AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251313
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
          CAGGAAAGGAATTCGGAGGGA	0	0	1
TGATATCTGAAAGGAGGTGAAGAAGATGTTA	1	68	1
GGAAAACAGAAAGAAGAATAACAAAAAGTAA	1	149	1
TGGTTAAAAAATGGGGACGCAGGGGTACGGC	1	182	0
CCCAGCCAGAAAGGGGATGCAATGCATCCCC	2	85	1
GATAAAGAAAAAGGGGATGCATTGCATCCCC	2	97	0
TTAATTTGGTCTGTGGATAAAGAAAAAGGGG	2	112	0
TTTTCTCCTTCAGGAGGTGAATGCC      	2	285	1
CTTTTACGTCCAGAAAACGAATATTTCTGTG	3	109	1
AGTCCAGATTATGTAAACGAAACACAGAAAT	3	131	0
AACAGTTTCGAAGAGAACGAAGAGGGAAATT	3	173	0
ATTATTGATTCAGAAGAGTAAAATTACTCTT	3	229	1
ATCCCTCCGGAAGGAGACACAACGA      	5	4	0
TTGTACAACACTGTGGAGGAACAGAAA    	5	45	1
          ******* ***
MAP Score: 12.6201

Motif 2
ATGCTTTTCTCCTTCAGGAGGTGAATGCC   	2	281	1
GCTGATATGGCTGACTGGAGGT          	4	14	1
CGTTGTGTCTCCTTCCGGAGGGATTCAATATG	5	11	1
TCTCTTTCAATCCCGAGGAGGTGTGATGA   	3	281	1
     AAAGGCCGTTGGGAGGTCGTCTAACGG	2	5	1
GTTGAAAATCTCCTCGGGATGTCGCTTGACAT	3	48	0
CTCTGGATCCGCTGGTGGAGGTTCGAGTCCTC	2	49	1
ATGATGATATCTGAAAGGAGGTGAAGAAGATG	1	64	1
TAGAACTGATACCGCTGGATGTGGTCATAGAG	1	97	1
GAAATATTCGTTTTCTGGACGTAAAAGTCGAT	3	104	0
AGGTCGTCTAACGGTAGGACGGCGGACTCTGG	2	23	1
          *** * ******
MAP Score: 10.6447

Motif 3
AGAACTGATACCGCTGGATGTGGTCATAGAGAT	1	98	1
TTTAACCAGGCCTCGAAACGAGGCTTTTTTTGT	1	205	1
    AAAGGCCGTTGGGAGGTCGTCTAACGGTA	2	6	1
GGTCGTCTAACGGTAGGACGGCGGACTCTGGAT	2	24	1
GACTCTGGATCCGCTGGTGGAGGTTCGAGTCCT	2	47	1
ATCCCCTTTCTGGCTGGGAGGGGAGGACTCGAA	2	70	0
  GGCATTCACCTCCTGAAGGAGAAAAGCATGA	2	279	0
TTGAAAATCTCCTCGGGATGTCGCTTGACATCA	3	46	0
TCTGCTGATATGGCTGACTGGAGGT        	4	11	1
ATATTGAATCCCTCCGGAAGGAGACACAACGA 	5	9	0
          **** **  ****
MAP Score: 10.02

Motif 4
TTCTTCACCTCCTTTCAGATATCATCATCC	1	62	0
TTGTTATTCTTCTTTCTGTTTTCCTGTGTT	1	143	0
TACGGCACTTACTTTTTGTTATTCTTCTTT	1	158	0
CAATGCATCCCCTTTTTCTTTATCCACAGA	2	104	1
TTCATAACAGACTTTTACTTTTCTCAAACG	2	178	1
TTTCACGGTAACGTTTACGTATGGTAATA 	3	9	0
CATCACGGTAACTTTCACGGTAACGTTTAC	3	21	0
CCTGGAATCGACTTTTACGTCCAGAAAACG	3	98	1
ACAGAAATATTCGTTTTCTGGACGTAAAAG	3	109	0
TTTCTGTGTTTCGTTTACATAATCTGGACT	3	132	1
ATTTCCCTCTTCGTTCTCTTCGAAACTGTT	3	174	1
GATTGTGAAAACTTTCTCTTTCAATCCCGA	3	267	1
          **********
MAP Score: 8.6804

Motif 5
CTTTTCCCTCCGAATTCCTTTCCTG          	0	0	0
TCAGTTCTAACATCTTCTTCACCTCCTTTCAGATA	1	71	0
TGTTATTCTTCTTTCTGTTTTCCTGTGTTTTTCCA	1	137	0
ACGGCACTTACTTTTTGTTATTCTTCTTTCTGTTT	1	152	0
TTCATAACAGACTTTTACTTTTCTCAAACGAAACA	2	178	1
ACATTTATACCATATGTGTTCTCTCAATCAAAGGA	2	225	0
AAGATTTTATATTCATGCTTTTCTCCTTCAGGAGG	2	267	1
AACGTTATTTCCAAATAATTTCCTGGAATCGACTT	3	77	1
GAAACACAGAAATATTCGTTTTCTGGACGTAAAAG	3	109	0
TTCTGTGTTTCGTTTACATAATCTGGACTCTTTTG	3	133	1
TCTAAATTTCCCTCTTCGTTCTCTTCGAAACTGTT	3	169	1
TCTCTTCGAAACTGTTTTTTATCTCTACTAATTAG	3	188	1
ACACAAGAGTAATTTTACTCTTCTGAATCAATAAT	3	229	0
TTGTACAATACATATTGAATCCCTCCGGAAGGAGA	5	18	0
          * * **  ** ****
MAP Score: 7.94819

Motif 6
          CAGGAAAGGAATTCGGAGGGA	0	0	1
GCTACATTTACAGGCGAAGGATGATGATATC	1	44	1
TGATATCTGAAAGGAGGTGAAGAAGATGTTA	1	68	1
CACAGGAAAACAGAAAGAAGAATAACAAAAA	1	145	1
ATTTTTTAACCAGGCCTCGAAACGAGGCTTT	1	201	1
CCCTCCCAGCCAGAAAGGGGATGCAATGCAT	2	81	1
TTTTCTCCTTCAGGAGGTGAATGCC      	2	285	1
CTTTTACGTCCAGAAAACGAATATTTCTGTG	3	109	1
ATTATTGATTCAGAAGAGTAAAATTACTCTT	3	229	1
TTGAATCCCTCCGGAAGGAGACACAACGA  	5	8	0
          ******* ***
MAP Score: 4.86933

Motif 7
AAAGGAATTCGGAGGGAAAAGT         	0	14	1
ATTTACAGGCGAAGGATGATGATATCTGAAA	1	49	1
ATATCTGAAAGGAGGTGAAGAAGATGTTAGA	1	70	1
CCTGGTTAAAAAATGGGGACGCAGGGGTACG	1	184	0
CTTTCTGGCTGGGAGGGGAGGACTCGAACCT	2	67	0
CTCCCAGCCAGAAAGGGGATGCAATGCATCC	2	83	1
TGGATAAAGAAAAAGGGGATGCATTGCATCC	2	99	0
ATTCACCTCCTGAAGGAGAAAAGCATGAATA	2	276	0
TTCTCCTTCAGGAGGTGAATGCC        	2	287	1
CGAAGAGAACGAAGAGGGAAATTTAGACCAA	3	165	0
TCCTCGGGATTGAAAGAGAAAGTTTTCACAA	3	269	0
GAATCCCTCCGGAAGGAGACACAACGA    	5	6	0
          ********* *
MAP Score: 3.39579

Motif 8
TTCCGATGCTACATTTACAGGCGAAGGATG	1	37	1
AGATGTTAGAACTGATACCGCTGGATGTGG	1	91	1
ACGAAACAATACTGATACAGTCCTTTGATT	2	205	1
ACCATACGTAAACGTTACCGTGAAAGTTAC	3	14	1
CGTTACCGTGAAAGTTACCGTGATGTCAAG	3	26	1
          **********
MAP Score: 0.641784