AlignACE 3.0 10/20/99
AlignACE2 -i EC_sum_all064_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943443019
 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
GGGTTCACTCTCGGAGTCTTCATGCGATGAGCAAG	0	270	1
CAAGAAGCGTTCCCAGAATCCATGCGAAATACCAC	1	26	0
CGGTGATTACCCCAAACGAACAGGCAAGAAGCGTT	1	50	0
TTTGCCTGATTCGACGTGTTCAAGCGCCAGCGCGG	1	82	0
TAAAAAATTATGGGCCGCTCCAGGCCCATAAATTT	2	24	1
GCCTGTTACCCGCTCTCTTTCAAGCAAGGGAAACG	3	17	0
ACTGTTCGGACGGTCAACATCAGGCACCGGTTGCC	4	21	1
AGGATGCGCCCGCGAATATTCATGCTAGTTTAGAC	6	40	0
CACGGTTTCGCCGTCGGTTTCAACCAGCATGGGCC	7	40	1
CCAGGAATAATCTTCATGTTCACGCGGCATAATCT	7	191	1
          *** *   **** **
MAP Score: 9.99204

Motif 2
TGAAACCGACGGCGAAACCGTGTTTAGCTC	7	32	0
AATTTCTATTGGGGCATGCGTGTGACCCTT	0	233	1
AGGATGAGTTGGCCAAACCGAAGACTCCTG	7	108	1
AATATTCGCGGGCGCATCCTGAAGAATTGG	6	55	1
CCAGAACCCCGTGGCAACCGGTGCCTGATG	4	38	0
GCCCATTGGGGGCCCATGCTGGTTGAAACC	7	55	0
    TCCTGTGGCTAACGCGCCACGCGAGC	7	6	1
GCTTGAACACGTCGAATCAGGCAAAGCCGG	1	92	1
CGAACAGTTTTTGGAAACCGAGA       	3	51	1
GCATGGATTCTGGGAACGCTTCTTGCCTGT	1	36	1
GCCCATGCTGGTTGAAACCGACGGCGAAAC	7	44	0
GATTGAGGTTTGGGAATGAGGGCAAGTTAA	2	69	0
CTGGACCGATGGCCCACGATAATTTAGCAG	4	98	0
TATTAACATGTTTGCAACCTTTCTTTACGC	0	159	1
TGATTCGACGTGTTCAAGCGCCAGCGCGGT	1	81	0
ATAATCTTCATGTTCACGCGGCATAATCTC	7	197	1
          **********
MAP Score: 6.72814

Motif 3
GTTTATTGTAAGGATTTTGCGGCGTAATATATAC	0	105	1
CGCTTCTTGCCTGTTCGTTTGGGGTAATCACCGC	1	52	1
ACGTCGAATCAGGCAAAGCCGGTCAAGAAGACAT	1	100	1
GCGATGTTGACTGTTCGGACGGTCAACATCAGGC	4	12	1
CATCAGGCACCGGTTGCCACGGGGTTCTGGTAGT	4	38	1
TCTCCCTTATCTGGACCGATGGCCCACGATAATT	4	104	0
CCAATTCTTCAGGATGCGCCCGCGAATATTCATG	6	51	0
GAGCTAAACACGGTTTCGCCGTCGGTTTCAACCA	7	32	1
GAATATCGTGAGGATGAGTTGGCCAAACCGAAGA	7	98	1
AATAATCTTCATGTTCACGCGGCATAATCTCCCG	7	196	1
TTCTTTGCCACGGGTTCCGTGGCGGGAGATTATG	7	218	0
          *** *  * *****
MAP Score: 4.86639

Motif 4
TGTTTATTGTAAGGATTTTGCGGCGTAATATATACG	0	104	1
ATGTTTGCAACCTTTCTTTACGCCGTTTTTGTGTGC	0	166	1
ATGCGTGTGACCCTTTCTAACGGGGTTCACTCTCGG	0	248	1
ACGCTTCTTGCCTGTTCGTTTGGGGTAATCACCGCG	1	51	1
TCGACGTGTTCAAGCGCCAGCGCGGTGATTACCCCA	1	71	0
ACCGGCTTTGCCTGATTCGACGTGTTCAAGCGCCAG	1	87	0
ACATCAGGCACCGGTTGCCACGGGGTTCTGGTAGTT	4	37	1
TCTAAACTAGCATGAATATTCGCGGGCGCATCCTGA	6	41	1
GCGGGCGCATCCTGAAGAATTGGCATAAAGCAGAAA	6	62	1
CGAGCTAAACACGGTTTCGCCGTCGGTTTCAACCAG	7	31	1
CAGCATGGGCCCCCAATGGGCGGCAGTCAGAACGGA	7	64	1
GAATAATCTTCATGTTCACGCGGCATAATCTCCCGC	7	195	1
ATTCTTTGCCACGGGTTCCGTGGCGGGAGATTATGC	7	217	0
          ** *  *   ******
MAP Score: 4.44566

Motif 5
CTGATTCGACGTGTTCAAGCGCCAGCGCGG	1	82	0
CTTTCTAACGGGGTTCACTCTCGGAGTCTT	0	260	1
CGCCGTTTTTGTGTGCATTCACATGGTATG	0	186	1
TATGATGAAAGTGTTCAAACAAATTTCTAT	0	212	1
TTATTAACATGTTTGCAACCTTTCTTTACG	0	158	1
TTTCGCCGTCGGTTTCAACCAGCATGGGCC	7	45	1
CACTCTCGGAGTCTTCATGCGATGAGCAAG	0	275	1
GAATATTCGCGGGCGCATCCTGAAGAATTG	6	54	1
AATAATCTTCATGTTCACGCGGCATAATCT	7	196	1
CGCCCATTGGGGGCCCATGCTGGTTGAAAC	7	56	0
          **********
MAP Score: 3.85504

Motif 6
TGCTTCAACAAAAACCTGTTTATTGTAAGGATTTTGCGGCGT	0	88	1
GAATGCACACAAAAACGGCGTAAAGAAAGGTTGCAAACATGT	0	164	0
AAGGAGCTAAAAATGTGGTATTTCGCATGGATTCTGGGAACG	1	12	1
GGTCAACATCAGGCACCGGTTGCCACGGGGTTCTGGTAGTTT	4	32	1
CACGCGAGCTAAACACGGTTTCGCCGTCGGTTTCAACCAGCA	7	27	1
GGGCGGCAGTCAGAACGGAATATCGTGAGGATGAGTTGGCCA	7	81	1
GAGTTGGCCAAACCGAAGACTCCTGAAAGGTTAGATGTATTG	7	113	1
ATTACTTACAAATTTCCGAGTATTCCCAGGAATAATCTTCAT	7	166	1
          **   * *  *   *   ****
MAP Score: 3.65404

Motif 7
TTGAAGCAAATTTGCATTTTTCGACGGTGATCAATTT	0	59	0
ACGCCGTTTTTGTGTGCATTCACATGGTATGATGAAA	0	185	1
GGGCATGCGTGTGACCCTTTCTAACGGGGTTCACTCT	0	244	1
GAGCTAAAAATGTGGTATTTCGCATGGATTCTGGGAA	1	15	1
GCAACAAAAGTTAGAGCTTTTAAACGCTGCTACTATA	2	106	0
   TCGCGATGTTGACTGTTCGGACGGTCAACATCAG	4	7	1
GTCAACATCAGGCACCGGTTGCCACGGGGTTCTGGTA	4	33	1
GCCCCCAATGGGCGGCAGTCAGAACGGAATATCGTGA	7	72	1
TAATAACCTTTTTATTCTTTGCCACGGGTTCCGTGGC	7	229	0
          ** *   ***   ****
MAP Score: 3.43984

Motif 8
ACGGGGTTCACTCTCGGAGTCTTCATGCGATGAGCAAGGAGT	0	267	1
GGTGATTACCCCAAACGAACAGGCAAGAAGCGTTCCCAGAAT	1	42	0
GCTGGCGCTTGAACACGTCGAATCAGGCAAAGCCGGTCAAGA	1	86	1
CAAACCTCAATCGCGCGCGTATAGTAGCAGCGTTTAAAAGCT	2	87	1
      TTTACATCCCGGTAATGCAACAAAAGTTAGAGCTTT	2	123	0
TGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAA	3	26	1
TTGACTGTTCGGACGGTCAACATCAGGCACCGGTTGCCACGG	4	18	1
ATGAATATTCGCGGGCGCATCCTGAAGAATTGGCATAAAGCA	6	52	1
CACGGTTTCGCCGTCGGTTTCAACCAGCATGGGCCCCCAATG	7	40	1
CATGGGCCCCCAATGGGCGGCAGTCAGAACGGAATATCGTGA	7	67	1
ATGAGTTGGCCAAACCGAAGACTCCTGAAAGGTTAGATGTAT	7	111	1
CATAATCTCCCGCCACGGAACCCGTGGCAAAGAATAAAAAGG	7	218	1
          *   ***   *  *  ***  *
MAP Score: 3.2999

Motif 9
GCCGTTTTTGTGTGCATTCACATGGTATGATGAAA	0	187	1
GCTAAAAATGTGGTATTTCGCATGGATTCTGGGAA	1	17	1
GAACGCTTCTTGCCTGTTCGTTTGGGGTAATCACC	1	49	1
 TCGCGATGTTGACTGTTCGGACGGTCAACATCAG	4	9	1
GGGATTCCTGTTTTTATACGTCTGGATGTCTAAAC	6	13	1
TAAACTAGCATGAATATTCGCGGGCGCATCCTGAA	6	43	1
TTCTGCTTTATGCCAATTCTTCAGGATGCGCCCGC	6	62	0
AGGAATAATCTTCATGTTCACGCGGCATAATCTCC	7	193	1
          **   ******  **
MAP Score: 3.08306

Motif 10
AAATTGGCTGAAAGGCGGTAATTTAGCTATA	0	29	1
ACGTATATATTACGCCGCAAAATCCTTACAA	0	110	0
TGCACACAAAAACGGCGTAAAGAAAGGTTGC	0	172	0
GACCCTTTCTAACGGGGTTCACTCTCGGAGT	0	256	1
         GTAAGGAGCTAAAAATGTGGTA	1	1	1
CGAATCAGGCAAAGCCGGTCAAGAAGACATC	1	104	1
TGCTTGAAAGAGAGCGGGTAACAGGCGAACA	3	26	1
GAATTGGCATAAAGCAGAAAATTTTCGCAAA	6	78	1
TTAGATGTATTGAGCAGTTAAATATTACTTA	7	143	1
          ******* ***
MAP Score: 2.95178

Motif 11
GCCTTTCAGCCAATTTGATCGAGAACAATTTATCT  	0	8	0
AAATTGATCACCGTCGAAAAATGCAAATTTGCTTCAA	0	59	1
ACCCCGTTAGAAAGGGTCACACGCATGCCCCAATAGA	0	237	0
GGAGCTAAAAATGTGGTATTTCGCATGGATTCTGGGA	1	14	1
GGTGATTACCCCAAACGAACAGGCAAGAAGCGTTCCC	1	47	0
GCGCTTGAACACGTCGAATCAGGCAAAGCCGGTCAAG	1	90	1
ATACGTCTGGATGTCTAAACTAGCATGAATATTCGCG	6	28	1
TGAATATTCGCGGGCGCATCCTGAAGAATTGGCATAA	6	53	1
GTTTCGCCGTCGGTTTCAACCAGCATGGGCCCCCAAT	7	44	1
GTTGGCCAAACCGAAGACTCCTGAAAGGTTAGATGTA	7	115	1
GGAGATTATGCCGCGTGAACATGAAGATTATTCCTGG	7	191	0
          * *  * ***  *** *
MAP Score: 1.51057

Motif 12
ATAAATTGATCACCGTCGAAAAATGCAAATTTGCT	0	57	1
GGGGTTCACTCTCGGAGTCTTCATGCGATGAGCAA	0	269	1
ATGTCTTCTTGACCGGCTTTGCCTGATTCGACGTG	1	99	0
ACTACCAGAACCCCGTGGCAACCGGTGCCTGATGT	4	37	0
CCCTTATCTGGACCGATGGCCCACGATAATTTAGC	4	100	0
CATGAATATTCGCGGGCGCATCCTGAAGAATTGGC	6	51	1
TAACGCGCCACGCGAGCTAAACACGGTTTCGCCGT	7	19	1
CGGTTTCGCCGTCGGTTTCAACCAGCATGGGCCCC	7	42	1
CGGGAGATTATGCCGCGTGAACATGAAGATTATTC	7	195	0
          * *** ** * ** *
MAP Score: 0.154047