AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251340
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0362	35	deoxyribonuclease IV
#1	TM1836	300	maltose ABC transporter, permease protein
#2	TM1840	250	alpha-amylase

Motif 1
ACCGGGAAAGGGGTAAGAAGC         	0	24	1
GCTCCTCTGTTGGTCGGAAGTTTCGCTTTC	1	38	1
TATCTGCTCACCGGTGGAGGTCCCGCAATG	1	92	1
TTACAAACTCGCGTTCGAAGGAGGAAGAGG	1	172	1
GCGTTCGAAGGAGGAAGAGGACAGGACTTC	1	182	1
ATATTCTTCCTCGTTGGAGGAATCAGCTTT	1	239	1
ACGCACCAGAGAGTTTGAAGTTCACAAAGC	1	264	0
ACTCTCTGGTGCGTTTGAAGAGGTGAGTGA	1	280	1
          **********
MAP Score: 5.01984

Motif 2
ATATATCTGCTCACCGGTGGAGGTCCCGCAATG	1	89	1
ATCATATTCTTCCTCGTTGGAGGAATCAGCTTT	1	236	1
TACAAACTCGCGTTCGAAGGAGGAAGAGGACAG	1	173	1
TTTCATTATATCACCGGGAAAGGGGTAAGAAGC	0	12	1
GCGAAACTTCCGACCAACAGAGGAGCCACAGTG	1	31	0
GTTAATTTATTGATCGTGGAATGTTTCGAAAAT	2	222	1
GGAGCCACAGTGGTCATCAGAAGCGGAAACGTG	1	10	0
AATGTCCGTGTGTCCAACAGGAGTTGTGGTTCC	1	125	0
          ** ***  *****
MAP Score: 5.00343

Motif 3
CTCTGTTGGTCGGAAGTTTCGCTTTCAACTT	1	42	1
TTCAACTTCAACAACTTTGTGAACATATATC	1	65	1
GTTGTGGTTCCAGCCATTGCGGGACCTCCAC	1	105	0
GTGTGTCCAACAGGAGTTGTGGTTCCAGCCA	1	120	0
GTTGGACACACGGACATTTTGGTCTCCTACG	1	140	1
GATTTTAACACCGAATTTTCGTGATGTCAAT	2	72	1
GATAGGGTTAACGGAATTTCGATATTTCTGA	2	148	0
ATATAAACAGACGGATTTGTGTTAATTTATT	2	202	1
         TCCTCATTTTCGAAACATTCCA	2	238	0
          ***** *****
MAP Score: 4.97359

Motif 4
   CACGTTTCCGCTTCTGATGACCACTGTGGCTC	1	7	1
GACCACTGTGGCTCCTCTGTTGGTCGGAAGTTTCG	1	28	1
GCTGGAACCACAACTCCTGTTGGACACACGGACAT	1	122	1
TGTCCTCTTCCTCCTTCGAACGCGAGTTTGTAAAC	1	170	0
GAAGAGGACAGGACTTCGGTTTTGCCAGTGCCATA	1	195	1
TCAGCTTTGTGAACTTCAAACTCTCTGGTGCGTTT	1	261	1
   TCACTCACCTCTTCAAACGCACCAGAGAGTTT	1	278	0
AACACCGATTCGAATCCAGATTGACATCACGAAAA	2	87	0
CAGAAATATCGAAATTCCGTTAACCCTATCGACAT	2	149	1
          *  **** ****  *
MAP Score: 2.60897

Motif 5
TCAACTTCAACAACTTTGTGAACATATATC	1	66	1
GACAGGACTTCGGTTTTGCCAGTGCCATAT	1	201	1
TTGGAGGAATCAGCTTTGTGAACTTCAAAC	1	252	1
ATTTTAACACCGAATTTTCGTGATGTCAAT	2	73	1
ATAGGGTTAACGGAATTTCGATATTTCTGA	2	148	0
TATAAACAGACGGATTTGTGTTAATTTATT	2	203	1
          **********
MAP Score: 2.55398

Motif 6
ACCACTGTGGCTCCTCTGTTGGTCGGAAGTTTC	1	29	1
TTTCAACTTCAACAACTTTGTGAACATATATCT	1	64	1
CTGGAACCACAACTCCTGTTGGACACACGGACA	1	123	1
TACGTTTACAAACTCGCGTTCGAAGGAGGAAGA	1	167	1
CGTTGGAGGAATCAGCTTTGTGAACTTCAAACT	1	250	1
       GGACACCTCCTTTAGATTACAAAGAG	2	3	1
TAAATTACTCATCAACTGTTTCATTCAGAAATA	2	124	1
          ***  ***** **
MAP Score: 0.905689

Motif 7
TTCATTATATCACCGGGAAAGGGGTAAGAAGC	0	13	1
TATATCTGCTCACCGGTGGAGGTCCCGCAATG	1	90	1
ACTCGCGTTCGAAGGAGGAAGAGGACAGGACT	1	178	1
CTGATTCCTCCAACGAGGAAGAATATGATGAT	1	233	0
TTAATTTATTGATCGTGGAATGTTTCGAAAAT	2	223	1
          ** ** ******
MAP Score: 0.613379