AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons030_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243052
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT573	127	hypothetical protein
#1	mutL	294	DNA Mismatch Repair
#2	CT663	300	hypothetical protein
#3	CT665	43	hypothetical protein
#4	CT666	26	hypothetical protein
#5	CT670	22	hypothetical protein
#6	pkn5	134	S/T Protein Kinase

Motif 1
ATATAAAAGCCGATTTTTTTGTTTTTTAAC	0	14	1
AGAAAAGCCGTTTTTTTGTTAAAAAACAAA	0	31	0
GGCTTTTCTTATTTTCTTTTGTAAAAATTG	0	52	1
TTGTAAAAATTGATTTTTTTTCTCAAATCA	0	70	1
TTACTTTATACAATTCTTTTTTGTTTCTCT	0	101	1
TTTGTTATTTTTATTTTTTTAGGAATTATC	1	13	0
ATATTAAAAACGTTTTTATTAATTAACTTG	1	82	0
AAAACATAATTAATTCTTTTTGCGTAAGTT	1	124	1
CGTTGCCTTGCAATTTTTTTTAACAGGAGG	1	176	1
CGTTCGTGCCCGATTTTTTTCTAAAATTCT	2	91	1
TTTTTTTCTAAAATTCTTTTGTACTTTAAA	2	104	1
ATAGAGGAGCCTTTTCTGTTTTCTCTTTCA	2	144	0
TGAGAAATCGTTTTTCTTTTTAAAGTAGGT	2	179	1
          **********
MAP Score: 14.4002

Motif 2
AAAACAAAAAAATCGGCTTTTATATGAAA        	0	2	0
GAAAATAAGAAAAGCCGTTTTTTTGTTAAAAAACAAA	0	31	0
TCTTTTGTAAAAATTGATTTTTTTTCTCAAATCAGTT	0	66	1
TACTTTATACAATTCTTTTTTGTTTCTCTGTTGTT  	0	102	1
TGTTAGTAGTAATTTGTTATTTTTATTTTTTTAGGAA	1	18	0
AGATCGTTAGAATTTAATATTGTTAGTAGTAATTTGT	1	38	0
CAAAATATTAAAAACGTTTTTATTAATTAACTTGTTA	1	79	0
AAAAAGAATTAATTATGTTTTATTAAAAGCAAAATAT	1	108	0
ATTTTTTTCTAAAATTCTTTTGTACTTTAAATTGAAA	2	103	1
TCGAGATGAGAAATCGTTTTTCTTTTTAAAGTAGGTA	2	173	1
          ***    **** **  *
MAP Score: 13.422