AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251327
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0335	26	dihydroorotase
#1	TM0337	278	conserved hypothetical protein
#2	TM0338	184	hypothetical protein
#3	TM0398	300	conserved hypothetical protein
#4	TM1205	300	conserved hypothetical protein
#5	TM1208	26	conserved hypothetical protein
#6	TM1632	62	conserved hypothetical protein

Motif 1
        ACTTTTCCCTCCGAATTCCTTT	0	14	0
CTAACATCTTCTTCACCTCCTTTCAGATAT	1	70	0
TTTTCCTGTGTTTTTCCACCAAAAATCTCT	1	125	0
GGTGATACTGTGTTTCTTCCCACAACACGT	1	252	1
      ATTTTGTCACCTCCTGCAAAATAT	2	4	1
TCGTTGCCCCTTTTCCCGCCGTGAAACGAG	2	92	1
AGGTTCGAGTCCTCCCCTCCCAGCCAGAAA	3	67	1
TATTCATGCTTTTCTCCTTCAGGAGGTGAA	3	276	1
       GGCATTCACCTCCTGAAGGAGAA	3	287	0
TGGAATCGACTTTTACGTCCAGAAAACGAA	4	100	1
TTGTGAAAACTTTCTCTTTCAATCCCGAGG	4	269	1
       TCATCACACCTCCTCGGGATTGA	4	287	0
    TCGTTGTGTCTCCTTCCGGAGGGATT	6	6	1
       TTTCTGTTCCTCCACAGTGTTGT	6	49	0
          **********
MAP Score: 13.7271

Motif 2
     ACTTTTCCCTCCGAATTCCTTTCCTG 	0	9	0
GATATCATCATCCTTCGCCTGTAAATGTAGCA	1	43	0
ATGTTAGAACTGATACCGCTGGATGTGGTCAT	1	93	1
GCCGTACCCCTGCGTCCCCATTTTTTAACCAG	1	182	1
          TTCCTCACGTGTTGTGGGAAGA	1	266	0
CATAAGAGTGTACCACCGGTGTATTAAAAATC	2	156	0
CGGCGGACTCTGGATCCGCTGGTGGAGGTTCG	3	42	1
GGGGATGCATTGCATCCCCTTTCTGGCTGGGA	3	84	0
GGGGATGCAATGCATCCCCTTTTTCTTTATCC	3	97	1
CATGCTTTTCTCCTTCAGGAGGTGAATGCC  	3	280	1
GATGTCAAGCGACATCCCGAGGAGATTTTCAA	4	47	1
ACTTTCTCTTTCAATCCCGAGGAGGTGTGATG	4	277	1
TCGTTGTGTCTCCTTCCGGAGGGATTCAATAT	6	10	1
    TTTCTGTTCCTCCACAGTGTTGTACAAT	6	44	0
          * * ********
MAP Score: 11.8862

Motif 3
          CAGGAAAGGAATTCGGAGGGA	0	0	1
TGATATCTGAAAGGAGGTGAAGAAGATGTTA	1	68	1
GAGATTTTTGGTGGAAAAACACAGGAAAACA	1	126	1
TGGTTAAAAAATGGGGACGCAGGGGTACGGC	1	182	0
CGTGTTGTGGGAAGAAACACAGTATCACCCT	1	250	0
TATTTTGCAGGAGGTGACAAAAT        	2	2	0
TTCTGGCTGGGAGGGGAGGACTCGAACCTCC	3	65	0
CCCAGCCAGAAAGGGGATGCAATGCATCCCC	3	85	1
GATAAAGAAAAAGGGGATGCATTGCATCCCC	3	97	0
TCACCTCCTGAAGGAGAAAAGCATGAATATA	3	274	0
TTTTCTCCTTCAGGAGGTGAATGCC      	3	285	1
CGAAGAGAACGAAGAGGGAAATTTAGACCAA	4	165	0
AACCTAATTAGTAGAGATAAAAAACAGTTTC	4	195	0
TTTCAATCCCGAGGAGGTGTGATGA      	4	285	1
ATCCCTCCGGAAGGAGACACAACGA      	6	4	0
GTACAACACTGTGGAGGAACAGAAA      	6	47	1
          ******* ***
MAP Score: 9.04196

Motif 4
GATGATGATATCTGAAAGGAGGTGAAGAAGAT	1	63	1
TTCTAAAATATTTTGCAGGAGGTGACAAAAT 	2	9	0
TCCAAAAAAATTTTTCTGTAAGGATTTTCGTT	2	65	1
      AAAGGCCGTTGGGAGGTCGTCTAACG	3	4	1
TGGGAGGTCGTCTAACGGTAGGACGGCGGACT	3	19	1
GCATCCCCTTTCTGGCTGGGAGGGGAGGACTC	3	73	0
CATGCTTTTCTCCTTCAGGAGGTGAATGCC  	3	280	1
AGAAATATTCGTTTTCTGGACGTAAAAGTCGA	4	105	0
TGCTGATATGGCTGACTGGAGGT         	5	13	1
TCGTTGTGTCTCCTTCCGGAGGGATTCAATAT	6	10	1
          **** * *****
MAP Score: 8.57856

Motif 5
TTAATTCTTATTTTGTGCTTAATATTCCGATGCTACAT	1	13	1
CTTTCTGTTTTCCTGTGTTTTTCCACCAAAAATCTCTA	1	124	0
GGCACTTACTTTTTGTTATTCTTCTTTCTGTTTTCCTG	1	147	0
AAACGAGGCTTTTTTTGTTTTAAAATACATAGGGTGAT	1	220	1
CATAGGGTGATACTGTGTTTCTTCCCACAACACGTGAG	1	247	1
TAGTATTGCCTTATTTGATTTTTAATACACCGGTGGTA	2	140	1
ACTGATACAGTCCTTTGATTGAGAGAACACATATGGTA	3	215	1
TAATCTGGACTCTTTTGGTCTAAATTTCCCTCTTCGTT	4	151	1
ATTACTCTTGTGTTGTGATTGTGAAAACTTTCTCTTTC	4	251	1
          *  **** ** * *   *
MAP Score: 7.04621

Motif 6
AGGAAAGGAATTCGGAGGGAAAAGT     	0	11	1
ATGATATCTGAAAGGAGGTGAAGAAGATGT	1	67	1
      TTCCTCACGTGTTGTGGGAAGAAA	1	264	0
AAAATATTTTGCAGGAGGTGACAAAAT   	2	7	0
TTTTTAATACACCGGTGGTACACTCTTATG	2	158	1
GGACTCTGGATCCGCTGGTGGAGGTTCGAG	3	46	1
CTTTTCTCCTTCAGGAGGTGAATGCC    	3	284	1
CCGTGAAAGTTACCGTGATGTCAAGCGACA	4	31	1
TCAAGCGACATCCCGAGGAGATTTTCAACG	4	51	1
TCTCTTTCAATCCCGAGGAGGTGTGATGA 	4	281	1
TGTGTCTCCTTCCGGAGGGATTCAATATGT	6	14	1
          **********
MAP Score: 6.55372

Motif 7
TCACCTCCTGCAAAATATTTTAGAATATTAC	2	16	1
TAGAATATTACCAAATATTTTGTCAAGTCTC	2	36	1
GTCAAGTCTCCAAAAAAATTTTTCTGTAAGG	2	57	1
ATCCACAGACCAAATTAATTTTTATGCCATA	3	125	1
AAATGTTATACACAAGATTTTATATTCATGC	3	254	1
AACGTTATTTCCAAATAATTTCCTGGAATCG	4	77	1
          ***** *****
MAP Score: 4.24799

Motif 8
GAGATTTTTGGTGGAAAAACACAGGAAAACA	1	126	1
AAAACAGAAAGAAGAATAACAAAAAGTAAGT	1	151	1
CGTGTTGTGGGAAGAAACACAGTATCACCCT	1	250	0
CTAATTATATGTAAAGAAAATCTCGTTTCAC	2	112	0
GCCATAACTGGAATAATTACACGGATGTTTC	3	150	1
TTTCGTTTGAGAAAAGTAAAAGTCTGTTATG	3	180	0
TTCACCTCCTGAAGGAGAAAAGCATGAATAT	3	275	0
CGAAGAGAACGAAGAGGGAAATTTAGACCAA	4	165	0
AACCTAATTAGTAGAGATAAAAAACAGTTTC	4	195	0
TATTGATTCAGAAGAGTAAAATTACTCTTGT	4	231	1
ATCCCTCCGGAAGGAGACACAACGA      	6	4	0
GTACAACACTGTGGAGGAACAGAAA      	6	47	1
          ******* ***
MAP Score: 2.12351

Motif 9
         ACTTTTCCCTCCGAATTCCTTTCCT	0	11	0
TTTTCCTGTGTTTTTCCACCAAAAATCTCTATGA	1	121	0
GGTGATACTGTGTTTCTTCCCACAACACGTGAGG	1	252	1
GCATCCCCTTTTTCTTTATCCACAGACCAAATTA	3	108	1
TATTCATGCTTTTCTCCTTCAGGAGGTGAATGCC	3	276	1
CTGGAATCGACTTTTACGTCCAGAAAACGAATAT	4	99	1
GAAAACTTTCTCTTTCAATCCCGAGGAGGTGTGA	4	273	1
    TCGTTGTGTCTCCTTCCGGAGGGATTCAAT	6	6	1
          * ***** ***  *
MAP Score: 1.26514