AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons032_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236188
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	aq_394	147	putative protein
#1	hdrA	57	heterodisulfide reductase subunit A
#2	aq_401	74	putative protein
#3	aq_402	27	putative protein
#4	aq_403	42	putative protein
#5	tsf	76	elongation factor EF-Ts
#6	aq_716	110	putative protein
#7	aq_1247	66	putative protein
#8	rpsB	91	ribosomal protein S02
#9	aq_2011	74	putative protein

Motif 1
GACAAAGACCAGCAGCTTCCACAGCTGTTA	0	103	1
TACTTGTGCTCCAAGCTTCTTTATAACAGC	0	126	0
GGGGGCTCTTGCCCCCTTCTATAAATCCTT	1	22	1
       TATTTTCCCTCCTAAAAGGATTT	1	44	0
        AGCACACCTCCCTTAAATTTAT	3	15	0
          TTCCCCTTCTCTCTCCTTTT	4	0	1
          TACCGCTCCCTCAAAAGGTT	4	32	0
CGGGATAGTTCACACTTTCCTCCCGCAAAA	5	12	1
        AACCTACCTCCCGACATTATTA	7	54	0
TTCTTTAAACCGCACCTTCCCCGCTTGGGT	8	16	1
CTTGGGTTGCCCCAGCTTCGGGGTGATGGG	8	39	1
TGGGTTTTGCCACCCTTCCCCATCACCCCG	8	57	0
      ACTTCACACCTCCTTGGGTTTTGC	8	77	0
          **********
MAP Score: 12.8716

Motif 2
GTCCGTTGTAAACTTCGGGGTCGTAGGGGT	0	76	0
AAAAGGATTTATAGAAGGGGGCAAGAGCCC	1	24	0
TTAAAAGGAGAGAGAAGGGGAA        	4	2	0
TAATTAGAAAAGATAAGCGGAGGT      	5	62	1
ATTTTATAGTAAATCCGCGGGCTAAAACCG	6	17	1
CCCGTATCATAGATACGCGGTTTTAGCCCG	6	34	0
CGCGTATCTATGATACGGGGACAGAAGCCG	6	45	1
GGGTTGCCCCAGCTTCGGGGTGATGGGGAA	8	42	1
          **********
MAP Score: 11.3006

Motif 3
     TGTCTTTTGCCCGCCTTTTGGCGGGC	2	5	1
TAAACCGCACCTTCCCCGCTTGGGTTGCCCC	8	21	1
CCCGCTTGGGTTGCCCCAGCTTCGGGGTGAT	8	35	1
        TATTTTCCCTCCTAAAAGGATTT	1	44	0
AGACCAGCAGCTTCCACAGCTGTTATAAAGA	0	108	1
CATGGGGGCTCTTGCCCCCTTCTATAAATCC	1	19	1
TACACAACGCTTGCCACACCTGGAAGATGAT	0	34	1
TTTTGCCACCCTTCCCCATCACCCCGAAGCT	8	52	0
CAGGCGGCTTCTGTCCCCGTATCATAGATAC	6	48	0
          ******* ***
MAP Score: 11.1416

Motif 4
ACCCCGAAGTTTACAACGGACAAAGACCAGCAG	0	85	1
TCCACAGCTGTTATAAAGAAGCTTGGAGCACAA	0	120	1
ATAAATCCTTTTAGGAGGGAAAATA        	1	42	1
TTGGCGGGCTTTAAAAATAAAAAAAATTAATGG	2	27	1
CTCAAAAGGTTTTAAAAGGAGAGAGAAGGGGAA	4	10	0
TTTTAAAACCTTTTGAGGGAGCGGTA       	4	26	1
TATAACAGGCTCAAAAGGGAACTTTTGCGGGAG	5	31	0
CCTGTTATAATTAGAAAAGATAAGCGGAGGT  	5	55	1
AAGCAGTTTTTTAAAATGAATCTTGTGAGGTCA	6	82	1
GAAGGATTTATTATAAAGAACAAATTGTAAGAT	7	22	1
GAAGGTGCGGTTTAAAGAAATAATT        	8	2	0
GTGCACGACTTTCTGAGGAATCTCATACTGAGT	9	23	0
          TTAAGATAAACATATTAAAGACT	9	61	0
          *** ** *** **
MAP Score: 7.28591

Motif 5
TTGCTATACACAACGCTTGCCACACCTGGAAGATG	0	28	1
TAGCTGACGACTACCCCTACGACCCCGAAGTTTAC	0	64	1
GCGGGATAGTTCACACTTTCCTCCCGCAAAAGTTC	5	11	1
TTTCTTTAAACCGCACCTTCCCCGCTTGGGTTGCC	8	15	1
TTGGGTTTTGCCACCCTTCCCCATCACCCCGAAGC	8	53	0
          * ** *** ** * *
MAP Score: 5.11818

Motif 6
AGCTTCCACAGCTGTTATAAAGAAGCTTGGAGCA	0	116	1
CCTTTTGGCGGGCTTTAAAAATAAAAAAAATTAA	2	23	1
AAAAATTAATGGAGATATAAATAGAGGTAAAGGA	2	48	1
TCCCTCAAAAGGTTTTAAAAGGAGAGAGAAGGGG	4	12	0
CCCTTTTGAGCCTGTTATAATTAGAAAAGATAAG	5	45	1
TTTAGCCCGCGGATTTACTATAAAATACAAGTA 	6	9	0
ACCTCCTGAAGGATTTATTATAAAGAACAAATTG	7	15	1
CGGGGAAGGTGCGGTTTAAAGAAATAATT     	8	5	0
          ** **** **  **
MAP Score: 4.37917

Motif 7
AGTCGTCAGCTATCATCTTCCAGGTGTGGCAAG	0	43	0
CTGACGACTACCCCTACGACCCCGAAGTTTACA	0	67	1
GGACAAAGACCAGCAGCTTCCACAGCTGTTATA	0	102	1
        TTCCCCTTCTCTCTCCTTTTAAAAC	4	2	1
        TACCGCTCCCTCAAAAGGTTTTAAA	4	27	0
GGATAGTTCACACTTTCCTCCCGCAAAAGTTCC	5	14	1
          AACCTACCTCCCGACATTATTAT	7	53	0
TTTCTTTAAACCGCACCTTCCCCGCTTGGGTTG	8	15	1
GCTTGGGTTGCCCCAGCTTCGGGGTGATGGGGA	8	38	1
GGGTTTTGCCACCCTTCCCCATCACCCCGAAGC	8	53	0
          ***** ** ** *
MAP Score: 2.08149

Motif 8
TTGTGTATAGCAACCCTTACGTTGGAAACA	0	11	0
TTGCTATACACAACGCTTGCCACACCTGGA	0	28	1
TAGCTGACGACTACCCCTACGACCCCGAAG	0	64	1
GGGGGCAAGAGCCCCCATGTATGTGTGT  	1	8	0
GGGGGCTCTTGCCCCCTTCTATAAATCCTT	1	22	1
  TGTCTTTTGCCCGCCTTTTGGCGGGCTT	2	8	1
    AGCACACCTCCCTTAAATTTATTGAA	3	11	0
TCCCGCAAAAGTTCCCTTTTGAGCCTGTTA	5	32	1
        ACCTCCGCTTATCTTTTCTAAT	5	64	0
ACCGCACCTTCCCCGCTTGGGTTGCCCCAG	8	24	1
TTGGGTTTTGCCACCCTTCCCCATCACCCC	8	58	0
          **********
MAP Score: 2.00551

Motif 9
CTACGACCCCGAAGTTTACAACGGACAAAGACCAG	0	80	1
GCCTTTTGGCGGGCTTTAAAAATAAAAAAAATTAA	2	22	1
TCCCTCAAAAGGTTTTAAAAGGAGAGAGAAGGGGA	4	11	0
TTTTGAGCCTGTTATAATTAGAAAAGATAAGCGGA	5	48	1
     TACTTGTATTTTATAGTAAATCCGCGGGCT	6	5	1
TGTGTAAGCAGTTTTTTAAAATGAATCTTGTGAGG	6	77	1
CTTACAATTTGTTCTTTATAATAAATCCTTCAGGA	7	18	0
CGGGGAAGGTGCGGTTTAAAGAAATAATT      	8	4	0
          *   **** ** ***
MAP Score: 0.23357