AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242944
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH123	91	sensory transduction histidine kinase
#1	MTH124	126	conserved protein
#2	MTH360	136	sensory transduction histidine kinase
#3	MTH444	133	sensory transduction histidine kinase
#4	MTH446	97	sensory transduction regulatory protein
#5	MTH468	98	sensory transduction histidine kinase
#6	MTH469	178	conserved protein
#7	MTH549	126	sensory transduction regulatory protein
#8	MTH786	139	sensory transduction histidine kinase related protein
#9	MTH1607	58	sensory transduction regulatory protein
#10	MTH1615	34	conserved protein
#11	MTH1618	118	conserved protein
#12	MTH1764	154	sensory transduction regulatory protein

Motif 1
TCATTTATTGGGTCAAGAGGGACCCTCCTACAAG	0	32	0
TTACAGTTCGCATCAAGCCCCCTCCAAATAGTAT	1	56	0
        CTCATCAAGATCTCTGTAAACCTCCC	1	110	0
TGTGTATCTACCGGAGGCCCACCGGGTATTAATT	2	24	0
AGCAGAGATCCGTGAAGAGCCATGCGTTTCATGG	3	65	0
AGCCGGACCTCTGGAAGAGCAGAGATCCGTGAAG	3	82	0
        GACCAGAAGAGGAGAGTCAGAAAAAT	3	117	0
    GCATGTCTTGAAGACCAGACACCAGTGAAG	4	6	1
ACCAGACACCAGTGAAGAGCCCACAATAAAATTT	4	23	1
CATTAACCGTAATGAAGAGGAACCGGA       	4	80	1
TGTGAATCCCATTGAAGACCATGGAGGGCGTGTG	5	70	1
GGATGAATTCCTTGAAAAGGCTAGGGAATTCAGT	6	58	0
GACAGAACTTAATCAGGAGCTGGCCAATCCCTGA	7	24	1
ACTCCAGTTCAGTCAGGATCAGCCTCAAGTTATA	8	28	0
CCCAGAGGGGCCTCAGGAGGTTTCATAG      	10	16	1
GTGGTTAATCCATCAGGAGCCGGGAAAAGATCTT	12	60	1
          * ********   *
MAP Score: 17.3577

Motif 2
TAACACCTTGTAGGAGGGTCCCTCTTGACC	0	26	1
TGACCCAATAAATGAGGTCCAGTACAACCT	0	51	1
TCACTCCAGTAAGGAGGTTGTACTGGACCT	0	65	0
TAAATACTATTTGGAGGGGGCTTGATGCGA	1	53	1
TGTGTATCTACCGGAGGCCCACCGGGTATT	2	28	0
CCTTTACGGTCATGAGGGTGTGTATCTACC	2	46	0
GTATACATAAAATGAGGTGGTATACTGGTT	2	98	0
ATTTCATGGATAAGAGGTTCCATGAAACGC	3	46	1
CTCTGCTCTTCCAGAGGTCCGGCTGATTTT	3	92	1
ATTGAAGACCATGGAGGGCGTGTGAGAA  	5	80	1
ATTATATCATTCGGAGGTGCTAAA      	6	164	1
AGAACTTAATCAGGAGCTGGCCAATCCCTG	7	27	1
CAGGTTTAAATAGGATGGGGGAATAGTTGA	7	72	1
GTTTTAAGTTCCGGGGGTGGCTGGCA    	7	110	1
TCTATTATAACTTGAGGCTGATCCTGACTG	8	23	1
AAATATTACTCAAGATGTTCATTGTGGGAG	8	111	1
TTTTATCTGCATGGATGTCCATTAATCAGT	9	10	0
   AACTATCCCAGAGGGGCCTCAGGAGGT	10	7	1
AGAGGGGCCTCAGGAGGTTTCATAG     	10	19	1
TCTCAATGTGCAAGATGTGGATGTTCTATT	11	78	1
GTTAATCCATCAGGAGCCGGGAAAAGATCT	12	63	1
          **********
MAP Score: 15.6727

Motif 3
TGAATTAATACCCGGTGGGCCTCCGGTAGATACACA	2	22	1
GGATCAGATACCTCACTGATGCAGGGA         	3	1	0
ACGCATGGCTCTTCACGGATCTCTGCTCTTCCAGAG	3	72	1
GGATCTCTGCTCTTCCAGAGGTCCGGCTGATTTTTC	3	88	1
ATTGTGGGCTCTTCACTGGTGTCTGGTCTTCAAGAC	4	14	0
AAACCTGAAACATTACAGGGCTCAGGGATTGGCCAG	7	43	0
ATGTTTTAAGTTCCGGGGGTGGCTGGCA        	7	108	1
CTGATCCTGACTGAACTGGAGTCTGGTCCTAACAAT	8	40	1
   AACTATCCCAGAGGGGCCTCAGGAGGTTTCATA	10	7	1
TCGTGGTTAATCCATCAGGAGCCGGGAAAAGATCTT	12	58	1
          **   * ** *** **
MAP Score: 8.93487

Motif 4
AGTACAACCTCCTTACTGGAGTGAACAATC      	0	71	1
GCGAACTGTAATGGACAGGAATGCAGTTGTAGGGAG	1	79	1
         TATGATCCTCCATGAATTAATACCCGG	2	1	1
CATTAAATACCTTTACGGTCATGAGGGTGTGTATCT	2	49	0
         TCCCTGCATCAGTGAGGTATCTGATCC	3	1	1
GTCTTGAAGACCAGACACCAGTGAAGAGCCCACAAT	4	14	1
TCTTGAGCTCATTAACCGTAATGAAGAGGAACCGGA	4	71	1
AGGGAACCTACCGGTCATTCCTGAACACAGAATCAC	5	17	1
TAACTTGAGGCTGATCCTGACTGAACTGGAGTCTGG	8	30	1
GGAGTCTGGTCCTAACAATATTGAACACTAAAATCT	8	57	1
    TTAACCATCTCCCACAATGAACATCTTGAGTA	8	117	0
  ACTGATTAATGGACATCCATGCAGATAAAATACA	9	8	1
          **   *  ** *****
MAP Score: 7.04999

Motif 5
CAGGAATGCAGTTGTAGGGAGGTTTACAGA	1	94	1
ACCGGGTATTAATTCATGGAGGATCATA  	2	8	0
CCGTAAAGGTATTTAATGGTAACCCGGATA	2	67	1
ATACCACCTCATTTTATGTATACTTTAAGA	2	105	1
ATACCTCACTGATGCAGGGA          	3	0	0
CACTCTTATCATTTCATGGATAAGAGGTTC	3	36	1
AGAGCCATGCGTTTCATGGAACCTCTTATC	3	54	0
AAGCCTGGAAATTTTATTGTGGGCTCTTCA	4	35	0
AAGGCTAGGGAATTCAGTGATTATGACCAT	6	46	0
GCCCTGTAATGTTTCAGGTTTAAATAGGAT	7	58	1
TGTATTTAAGATTTTAGTGTTCAATATTGT	8	71	0
       ACTGATTAATGGACATCCATGCA	9	3	1
ATTTAGGATTATTTTAGTGATAA       	12	141	1
          **********
MAP Score: 4.72179

Motif 6
TTGTTCACTCCAGTAAGGAGGTTGTACTGGACCT	0	65	0
ATCTTAAATACTATTTGGAGGGGGCTTGATGCGA	1	49	1
TTGATGCGAACTGTAATGGACAGGAATGCAGTTG	1	74	1
AATACCTTTACGGTCATGAGGGTGTGTATCTACC	2	46	0
AGCTCATTAACCGTAATGAAGAGGAACCGGA   	4	76	1
ATGTGAATCCCATTGAAGACCATGGAGGGCGTGT	5	69	1
GGACAGAACTTAATCAGGAGCTGGCCAATCCCTG	7	23	1
GTTTCAGGTTTAAATAGGATGGGGGAATAGTTGA	7	68	1
GACTCCAGTTCAGTCAGGATCAGCCTCAAGTTAT	8	29	0
GTGTTCAATATTGTTAGGACCAGACTCCAGTTCA	8	51	0
TCAAGATGTTCATTGTGGGAGATGGTTAA     	8	120	1
ACCATCTCAATGTGCAAGATGTGGATGTTCTATT	11	74	1
GATGGTTAATCTATCAGGAAGAGTAAAAAAATCT	12	10	1
CGTGGTTAATCCATCAGGAGCCGGGAAAAGATCT	12	59	1
          * ** **** * **
MAP Score: 3.52361

Motif 7
GGATCAGATACCTCACTGATGCAGGGA         	3	1	0
CTGATCCACTCTTATCATTTCATGGATAAGAGGTTC	3	30	1
CCGTGAAGAGCCATGCGTTTCATGGAACCTCTTATC	3	54	0
CTTCACGGATCTCTGCTCTTCCAGAGGTCCGGCTGA	3	82	1
ACTGAATTCCCTAGCCTTTTCAAGGAATTCATCCCT	6	58	1
TAATCAGGAGCTGGCCAATCCCTGAGCCCTGTAATG	7	33	1
        TGCCAGCCACCCCCGGAACTTAAAACAT	7	108	0
GTAAAAAAATCTTCCCCTACCGAGGATCGTGGTTAA	12	32	1
AAGATCTTTTCCCGGCTCCTGATGGATTAACCACGA	12	58	0
GGGAAAAGATCTTCTCCTCCGCTGGAGGACATAACT	12	81	1
          **   *   *******
MAP Score: 3.33512

Motif 8
   CTCATCAAGATCTCTGTAAACCTCCCTACAACTGC	1	101	0
AGGTATTTAATGGTAACCCGGATATAACCAGTATACCA	2	73	1
CTGGAAGAGCAGAGATCCGTGAAGAGCCATGCGTTTCA	3	68	0
CTTGAAGACCAGACACCAGTGAAGAGCCCACAATAAAA	4	16	1
          TGGAAACAGGGAACCTACCGGTCATTCC	5	0	1
TTGAAAGGGATGAATTCCTTGAAAAGGCTAGGGAATTC	6	61	0
GAAACATTACAGGGCTCAGGGATTGGCCAGCTCCTGAT	7	35	0
TTAATCCATCAGGAGCCGGGAAAAGATCTTCTCCTCCG	12	64	1
          ***   * *****    *
MAP Score: 2.91673

Motif 9
TCCTGTGAAAATGATAAATCTCTTATCTTGGTTT	1	14	1
TGAACACAGAATCACAATTAACTTAATAGGTATG	5	38	1
TTTCAATCCTATCAAAAAAATTTTTTGAGCACCC	6	93	1
TCCGAATGATATAATAATTATCTGGTTTTTTGAT	6	145	0
AACAATATTGAACACTAAAATCTTAAATACATTG	8	70	1
ACCATCTCCCACAATGAACATCTTGAGTAATATT	8	112	0
TAAAATACAGAATACAAAAATTTTTATACAGCC 	9	35	1
TAAATATGGAAACACAAAGCACTTATAATATTCT	11	23	1
TATCAGGAAGAGTAAAAAAATCTTCCCCTACCGA	12	21	1
     TTATCACTAAAATAATCCTAAATAATTCT	12	135	0
          *  * *** *****
MAP Score: 2.26798