AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_fusions004_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238389
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0363	300	chemotaxis histidine kinase (cheA)
#1	TP0365	21	chemotaxis protein (cheX)
#2	TP0519	300	response regulatory protein (atoC)
#3	TP0872	75	flagellar filament cap protein (fliD)
#4	TP0875	39	conserved hypothetical protein
#5	TP0876	46	conserved hypothetical protein
#6	TP0907	62	conserved hypothetical protein
#7	TP0911	21	conserved hypothetical protein

Motif 1
ACCCAAGACGACCGCGCGTGGGTAGAAAGCTG	0	33	1
TGGGTAGAAAGCTGCGAGAGGGTCTGGTTTTG	0	51	1
CTACTCCTCTACCGAGCGGTGGGGGTCTACGT	0	99	0
CTCCTTGTATGCCGCGGGACTGGTCCTACTCC	0	124	0
AGGAGTAACCACCGAGGGCGAGAAACCGACCT	0	151	1
GACAAACGTACCTGCGCGCGGGCCATGGCGGA	0	183	1
GTCAAGGGATGCAGCGGGTGGCGGGGTCTTTT	0	238	1
          GCCGCGCGTGGGGTTTTTTTGA	3	0	1
CTCGAAAGCTGCGGAGAGTGGATCAAGACTCC	3	45	0
         CGCGGCGAGTCTACCGTTTTTAA	4	26	0
GCAAAAAGGCAAAGAGGGCGGGGTGT      	5	30	1
CTGCAACAAGGCCGCAAGACGGAAAAGGAGCC	6	11	0
          ** ***** ***
MAP Score: 26.0022

Motif 2
GTAGAAAGCTGCGAGAGGGTCTGGTTTTGATAAAAG	0	54	1
CGGCCTTGTTGCAGGCGGTGTGTGGTGGGTTATGGA	6	29	1
AAGGGATGCAGCGGGTGGCGGGGTCTTTTGGACGTT	0	241	1
     TTAGCGCATGAGGAGTGGTGT          	1	5	1
CTCTACTGTTGGACGGGGTACGTGTTTTACTCTCCT	2	186	1
AAAACTGAAGGTACGGGGTTAGGGTTAACCTTAACG	2	109	1
       GCCGCGCGTGGGGTTTTTTTGAAGGGAAC	3	3	1
TACTCCTCTACCGAGCGGTGGGGGTCTACGTTTGGA	0	94	0
AAACGTACCTGCGCGCGGGCCATGGCGGAGTCTATT	0	186	1
CTCGGCTGATGGAAGTGTCAAGGGATGCAGCGGGTG	0	222	1
TATGTCTTAGGTGGGTGGATATTTTTTCTTGTAAAA	2	251	0
TTTCGGATACAGGAGAGGGAATTGATGCCCGAAATA	2	41	1
TTGCAAAAAGGCAAAGAGGGCGGGGTGT        	5	28	1
          GGTGGCGGTAGTGTGCGTCTG     	7	5	0
          *** * **   *** *
MAP Score: 19.7986

Motif 3
GCAGCTTTCTACCCACGCGCGGTCGTCTTGGG	0	34	0
TCAAAACCAGACCCTCTCGCAGCTTTCTACCC	0	52	0
ATCCAAACGTAGACCCCCACCGCTCGGTAGAG	0	93	1
CTCCGCCATGGCCCGCGCGCAGGTACGTTTGT	0	184	0
AGCCGAGAATAGACTCCGCCATGGCCCGCGCG	0	197	0
CAAAAGACCCCGCCACCCGCTGCATCCCTTGA	0	239	0
GTTAAGGTTAACCCTAACCCCGTACCTTCAGT	2	112	0
GGAGAGTAAAACACGTACCCCGTCCAACAGTA	2	189	0
GAAAAAATATCCACCCACCTAAGACATACGAG	2	259	1
TTCAAAAAAACCCCACGCGCGGC         	3	1	0
GAGTGGATCAAGACTCCAGCCGAGTTCCCTTC	3	30	0
GAGTCTTGATCCACTCTCCGCAGCTTTCGAGG	3	46	1
TAAAAACGGTAGACTCGCCGCG          	4	27	1
          ACACCCCGCCCTCTTTGCCTTT	5	34	0
ATAACCCACCACACACCGCCTGCAACAAGGCC	6	30	0
   CAGACGCACACTACCGCCACC        	7	7	1
          **** * *****
MAP Score: 16.7022

Motif 4
GGAGTCTATTCTCGGCTGATGGAAGTGTCAAGGGATGCAGCGGG	0	212	1
TGGACGTTGCCTTGACCAAAGGCTGAGAATGCGGGAAGATT   	0	269	1
TCGCAGCTTTCTACCCACGCGCGGTCGTCTTGGGTATCGATTGG	0	24	0
CGGCTCCTTTTCCGTCTTGCGGCCTTGTTGCAGGCGGTGTGTGG	6	10	1
GAGAAACCGACCTGACAAACGTACCTGCGCGCGGGCCATGGCGG	0	170	1
     AATGACTCCTCGAAAGCTGCGGAGAGTGGATCAAGACTC	3	46	0
         GCCGCGCGTGGGGTTTTTTTGAAGGGAACTCGGCT	3	1	1
TGCTTCCTGTCTTGCAAAAAGGCAAAGAGGGCGGGGTGT     	5	17	1
AACGTAGACCCCCACCGCTCGGTAGAGGAGTAGGACCAGTCCCG	0	98	1
AGGAGTAGGACCAGTCCCGCGGCATACAAGGAGTAACCACCGAG	0	123	1
ACTTCACTACTAAAACTGAAGGTACGGGGTTAGGGTTAACCTTA	2	98	1
          ** * *  * **    *     **
MAP Score: 14.77

Motif 5
          GGCTGGCGTGTCCGCCAATCGATACCCA	0	0	1
ACCGCGCGTGGGTAGAAAGCTGCGAGAGGGTCTGGTTT	0	43	1
TCTACCGAGCGGTGGGGGTCTACGTTTGGATCCACTTT	0	86	0
CCCACCGCTCGGTAGAGGAGTAGGACCAGTCCCGCGGC	0	108	1
AAGTGTCAAGGGATGCAGCGGGTGGCGGGGTCTTTTGG	0	234	1
CTTGACCAAAGGCTGAGAATGCGGGAAGATT       	0	279	1
TAAAGAACATGGCGGTGACATCAGTGTGTCCTCTACTG	2	156	1
GGGGTTTTTTTGAAGGGAACTCGGCTGGAGTCTTGATC	3	19	1
CCTCGAAAGCTGCGGAGAGTGGATCAAGACTCCAGCCG	3	40	0
CTTGCAAAAAGGCAAAGAGGGCGGGGTGT         	5	27	1
CTTGCGGCCTTGTTGCAGGCGGTGTGTGGTGGGTTATG	6	25	1
       GGTGGCGGTAGTGTGCGTCTG          	7	0	0
          *** * **  ** *   *
MAP Score: 11.217

Motif 6
CCAAGACGACCGCGCGTGGGTAGAAAGCTGCGAG	0	35	1
TAGAAAGCTGCGAGAGGGTCTGGTTTTGATAAAA	0	55	1
ACTCCTCTACCGAGCGGTGGGGGTCTACGTTTGG	0	95	0
CTCCTTGTATGCCGCGGGACTGGTCCTACTCCTC	0	122	0
AACGTACCTGCGCGCGGGCCATGGCGGAGTCTAT	0	187	1
CAAGGGATGCAGCGGGTGGCGGGGTCTTTTGGAC	0	240	1
TTCGGATACAGGAGAGGGAATTGATGCCCGAAAT	2	42	1
TAAAACTGAAGGTACGGGGTTAGGGTTAACCTTA	2	108	1
      GCCGCGCGTGGGGTTTTTTTGAAGGGAA	3	4	1
AAAAAGGCAAAGAGGGCGGGGTGT          	5	32	1
TGTTGCAGGCGGTGTGTGGTGGGTTATGGATAGA	6	35	1
          ** * **** * **
MAP Score: 8.36373

Motif 7
ATCGATACCCAAGACGACCGCGCGTGGGTAG	0	27	1
CCAAACGTAGACCCCCACCGCTCGGTAGAGG	0	95	1
GAGGAGTAGGACCAGTCCCGCGGCATACAAG	0	122	1
CGAGGGCGAGAAACCGACCTGACAAACGTAC	0	163	1
CCGACCTGACAAACGTACCTGCGCGCGGGCC	0	176	1
ATAGACTCCGCCATGGCCCGCGCGCAGGTAC	0	190	0
AAAGACCCCGCCACCCGCTGCATCCCTTGAC	0	238	0
         ACACCACTCCTCATGCGCTAA 	1	9	0
GGAGAGTAAAACACGTACCCCGTCCAACAGT	2	190	0
GAAAAAATATCCACCCACCTAAGACATACGA	2	259	1
CAAAAAAACCCCACGCGCGGC          	3	0	0
GAGTCTTGATCCACTCTCCGCAGCTTTCGAG	3	46	1
TAAAAACGGTAGACTCGCCGCG         	4	27	1
GCAAGACAGGAAGCACTCTGCG         	5	1	0
        ACACCCCGCCCTCTTTGCCTTTT	5	33	0
CACCGCCTGCAACAAGGCCGCAAGACGGAAA	6	18	0
AACCCACCACACACCGCCTGCAACAAGGCCG	6	29	0
       CAGACGCACACTACCGCCACC   	7	3	1
          ****** ****
MAP Score: 5.99278

Motif 8
TCCGCCAATCGATACCCAAGACGACCGCGCGTGGGTAGAAAGCTG	0	20	1
GGGACTGGTCCTACTCCTCTACCGAGCGGTGGGGGTCTACGTTTG	0	96	0
GAGAAACCGACCTGACAAACGTACCTGCGCGCGGGCCATGGCGGA	0	170	1
CGGCTGATGGAAGTGTCAAGGGATGCAGCGGGTGGCGGGGTCTTT	0	224	1
TGGACGTTGCCTTGACCAAAGGCTGAGAATGCGGGAAGATT    	0	269	1
AGCCGTACTTCACTACTAAAACTGAAGGTACGGGGTTAGGGTTAA	2	92	1
TCCTTATTCTTTACTCGTATGTCTTAGGTGGGTGGATATTTTTTC	2	259	0
AGCCGAGTTCCCTTCAAAAAAACCCCACGCGCGGC          	3	0	0
     AATGACTCCTCGAAAGCTGCGGAGAGTGGATCAAGACTCC	3	45	0
TGCTTCCTGTCTTGCAAAAAGGCAAAGAGGGCGGGGTGT      	5	17	1
CACCACACACCGCCTGCAACAAGGCCGCAAGACGGAAAAGGAGCC	6	11	0
          *    * ** *     *   * ***
MAP Score: 0.90292

Motif 9
CGATACCCAAGACGACCGCGCGTGGGTAGAAAGCTGC	0	29	1
CGCGTGGGTAGAAAGCTGCGAGAGGGTCTGGTTTTGA	0	47	1
AGACTCCGCCATGGCCCGCGCGCAGGTACGTTTGTCA	0	182	0
AAGTGTCAAGGGATGCAGCGGGTGGCGGGGTCTTTTG	0	234	1
GACCAAAGGCTGAGAATGCGGGAAGATT         	0	282	1
GTCCTCTACTGTTGGACGGGGTACGTGTTTTACTCTC	2	183	1
          GCCGCGCGTGGGGTTTTTTTGAAGGGA	3	0	1
TTGCAAAAAGGCAAAGAGGGCGGGGTGT         	5	28	1
TTGCGGCCTTGTTGCAGGCGGTGTGTGGTGGGTTATG	6	26	1
          *  **  *****  * *
MAP Score: 0.569917

Motif 10
          GGCTGGCGTGTCCGCCAATCGA	0	0	1
TCTACCCACGCGCGGTCGTCTTGGGTATCGAT	0	27	0
AGCTGCGAGAGGGTCTGGTTTTGATAAAAGTG	0	60	1
CGAGCGGTGGGGGTCTACGTTTGGATCCACTT	0	87	0
TGTATGCCGCGGGACTGGTCCTACTCCTCTAC	0	119	0
GGGATGCAGCGGGTGGCGGGGTCTTTTGGACG	0	243	1
CTGAAGGTACGGGGTTAGGGTTAACCTTAACG	2	113	1
ACTGTTGGACGGGGTACGTGTTTTACTCTCCT	2	190	1
       GCCGCGCGTGGGGTTTTTTTGAAGG	3	3	1
AAGGGAACTCGGCTGGAGTCTTGATCCACTCT	3	31	1
         CGCGGCGAGTCTACCGTTTTTAA	4	26	0
CTTGTTGCAGGCGGTGTGTGGTGGGTTATGGA	6	33	1
          *** ** *****
MAP Score: 0.465207