AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251352
 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
GACCACTGTGGCTCCTCTGTTGGTCGGAAGTTTCGCTTTC	1	28	1
ACATATATCTGCTCACCGGTGGAGGTCCCGCAATGGCTGG	1	87	1
GCTGGAACCACAACTCCTGTTGGACACACGGACATTTTGG	1	122	1
GAGCCACAGTGGTCATCAGAAGCGGAAACGTG        	1	2	0
GTCCTGTCCTCTTCCTCCTTCGAACGCGAGTTTGTAAACG	1	169	0
GAAGAGGACAGGACTTCGGTTTTGCCAGTGCCATATCCAT	1	195	1
   TCACTCACCTCTTCAAACGCACCAGAGAGTTTGAAGT	1	273	0
TCATCATATTCTTCCTCGTTGGAGGAATCAGCTTTGTGAA	1	234	1
          * ** ** ** *  *    *
MAP Score: 4.64838

Motif 2
CTCTGTTGGTCGGAAGTTTCGCTTTCAACTT	1	42	1
GTTGTGGTTCCAGCCATTGCGGGACCTCCAC	1	105	0
GTGTGTCCAACAGGAGTTGTGGTTCCAGCCA	1	120	0
GTTGGACACACGGACATTTTGGTCTCCTACG	1	140	1
GATTTTAACACCGAATTTTCGTGATGTCAAT	2	72	1
CTGTTTCATTCAGAAATATCGAAATTCCGTT	2	139	1
ATATAAACAGACGGATTTGTGTTAATTTATT	2	202	1
         TCCTCATTTTCGAAACATTCCA	2	238	0
          ***** *****
MAP Score: 3.534

Motif 3
GTGGCTCCTCTGTTGGTCGGAAGTTTCGCTTTCAACT	1	35	1
GCCAGTGCCATATCCATCATCATATTCTTCCTCGTTG	1	218	1
ATCATATTCTTCCTCGTTGGAGGAATCAGCTTTGTGA	1	236	1
TACAAAGAGTTTACCGTCAGAAAATTCACAAAATGTT	2	27	1
TAACACCGAATTTTCGTGATGTCAATCTGGATTCGAA	2	77	1
GTTTTTAAATTACTCATCAACTGTTTCATTCAGAAAT	2	119	1
AAATATCGAAATTCCGTTAACCCTATCGACATGTTAT	2	152	1
GTTAATTTATTGATCGTGGAATGTTTCGAAAATGAGG	2	222	1
          *  **** *    ****
MAP Score: 3.09681

Motif 4
CACTGTGGCTCCTCTGTTGGTCGGAAGTTTCGCTTTCAACTT	1	31	1
GAACATATATCTGCTCACCGGTGGAGGTCCCGCAATGGCTGG	1	85	1
CGTTTACAAACTCGCGTTCGAAGGAGGAAGAGGACAGGACTT	1	169	1
CATCATCATATTCTTCCTCGTTGGAGGAATCAGCTTTGTGAA	1	232	1
ACTTCAAACTCTCTGGTGCGTTTGAAGAGGTGAGTGA     	1	273	1
TTGTGTTAATTTATTGATCGTGGAATGTTTCGAAAATGAGGA	2	218	1
          **   *  **  *** *    *
MAP Score: 2.8466

Motif 5
         CGTTTCATTATATCACCGGGAAAGGGGTAAGAAGC  	0	1	1
CAACAACTTTGTGAACATATATCTGCTCACCGGTGGAGGTCCCGCA	1	73	1
AGACCAAAATGTCCGTGTGTCCAACAGGAGTTGTGGTTCCAGCCAT	1	119	0
CCGAAGTCCTGTCCTCTTCCTCCTTCGAACGCGAGTTTGTAAACGT	1	168	0
TGCCATATCCATCATCATATTCTTCCTCGTTGGAGGAATCAGCTTT	1	223	1
        TCACTCACCTCTTCAAACGCACCAGAGAGTTTGAAGTT	1	272	0
AATTTTCGTGATGTCAATCTGGATTCGAATCGGTGTTTTTAAATTA	2	85	1
TGAATTGGGTGTTAATATAAACAGACGGATTTGTGTTAATTTATTG	2	188	1
TTAATTTATTGATCGTGGAATGTTTCGAAAATGAGGA         	2	223	1
          **     * *     ** *   * **
MAP Score: 1.12122