AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251402
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0521	81	heat shock protein HslV
#1	TM0524	209	conserved hypothetical protein
#2	TM0526	30	host factor I
#3	TM1243	43	phosphoribosylaminoimidazole-succinocarboxamide synthase

Motif 1
GTATCATCTTAAATGAGGAGGTGCGAAC      	0	4	0
CAATTTCTCAAATAAAGGAAATGGTATCATCTTA	0	27	0
AGTTAAAATAACTTGAGGAGGTGTTGAACC    	0	61	1
  ACTGAGGCCAAGAAGGCGGAAGCATTTCAGAG	1	8	1
GATCATAAAGAAAAGAAGCGTCAGAAGTCCCAGA	1	46	0
GCTATCACAACTATCAGGTGGCACTGGAGAAGCA	1	96	1
AAATACCAGGAATTGAAGACAAAGATAGAGGAAC	1	146	1
ACGAGAAGCTCTTAGAGGTGATAGAGA       	1	192	1
TTTGAAATCACATCGAGGGGGGAG          	2	16	1
ATAGAATTTTCAAAAAGGGCGGGGAGGCGAGCGT	3	19	1
          * * **** ** **
MAP Score: 7.43888

Motif 2
          GTTCGCACCTCCTCATTTAAGATGATACCATT	0	0	1
CATTTAAGATGATACCATTTCCTTTATTTGAGAAATTGAGTT	0	23	1
        GGTTCAACACCTCCTCAAGTTATTTTAACTCAAT	0	57	0
AGATTAACTCTGAAATGCTTCCGCCTTCTTGGCCTCAGT   	1	7	0
ATCTGGGACTTCTGACGCTTCTTTTCTTTATGATCTTTGTTT	1	45	1
CTCTATCTTTGTCTTCAATTCCTGGTATTTCGACATCAACCG	1	134	0
CTCGTTCAGCGCTTTCTGTTCCTCTATCTTTGTCTTCAATTC	1	155	0
        ACGCTCGCCTCCCCGCCCTTTTTGAAAATTCTAT	3	19	0
          *    *  *****    **  *
MAP Score: 4.03462

Motif 3
TATCATCTTAAATGAGGAGGTGCGAAC        	0	2	0
GTTAAAATAACTTGAGGAGGTGTTGAACC      	0	62	1
 ACTGAGGCCAAGAAGGCGGAAGCATTTCAGAGTT	1	9	1
TCACAACTATCAGGTGGCACTGGAGAAGCACAATC	1	100	1
GAAGACAAAGATAGAGGAACAGAAAGCGCTGAACG	1	160	1
ATTTTGAAATCACATCGAGGGGGGAG         	2	14	1
AGAATTTTCAAAAAGGGCGGGGAGGCGAGCGT   	3	21	1
          ** * ***** *  *
MAP Score: 1.14026