AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons029_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236090
 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
ATGTATACATATTTTAAGTTTCGTAAAATATTC	0	19	1
TTAACATAAAATTTTAAGTCTGGA         	1	1	0
CCCTCCACCGATTTTTGGCCTCCCGCCCGGGAG	2	207	1
  CGCTATTTATTTTAGAAAGGGCCTCCCGGGC	2	231	0
  AGAGATTTATTTTAGGCTTAGCTTATCTTTT	3	15	0
  AATTGATTATTTTAAACGAAGGGGTTTAAAT	4	279	0
GAGTTATATTATTTTTAGGCTTGGGTGTCAACG	5	98	1
GAAAACCTTGATTTTAATCATCCTGATAGGGTA	5	181	1
TTAAAACTTCATTTTAAAATTAGAAACCT    	6	6	0
TTTCAAAACAATTTTAAAACTTCATTTTAAAAT	6	19	0
        TTATTTTTAATTTAGCTTTTCAAGA	8	194	0
          ********  * *
MAP Score: 11.5524

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
CGATTTTTGGCCTCCCGCCCGGGAGGCCCTTTC	2	215	1
GTTCACCGCTATTACTTCCTGCCCCTCTTCCCT	4	78	1
TCCTGCCCCTCTTCCCTCATGCTTTTGGGAACG	4	94	1
CGTGGATTACCCCCCTTCCGCGGAAAGCGTTCC	4	121	0
GGTAAAGGGGCATACCTCACCCCTTATGTCAAG	4	213	1
AGCTCTTTGTCAACCTTCACGTCCATAACTCTT	4	244	1
          CTAACCTCCTCATAGATTTTTAT	5	287	0
         ACTGACCTCCTTTCAAAACAATTT	6	38	0
       TTCCGAACCTCCGTTTCGTGTGGTGG	7	24	0
          *  ******** *
MAP Score: 11.546

Motif 4
TACGAGAGAGGTTATTTTAACATAAAATTTTAAGTCTGG	1	11	0
TGACAGTTATAATAATATTACAATAAAATATAACTTGTT	2	59	0
GAAGAAGTTAGGAGAACTTGCAAAAAAATTTCAATTGCA	2	121	1
TTGCAAAAAAATTTCAATTGCATAAATTTAATAGTAGAG	2	138	1
AAAGTTCCATAAAATTTTTCCGTAAAAGTG         	5	1	0
AAAATATTCTGTAAAAGTTCCATAAAATTTTTCCGTAAA	5	14	0
AAAATTTTATGGAACTTTTACAGAATATTTTTACCTGTT	5	22	1
TAAAAATAATATAACTCCTTCAAAAAAGTTAAACAACAG	5	76	0
GGGTGTCAACGTATTCATTTCAAAAAAATTGAAGGAGTT	5	120	1
TGTTGTCAACAACGATTTTGTATAAAAATCTATGAGGAG	5	266	1
       ACTGACCTCCTTTCAAAACAATTTTAAAACTT	6	30	0
TCACTGTTTAAAACCTTTTTCACAAAGTTCGGATAGGCT	8	125	0
          *      ** ** **** *
MAP Score: 10.7834

Motif 5
       TCTCCCCTCTTTTCCCGCTTTTAT	2	3	1
GTGAGAAAGCCCCTCCCTCCCCCCACCTCCC	2	179	1
CCCTCCCTCCCCCCACCTCCCTCCACCGATT	2	189	1
TTACTTCCTGCCCCTCTTCCCTCATGCTTTT	4	89	1
TCGTGGATTACCCCCCTTCCGCGGAAAGCGT	4	124	0
          **** ******
MAP Score: 8.07286

Motif 6
ATATTTTAAGTTTCGTAAAATATTCCT   	0	27	1
AAATAACCTCTCTCGTAAAAGGAGGCATCG	1	33	1
GCCCCTTTACCTTCGTGAAGAGTAAACTCG	4	194	0
CATAAAATTTTTCCGTAAAAGTG       	5	3	0
TCTGTAAAAGTTCCATAAAATTTTTCCGTA	5	16	0
GGTAAAAATATTCTGTAAAAGTTCCATAAA	5	27	0
TTAAACAACAGTCCGTAAAGGAGAAGAACA	5	57	0
TCAACAACGATTTTGTATAAAAATCTATGA	5	271	1
ACTCCGCAAATCACGTAAAGAAACT     	8	5	0
CTACCGATAATTCCGTCAAGCCCCTTTTTC	8	69	1
TTCGGATAGGCTTTGTAAAAGCAAAAGAGC	8	107	0
CCTATCCGAACTTTGTGAAAAAGGTTTTAA	8	127	1
          **********
MAP Score: 6.76581

Motif 7
         TCTCCCCTCTTTTCCCGCTTTTA	2	1	1
GAGGGGCTTTCTCACCTCTCTACTATTAAATT	2	162	0
GAGGTGAGAAAGCCCCTCCCTCCCCCCACCTC	2	176	1
CCTCCCTCCCCCCACCTCCCTCCACCGATTTT	2	190	1
CCCGCCCGGGAGGCCCTTTCTAAAATAAATAG	2	228	1
TTAGGCTTAGCTTATCTTTTTCAAT       	3	3	0
CTATTACTTCCTGCCCCTCTTCCCTCATGCTT	4	86	1
TCGTGGATTACCCCCCTTCCGCGGAAAGCGTT	4	123	0
GGGGTGAGGTATGCCCCTTTACCTTCGTGAAG	4	204	0
AGGGGCATACCTCACCCCTTATGTCAAGCTCT	4	218	1
CCCTTATGTCAAGCTCTTTGTCAACCTTCACG	4	233	1
TTTACCTGTTCTTCTCCTTTACGGACTGTTGT	5	51	1
GTTTTCTATGCTCCCCAATTTCCTTTTGAACT	5	155	0
         ACTGACCTCCTTTCAAAACAATT	6	39	0
       TTCCGAACCTCCGTTTCGTGTGGTG	7	25	0
TAATTCCGTCAAGCCCCTTTTTCATTCCTGCG	8	76	1
TTTTTCATTCCTGCGCTCTTTTGCTTTTACAA	8	93	1
TTCACTGTTTAAAACCTTTTTCACAAAGTTCG	8	133	0
          *  *********
MAP Score: 0.839666