AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions004_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243007
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH296	300	unknown
#1	MTH297	29	DNA-dependent RNA polymerase, subunit A' 
#2	MTH1048	300	DNA-dependent RNA polymerase, subunit H 
#3	MTH1049	40	DNA-dependent RNA polymerase, subunit B'' 
#4	MTH1050	22	DNA-dependent RNA polymerase, subunit B' 
#5	MTH1051	38	DNA-dependent RNA polymerase, subunit A' 

Motif 1
AGGCTTCCCTGAGGCTTAAGCCGGAGGACCCACCGTTAA	0	99	1
TCGGGGATCTGATCCCTGAGCCAGGGGGGTTATATTATG	0	215	1
GTGAATGCGGGGAGCTTAATCGTGATGGGGCAAACTACT	0	264	1
TCTCATTCTAGAGACTTGCCCTGGTGGTGTAGGGGCTAT	2	97	1
CGCCCTGGCCGGGAATTGAACCCGAGTCGCGGGCTCGAC	2	147	0
CAGAGCGCTTGGCTTTTAACCAAGTGGTCGCGGGTTCAA	2	214	1
CGGGCCCGACGGGAATTGAACCCGCGACCACTTGGTTAA	2	229	0
ATTTTACGGTGACTTTTTATCTGGAGGACTGAATT    	2	275	1
          **   ** * *  * ** *
MAP Score: 15.3458

Motif 2
CTTTAGGCTTCCCTGAGGCTTAAGCCGGAGGACCCACCGTTAA	0	95	1
GGAGGACCCACCGTTAAACCTTTTCCAGATGAGGGTATACATT	0	121	1
CCGAAGTGAACCATTATATGATCCCATGCAGTCATTCTGCACA	0	176	0
CCCCCCTGGCTCAGGGATCAGATCCCCGAAGTGAACCATTATA	0	201	0
TGTCGTGAATGCGGGGAGCTTAATCGTGATGGGGCAAACTACT	0	260	1
          CCAAAAAATAACTCAGAGGAGAGAATAAC    	1	0	1
ATGCTCTCATTCTAGAGACTTGCCCTGGTGGTGTAGGGGCTAT	2	93	1
AACGCCCTGGCCGGGAATTGAACCCGAGTCGCGGGCTCGACAG	2	145	0
TTTCCTGAGGGCCCGTAGCTCAGTCTGGCAGAGCGCTTGGCTT	2	186	1
CTGGCAGAGCGCTTGGCTTTTAACCAAGTGGTCGCGGGTTCAA	2	210	1
TCTAATTTTACGGTGACTTTTTATCTGGAGGACTGAATT    	2	271	1
          **  **  *    **  *  * *
MAP Score: 12.9803

Motif 3
   TTTTCCACCGGGAGGCTGTTAA     	4	7	1
GAGGCTTAAGCCGGAGGACCCACCGTTAAA	0	109	1
CAGGGCGTTTCCTGAGGGCCCGTAGCTCAG	2	179	1
GGTTCAATTCCCGTCGGGCCCGCTATCTAA	2	246	1
TAGGGGCTATCATGCGGGCCTGTCGAGCCC	2	126	1
TGTCGTGAATGCGGGGAGCTTAATCGTGAT	0	260	1
GACTTTTTATCTGGAGGACTGAATT     	2	285	1
ATCCCTGAGCCAGGGGGGTTATATTATGGT	0	226	1
TTGAACCCGAGTCGCGGGCTCGACAGGCCC	2	141	0
AAGCCTAAAGGTGGAGGCCTAATGAGGGAT	0	75	0
GCTTAAGCCTCAGGGAAGCCTAAAGGTGGA	0	90	0
TAACCAAGTGGTCGCGGGTTCAATTCCCGT	2	230	1
          **********
MAP Score: 11.3416

Motif 4
ACCTTTAGGCTTCCCTGAGGCTTAAGCCGGA	0	93	1
TGGAAAAGGTTTAACGGTGGGTCCTCCGGCT	0	117	0
CATATAATGGTTCACTTCGGGGATCTGATCC	0	199	1
TCTGATCCCTGAGCCAGGGGGGTTATATTAT	0	222	1
GTTTACTGTCGTGAATGCGGGGAGCTTAATC	0	254	1
GTGTAGGGGCTATCATGCGGGCCTGTCGAGC	2	123	1
GGCCAGGGCGTTTCCTGAGGGCCCGTAGCTC	2	176	1
GCGGGTTCAATTCCCGTCGGGCCCGCTATCT	2	243	1
ACCGTAAAATTAGATAGCGGGCCCGACGGGA	2	254	0
         TTTTCCACCGGGAGGCTGTTAA	4	1	1
          ** ********
MAP Score: 6.47971

Motif 5
CTATTACGAACGTGTGGTCCGGTACACCATT	0	23	0
AAGCCTAAAGGTGGAGGCCTAATGAGGGATG	0	74	0
AGGCCTCCACCTTTAGGCTTCCCTGAGGCTT	0	85	1
TTTAGGCTTCCCTGAGGCTTAAGCCGGAGGA	0	96	1
GAGGCTTAAGCCGGAGGACCCACCGTTAAAC	0	109	1
ACCCCCCTGGCTCAGGGATCAGATCCCCGAA	0	214	0
ATCCCTGAGCCAGGGGGGTTATATTATGGTT	0	226	1
GTCGTGAATGCGGGGAGCTTAATCGTGATGG	0	261	1
AGGGGCTATCATGCGGGCCTGTCGAGCCCGC	2	127	1
TGAACCCGAGTCGCGGGCTCGACAGGCCCGC	2	139	0
AATTCCCGGCCAGGGCGTTTCCTGAGGGCCC	2	169	1
AGGGCGTTTCCTGAGGGCCCGTAGCTCAGTC	2	180	1
CTCAGTCTGGCAGAGCGCTTGGCTTTTAACC	2	204	1
GTTCAATTCCCGTCGGGCCCGCTATCTAATT	2	247	1
GACTTTTTATCTGGAGGACTGAATT      	2	285	1
AAGATCAACACTGCAGGATCATTTCATCATC	3	15	1
   TTTTCCACCGGGAGGCTGTTAA      	4	7	1
          * *********
MAP Score: 5.89389

Motif 6
CCACCTTTAGGCTTCCCTGAGGCTTAAGCCGGAGGACCCACC	0	91	1
TATAATGGTTCACTTCGGGGATCTGATCCCTGAGCCAGGGGG	0	201	1
TTACTGTCGTGAATGCGGGGAGCTTAATCGTGATGGGGCAAA	0	256	1
TTGCCCTGGTGGTGTAGGGGCTATCATGCGGGCCTGTCGAGC	2	112	1
CTGTCGAGCCCGCGACTCGGGTTCAATTCCCGGCCAGGGCGT	2	145	1
GGCGTTTCCTGAGGGCCCGTAGCTCAGTCTGGCAGAGCGCTT	2	182	1
TTTTAACCAAGTGGTCGCGGGTTCAATTCCCGTCGGGCCCGC	2	227	1
          *  * *  ** * * *  *  *
MAP Score: 5.26074

Motif 7
TGGTCCGGTACACCATTTAATAAAAATATT	0	10	0
CCGGAGGACCCACCGTTAAACCTTTTCCAG	0	119	1
CTGCACACTGTACAATATAAATGTATACCC	0	153	0
GACTGCATGGGATCATATAATGGTTCACTT	0	186	1
GACAGTAAACCATAATATAACCCCCCTGGC	0	234	0
GATAAAAAGTCACCGTAAAATTAGATAGCG	2	266	0
CTGCAGTGTTGATCTTAAAAA         	3	1	0
AGGATCATTTCATCATCTAAT         	3	29	1
          **********
MAP Score: 1.05898