AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241392
 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
CATGCGCTTTAAAAAGTTTTGGTTCGCCCA	3	103	1
TGCGTCAGGTAAAAAGTTTTCCCATCATAA	5	150	0
        TCAAAAAGTTTTTTATTTTTGA	6	2	1
GGGAGTGATGAAAAAGTTCTCTGGAAAAGA	3	65	0
GAGGATTATTAAAAATTTCTCACCAAACGC	4	27	1
ATACAAAGACATAAATTTTTTTGAAAAGAA	0	50	1
AAATGGGATTAAAAAATTTGGCGTTTGGCC	7	24	0
AAGAGTACGGATAAAGGTTTAGGAGTCATC	1	254	1
          **********
MAP Score: 14.7464

Motif 2
     CGCTCCTCCTCGCCCCAAGGTAAAAAAGTTTTATTG	0	5	1
ACGCTCGTGGCCCGCAGGGGGATGTTGTAAGAATATGCAAC	1	155	1
   TTAAAACCACCTCTAACTCCTTTAGAAAAGAAGTAAAA	3	7	1
TCACTCCCACCACCAGCATGCGCTTTAAAAAGTTTTGGTTC	3	87	1
   TTTCCTACAAAGGTAAGTAGTTTTTAAAACTTAGCTTG	3	154	0
TTAAAAATTTCTCACCAAACGCTTTTATAAGTTCGTTACTT	4	35	1
     GCTCTCACAACAGCGTTTTTTTGAAGAACTCTGAAG	5	5	1
ACTCTGAAGTCACTTAACAGCCATTTCAAAAGCTGGATTTA	5	37	1
AGCACGGAAGCAAACAAGAGAAAAGTTTAAATCCAGCTTTT	5	64	0
       TATCACAATTAGGGAAATTCAAAAATAAAAAACT	6	16	0
ATAGCTCTAACCCTCCTACCATTCTTCCAAAACACACATAT	8	46	1
          ***    * *    **  ***
MAP Score: 7.30155

Motif 3
TTAATAAACCTAACTGCCAATTCTTTTCAAAA	0	68	0
ATGTTGTAAGAATATGCAACTTCCTTAGGTTG	1	176	1
AGGAAAAGAAAATGTGCATCTTTTGTCCATCT	2	14	0
AGCTAAGTTTTAAAAACTACTTACCTTTGTAG	3	156	1
TGAAGTCACTTAACAGCCATTTCAAAAGCTGG	5	41	1
          TATTTTCTACTTTGATGCGTCA	5	173	0
TAATCCCATTTATTAGCCACTTTCC       	7	43	1
CTATTTCAGCAATCTGCTATTTGACGTTTCCC	8	14	1
          *** *** ****
MAP Score: 0.345497

Motif 4
          CGCTCCTCCTCGCCCCAAGGTAA	0	0	1
TCGGGTCTATCGCAGCACCACGCTTTGAGGGGT	1	68	0
GATAGCTGGAAACATCGCCCCCCTCGTTGATTA	1	119	0
ATATTCTTACAACATCCCCCTGCGGGCCACGAG	1	158	0
ACTTTTTCATCACTCCCACCACCAGCATGCGCT	3	78	1
AAGGTAATTGCACTGCTGCAAGCTAAGTTTTAA	3	136	1
TTTAGCGGGCAGCACCAGCACGGAAGCAAACAA	5	88	0
          **** * ** ***
MAP Score: 0.29221