AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons035_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243169
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT145	185	Serine/threonine Protein Kinase
#1	sohB	102	Protease
#2	uvrD	80	DNA Helicase

Motif 1
GCGGTGTAAATAGAAAAGAGCTCCG        	0	2	0
TAACTAAAGCAAGCTAAGCGGTGTAAATAGAAA	0	19	0
TAGCTTGCTTTAGTTAAGCGGTTCCTTTTTATC	0	36	1
TTATCAAAACAAAATAAGAGATCTTTTGTTGTA	0	64	1
GGAAAGCTACAAGTATAGTACTGGGAAGAGCAA	0	105	1
GTACTGGGAAGAGCAAATCGCTTAATAGGTTCA	0	122	1
TAATAGGTTCAAGTAAAGAAACTTCGCAATAAG	0	144	1
ACTTCGCAATAAGGTTAGAGGTCCCGAGGAG  	0	164	1
   TCTTGAGAAGAAAAGGACCTGGAGTATAGT	1	7	1
AAAGGACCTGGAGTATAGTATTCCAGGTCTTTT	1	21	1
          *** **** * **
MAP Score: 7.82018

Motif 2
 CGGAGCTCTTTTCTATTTACACCGCTTAG	0	9	1
AGTTAAGCGGTTCCTTTTTATCAAAACAAA	0	47	1
TTATTTAAAAATTCTTTTTATAATCCCCCT	1	59	1
TCCAGGTCCTTTTCTTCTCAAGA       	1	3	0
GGTCTTTTAATTTTTATTTAAAAATTCTTT	1	46	1
GATCTCTTATTTTGTTTTGATAAAAAGGAA	0	57	0
          **********
MAP Score: 2.91406