AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249425
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0230	192	283aa long hypothetical nucleotide-binding protein
#1	APE0402	62	204aa long hypothetical membrane-associated ATPase gamma chain
#2	APE0404	32	466aa long hypothetical membrane-associated ATPase beta chain
#3	APE0673	121	686aa long hypothetical protein
#4	APE0675	143	117aa long hypothetical methionyl-tRNA synthetase
#5	APE0676	21	274aa long hypothetical 3-methyl-2-oxobutanoate hydroxymethyl transferase
#6	APE1592	40	475aa long hypothetical cysteinyl-tRNA synthetase

Motif 1
TATATGGATGGGAAGCCGGGATGGGACAGCC	0	41	0
AATTTCTTGTCTACTCAGGAGGGTGGCAGAG	0	118	1
GAGTACAAGGCTATCGCGGAGCGG       	0	178	1
TTTATCCACTCTAGCGTGGGAGGTGTAAGGT	1	17	1
TGCTTTGGCTGTAGACCCGAGGAAA      	1	47	1
GTTCCGCCGGTTACTCCGGAGACTTATTAAT	3	34	0
AGAAATTCCCGTGGCGCGGAGTTCCGCCGGT	3	54	0
ATTACGCTTGCTCTCCCAGGGCTAATTGGGA	3	87	1
GGGCTAATTGGGATTGCGGGGGACGG     	3	105	1
CCCCCGGAAGGGAGCCTGGGGGTGTTGTGAG	4	43	0
CGACACTGAACACCCCCGGAAGGGAGCCTGG	4	55	0
GGTGTTCAGTGTCGCCTGGGGTCGTCACCCC	4	72	1
GCCTGGGGTCGTCACCCCGGGAATTAGATTC	4	85	1
AGATTCTTTATCCTCCCGGAGGGATATTTCA	4	110	1
TAGATGGGGTGGAGCCTGGGGC         	6	1	0
TCCACCCCATCTACCCCGGGGTTTCAGGCGG	6	19	1
          *** *******
MAP Score: 23.3036

Motif 2
ACACCCTTTTATGCCAACCCCCCTATTGGCTG	0	14	1
CCCCTATTGGCTGTCCCATCCCGGCTTCCCAT	0	33	1
GTAGACAAGAAATTACCCCTCCTACTATCTGA	0	100	0
CTTAGAAGCTCTGCCACCCTCCTGAGTAGACA	0	125	0
CCTACTTACCCTGAATCCCTTAGAAGCTCTGC	0	143	0
    CAAATGCTTTATCCACTCTAGCGTGGGA	1	6	1
GCCAAAGCACCTTACACCTCCCACGCTAGAGT	1	24	0
GGTGCTTTGGCTGTAGACCCGAGGAAA     	1	45	1
CTTAATTACGCTTGCTCTCCCAGGGCTAATTG	3	83	1
GGCTGAACTCCTCACAACACCCCCAGGCTCCC	4	33	1
ACAACACCCCCAGGCTCCCTTCCGGGGGTGTT	4	46	1
CCAGGCGACACTGAACACCCCCGGAAGGGAGC	4	59	0
AATTCCCGGGGTGACGACCCCAGGCGACACTG	4	78	0
GAATTAGATTCTTTATCCTCCCGGAGGGATAT	4	105	1
         GAAGCCTACACCCTATCCAGG  	5	8	0
      GCCCCAGGCTCCACCCCATCTACCCC	6	4	1
      CCGCCTGAAACCCCGGGGTAGATGGG	6	24	0
          *** * ******
MAP Score: 21.1249

Motif 3
GCTGAAATATCCCTCCGGGAGGATAAAGAA	4	113	0
CTCCTCACAACACCCCCAGGCTCCCTTCCG	4	40	1
CGACACTGAACACCCCCGGAAGGGAGCCTG	4	56	0
CCTGGGGTCGTCACCCCGGGAATTAGATTC	4	86	1
ATTGGCTGTCCCATCCCGGCTTCCCATCCA	0	38	1
CCCGGGGTGACGACCCCAGGCGACACTGAA	4	76	0
CCACCCCATCTACCCCGGGGTTTCAGGCGG	6	20	1
AGCTCTGCCACCCTCCTGAGTAGACAAGAA	0	121	0
ATTACGCTTGCTCTCCCAGGGCTAATTGGG	3	87	1
         CCGCTCCGCGATAGCCTTGTA	0	181	0
        AACCCCCCTAAAGGGTCGGACA	4	2	1
CGGAACTCCGCGCCACGGGAATTTCTTAAT	3	59	1
TTCCGCCGGTTACTCCGGAGACTTATTAAT	3	34	0
       CCGTCCCCCGCAATCCCAATTAG	3	108	0
GCCCCAGGCTCCACCCCATCTACCCCGGGG	6	10	1
AATGCTTTATCCACTCTAGCGTGGGAGGTG	1	12	1
         CCCACACCATGTCTAGAGAGC	2	21	0
          **********
MAP Score: 18.289

Motif 4
   GGCAACACCCTTTTATGCCAACCCCCCTATTGGCTGTCCCA	0	7	1
TATTGGCTGTCCCATCCCGGCTTCCCATCCATATATCCTTGATA	0	37	1
TACCCTGAATCCCTTAGAAGCTCTGCCACCCTCCTGAGTAGACA	0	125	0
TAGCCTTGTACTCACTCCTACTTACCCTGAATCCCTTAGAAGCT	0	147	0
ACAGCCAAAGCACCTTACACCTCCCACGCTAGAGTGGATAAAGC	1	15	0
      TTTCCTCGGGTCTACAGCCAAAGCACCTTACACCTCCC	1	34	0
TAATAAGTCTCCGGAGTAACCGGCGGAACTCCGCGCCACGGGAA	3	36	1
          CCGTCCCCCGCAATCCCAATTAGCCCTGGGAGAG	3	97	0
CAAGGCTGAACTCCTCACAACACCCCCAGGCTCCCTTCCGGGGG	4	30	1
CCCCAGGCGACACTGAACACCCCCGGAAGGGAGCCTGGGGGTGT	4	49	0
GAATCTAATTCCCGGGGTGACGACCCCAGGCGACACTGAACACC	4	72	0
         GCCCCAGGCTCCACCCCATCTACCCCGGGGTTTCA	6	1	1
          * *    *  *  **** *    *
MAP Score: 16.9086

Motif 5
TTTATGCCAACCCCCCTATTGGCTGTCCCATCCC	0	21	1
AATTTCTTGTCTACTCAGGAGGGTGGCAGAGCTT	0	118	1
GAGTACAAGGCTATCGCGGAGCGG          	0	178	1
AATGCTTTATCCACTCTAGCGTGGGAGGTGTAAG	1	12	1
        AACCCCCCTAAAGGGTCGGACAAGGC	4	2	1
CCGGAAGGGAGCCTGGGGGTGTTGTGAGGAGTTC	4	37	0
CCCCCAGGCTCCCTTCCGGGGGTGTTCAGTGTCG	4	52	1
GGTGTTCAGTGTCGCCTGGGGTCGTCACCCCGGG	4	72	1
AAGAATCTAATTCCCGGGGTGACGACCCCAGGCG	4	84	0
GCTGAAATATCCCTCCGGGAGGATAAAGAATCTA	4	109	0
TCCACCCCATCTACCCCGGGGTTTCAGGCGG   	6	19	1
          ****** ** *  *
MAP Score: 8.81813

Motif 6
GCTGTCCCATCCCGGCTTCCCATCCATATATCCT	0	42	1
ATCCATATATCCTTGATAAATAGCTTCAAATGCT	0	63	1
GGGGTAATTTCTTGTCTACTCAGGAGGGTGGCAG	0	113	1
GGAGTGAGTACAAGGCTATCGCGGAGCGG     	0	173	1
CTTACACCTCCCACGCTAGAGTGGATAAAGCATT	1	12	0
TGTAAGGTGCTTTGGCTGTAGACCCGAGGAAA  	1	40	1
   CCCACACCATGTCTAGAGAGCCACAGTAAAG	2	11	0
TTAATAAGTCTCCGGAGTAACCGGCGGAACTCCG	3	35	1
ACCGGCGGAACTCCGCGCCACGGGAATTTCTTAA	3	54	1
CCAATTAGCCCTGGGAGAGCAAGCGTAATTAAGA	3	82	0
CCAGGGCTAATTGGGATTGCGGGGGACGG     	3	102	1
AAGGGTCGGACAAGGCTGAACTCCTCACAACACC	4	20	1
CACAACACCCCCAGGCTCCCTTCCGGGGGTGTTC	4	45	1
GGTGACGACCCCAGGCGACACTGAACACCCCCGG	4	67	0
AATCTAATTCCCGGGGTGACGACCCCAGGCGACA	4	81	0
          CCTGGATAGGGTGTAGGCTTC   	5	0	1
       GCCCCAGGCTCCACCCCATCTACCCCG	6	3	1
CCCCATCTACCCCGGGGTTTCAGGCGG       	6	23	1
          ** ****  ** **
MAP Score: 7.05528

Motif 7
  GGCAACACCCTTTTATGCCAACCCCCCTATTGGCTGT	0	8	1
AACCCCCCTATTGGCTGTCCCATCCCGGCTTCCCATCCA	0	29	1
      TTTCCTCGGGTCTACAGCCAAAGCACCTTACAC	1	39	0
CAAGGCTGAACTCCTCACAACACCCCCAGGCTCCCTTCC	4	30	1
TCAGTGTCGCCTGGGGTCGTCACCCCGGGAATTAGATTC	4	77	1
   GCTTCACCACGCTGAAATATCCCTCCGGGAGGATAA	4	117	0
         GCCCCAGGCTCCACCCCATCTACCCCGGGG	6	1	1
          * **   *  ** ***  *
MAP Score: 3.10995