AlignACE 3.0 10/20/99
AlignACE2 -i BB/BB_operons021_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237662
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	BB0147	50	flagellar filament 41 kDa core protein (flaB)
#1	BB0180	83	flagellar protein, putative {Borrelia burgdorferi
#2	BB0359	64	carboxyl-terminal protease (ctp)

Motif 1
CCAAAGTCAGAAATTTAAATTTTATCATGGAGGAATG	0	19	1
          ACTTTAATGTATTATAACACAATAAAA	1	0	1
AAAAAAGACAAAATTGATTTGTAAATATGTTTATAAT	1	33	1
TATGAAATTAATTATAAGCTATTATAAACATATTTAC	1	53	0
TTATTTCCATAATATAATATTTTAAAACT        	2	2	0
TTATGGAAATAAAATCAAGTTTTAATTTTTGCATTAG	2	27	1
          * *** *  * ***  *
MAP Score: 7.0532

Motif 2
TTTGCCAAAGTCAGAAATTTAAATTTTATCATG	0	15	1
ATTTTATCATGGAGGAATGATAT          	0	37	1
      ACTTTAATGTATTATAACACAATAAAA	1	4	1
AAATTAATTATAAGCTATTATAAACATATTTAC	1	53	0
       TTTTATGAAATTAATTATAAGCTATT	1	67	0
AATATTATATTATGGAAATAAAATCAAGTTTTA	2	18	1
CATTCCTAATGCAAAAATTAAAACTTGATTTTA	2	36	0
AATTTTTGCATTAGGAATGAATAA         	2	50	1
          * ** ***** **
MAP Score: 2.69878