AlignACE 3.0 10/20/99
AlignACE2 -i EC_operons051_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943441887
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	cydA	300	cytochrome d terminal oxidase, polypeptide subunit I
#1	ybgE	127	orf, hypothetical protein
#2	ybgC	149	orf, hypothetical protein
#3	tolA	64	membrane spanning protein, required for outer membrane integrity
#4	tolB	132	periplasmic protein involved in the tonb-independent uptake of group A colicins
#5	pal	34	peptidoglycan-associated lipoprotein
#6	b3007	103	orf, hypothetical protein
#7	yiaD	266	putative outer membrane protein

Motif 1
TGTGGCTAACGCGCCACGCGAGCTAAACACGGTTT	7	13	1
AAGACTCCGAGAGTGAACCCCGTTAGAAAGGGTCA	0	255	0
GATCAAATTGGCTGAAAGGCGGTAATTTAGCTATA	0	25	1
ACGTGTTCAAGCGCCAGCGCGGTGATTACCCCAAA	1	69	0
AATTTCTATTGGGGCATGCGTGTGACCCTTTCTAA	0	233	1
TTCTGGGAACGCTTCTTGCCTGTTCGTTTGGGGTA	1	43	1
GTTTCCAAAAACTGTTCGCCTGTTACCCGCTCTCT	3	34	0
ATTATGGGCCGCTCCAGGCCCATAAATTTTTACGC	2	30	1
ACGTCGAATCAGGCAAAGCCGGTCAAGAAGACATC	1	100	1
CGTGGCGGGAGATTATGCCGCGTGAACATGAAGAT	7	200	0
AAACGCTGCTACTATACGCGCGCGATTGAGGTTTG	2	87	0
ATCTCCCGCCACGGAACCCGTGGCAAAGAATAAAA	7	222	1
ACAAATTTCCGAGTATTCCCAGGAATAATCTTCAT	7	173	1
AAAATTTTCTGCTTTATGCCAATTCTTCAGGATGC	6	68	0
TTATTGTAAGGATTTTGCGGCGTAATATATACGTG	0	107	1
GCGCGCGATTGAGGTTTGGGAATGAGGGCAAGTTA	2	70	0
          ***  * *** ** *
MAP Score: 6.97614

Motif 2
CGTAATATATACGTGGGATCAATTTGAGTTTTTATTAA	0	127	1
GACCCTTTCTAACGGGGTTCACTCTCGGAGTCTTCATG	0	256	1
TTCGCATGGATTCTGGGAACGCTTCTTGCCTGTTCGTT	1	33	1
TCTTTAAAAAATTATGGGCCGCTCCAGGCCCATAAATT	2	20	1
AGGTTTGGGAATGAGGGCAAGTTAAGGGAGCGTAAAAA	2	56	0
CGCTGCTACTATACGCGCGCGATTGAGGTTTGGGAATG	2	81	0
AGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGA	3	36	1
TAGCATGAATATTCGCGGGCGCATCCTGAAGAATTGGC	6	48	1
       GCCATTTGCGAAAATTTTCTGCTTTATGCCA	6	82	0
ACTGCCGCCCATTGGGGGCCCATGCTGGTTGAAACCGA	7	53	0
TTATTCTTTGCCACGGGTTCCGTGGCGGGAGATTATGC	7	217	0
          **  ***  ** *   **
MAP Score: 6.65805

Motif 3
TCTATTGGGGCATGCGTGTGACCCTTTCTAACGGGGTTCACTCTCG	0	237	1
     GACTCCTTGCTCATCGCATGAAGACTCCGAGAGTGAACCCC	0	269	0
TGTTCAAGCGCCAGCGCGGTGATTACCCCAAACGAACAGGCAAGAA	1	55	0
CTACTATACGCGCGCGATTGAGGTTTGGGAATGAGGGCAAGTTAAG	2	68	0
GAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGA         	3	37	1
CCCGTGGCAACCGGTGCCTGATGTTGACCGTCCGAACAGTCAACAT	4	15	0
GCTAAATTATCGTGGGCCATCGGTCCAGATAAGGGAGATATG    	4	100	1
CATGAATATTCGCGGGCGCATCCTGAAGAATTGGCATAAAGCAGAA	6	51	1
GCTAACGCGCCACGCGAGCTAAACACGGTTTCGCCGTCGGTTTCAA	7	17	1
TTTCAACCAGCATGGGCCCCCAATGGGCGGCAGTCAGAACGGAATA	7	57	1
AACGGAATATCGTGAGGATGAGTTGGCCAAACCGAAGACTCCTGAA	7	94	1
TCTTCATGTTCACGCGGCATAATCTCCCGCCACGGAACCCGTGGCA	7	201	1
          *  ***       *   *   *** *
MAP Score: 5.42881

Motif 4
CAATTTGATCGAGAACAATTTATCT        	0	2	0
TTTTTCGACGGTGATCAATTTATAGCTAAATTA	0	47	0
ATATATACGTGGGATCAATTTGAGTTTTTATTA	0	131	1
AGAAATTTGTTTGAACACTTTCATCATACCATG	0	207	0
CATGGATTCTGGGAACGCTTCTTGCCTGTTCGT	1	37	1
CGGGTAACAGGCGAACAGTTTTTGGAAACCGAG	3	40	1
   GCCATTTGCGAAAATTTTCTGCTTTATGCC	6	83	0
          * ***** *** *
MAP Score: 5.13005

Motif 5
AATTTCTATTGGGGCATGCGTGTGACCCTTTCTAACGGGGTTCA	0	233	1
TCTAACGGGGTTCACTCTCGGAGTCTTCATGCGATGAGCAAGGA	0	263	1
GAACAGGCAAGAAGCGTTCCCAGAATCCATGCGAAATACCACAT	1	24	0
GCTGCTACTATACGCGCGCGATTGAGGTTTGGGAATGAGGGCAA	2	74	0
AAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGA   	3	33	1
CGATGTTGACTGTTCGGACGGTCAACATCAGGCACCGGTTGCCA	4	13	1
TAAATTATCGTGGGCCATCGGTCCAGATAAGGGAGATATG    	4	102	1
      TCCTGTGGCTAACGCGCCACGCGAGCTAAACACGGTTT	7	4	1
TAAACACGGTTTCGCCGTCGGTTTCAACCAGCATGGGCCCCCAA	7	36	1
GAGGATGAGTTGGCCAAACCGAAGACTCCTGAAAGGTTAGATGT	7	107	1
TTATGCCGCGTGAACATGAAGATTATTCCTGGGAATACTCGGAA	7	179	0
CGCGGCATAATCTCCCGCCACGGAACCCGTGGCAAAGAATAAAA	7	213	1
          *   *   **    *  * *** *
MAP Score: 4.16773

Motif 6
GCAAATTTGCATTTTTCGACGGTGATCAATTTAT	0	57	0
GTTTATTGTAAGGATTTTGCGGCGTAATATATAC	0	105	1
TTTCTTTACGCCGTTTTTGTGTGCATTCACATGG	0	178	1
TGTTCAAACAAATTTCTATTGGGGCATGCGTGTG	0	223	1
TGCGTGTGACCCTTTCTAACGGGGTTCACTCTCG	0	249	1
CGCTTCTTGCCTGTTCGTTTGGGGTAATCACCGC	1	52	1
TTTCCAAAAACTGTTCGCCTGTTACCCGCTCTCT	3	34	0
GCGATGTTGACTGTTCGGACGGTCAACATCAGGC	4	12	1
CATCAGGCACCGGTTGCCACGGGGTTCTGGTAGT	4	38	1
GAGCTAAACACGGTTTCGCCGTCGGTTTCAACCA	7	32	1
TCACGATATTCCGTTCTGACTGCCGCCCATTGGG	7	75	0
AATAATCTTCATGTTCACGCGGCATAATCTCCCG	7	196	1
TTCTTTGCCACGGGTTCCGTGGCGGGAGATTATG	7	218	0
          * ****   *****
MAP Score: 3.71596

Motif 7
       AGATAAATTGTTCTCGATCAAATTGGCTG	0	3	1
AATTTAGCTATAAATTGATCACCGTCGAAAAATGCA	0	48	1
TTTTATTAACATGTTTGCAACCTTTCTTTACGCCGT	0	156	1
CAATAGAAATTTGTTTGAACACTTTCATCATACCAT	0	208	0
TACGCTCCCTTAACTTGCCCTCATTCCCAAACCTCA	2	60	1
TTGTGTATTTTAGTTTGTTAACATTCTGCTAAATTA	4	73	1
          *** ***  * *  **
MAP Score: 3.67159

Motif 8
CGGCGTAATATATACGTGGGATCAATTTGAGT	0	124	1
GCAACCTTTCTTTACGCCGTTTTTGTGTGCAT	0	172	1
TTTGTGTGCATTCACATGGTATGATGAAAGTG	0	193	1
GTGTGACCCTTTCTAACGGGGTTCACTCTCGG	0	252	1
ACGCTGCTACTATACGCGCGCGATTGAGGTTT	2	88	0
CAGGCACCGGTTGCCACGGGGTTCTGGTAGTT	4	41	1
TTCTGCTAAATTATCGTGGGCCATCGGTCCAG	4	96	1
CTAGCATGAATATTCGCGGGCGCATCCTGAAG	6	47	1
CCACGCGAGCTAAACACGGTTTCGCCGTCGGT	7	26	1
AATCTTCATGTTCACGCGGCATAATCTCCCGC	7	199	1
TTTTTATTCTTTGCCACGGGTTCCGTGGCGGG	7	226	0
          ** ******* *
MAP Score: 3.39294

Motif 9
ATTGTAAGGATTTTGCGGCGTAATATATACGTGGGA	0	109	1
CCTTATCTGGACCGATGGCCCACGATAATTTAGCAG	4	98	0
AGCATGAATATTCGCGGGCGCATCCTGAAGAATTGG	6	49	1
          TCCTGTGGCTAACGCGCCACGCGAGC	7	0	1
GCTGGTTGAAACCGACGGCGAAACCGTGTTTAGCTC	7	32	0
ACTGCCGCCCATTGGGGGCCCATGCTGGTTGAAACC	7	55	0
ATCGTGAGGATGAGTTGGCCAAACCGAAGACTCCTG	7	102	1
TTTCCGAGTATTCCCAGGAATAATCTTCATGTTCAC	7	178	1
ATCTTCATGTTCACGCGGCATAATCTCCCGCCACGG	7	200	1
CCGCCACGGAACCCGTGGCAAAGAATAAAAAGGTTA	7	227	1
          ****  ***  *  **
MAP Score: 2.75461

Motif 10
TAATATATACGTGGGATCAATTTGAGTTTTTATTAACATGT	0	129	1
AATTTCTATTGGGGCATGCGTGTGACCCTTTCTAACGGGGT	0	233	1
TCAAGCGCCAGCGCGGTGATTACCCCAAACGAACAGGCAAG	1	57	0
AAAAATTTATGGGCCTGGAGCGGCCCATAATTTTTTAAAGA	2	20	0
AAATTTTTACGCTCCCTTAACTTGCCCTCATTCCCAAACCT	2	53	1
CCTCAATCGCGCGCGTATAGTAGCAGCGTTTAAAAGCTCTA	2	91	1
GCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAA	3	27	1
ATGAATATTCGCGGGCGCATCCTGAAGAATTGGCATAAAGC	6	52	1
      TCCTGTGGCTAACGCGCCACGCGAGCTAAACACGG	7	4	1
CAACCAGCATGGGCCCCCAATGGGCGGCAGTCAGAACGGAA	7	60	1
TCATGTTCACGCGGCATAATCTCCCGCCACGGAACCCGTGG	7	204	1
          * ***   * *  ***    *
MAP Score: 1.70437