AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243152
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH187	142	conserved protein
#1	MTH189	99	unknown
#2	MTH1246	30	NADH dehydrogenase I, subunit N 
#3	MTH1251	147	conserved protein
#4	MTH1667	219	unknown
#5	MTH1708	300	carbon monoxide dehydrogenase, alpha subunit 
#6	MTH1710	21	carbon monoxide dehydrogenase, alpha subunit 
#7	MTH1740	86	pyruvate oxidoreductase, gamma subunit 

Motif 1
AGCTGTTCAACAGCGGGTTCCCCTATTTCAGATAGGAGC	0	10	0
TTGAACAGCTCATTGAGGCCCTTGATGACAGTGACAAAT	0	39	1
CCCAGGGCTGCTGCGGCCCCCCTCCTAACAGATTTGTCA	0	70	0
GATCCCAGAGCAGTTGAACCCCTCATAAAGGCT      	0	119	1
AAGGTCCGGCCATGGTAAACCCTTCACCCCATCACACTG	1	17	0
TTCAGTGTGCATTCAACCTCCCTGAGGTCATTTCCTTCC	1	54	1
CTTGAAGGGGAAGAGGCTGCCGTAATAACCCCATGAGTC	3	12	0
AGTGTTTAATCATCGGATCCCCTATTTTATTACGATTTA	3	49	1
TAATAGCCATCAGAATGTCCCCTGGAAACTGGGGATATC	4	34	1
ATTATATTTCCAGGAGATTCCTTGATATCCCCAGTTTCC	4	57	0
ATCTCCTGGAAATATAATCCCCTTCTAACTCTGTAAAAA	4	78	1
ATACTGGTTAAAGTGGTTTCCTTTTTTACAGAGTTAGAA	4	100	0
TATTACTAATCTTCGGTTTCCCTTATATTGTGGTAATAT	5	57	1
GACCCCCGGCAATGGTCATCCCTCCGCTCAGGGTGCGAT	5	94	0
GGATTATTACCATTATACACCCTGAGACCCCCGGCAATG	5	119	0
          *** **   ****     *
MAP Score: 20.1884

Motif 2
  GCTCCTATCTGAAATAGGGGAACCCGCTGTT	0	8	1
AGTGACAAATCTGTTAGGAGGGGGGCCGCAGCA	0	68	1
TTGGAGATCCCAGAGCAGTTGAACCCCTCATAA	0	114	1
   TCCGGTTCAGTGTGATGGGGTGAAGGGTTT	1	7	1
GAAATGACCTCAGGGAGGTTGAATGCACACTGA	1	55	0
   GGGGTTACTGAAAGATGGAAGGAAATGACC	1	79	0
AGAATGTCCCCTGGAAACTGGGGATATCAAGGA	4	45	1
CTTTTTTACAGAGTTAGAAGGGGATTATATTTC	4	86	0
GTTACAGTACCAGCGGGAGGGGGTTATATAAAC	4	150	1
GTTATATAAACAGAAAAACGGAATGTCTGTGTC	4	172	1
       GATCAGGATAGCTGGGACAATCGGGA	4	203	0
ATATCGCACCCTGAGCGGAGGGATGACCATTGC	5	92	1
GGGGATGTGCCAGATAGGCGGAGGATTATTACC	5	147	0
         TCAGGATAATGGAGGAATTCA   	6	1	1
ATGATTAACAATGAGAAATGGAGGTAAACT   	7	66	1
          *** * ** ****
MAP Score: 18.8533

Motif 3
   TCCGGTTCAGTGTGATGGGGTGAAGGGTTTACCA	1	7	1
   GGGGTTACTGAAAGATGGAAGGAAATGACCTCAG	1	75	0
          AGGACTCATGGGGTTATTACGGCAGCC	3	0	1
TATTGGTACTAAAGAGAAGGGAGCTATAAA       	3	127	1
AGAATGTCCCCTGGAAACTGGGGATATCAAGGAATCT	4	45	1
TTTTTTACAGAGTTAGAAGGGGATTATATTTCCAGGA	4	81	0
GTTACAGTACCAGCGGGAGGGGGTTATATAAACAGAA	4	150	1
      GATCAGGATAGCTGGGACAATCGGGACACAG	4	198	0
         TCAGGATAATGGAGGAATTCA       	6	1	1
TTGGTCAACTAAAATTAATGGGGGTAACGAA      	7	4	0
ATGATTAACAATGAGAAATGGAGGTAAACT       	7	66	1
          * *    ******  **
MAP Score: 12.4522

Motif 4
TCAACAGCGGGTTCCCCTATTTCAGATAGGAGC   	0	7	0
ATCTCCAATGTTACCCAGGGCTGCTGCGGCCCCCCT	0	86	0
TAACATTGGAGATCCCAGAGCAGTTGAACCCCTCAT	0	109	1
GTGCATTCAACCTCCCTGAGGTCATTTCCTTCCATC	1	60	1
GAGGTCATTTCCTTCCATCTTTCAGTAACCCC    	1	77	1
TACGGCAGCCTCTTCCCCTTCAAGTGTTTAATCATC	3	27	1
TTAATCATCGGATCCCCTATTTTATTACGATTTATA	3	54	1
    TTTATAGCTCCCTTCTCTTTAGTACCAATAAT	3	125	0
GCCATCAGAATGTCCCCTGGAAACTGGGGATATCAA	4	39	1
GGTTAAAGTGGTTTCCTTTTTTACAGAGTTAGAAGG	4	98	0
ACTTTAACCAGTATCCACATATTAGGTTACAGTACC	4	125	1
TATATAACCCCCTCCCGCTGGTACTGTAACCTAATA	4	144	0
GGGACACAGACATTCCGTTTTTCTGTTTATATAACC	4	171	0
GTGTCCCGATTGTCCCAGCTATCCTGATC       	4	200	1
TAATCTTCGGTTTCCCTTATATTGTGGTAATATCGC	5	63	1
CGGCAATGGTCATCCCTCCGCTCAGGGTGCGATATT	5	91	0
      TTCGTTACCCCCATTAATTTTAGTTGACCA	7	4	1
          * **** * * *  **
MAP Score: 10.1731

Motif 5
CTGTTGAACAGCTCATTGAGGCCCTTGATG	0	36	1
GGGTTCAACTGCTCTGGGATCTCCAATGTT	0	110	0
      TCCGGTTCAGTGTGATGGGGTGAA	1	4	1
ATGGCCGGACCTTCAGTGTGCATTCAACCT	1	43	1
AAGGAAATGACCTCAGGGAGGTTGAATGCA	1	61	0
TCATCCCTCCGCTCAGGGTGCGATATTACC	5	88	0
TTGCCGGGGGTCTCAGGGTGTATAATGGTA	5	121	1
TACCTCCATTTCTCATTGTTAATCATTATA	7	62	0
          **********
MAP Score: 9.31255

Motif 6
TCCTATCTGAAATAGGGGAACCCGCTGTTG	0	12	1
CAAATCTGTTAGGAGGGGGGCCGCAGCAGC	0	73	1
CAGTGTGATGGGGTGAAGGGTTTACCATGG	1	17	1
GTTACTGAAAGATGGAAGGAAATGACCTCA	1	76	0
GGAATCTAACAGGTGAGGAATT        	2	18	1
AAACACTTGAAGGGGAAGAGGCTGCCGTAA	3	26	0
ATTGGTACTAAAGAGAAGGGAGCTATAAA 	3	128	1
TTACAGTACCAGCGGGAGGGGGTTATATAA	4	151	1
ATCGCACCCTGAGCGGAGGGATGACCATTG	5	94	1
TGTGCCAGATAGGCGGAGGATTATTACCAT	5	145	0
CTTTTTAATAAATGGTGGGGATGTGCCAGA	5	166	0
   TCAGGATAATGGAGGAATTCA      	6	7	1
AACTAAAATTAATGGGGGTAACGAA     	7	5	0
AACAATGAGAAATGGAGGTAAACT      	7	72	1
          **********
MAP Score: 5.67052

Motif 7
CTATTTTATTACGATTTATATAGAAAACTTTA	3	70	1
TTTATATAGAAAACTTTATATTATCATAAATA	3	84	1
AATTAACATGATTATTTATGATAATATAAAGT	3	96	0
TAATCACTTCAACCTTTATATTATATGAATGT	5	27	0
CGGGGGTCTCAGGGTGTATAATGGTAATAATC	5	125	1
GCACATCCCCACCATTTATTAAAAAGGTCCAT	5	170	1
GACAATGCACAAAGTTTATATATAGATTCCAT	5	219	1
ACAATTATTAATGATTTATAATGATGTTTTTA	5	256	0
TTAGTTGACCAACATGTATATATATTAAAAAT	7	29	1
ATATATATTAAAAATTTATAATGATTAACAAT	7	46	1
          *  *********
MAP Score: 4.96529

Motif 8
TTCAACAGCGGGTTCCCCTATTTCAGATAGGAG	0	11	0
GGGCTGCTGCGGCCCCCCTCCTAACAGATTTGT	0	72	0
CCAGAGCAGTTGAACCCCTCATAAAGGCT    	0	123	1
TGGTAAACCCTTCACCCCATCACACTGAACCGG	1	11	0
TCACCTGTTAGATTCCTCATTTTA         	2	1	0
       AATTCCTCACCTGTTAGATTCCTCAT	2	14	0
TACGGCAGCCTCTTCCCCTTCAAGTGTTTAATC	3	27	1
TTTAATCATCGGATCCCCTATTTTATTACGATT	3	53	1
AGATTCCTTGATATCCCCAGTTTCCAGGGGACA	4	49	0
CCTGGAAATATAATCCCCTTCTAACTCTGTAAA	4	82	1
ACTAATCTTCGGTTTCCCTTATATTGTGGTAAT	5	61	1
CCTATCTGGCACATCCCCACCATTTATTAAAAA	5	162	1
        TGAATTCCTCCATTATCCTGA    	6	6	0
       TTCGTTACCCCCATTAATTTTAGTTG	7	3	1
          *  ****** ***
MAP Score: 2.85292