AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons029_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236069
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	proS	44	proline-tRNA synthetase
#1	rplT	54	ribosomal protein L20
#2	aq_1666	252	hypothetical protein
#3	thrS	36	threonyl-tRNA synthetase
#4	pheT	300	phenylalanyl-tRNA synthetase beta subunit
#5	infC	300	initiation factor IF-3
#6	aco	52	aconitase
#7	aq_1791	40	putative protein
#8	ntrC2	209	transcriptional regulator (NtrC family)

Motif 1
    GCGATGCCTCCTTTTACGAGAGAGGTT	1	37	0
      TCTCCCCTCTTTTCCCGCTTTTATT	2	4	1
AGGTGAGAAAGCCCCTCCCTCCCCCCACCTC	2	177	1
CCCCTCCCTCCCCCCACCTCCCTCCACCGAT	2	188	1
CCGATTTTTGGCCTCCCGCCCGGGAGGCCCT	2	214	1
ATTACTTCCTGCCCCTCTTCCCTCATGCTTT	4	88	1
TCGTGGATTACCCCCCTTCCGCGGAAAGCGT	4	124	0
CTCAGGATTTGTCCCGTTTCCATTTCTTCCA	4	160	1
GGTGAGGTATGCCCCTTTACCTTCGTGAAGA	4	203	0
TCTTTGTCAACCTTCACGTCCATAACTCTTA	4	247	1
TTTCTATGCTCCCCAATTTCCTTTTGAACTC	5	154	0
   TTCCGAACCTCCGTTTCGTGTGGTGGAC	7	22	0
ATTCCGTCAAGCCCCTTTTTCATTCCTGCGC	8	78	1
AAGGTAAGGCGCTTCGTTCCGAAGAAAGTTC	8	165	1
          ***** *****
MAP Score: 17.8591

Motif 2
TATAACTGTCAATGGTTTGAAAACTACGGAGA	2	87	1
ATGCAATTGAAATTTTTTTGCAAGTTCTCCTA	2	129	0
CTCTACTATTAAATTTATGCAATTGAAATTTT	2	145	0
TTTACGGAAAAATTTTATGGAACTTTTACAGA	5	14	1
ACTGTTGTTTAACTTTTTTGAAGGAGTTATAT	5	75	1
GAACTCCTTCAATTTTTTTGAAATGAATACGT	5	128	0
CTGATAGGGTAAAGTTCAGGAAGCTTTCTTAC	5	203	1
TTGACAACATAAAGTTTAGGAATAAAACGCTC	5	243	0
GAAGTTTTAAAATTGTTTTGAAAGGAGGTCAG	6	29	1
AGCCTATCCGAACTTTGTGAAAAAGGTTTTAA	8	125	1
CGTTCCGAAGAAAGTTCTTGAAAAGCTAAATT	8	179	1
          ** *** *****
MAP Score: 12.5077

Motif 3
TTATGTTAAAATAACCTCTCTCGTAAAAGGAGG	1	25	1
         TCTCCCCTCTTTTCCCGCTTTTAT	2	1	1
GCAAGTTCTCCTAACTTCTTCATTCTCCGTAGT	2	109	0
GAGGGGCTTTCTCACCTCTCTACTATTAAATTT	2	161	0
GAGGTGAGAAAGCCCCTCCCTCCCCCCACCTCC	2	176	1
CCTCCCTCCCCCCACCTCCCTCCACCGATTTTT	2	190	1
TATTTTAGAAAGGGCCTCCCGGGCGGGAGGCCA	2	222	0
GTTCACCGCTATTACTTCCTGCCCCTCTTCCCT	4	78	1
TCCTGCCCCTCTTCCCTCATGCTTTTGGGAACG	4	94	1
TCGTGGATTACCCCCCTTCCGCGGAAAGCGTTC	4	122	0
GGTAAAGGGGCATACCTCACCCCTTATGTCAAG	4	213	1
AGCTCTTTGTCAACCTTCACGTCCATAACTCTT	4	244	1
          CTAACCTCCTCATAGATTTTTAT	5	287	0
         ACTGACCTCCTTTCAAAACAATTT	6	38	0
       TTCCGAACCTCCGTTTCGTGTGGTGG	7	24	0
AACGAAGCGCCTTACCTTTTCACTGTTTAAAAC	8	150	0
          *  ******** *
MAP Score: 11.0294

Motif 4
CTACGGAGAATGAAGAAGTTAGGAGAACTTG	2	110	1
        ATTGAAAAAGATAAGCTAAGCCT	3	2	1
ATTAAGAAAGTGAAATGAAAATACTCCTATT	4	17	0
GTAATAGCGGTGAACCAGATAGGTGAAAACC	4	62	0
TCGCCTTGGAAGAAATGGAAACGGGACAAAT	4	166	0
TTTACCTTCGTGAAGAGTAAACTCGCCTTGG	4	188	0
GTAAAGGAGAAGAACAGGTAAAAATATTCTG	5	42	0
TTAACTTTTTTGAAGGAGTTATATTATTTTT	5	83	1
TCAATTTTTTTGAAATGAATACGTTGACACC	5	121	0
TTGAAGGAGTTCAAAAGGAAATTGGGGAGCA	5	148	1
TTAATCATCCTGATAGGGTAAAGTTCAGGAA	5	194	1
TAAAAATCTATGAGGAGGTTAG         	5	288	1
TTCCGAATATTGAAAGGATAACTCCGCAAAT	8	24	0
TTTTAAACAGTGAAAAGGTAAGGCGCTTCGT	8	151	1
AGAAAGTTCTTGAAAAGCTAAATTAAAAATA	8	187	1
          ***** *****
MAP Score: 10.5318

Motif 5
     AGGAATATTTTACGAAACTTAAAATATGTA	0	24	0
CTCTTTTCCCGCTTTTATTAATCCTCTTATGATAG	2	16	1
CTTCCCTCATGCTTTTGGGAACGCTTTCCGCGGAA	4	104	1
CTTATGTCAAGCTCTTTGTCAACCTTCACGTCCAT	4	235	1
TTTACGGAAAAATTTTATGGAACTTTTACAGAATA	5	14	1
TCCTTTACGGACTGTTGTTTAACTTTTTTGAAGGA	5	65	1
AGAAAACCTTGATTTTAATCATCCTGATAGGGTAA	5	180	1
GCGCTCTTTTGCTTTTACAAAGCCTATCCGAACTT	8	105	1
TTACCTTTTCACTGTTTAAAACCTTTTTCACAAAG	8	137	0
TTTTAATTTAGCTTTTCAAGAACTTTCTTCGGAAC	8	180	0
          ******    * ***
MAP Score: 10.469

Motif 6
GAATATTTTACGAAACTTAAAATATGTATACATTT	0	17	0
         TCCAGACTTAAAATTTTATGTTAAAA	1	1	1
TCTCACCTCTCTACTATTAAATTTATGCAATTGAA	2	150	0
GCCCGGGAGGCCCTTTCTAAAATAAATAGCG    	2	231	1
AAAAGATAAGCTAAGCCTAAAATAAATCTCT    	3	15	1
ATTTAAACCCCTTCGTTTAAAATAATCAATT    	4	279	1
CGTTGACACCCAAGCCTAAAAATAATATAACTCCT	5	96	0
TACCCTATCAGGATGATTAAAATCAAGGTTTTCTA	5	179	0
    AGGTTTCTAATTTTAAAATGAAGTTTTAAAA	6	6	1
TCTTGAAAAGCTAAATTAAAAATAA          	8	194	1
          * *   ******* *
MAP Score: 9.47455

Motif 7
GAAAACTACGGAGAATGAAGAAGTTAGGAGAACTTGC	2	105	1
GCATAAATTTAATAGTAGAGAGGTGAGAAAGCCCCTC	2	157	1
       ATTGAAAAAGATAAGCTAAGCCTAAAATAA	3	3	1
AGAGCTTGACATAAGGGGTGAGGTATGCCCCTTTACC	4	213	0
ACAACAGTCCGTAAAGGAGAAGAACAGGTAAAAATAT	5	46	0
AGTTCAAAAGGAAATTGGGGAGCATAGAAAACCTTGA	5	155	1
TAATCATCCTGATAGGGTAAAGTTCAGGAAGCTTTCT	5	195	1
AATCGTTGTTGACAACATAAAGTTTAGGAATAAAACG	5	246	0
TTGTATAAAAATCTATGAGGAGGTTAG          	5	283	1
AAAGGTTTTAAACAGTGAAAAGGTAAGGCGCTTCGTT	8	146	1
          ** *  *  *** * **
MAP Score: 6.67612

Motif 8
TCCAGACTTAAAATTTTATGTTAAAATAACCTCTCTCGT	1	10	1
ATGCAATTGAAATTTTTTTGCAAGTTCTCCTAACTTCTT	2	122	0
GATAGGTGAAAACCTCTGGGAGATTATAATTAAGAAAGT	4	37	0
CCCTTATGTCAAGCTCTTTGTCAACCTTCACGTCCATAA	4	233	1
TTTTACGGAAAAATTTTATGGAACTTTTACAGAATATTT	5	13	1
ACTGTTGTTTAACTTTTTTGAAGGAGTTATATTATTTTT	5	75	1
GAACTCCTTCAATTTTTTTGAAATGAATACGTTGACACC	5	121	0
CCTTGATTTTAATCATCCTGATAGGGTAAAGTTCAGGAA	5	186	1
TTTTATTCCTAAACTTTATGTTGTCAACAACGATTTTGT	5	248	1
ATTTTGTATAAAAATCTATGAGGAGGTTAG         	5	280	1
AACAATTTTAAAACTTCATTTTAAAATTAGAAACCT   	6	7	0
CACTGTTTAAAACCTTTTTCACAAAGTTCGGATAGGCTT	8	124	0
CGTTCCGAAGAAAGTTCTTGAAAAGCTAAATTAAAAATA	8	179	1
          **  *** **  *   * *
MAP Score: 5.93015

Motif 9
CTCCTTTTACGAGAGAGGTTATTTTAACAT	1	27	0
ATAAAAGCGGGAAAAGAGGGGAGA      	2	4	0
CTACGGAGAATGAAGAAGTTAGGAGAACTT	2	110	1
AATTTAATAGTAGAGAGGTGAGAAAGCCCC	2	162	1
GTGGGGGGAGGGAGGGGCTTTCTCACCTCT	2	175	0
ATCGGTGGAGGGAGGTGGGGGGAGGGAGGG	2	189	0
AAAGCATGAGGGAAGAGGGGCAGGAAGTAA	4	89	0
CCCCTTCCGCGGAAAGCGTTCCCAAAAGCA	4	113	0
CGCTTTCCGCGGAAGGGGGGTAATCCACGA	4	125	1
TCTTCACGAAGGTAAAGGGGCATACCTCAC	4	203	1
TTATTTTAAACGAAGGGGTTTAAATTTAAG	4	274	0
 CACTTTTACGGAAAAATTTTATGGAACTT	5	9	1
TTAACTTTTTTGAAGGAGTTATATTATTTT	5	83	1
TTTTTTGAAATGAATACGTTGACACCCAAG	5	117	0
TCAAAAAAATTGAAGGAGTTCAAAAGGAAA	5	139	1
TAAAAATCTATGAGGAGGTTAG        	5	288	1
AAATTGTTTTGAAAGGAGGTCAGT      	6	38	1
GCGCAGGAATGAAAAAGGGGCTTGACGGAA	8	79	0
CCGAACTTTGTGAAAAAGGTTTTAAACAGT	8	132	1
          **********
MAP Score: 5.04838

Motif 10
TTTATGTTAAAATAACCTCTCTCGTAAAAGGAGG	1	24	1
         TCTCCCCTCTTTTCCCGCTTTTATT	2	1	1
AGAGGTGAGAAAGCCCCTCCCTCCCCCCACCTCC	2	175	1
CCCTCCCTCCCCCCACCTCCCTCCACCGATTTTT	2	189	1
AGTGAAATGAAAATACTCCTATTCATAACG    	4	6	0
GCTATTACTTCCTGCCCCTCTTCCCTCATGCTTT	4	85	1
GTTCTCGTGGATTACCCCCCTTCCGCGGAAAGCG	4	125	0
AGGGGCATACCTCACCCCTTATGTCAAGCTCTTT	4	218	1
TCTTAAATTTAAACCCCTTCGTTTAAAATAATCA	4	273	1
          ACTGACCTCCTTTCAAAACAATTT	6	38	0
ATAATTCCGTCAAGCCCCTTTTTCATTCCTGCGC	8	75	1
GTGAAAAGGTAAGGCGCTTCGTTCCGAAGAAAGT	8	160	1
          *   ****** ***
MAP Score: 2.63235

Motif 11
       TCTCCCCTCTTTTCCCGCTTTTATTA	2	3	1
TGAGAAAGCCCCTCCCTCCCCCCACCTCCCTCC	2	180	1
CCTCCCCCCACCTCCCTCCACCGATTTTTGGCC	2	194	1
TTACTTCCTGCCCCTCTTCCCTCATGCTTTTGG	4	89	1
GGTAAAGGGGCATACCTCACCCCTTATGTCAAG	4	213	1
          ** *****  ***
MAP Score: 1.20368

Motif 12
       TCTCCCCTCTTTTCCCGCTTTTATTAATCCTCTTATGATAG	2	3	1
CCACCTCCCTCCACCGATTTTTGGCCTCCCGCCCGGGAGGCCCTTTCT	2	201	1
GAGGTTTTCACCTATCTGGTTCACCGCTATTACTTCCTGCCCCTCTTC	4	60	1
ACTTCCTGCCCCTCTTCCCTCATGCTTTTGGGAACGCTTTCCGCGGAA	4	91	1
CCACGAGAACCCTCAGGATTTGTCCCGTTTCCATTTCTTCCAAGGCGA	4	149	1
GCATACCTCACCCCTTATGTCAAGCTCTTTGTCAACCTTCACGTCCAT	4	222	1
CTTTTTCATTCCTGCGCTCTTTTGCTTTTACAAAGCCTATCCGAACTT	8	92	1
          ** *     **  **  *        **
MAP Score: 0.603994