AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_sum_all052_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237212
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0238	67	hypothetical protein
#1	TM0239	39	glucose-1-phosphate adenylyltransferase
#2	TM0242	146	hypothetical protein

Motif 1
  AGTAGAACCACCTCTGAAGGAATTTTAACA	0	8	1
 TTTTCTTACCTCCTGTCTGGAAAAGCTTTAA	0	46	0
    TCTTCACACCTCTCTTCCTTCGTTCACT	1	21	0
       GTTCTCTTGTCATGGAAGTCCTTTT	2	3	1
GTCCTTTTTGCTCTTCTCATCGTCACAGTGAT	2	27	1
GTCACAGTGATCTTTTTCACGGTTTGCAGTGT	2	48	1
TTTGCAGTGTTTCCATTCATGCGAGAAGGATA	2	70	1
AGGATATTTTTACTTTACAGGGAAAGAGAAAT	2	96	1
          * ******* **
MAP Score: 3.45969

Motif 2
TATTTAAAGCTTTTCCAGACAGGAGGTAAGAAAA  	0	43	1
   TAGAATTCTTTAGTGAACGAAGGAAGAGAGGTG	1	7	1
GCAAAAAGGACTTCCATGACAAGAGAAC        	2	2	0
AAAAGATCACTGTGACGATGAGAAGAGCAAAAAGGA	2	28	0
GCAGTGTTTCCATTCATGCGAGAAGGATATTTTTAC	2	73	1
ATATTTTTACTTTACAGGGAAAGAGAAATAGCTGAA	2	99	1
          * * *  *  ******
MAP Score: 2.29212

Motif 3
AAGCTTTTCCAGACAGGAGGTAAGAAAA   	0	49	1
AATTCTTTAGTGAACGAAGGAAGAGAGGTGT	1	13	1
GAAGGAAGAGAGGTGTGAAGA          	1	28	1
AGGACTTCCATGACAAGAGAAC         	2	1	0
CGATGAGAAGAGCAAAAAGGACTTCCATGAC	2	18	0
ATCACTGTGACGATGAGAAGAGCAAAAAGGA	2	28	0
CACTGCAAACCGTGAAAAAGATCACTGTGAC	2	48	0
TTTCCATTCATGCGAGAAGGATATTTTTACT	2	79	1
TTTTTACTTTACAGGGAAAGAGAAATAGCTG	2	102	1
AAAGAGAAATAGCTGAAAGAACCGCAGATGG	2	118	1
          *** *******
MAP Score: 1.61224