AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i248_cell_division_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	smc	100	chromosome segregation SMC protein homolg
#2	ftsE	233	cell-division ATP-binding protein

Motif number 1

          AATCCCCCTTATGACTCAGG	1	1	1	AATCCCCCTT	    0.996706	-100
TACATACTGAAATCCCCCTGAGTCATAAGG	1	17	0	AATCCCCCTG	    0.992733	-84
       AGCGATCCTCCTTATGTAATAAG	1	88	0	GATCCTCCTT	    0.992157	-13
     GATAAAAACATCCTTGCCGAGTGCT	2	6	1	AAACATCCTT	    0.988073	-228
CAAGGCATAAAAACATCCTTGCCAGCACTC	2	29	0	AAACATCCTT	    0.988073	-205
          **********

Masking position 2
Map Score:   9.15049

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 52
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 2

   AATCCCCCTTATGACTCAGGGGGATTTCA	1	8	1	CTTATGACAG	    0.962878	-93
TATGCCGTCTTATTTGACCAATGTTTATGATA	1	45	1	TATTTGACAT	    0.955161	-56
TTGACCAATGTTTATGATAGAATTGAAATACT	1	58	1	TTTATGATAA	    0.798168	-43
AATTGAAATACTTATTACATAAGGAGGATCGC	1	78	1	CTTATTACAA	    0.923316	-23
ATTACAGTTTCTTTTCATTCATATTGTCAAGG	2	54	0	CTTTTCATAT	    0.886451	-180
ATTATGTCTAAATTTGACGTATAATGAAGTGT	2	89	1	AATTTGACAT	    0.893964	-145
GATTTTTCATCTTTTTACAAATGAATGGGTCA	2	141	1	CTTTTTACAT	    0.974046	-93
CATTCGACAATTTATGACCCATTCATTTGTAA	2	155	0	TTTATGACAT	    0.970555	-79
TCTTTTATATCATTTTATCTATCACACGGTCA	2	200	0	CATTTTATAT	    0.874711	-34
          ********  **

Masking position 7
Map Score:   5.32742

Number of sites scoring better than the average of aligned sites = 1146
Number in coding regions = 974
Number in noncoding regions = 172
Number of orfs with sites within 600 bp upstream = 207
Fraction of orfs with sites within 600 bp upstream = 0.0332477


Motif number 3

CCCCCTGAGTCATAAGGGGGATT       	1	4	0	CATAAGGGGG	    0.984144	-97
ATACTTATTACATAAGGAGGATCGCT    	1	85	1	CATAAGGAGG	     0.99063	-16
GCCAGCACTCGGCAAGGATGTTTTTATC  	2	9	0	GGCAAGGATG	    0.993983	-225
GCCGAGTGCTGGCAAGGATGTTTTTATGCC	2	26	1	GGCAAGGATG	    0.993983	-208
          **********

Masking position 5
Map Score:   3.66461

Number of sites scoring better than the average of aligned sites = 68
Number in coding regions = 47
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 4

GACTCAGGGGGATTTCAGTATGTATGCCGTC	1	23	1	GATTTCATAT	    0.934231	-78
ATGTAATAAGTATTTCAATTCTATCATAAAC	1	67	0	TATTTCATTC	    0.983468	-34
GACATAATACTATTACAGTTTCTTTTCATTC	2	66	0	TATTACATTT	    0.947046	-168
GAAAGTTCCCTTTTTCAATACACTTCATTAT	2	109	0	TTTTTCATAC	    0.945202	-125
AACTTTCAGATTTTTCATCTTTTTACAAATG	2	133	1	TTTTTCACTT	    0.934237	-101
CCTAATCTTTTATATCATTTTATCTATCACA	2	206	0	TATATCATTT	     0.94704	-28
          ******* ***

Masking position 7
Map Score:   2.59002

Number of sites scoring better than the average of aligned sites = 892
Number in coding regions = 702
Number in noncoding regions = 190
Number of orfs with sites within 600 bp upstream = 212
Fraction of orfs with sites within 600 bp upstream = 0.0340508


Motif number 5

          **********

No masking
Map Score:   -6.1574e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -6.1574e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   -6.1574e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0