AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons034_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238551
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	atpE	300	ATP Synthase Subunit E
#1	CPn0087	48	CT309 hypothetical protein
#2	atpK	94	ATP Synthase Subunit K
#3	valS	133	Valyl tRNA Synthetase
#4	CPn0095	62	S/T Protein Kinase
#5	rl31	80	L31 Ribosomal Protein
#6	pfrA	238	Peptide Chain Releasing Factor
#7	rl19	27	L19 Ribosomal Protein
#8	rnhB_1	55	Ribonuclease HII
#9	rpe	300	Ribulose-P Epimerase
#10	CPn0397	300	PP2C phosphatase family

Motif 1
ATTCTTTTAGAAAAGAATTTTCTTTAAAAAA	0	264	0
GTATAAAAAGAAAAGAATTTTTAATAAGAAA	9	104	1
CCTTATCTCCAAATGCATTTTCATTAGTGAA	9	47	1
GAATAATGAAAAAAGCATTCTCTTTACTATT	10	69	0
      AAGAAAGAGAATTTTAGGTGGTATA	7	4	1
TGAAGATATCAAAGCAATTTTCTTCTAGAAC	0	143	1
CCCATTTATAAAACCCATTCTCAGGCTCTCA	6	26	1
CCTCACAAAAAAACCCATTCTCGGGCTTGAG	6	53	0
CAAACATAGAAAGGCAATTCTTCTTTTTTGA	0	54	1
TATTATAAAGAATTGAATTTTCCTGACGAAA	10	207	0
TTCTATGTTTATAGGAATTTTTTCTTAGAGA	0	86	1
CAAGGTGTTTTAGAGAATTTTTTATCTGATT	6	179	1
TCTTAAAGGCAAGGGAAGTTTA         	2	1	0
          *** *******
MAP Score: 16.2003

Motif 2
AAAGTAGGCCTTCTTCTAGATCCAAAGATT	0	20	0
CTTTCTATGTTTGTTTGAAAGTAGGCCTTC	0	37	0
TAGGAATTTTTTCTTAGAGAGTTAGAGGAG	0	97	1
CAAAGCAATTTTCTTCTAGAACATCTCTGC	0	152	1
GAAAAGAATTTTCTTTAAAAAAGATGTTAT	0	256	0
TTACCGCTTATTCTTTTAGAAAAGAATTTT	0	274	0
TTTATGCTGCTTTTTCTAAAAATAGGGCAT	3	32	0
TAGCTCGACATACTTCGAGAGGATTCTACA	5	20	0
       AACTTCTTTTAGATTTCCCATTT	6	3	1
GAGAATGGGTTTTTTTGTGAGGGCTTTCTC	6	62	1
CATTGAACATTTCTTATTAAAAATTCTTTT	9	114	0
TGTTCAATGGTTCTTTGAAATATATTCGTT	9	135	1
TATCAAATTTTTCTTTGTAATTAATGATCA	10	147	1
GAAAATTCAATTCTTTATAATAATGATATG	10	216	1
          **********
MAP Score: 13.5198

Motif 3
TTCTATGTTTATAGGAATTTTTTCTTAGAGAGTTAGAGG	0	86	1
AGAGGAGAGCATGGGATTTATCTTGAAGATATCAAAGCA	0	120	1
TGAAGATATCAAAGCAATTTTCTTCTAGAACATCTCTGC	0	143	1
TTTGTGGATCAGTTGAATTAAATGCTAGAATGACATAAA	0	195	1
TGGAATCATAATAACATCTTTTTTAAAGAAAATTCTTTT	0	246	1
   GACGACAACTTTAAATATTGAGAAGATCTTTTCATG	1	22	0
TTCCTAGGTCACGATAATTTTGAAATAGATAACGTTAGA	6	123	1
GTATAAAAAGAAAAGAATTTTTAATAAGAAATGTTCAAT	9	104	1
CATAATACAGAACGAATATATTTCAAAGAACCATTGAAC	9	136	0
TACATCAACCAGTAAATATAAATAGTAGAAAGTTAAAGC	9	226	1
CAACTTCACTACGCTAAATTTAAAGTAGAGTGAGCTTTA	9	259	0
ATTAATTACAAAGAAAAATTTGATAAATAATCGCCCTAG	10	133	0
TATTATAAAGAATTGAATTTTCCTGACGAAATCATAATT	10	199	0
          *    ** ***    ****
MAP Score: 13.2471

Motif 4
    CCCAATAGGGAATCTTTGGATCTAGAA	0	6	1
CAAACATAGAAAGGCAATTCTTCTTTTTTGA	0	54	1
TGAAGATATCAAAGCAATTTTCTTCTAGAAC	0	143	1
ATTTTCTTCTAGAACATCTCTGCAACCCGTT	0	159	1
ATCTTTTTTAAAGAAAATTCTTTTCTAAAAG	0	261	1
TTAAATATTGAGAAGATCTTTTCATGACTTT	1	17	0
         GACGACAACTTTAAATATTGAG	1	36	0
CGAACTTGACAAGATTTCTTTCATGTTCCTC	2	32	0
TTCTAAAAATAGGGCATGTTTATGATTTGAT	3	18	0
CTAAGTTTACAGGGTATTTCTTAGTAGAGAT	3	91	1
          AAGATATTTCTGTAGAATCCT	5	0	1
TTCCTAGGTCACGATAATTTTGAAATAGATA	6	123	1
AAGGTGTTTTAGAGAATTTTTTATCTGATTC	6	180	1
      AAGAAAGAGAATTTTAGGTGGTATA	7	4	1
TATAAAAAGAAAAGAATTTTTAATAAGAAAT	9	105	1
GATAATAGTAAAGAGAATGCTTTTTTCATTA	10	66	1
TGATTTCGTCAGGAAAATTCAATTCTTTATA	10	204	1
ATATGAAATTAGAGAATGTCTATAGGGGCGG	10	241	1
TTTGTGATCCAGGATCTCTTTAGGAGCACTT	10	278	1
GGATCTCTTTAGGAGCACTTT          	10	289	1
          **** ******
MAP Score: 7.72256

Motif 5
AAGGCAATTCTTCTTTTTTGAATTCTATGTTTATAGGA	0	64	1
TAATAACATCTTTTTTAAAGAAAATTCTTTTCTAAAAG	0	254	1
        AATATTTTACCGCTTATTCTTTTAGAAAAG	0	280	0
TCTATTTTATTATCTTTATGCTGCTTTTTCTAAAAATA	3	38	0
       GCCTCCCTTTCCAATAATTCTAACAATATCA	4	41	0
CGAGAATGGGTTTTTTTGTGAGGGCTTTCTCTCTTGCA	6	61	1
TATACCAAGGTGTTTTAGAGAATTTTTTATCTGATTCC	6	174	1
CATTTGATACTGATTTTTCACCACTTTTTAGGGATTC 	6	211	1
CTTCATATTGTCTTATTTTGATTTTTATAATCTATAGT	8	22	1
ACAGAAAGATTAATCTTGGGATTTTTGTATAAAAAGAA	9	78	1
CCATTGAACATTTCTTATTAAAAATTCTTTTCTTTTTA	9	107	0
GAGTGAGCTTTAACTTTCTACTATTTATATTTACTGGT	9	233	0
TGATCCAGGATCTCTTTAGGAGCACTTT          	10	282	1
          *  ****  **   ** *
MAP Score: 7.40346

Motif 6
ACAAACATAGAAAGGCAATTCTTCTTTTTTGAA	0	53	1
AGATAATAGTAAAGAGAATGCTTTTTTCATTAT	10	65	1
CATCTTTTTTAAAGAAAATTCTTTTCTAAAAGA	0	260	1
      CCCAATAGGGAATCTTTGGATCTAGAA	0	4	1
CATTGTATGAATAGAAAATGAATACGGACTACT	9	177	0
       AAGAAAGAGAATTTTAGGTGGTATAT	7	3	1
TTTTGTATAAAAAGAAAAGAATTTTTAATAAGA	9	100	1
TTTTCTAAAAATAGGGCATGTTTATGATTTGAT	3	18	0
AAAGCAGCATAAAGATAATAAAATAGAACTATG	3	49	1
TTCTATGTTTATAGGAATTTTTTCTTAGAGAGT	0	86	1
GGATTATGATATAGCAAATATATTGTGATTCTA	9	16	0
CCAAGGTGTTTTAGAGAATTTTTTATCTGATTC	6	178	1
TTCCTCTCTTAAAGGCAAGGGAAGTTTA     	2	5	0
GTAATTATTTAAAGGTATTTGAAGGGAGCACAT	2	62	1
          ***** ***  **
MAP Score: 6.62496

Motif 7
AATTCTATGTTTATAGGAATTTTTTCTTAGAGAGTTA	0	84	1
ATTAGTGGAATCATAATAACATCTTTTTTAAAGAAAA	0	241	1
AACATCTTTTTTAAAGAAAATTCTTTTCTAAAAGAAT	0	258	1
TTTAATAAAGTCATGAAAAGATCTTCTCAATATTTAA	1	11	1
AAGTTCGTAATTATTTAAAGGTATTTGAAGGGAGCAC	2	56	1
GCCTGTATCAGTATACCAAGGTGTTTTAGAGAATTTT	6	163	1
AGAGAATTTTTTATCTGATTCCATTTGATACTGATTT	6	190	1
  GGAGGTTAGAATCACAATATATTTGCTATATCATA	9	8	1
TCTGTTTCACTAATGAAAATGCATTTGGAGATAAGGA	9	46	0
TGAACATTTCTTATTAAAAATTCTTTTCTTTTTATAC	9	104	0
GTTCAATGGTTCTTTGAAATATATTCGTTCTGTATTA	9	136	1
AAGATAATAGTAAAGAGAATGCTTTTTTCATTATTCA	10	64	1
          * **   **  * ****
MAP Score: 5.69455

Motif 8
AAAAAGAAGAATTGCCTTTCTATGTTTGTTTGAA	0	48	0
CTATGTTTATAGGAATTTTTTCTTAGAGAGTTAG	0	88	1
AGAGGAGAGCATGGGATTTATCTTGAAGATATCA	0	120	1
TGAAGATATCAAAGCAATTTTCTTCTAGAACATC	0	143	1
TTCTTTTAGAAAAGAATTTTCTTTAAAAAAGATG	0	260	0
  AATATTTTACCGCTTATTCTTTTAGAAAAGAA	0	278	0
CTCTAAGTTTACAGGGTATTTCTTAGTAGAGATC	3	89	1
CAAGCCCGAGAATGGGTTTTTTTGTGAGGGCTTT	6	55	1
AAGGTGTTTTAGAGAATTTTTTATCTGATTCCAT	6	180	1
AAGACTTCATATTGTCTTATTTTGATTTTTATAA	8	18	1
CTTATCTCCAAATGCATTTTCATTAGTGAAACAG	9	48	1
TTCTTATTAAAAATTCTTTTCTTTTTATACAAAA	9	100	0
TCAAAGAACCATTGAACATTTCTTATTAAAAATT	9	119	0
TAGTAAAGAGAATGCTTTTTTCATTATTCATCCT	10	71	1
CCTTAGGTTAATTGACCTTTCCAGCCTAGCTCTA	10	102	1
GCGATTATTTATCAAATTTTTCTTTGTAATTAAT	10	138	1
ATTATAAAGAATTGAATTTTCCTGACGAAATCAT	10	203	0
          *  *  ********
MAP Score: 3.02538

Motif 9
ACAAACATAGAAAGGCAATTCTTCTTTTTTGAATTC	0	53	1
AACATCTCTGCAACCCGTTTCTTATTTGTGGATCAG	0	171	1
CATCTTTTTTAAAGAAAATTCTTTTCTAAAAGAATA	0	260	1
TCCCATTTATAAAACCCATTCTCAGGCTCTCAAGCC	6	25	1
CCCTCACAAAAAAACCCATTCTCGGGCTTGAGAGCC	6	49	0
       AAGAAAGAGAATTTTAGGTGGTATATT  	7	3	1
AGTGAAACAGAAAGATTAATCTTGGGATTTTTGTAT	9	72	1
TTCTTATTAAAAATTCTTTTCTTTTTATACAAAAAT	9	98	0
TAAATAGTAGAAAGTTAAAGCTCACTCTACTTTAAA	9	244	1
AGATAATAGTAAAGAGAATGCTTTTTTCATTATTCA	10	65	1
TTCGTCAGGAAAATTCAATTCTTTATAATAATGATA	10	208	1
          ***    ******  *
MAP Score: 0.480184