AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions002_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234357
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	aq_027	72	hypothetical protein
#1	aq_028	46	putative protein
#2	aq_035	32	hypothetical protein
#3	aq_083	264	hypothetical protein
#4	folK	300	folate biosynthesis 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
#5	aq_265	104	hypothetical protein
#6	aq_340	28	hypothetical protein
#7	aq_341	300	hypothetical protein
#8	aq_367	44	hypothetical protein
#9	gidA2	32	glucose inhibited division protein A
#10	aq_1151	48	hypothetical protein
#11	lysC	35	aspartokinase
#12	aq_1455	300	hypothetical protein

Motif 1
GAAAGCCGTAGAAGAGCTCAAGGAAAAGAACTTC   	0	48	1
ACCTTACTCTAAAAAAGAGCTGGAAGAAACGCCCGAG	3	23	1
CGAGAAGGTGGGAAATCGTAAAGAGAATAGCCCCTTC	3	56	1
CCTTGTAAAAGTAAACGATAAAGAAAACAAGAACGCT	3	95	1
CTGAGGAGGAAAAACCTCACGGGAAAGGTTACTATGG	3	130	1
TATACAGAAGAGCCAAAAAAGGGAAAAATCCCATAGT	3	160	0
ATTGCTGGACGTTCCATTTCTGGAAAGGATAAC    	3	241	1
AAGCTCGCCGGAAGCGTTGCAAGAGAAGGTGCTATTG	4	85	0
ATTTGTTTTAAGATATTCTAAGGAGAGGTTAGTATGA	4	205	0
AGCTTTATCAGGTGCAATAAAGGAAAGTTCAAGT   	4	276	1
CTTTAAATATAATCATTATCAGGAGTAATCTTATGGA	5	65	0
TAATGATTATATTTAAAGTAGGGAAAATAA       	5	84	1
AAAAATATACAATAAAGAACTGGAAAAAAGGCAGAAT	7	36	1
TCTTCTAACGGAAGCGGTAAAGGAAAACCTATTCGTA	7	92	1
CTTCAAAGATGGGCTGGTAATGGAATACGAATAGGTT	7	117	0
GCCCATCTTTGAAGCAAAAACGGGAAATTTGGCAGGA	7	140	1
CAGGATTTGAGGCACTGGTCAGGATAAAGAAGGAAAG	7	172	1
GAATGAGTTTATAAACTTTCTGGAAAATTCCCATTAC	7	220	1
CCATTACCTTGATTACTTCAGGGAATGGGCTTTAAAG	7	250	1
ATGGGCTTTAAAGGAAGTGACGGATAAAATAAAAAA 	7	274	1
        TAGAAACTTATACGGAAAATTACGAATAC	10	2	1
GAGCATTTCGGGCGTTCCGAAGGAAAGGGCAAATTTA	12	13	0
AAAAGAAATAAACAAGATGAAAGAAAAGATAAAGTAT	12	64	1
GTATGTACTTGAGGATAAGAAGGAAGAAGAGAATATC	12	139	1
TGCAACCATTGTATCTTTAAAGGAGAAGGAGGT    	12	277	1
          **  *    * ******
MAP Score: 20.6729

Motif 2
ACACCCCAAGGACAGGGAAAAAGCTCTGAAAG	0	21	1
CTCTAAAAAAGAGCTGGAAGAAACGCCCGAGA	3	29	1
AACGCCCGAGAAGGTGGGAAATCGTAAAGAGA	3	50	1
CAAGAACGCTGAGGAGGAAAAACCTCACGGGA	3	122	1
GAAGAGCCAAAAAAGGGAAAAATCCCATAGTA	3	159	0
ATCCTTTCCAGAAATGGAACGTCCAGCAATAT	3	239	0
CCCATCTAGTAAAGAGGGACAAGTTCGGAAGA	4	18	0
CCAAAGCTAAAAATTGGAAGGATTGAAGTAGA	4	168	0
ATTATATTTAAAGTAGGGAAAATAA       	5	89	1
       GCCAAACAGGAAGGTTATAACGTAG	7	3	1
ATACAATAAAGAACTGGAAAAAAGGCAGAATC	7	42	1
CTTTGAAGCAAAAACGGGAAATTTGGCAGGAT	7	146	1
GGTCAGGATAAAGAAGGAAAGATACATTACCC	7	188	1
CGTTCCGAAGGAAAGGGCAAATTTATCA    	12	6	0
AGAAATAAACAAGATGAAAGAAAAGATAAAGT	12	67	1
ACTTGAGGATAAGAAGGAAGAAGAGAATATCC	12	145	1
GTAAGTAGCAAAGCCGAAAAGTGGGGAGTCAA	12	192	0
          ***  *******
MAP Score: 19.0318

Motif 3
GAAAATCTACACCCCAAGGACAGGGAAAAAGCTCTGAAAG	0	13	1
AAAAGCTCTGAAAGCCGTAGAAGAGCTCAAGGAAAAGAAC	0	39	1
 GATTTTTTTACCTCCTGAAAAAATCTAAAATTAAATTTT	1	9	1
AATTTAACCTTACTCTAAAAAAGAGCTGGAAGAAACGCCC	3	17	1
AGCTGGAAGAAACGCCCGAGAAGGTGGGAAATCGTAAAGA	3	40	1
TAGCCCCTTCAGCCTTGTAAAAGTAAACGATAAAGAAAAC	3	83	1
CATATACAGAAGAGCCAAAAAAGGGAAAAATCCCATAGTA	3	159	0
TGTAAAGGAAACCGCTTAAAAAGCCTATAATACATATTGC	3	206	1
TCCTGGGAAAAGCTCGCCGGAAGCGTTGCAAGAGAAGGTG	4	91	0
  CCTTTTTTACCTCTATGAAAGTAATTAATTACTTATTG	5	8	1
GGAAGGTTATAACGTAGTAAAAATATACAATAAAGAACTG	7	18	1
TATACAATAAAGAACTGGAAAAAAGGCAGAATCTTTCATT	7	41	1
GCTCCTTCAAAGCACACAAAAAGAAATAAACAAGATGAAA	12	46	1
ATCGGGTCCTATCTCCCCGTAAGTAGCAAAGCCGAAAAGT	12	202	0
          * * *   *****     **
MAP Score: 12.2149

Motif 4
TTTTTTACCTCCTGAAAAAATCTAAAATTA	1	13	1
       ATACCTTATAAAGTATATATACT	2	19	0
GCCCCTTCAGCCTTGTAAAAGTAAACGATA	3	85	1
TATATGCTTTCGTTGTAAAGGAAACCGCTT	3	193	1
AAAGGAAACCGCTTAAAAAGCCTATAATAC	3	209	1
GTTGGTATATCCTGGGAAAAGCTCGCCGGA	4	110	0
ACTAACCTCTCCTTAGAATATCTTAAAACA	4	209	1
CTTTATTGCACCTGATAAAGCTTACTGGAC	4	268	0
TAAGATTACTCCTGATAATGATTATATTTA	5	69	1
AAGGTTATAACGTAGTAAAAATATACAATA	7	20	1
TCAAAGATGGGCTGGTAATGGAATACGAAT	7	122	0
GTTGCAGTTTCGTTGTAAAGCTTTACCTTT	12	253	0
          **********
MAP Score: 8.18447

Motif 5
AGGTGGGAAATCGTAAAGAGAATAGCCCCTT	3	61	1
TAAAAGTAAACGATAAAGAAAACAAGAACGC	3	100	1
ACAGAAGAGCCAAAAAAGGGAAAAATCCCAT	3	163	0
TATGCTTTCGTTGTAAAGGAAACCGCTTAAA	3	195	1
TTATCCTTTCCAGAAATGGAACGTCCAGCAA	3	242	0
TTATCAGGTGCAATAAAGGAAAGTTCAAGT 	4	280	1
        CTCCGTAAAGAATTAGAATAATA	6	15	0
         GCCAAACAGGAAGGTTATAACG	7	1	1
TAAAAATATACAATAAAGAACTGGAAAAAAG	7	35	1
CTAACGGAAGCGGTAAAGGAAAACCTATTCG	7	96	1
AAAGATGGGCTGGTAATGGAATACGAATAGG	7	119	0
AGGGAATGGGCTTTAAAGGAAGTGACGGATA	7	269	1
TTCAAAGCACACAAAAAGAAATAAACAAGAT	12	51	1
CCTCCTTCTCCTTTAAAGATACAATGGTTGC	12	278	0
          * *********
MAP Score: 6.62769

Motif 6
TACACCCCAAGGACAGGGAAAAAGCTCTGAA	0	20	1
TCTTTTTTAGAGTAAGGTTAAATTAGTAGTT	3	10	0
GTGGGAAATCGTAAAGAGAATAGCCCCTTCA	3	63	1
CTTCAGCCTTGTAAAAGTAAACGATAAAGAA	3	89	1
CAAGAACGCTGAGGAGGAAAAACCTCACGGG	3	122	1
AAACCTCACGGGAAAGGTTACTATGGGATTT	3	141	1
AGAAGAGCCAAAAAAGGGAAAAATCCCATAG	3	161	0
TGCTTTCGTTGTAAAGGAAACCGCTTAAAAA	3	197	1
TTCCATTTCTGGAAAGGATAAC         	3	252	1
CCCATCTAGTAAAGAGGGACAAGTTCGGAAG	4	19	0
GATATTCTAAGGAGAGGTTAGTATGAACTTA	4	200	0
AATTACTTTCATAGAGGTAAAAAAGG     	5	5	0
ATACAATAAAGAACTGGAAAAAAGGCAGAAT	7	42	1
AACGGAAGCGGTAAAGGAAAACCTATTCGTA	7	98	1
CTTCAAAGATGGGCTGGTAATGGAATACGAA	7	123	0
TGGTCAGGATAAAGAAGGAAAGATACATTAC	7	187	1
AGTAATCAAGGTAATGGGAATTTTCCAGAAA	7	236	0
GCGTTCCGAAGGAAAGGGCAAATTTATCA  	12	8	0
ACAAGATGAAAGAAAAGATAAAGTATCCCGA	12	75	1
TCGCTATACAAGAGAAGTTAAAAGTGAGTTC	12	104	0
TAAGGACTTCAGAAAGGTAAAGCTTTACAAC	12	241	1
          ******* ***
MAP Score: 3.86438

Motif 7
CCCAAGGACAGGGAAAAAGCTCTGAAAGCCGTA	0	25	1
AAATCGTAAAGAGAATAGCCCCTTCAGCCTTGT	3	68	1
AACGCTGAGGAGGAAAAACCTCACGGGAAAGGT	3	126	1
AAAACCTCACGGGAAAGGTTACTATGGGATTTT	3	140	1
AGCCAAAAAAGGGAAAAATCCCATAGTAACCTT	3	154	0
AAGCAAAAACGGGAAATTTGGCAGGATTTGAGG	7	151	1
ATAAACTTTCTGGAAAATTCCCATTACCTTGAT	7	230	1
GATTACTTCAGGGAATGGGCTTTAAAGGAAGTG	7	260	1
GAAGGAAGAAGAGAATATCCTCATATCTCAGAA	12	157	1
          *******  * **
MAP Score: 2.01571