AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241374
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0208	112	signal-transducing histidine kinase
#1	AF1466	300	conserved hypothetical protein
#2	AF1467	70	signal-transducing histidine kinase
#3	AF1721	182	signal-transducing histidine kinase
#4	AF1766	74	amino-acid ABC transporter, periplasmic binding protein/protein kinase
#5	AF2032	185	signal-transducing histidine kinase, putative
#6	AF2420	40	signal-transducing histidine kinase, putative
#7	AF2421	58	leucyl-tRNA synthetase (leuS)
#8	AF2425	85	methanol dehydrogenase regulatory protein (moxR)

Motif 1
CCCCAAGGTAAAAAAGTTTTATTGGTTTAT	0	22	1
TGCGTCAGGTAAAAAGTTTTCCCATCATAA	5	150	0
        TCAAAAAGTTTTTTATTTTTGA	6	2	1
CATGCGCTTTAAAAAGTTTTGGTTCGCCCA	3	103	1
GGGAGTGATGAAAAAGTTCTCTGGAAAAGA	3	65	0
GAGGATTATTAAAAATTTCTCACCAAACGC	4	27	1
ATACAAAGACATAAATTTTTTTGAAAAGAA	0	50	1
AAGAGTACGGATAAAGGTTTAGGAGTCATC	1	254	1
          **********
MAP Score: 15.7495

Motif 2
AGAATTGGCAGTTAGGTTTATTAATTACCTCAACGTAATAACA	0	76	1
AACGAGGGGGGCGATGTTTCCAGCTATCCGCACGCTCGTGGCC	1	124	1
CTCTTTTCCAGAGAACTTTTTCATCACTCCCACCACCAGCATG	3	64	1
ACTGCTGCAAGCTAAGTTTTAAAAACTACTTACCTTTGTAGGA	3	147	1
AGCGTTTGGTGAGAAATTTTTAATAATCCTCACGAACATCCGA	4	15	0
TCTCACAACAGCGTTTTTTTGAAGAACTCTGAAGTCACTTAAC	5	12	1
 TCAAAAAGTTTTTTATTTTTGAATTTCCCTAATTGTGATA  	6	9	1
AATCTGCTATTTGACGTTTCCCATAGCTCTAACCCTCCTACCA	8	24	1
          * **  ***   *     *  **
MAP Score: 4.35493

Motif 3
TTACCTTGGGGCGAGGAGGAGCG        	0	2	0
ACCCCTCAAAGCGTGGTGCTGCGATAGACCC	1	68	1
TAATCAACGAGGGGGGCGATGTTTCCAGCTA	1	119	1
CGGGCCACGAGCGTGCGGATAGCTGGAAACA	1	138	0
CTCGTGGCCCGCAGGGGGATGTTGTAAGAAT	1	158	1
TTTTTAAAGCGCATGCTGGTGGTGGGAGTGA	3	87	0
TTAAAACTTAGCTTGCAGCAGTGCAATTACC	3	138	0
TTGTTTGCTTCCGTGCTGGTGCTGCCCGCTA	5	88	1
          ****** ****
MAP Score: 4.33852

Motif 4
GGCGATGTTTCCAGCTATCCGCACGCTCGTGGCCCG	1	133	1
GATGGGAAAAACTGCTGACCGTAAACTCAAGTATCC	1	213	0
TGACTCCTAAACCTTTATCCGTACTCTTATGTCGAT	1	246	0
TTTTCCAGAGAACTTTTTCATCACTCCCACCACCAG	3	67	1
ATTATTAAAAATTTCTCACCAAACGCTTTTATAAGT	4	31	1
TGATGGGAAAACTTTTTACCTGACGCATCAAAGTAG	5	153	1
  CTTTTGGTCAATCAGGCCAAACGCCAAATTTTTT	7	8	1
CTGCTATTTGACGTTTCCCATAGCTCTAACCCTCCT	8	27	1
ACCCTCCTACCATTCTTCCAAAACACACATATATTG	8	55	1
          ** ***  **  ** *
MAP Score: 4.33441

Motif 5
     CGCTCCTCCTCGCCCCAAGGTAAAAAAG	0	5	1
TATTAATTACCTCAACGTAATAACAATA     	0	94	1
AGCAGTTTTTCCCATCGACATAAGAGTACGGAT	1	233	1
AGGTTTAGGAGTCATCAACCTAAAATTACCTGG	1	268	1
AATGATAACTCTCATCACTTTAATTGTTATGAT	5	124	1
AAAAAGTTTTCCCATCATAACAATTAAAGTGAT	5	137	0
TTTGACGTTTCCCATAGCTCTAACCCTCCTACC	8	33	1
          *******   ***
MAP Score: 2.52616

Motif 6
GGCAGTTAGGTTTATTAATTACCTCAACGTAATAACAATA   	0	82	1
GTCAGCAGTTTTTCCCATCGACATAAGAGTACGGATAAAGGTT	1	230	1
GCACATTTTCTTTTCCTCTTTCTTAAATGCCCTTGAACCCTTT	2	29	1
TTTTACTTCTTTTCTAAAGGAGTTAGAGGTGGTTTTAA     	3	5	0
GAAAAAGTTCTCTGGAAAAGAGTTCATTGTAGTACAGCTTTTA	3	43	0
GAACCAAAACTTTTTAAAGCGCATGCTGGTGGTGGGAGTGATG	3	85	0
GTAAGTAGTTTTTAAAACTTAGCTTGCAGCAGTGCAATTACCT	3	137	0
CACCAAACGCTTTTATAAGTTCGTTACTTTATTTTAC      	4	47	1
GGGAAAACTTTTTACCTGACGCATCAAAGTAGAAAATA     	5	157	1
AGTTTTTTATTTTTGAATTTCCCTAATTGTGATA         	6	16	1
ATATGTGTGTTTTGGAAGAATGGTAGGAGGGTTAGAGCTATGG	8	44	0
          ***   *    * * *  **  *
MAP Score: 2.39325

Motif 7
     CGCTCCTCCTCGCCCCAAGGTAAAAAAGTTT	0	5	1
ATGCAAGGGACCCCTCAAAGCGTGGTGCTGCGATAG	1	59	1
CTGGAAACATCGCCCCCCTCGTTGATTATTGGAGTC	1	111	0
ATGTTTCCAGCTATCCGCACGCTCGTGGCCCGCAGG	1	137	1
AGGTTGATGACTCCTAAACCTTTATCCGTACTCTTA	1	253	0
TTCTTAAATGCCCTTGAACCCTTTGTTGGTTG    	2	48	1
   TTAAAACCACCTCTAACTCCTTTAGAAAAGAAG	3	7	1
ACTTTTTCATCACTCCCACCACCAGCATGCGCTTTA	3	78	1
TTAAAAATTTCTCACCAAACGCTTTTATAAGTTCGT	4	35	1
         GCTCTCACAACAGCGTTTTTTTGAAGA	5	1	1
CGAATGATAACTCTCATCACTTTAATTGTTATGATG	5	122	1
ATAGCTCTAACCCTCCTACCATTCTTCCAAAACACA	8	46	1
          * **** ***  *  *
MAP Score: 1.73323

Motif 8
   CCAAATGCGAAGGAGCTACAATCAATTGTAGAT	1	7	1
GTAGATTACACGAGGGCACTGGATGCAAGGGACCCC	1	37	1
CAATAATCAACGAGGGGGGCGATGTTTCCAGCTATC	1	116	1
CTGCGGGCCACGAGCGTGCGGATAGCTGGAAACATC	1	136	0
GCTCGTGGCCCGCAGGGGGATGTTGTAAGAATATGC	1	157	1
ACTCTTATGTCGATGGGAAAAACTGCTGACCGTAAA	1	224	0
TTAAAGCGCATGCTGGTGGTGGGAGTGATGAAAAAG	3	79	0
TTTGCTTCCGTGCTGGTGCTGCCCGCTAAAACGAAT	5	91	1
          *** ** ** *   **
MAP Score: 0.722838

Motif 9
CTTTTTTACCTTGGGGCGAGGAGGAGCG   	0	7	0
ACCCCTCAAAGCGTGGTGCTGCGATAGACCC	1	68	1
TAATCAACGAGGGGGGCGATGTTTCCAGCTA	1	119	1
GTGGCCCGCAGGGGGATGTTGTAAGAATATG	1	161	1
TTAAAGCGCATGCTGGTGGTGGGAGTGATGA	3	84	0
TTTGCTTCCGTGCTGGTGCTGCCCGCTAAAA	5	91	1
ATCACTTTAATTGTTATGATGGGAAAACTTT	5	137	1
          ******** **
MAP Score: 0.645236