	1	135	1
AACGTCTAACCTAAGAGGATCTCTTTCCCC	1	149	0
CTTCTACATTCTCAGAGGAAAGTTTATAGA	1	220	1
TTCCCTTAAACTCAGAGGAATTTTACCAAA	2	90	1
AAACCTAAAAGACAGGGGTAGAACTTTCCT	2	175	0
TTTGTACCTTCAAAGGGATATATTGAAAAT	3	45	1
TCAAGAAGAACCAAGGGAAAAAGAAAAATT	3	75	0
GCCTAGCCTTCAAAGTGAAAAATGTCAATC	3	114	0
TTTTTCTGGACTTAGAGGTTCTCTCTATTA	3	148	1
    ATTTTAGTTAGAGGAAAATACTTGAC	4	6	1
CAAAGCCCTTCTCAGGGGGAAGAGACACGA	5	91	1
GCGGGTGTAGCTCAGTGGTAGAGCGTCACG	5	190	1
          **********
MAP Score: 10.541

Motif 2
AACTCAAAAACAATGGAGTTTTTCTTAATCCCTTATC	0	13	1
TCCCTTATCTCTGAGCAATTTTAAACAGTAGATACAA	0	41	1
ACAGTAGATACAAACTATTTTTTTTGAAAAAATAAAA	0	65	1
TTAATCCCTTCTAGATATTTTTTAGAAGTTGTATATA	0	140	1
GTATAGCGAAATATGCAATCTTTTAAAATCGCTCCCT	0	201	1
GATCACTTCCTAATGTATTTTTAGAAAGGGGAAAGAG	1	122	1
AGAGGAAAGTTTATAGATTTTTTATTATTCCTATGTA	1	233	1
AAAATTCACCCCAAGCACTTTTTAAAAAGGTTTTTCT	1	273	0
CAGCTTCTTTTGAAACAGTCTTAATTAGTTTTATGTT	2	16	0
CCCTTAAACTCAGAGGAATTTTACCAAATTTGCTGGT	2	92	1
ATACTTGACCCAAGAAAGTCTTAAACATAGAATTCGA	4	27	1
CGTAGACAGCCTAAAAAGTCTTAGCTACGTTCCTAGG	4	91	1
TGCTAAATCAATGAAAAATTTTATCAAAGCCCTTCTC	5	67	1
GTTTAGATTTTTGAAGAGTTTTTAGCAACGACTAGAG	5	140	0
          * * * * *****   *
MAP Score: 9.93275

Motif 3
AACAATGGAGTTTTTCTTAATCCCTTATCTCT	0	21	1
AAAAAGACGATTTGCCTTAAACACGAGTCTTT	0	100	1
AATACGGCTCTTTTTCTCTAGGGTAAAAAGAG	0	236	0
        AATTGTCCTTATGCTCGGCTATAT	0	286	0
GGAGTTGCCGCTTTCTTCAGACAGTTCAAGAG	1	91	1
AAGAGGATCTCTTTCCCCTTTCTAAAAATACA	1	135	0
AATCTATAAACTTTCCTCTGAGAATGTAGAAG	1	220	0
TTTAAAAAGGTTTTTCTTATTACATAGGAATA	1	258	0
TTGTGCATAACTTTCCCTTAAACTCAGAGGAA	2	78	1
AGGGGTAGAACTTTCCTTAAGCATATACGAAA	2	160	0
ACTTAGGCAGCCTTCCTTTTACCCGAAAAGAC	3	12	0
TTGAAAATAATTTTTCTTTTTCCCTTGGTTCT	3	67	1
GGGTCAAGTATTTTCCTCTAACTAAAAT    	4	6	0
      TTGCGTTTCCTCATCAAATAATTTTC	4	162	0
ATTCGTGTCTCTTCCCCCTGAGAAGGGCTTTG	5	91	0
CTAAACTATTCTTTTCTTTGCGGGTGTAGCTC	5	171	1
CATCACCCGCTTTTCCTTTCAAGTCTAATAAA	5	251	1
          *********  *
MAP Score: 8.21041

Motif 4
GAAAGAGATCCTCTTAGGTTAGACGTTTAG	1	152	1
TTAGGTTAGACGTTTAGGTTTGGTAGTATT	1	165	1
GGTAAAATTCCTCTGAGTTTAAGGGAAAGT	2	87	0
CTACCCCTGTCTTTTAGGTTTTT       	2	184	1
      GAGTCTTTTCGGGTAAAAGGAAGG	3	4	1
CAATATATCCCTTTGAAGGTACAAAAACTT	3	40	0
ACATTTTTCACTTTGAAGGCTAGGCTGGTT	3	119	1
TTTTTCTGGACTTAGAGGTTCTCTCTATTA	3	148	1
CTATTCTTTTCTTTGCGGGTGTAGCTCAGT	5	176	1
          **********
MAP Score: 6.08876

Motif 5
ATTGCTCAGAGATAAGGGATTAAGAAAAACTCCATTGTTTT	0	19	0
AAAAAATATCTAGAAGGGATTAAAGATTAGGAAAGACTCGT	0	122	0
ACGGCTCTTTTTCTCTAGGGTAAAAAGAGGGAGCGATTTTA	0	224	0
CAGACAAATATAGCCGAGCATAAGGACAATT          	0	279	1
    TTATGTTTGACAAGCACAAGGTGGATGCCACTCTATA	1	6	1
AGTGATCTCTTGAACTGTCTGAAGAAAGCGGCAACTCCTAA	1	88	0
AATGTATTTTTAGAAAGGGGAAAGAGATCCTCTTAGGTTAG	1	133	1
     GAGTCTTTTCGGGTAAAAGGAAGGCTGCCTAAGTTT	3	5	1
AATATATCCCTTTGAAGGTACAAAAACTTAGGCAGCCTTCC	3	28	0
ATCAAGAAGAACCAAGGGAAAAAGAAAAATTATTTTCAATA	3	65	0
TAGGCTGGTTTTTTCTGGACTTAGAGGTTCTCTCTATTAAG	3	139	1
       TTCTCCTCTGGAATAAGAGTGGATAATATAATCT	5	3	1
TTAGCATGGGTAAACAGGTACAAGTAAGCAGATTATATTAT	5	32	0
ATCAAAGCCCTTCTCAGGGGGAAGAGACACGAATTTCTATG	5	89	1
          *   * **   *****    *
MAP Score: 4.01521

Motif 6
TCTGAGCAATTTTAAACAGTAGATACAAACTATTTTT	0	50	1
AAATCGTCTTTTTTTATTTTTTCAAAAAAAATAGTTT	0	76	0
TTCTAAAAAATATCTAGAAGGGATTAAAGATTAGGAA	0	130	0
AATTAGCGCATATATACAACTTCTAAAAAATATCTAG	0	150	0
TTGCATCTATTTTGTAGTATAGCGAAATATGCAATCT	0	185	1
TCGCTCCCTCTTTTTACCCTAGAGAAAAAGAGCCGTA	0	229	1
AAAAGAGCCGTATTTACTGGAGCGACAGACAAATATA	0	254	1
TCCTAATGTATTTTTAGAAAGGGGAAAGAGATCCTCT	1	129	1
CTTTTTAGGCTGTCTACGTCAGCAACAAGCTTAGACA	4	72	0
TACTTGTACCTGTTTACCCATGCTAAATCAATGAAAA	5	47	1
          * * ***    ** ***
MAP Score: 3.49354

Motif 7
AATCGCTCCCTCTTTTTACCCTAGAGAAAAAGAGCCGT	0	227	1
CCTAAGAGGATCTCTTTCCCCTTTCTAAAAATACATTA	1	132	0
AAAAGGTTTTTCTTATTACATAGGAATAATAAAAAATC	1	248	0
AAATAATTTTTCTTTTTCCCTTGGTTCTTCTTGATCAT	3	71	1
TAATGTCTAAGCTTGTTGCTGACGTAGACAGCCTAAAA	4	69	1
AAAAGTCTTAGCTACGTTCCTAGGGTCATTTCGTGATC	4	104	1
TATTATCCACTCTTATTCCAGAGGAGAA          	5	0	0
CTTACTTGTACCTGTTTACCCATGCTAAATCAATGAAA	5	45	1
TGGTAGAGCGTCACGTTGCCAACGTGAAGGTCGTGAGT	5	205	1
          ***  ** ** * *   *
MAP Score: 2.6215

Motif 8
TCAGAGATAAGGGATTAAGAAAAACTCCATT	0	24	0
TTTTCTCTAGGGTAAAAAGAGGGAGCGATTT	0	226	0
TTTTACCCTAGAGAAAAAGAGCCGTATTTAC	0	240	1
AAATATAGCCGAGCATAAGGACAATT     	0	284	1
AAATTCCTCTGAGTTTAAGGGAAAGTTATGC	2	82	0
GAGTCTTTTCGGGTAAAAGGAAGGCTGCCTA	3	10	1
GAAGAACCAAGGGAAAAAGAAAAATTATTTT	3	70	0
ATTATTTGATGAGGAAACGCAA         	4	166	1
  TTCTCCTCTGGAATAAGAGTGGATAATAT	5	8	1
GATTTAGCATGGGTAAACAGGTACAAGTAAG	5	45	0
TTAGACTTGAAAGGAAAAGCGGGTGATGAGG	5	248	0
TTTCAAGTCTAATAAAAAGGGTTGTCTT   	5	267	1
          *** *******
MAP Score: 2.23657

Motif 9
AATCCCTTATCTCTGAGCAATTTTAAACAG	0	39	1
GAAAGAGATCCTCTTAGGTTAGACGTTTAG	1	152	1
TTAGGTTAGACGTTTAGGTTTGGTAGTATT	1	165	1
CTTCTACATTCTCAGAGGAAAGTTTATAGA	1	220	1
TTCCCTTAAACTCAGAGGAATTTTACCAAA	2	90	1
CTACCCCTGTCTTTTAGGTTTTT       	2	184	1
TTTTTCTGGACTTAGAGGTTCTCTCTATTA	3	148	1
          **********
MAP Score: 1.12943

Motif 10
AACTCAAAAACAATGGAGTTTTTCTTAATCCCTTATCTC	0	13	1
ATTTGCCTTAAACACGAGTCTTTCCTAATCTTTAATCCC	0	109	1
TCAGACAGTTCAAGAGATCACTTCCTAATGTATTTTTAG	1	107	1
TCTACATTCTCAGAGGAAAGTTTATAGATTTTTTATTAT	1	222	1
TTTCTTATTACATAGGAATAATAAAAAATCTATAAACTT	1	239	0
CCCTTAAACTCAGAGGAATTTTACCAAATTTGCTGGTTT	2	92	1
CTTTTCGGGTAAAAGGAAGGCTGCCTAAGTTTTTGTACC	3	14	1
TTGTACCTTCAAAGGGATATATTGAAAATAATTTTTCTT	3	46	1
TAGCTACGTTCCTAGGGTCATTTCGTGATCGGGAACGTA	4	112	1
CGTATGGACACAACTGAAAATTATTTGATGAGGAAACGC	4	147	1
          **  ***    *   ****
MAP Score: 0.694234