AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242995
 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
CTTTAGGCTTCCCTGAGGCTTAAGCCGGAGGACCCACCGTTAA	0	95	1
GGAGGACCCACCGTTAAACCTTTTCCAGATGAGGGTATACATT	0	121	1
CCGAAGTGAACCATTATATGATCCCATGCAGTCATTCTGCACA	0	176	0
CCCCCCTGGCTCAGGGATCAGATCCCCGAAGTGAACCATTATA	0	201	0
TGTCGTGAATGCGGGGAGCTTAATCGTGATGGGGCAAACTACT	0	260	1
ATGCTCTCATTCTAGAGACTTGCCCTGGTGGTGTAGGGGCTAT	2	93	1
AACGCCCTGGCCGGGAATTGAACCCGAGTCGCGGGCTCGACAG	2	145	0
TTTCCTGAGGGCCCGTAGCTCAGTCTGGCAGAGCGCTTGGCTT	2	186	1
CTGGCAGAGCGCTTGGCTTTTAACCAAGTGGTCGCGGGTTCAA	2	210	1
TCTAATTTTACGGTGACTTTTTATCTGGAGGACTGAATT    	2	271	1
          **  **  *    **  *  * *
MAP Score: 13.4442

Motif 2
GACTTTTTATCTGGAGGACTGAATT       	2	285	1
GAGGCTTAAGCCGGAGGACCCACCGTTAAACC	0	109	1
TAAAATTAGATAGCGGGCCCGACGGGAATTGA	2	249	0
ATCCCTGAGCCAGGGGGGTTATATTATGGTTT	0	226	1
TGAACCCGAGTCGCGGGCTCGACAGGCCCGCA	2	138	0
   TTTTCCACCGGGAGGCTGTTAA       	4	7	1
AAGATCAACACTGCAGGATCATTTCATCATCT	3	15	1
AACCAAGTGGTCGCGGGTTCAATTCCCGTCGG	2	231	1
GTCGTGAATGCGGGGAGCTTAATCGTGATGGG	0	261	1
AAGCCTAAAGGTGGAGGCCTAATGAGGGATGG	0	73	0
GCCAAGCGCTCTGCCAGACTGAGCTACGGGCC	2	195	0
TTTAGGCTTCCCTGAGGCTTAAGCCGGAGGAC	0	96	1
AGGGCGTTTCCTGAGGGCCCGTAGCTCAGTCT	2	180	1
ATGGTTCACTTCGGGGATCTGATCCCTGAGCC	0	205	1
          * ***** ****
MAP Score: 12.5489

Motif 3
GGTTCAATTCCCGTCGGGCCCGCTATCTAA	2	246	1
GAGGCTTAAGCCGGAGGACCCACCGTTAAA	0	109	1
   TTTTCCACCGGGAGGCTGTTAA     	4	7	1
CAGGGCGTTTCCTGAGGGCCCGTAGCTCAG	2	179	1
GACTTTTTATCTGGAGGACTGAATT     	2	285	1
TTGAACCCGAGTCGCGGGCTCGACAGGCCC	2	141	0
GATCCCTGAGCCAGGGGGGTTATATTATGG	0	225	1
TGTCGTGAATGCGGGGAGCTTAATCGTGAT	0	260	1
TAGGGGCTATCATGCGGGCCTGTCGAGCCC	2	126	1
AAGCCTAAAGGTGGAGGCCTAATGAGGGAT	0	75	0
TGCCCTGGTGGTGTAGGGGCTATCATGCGG	2	113	1
CTTTAGGCTTCCCTGAGGCTTAAGCCGGAG	0	95	1
GTAGCTCAGTCTGGCAGAGCGCTTGGCTTT	2	200	1
TAACCAAGTGGTCGCGGGTTCAATTCCCGT	2	230	1
          **********
MAP Score: 10.2599

Motif 4
TATTTTTATTAAATGGTGTACCGGACCACACGTTCGTAATAG	0	12	1
CCTCAGGGAAGCCTAAAGGTGGAGGCCTAATGAGGGATGGTG	0	71	0
CTTCCCTGAGGCTTAAGCCGGAGGACCCACCGTTAAACCTTT	0	102	1
ATCATATAATGGTTCACTTCGGGGATCTGATCCCTGAGCCAG	0	197	1
GGTGGTGTAGGGGCTATCATGCGGGCCTGTCGAGCCCGCGAC	2	119	1
CCGCGACTCGGGTTCAATTCCCGGCCAGGGCGTTTCCTGAGG	2	154	1
CGCTCTGCCAGACTGAGCTACGGGCCCTCAGGAAACGCCCTG	2	179	0
GGCCCGACGGGAATTGAACCCGCGACCACTTGGTTAAAAGCC	2	224	0
GTCACCGTAAAATTAGATAGCGGGCCCGACGGGAATTGAACC	2	246	0
          *  * *    **** **    *
MAP Score: 8.76036

Motif 5
AGTTCACCATCCCTCATTAGGCCTCCACCTTTAGG	0	67	1
CATTAGGCCTCCACCTTTAGGCTTCCCTGAGGCTT	0	81	1
CGGTGGGTCCTCCGGCTTAAGCCTCAGGGAAGCCT	0	99	0
TTAAACCTTTTCCAGATGAGGGTATACATTTATAT	0	134	1
ATATAACCCCCCTGGCTCAGGGATCAGATCCCCGA	0	215	0
GTTTGCCCCATCACGATTAAGCTCCCCGCATTCAC	0	264	0
GATAGCCCCTACACCACCAGGGCAAGTCTCTAGAA	2	102	0
GGTGTAGGGGCTATCATGCGGGCCTGTCGAGCCCG	2	122	1
GGAATTGAACCCGAGTCGCGGGCTCGACAGGCCCG	2	140	0
CGGGTTCAATTCCCGGCCAGGGCGTTTCCTGAGGG	2	162	1
CTCTGCCAGACTGAGCTACGGGCCCTCAGGAAACG	2	184	0
CTTTTAACCAAGTGGTCGCGGGTTCAATTCCCGTC	2	226	1
CGCGGGTTCAATTCCCGTCGGGCCCGCTATCTAAT	2	242	1
      TTTTCCACCGGGAGGCTGTTAA       	4	4	1
          **  * * ***** *
MAP Score: 7.48242

Motif 6
CGTTCGTAATAGAGAACTATTACGAAGTTC	0	42	1
AACTCAGAGGAGAGAATAAC          	1	19	1
GCAGGTAACTAGAGAACAATGGAATGCTCT	2	70	1
CTCTAGAATGAGAGCATTCCATTGTTCTCT	2	80	0
AATGGATTTAAGGGAATAACAAAAAGGAGA	5	11	1
AACAAAAAGGAGAGAATACC          	5	28	1
          **********
MAP Score: 5.62082

Motif 7
CACCTTTAGGCTTCCCTGAGGCTTAAGCCGG	0	92	1
TCATATAATGGTTCACTTCGGGGATCTGATC	0	198	1
TCGGGGATCTGATCCCTGAGCCAGGGGGGTT	0	215	1
TTATATTATGGTTTACTGTCGTGAATGCGGG	0	244	1
CGCGACTCGGGTTCAATTCCCGGCCAGGGCG	2	155	1
CGGCCAGGGCGTTTCCTGAGGGCCCGTAGCT	2	175	1
GTGGTCGCGGGTTCAATTCCCGTCGGGCCCG	2	237	1
          ******** **
MAP Score: 2.23271