AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i315_mixed29_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	pksG	224	pksG

Motif number 1

TCAAGGTATGCCGTTCCGCCAAAGACATTC	1	37	0	CCGTTCCGCC	    0.994727	-188
GAACGGCATACCTTGATGTCATGGAGCTGG	1	51	1	CCTTGATGTC	    0.962662	-174
CTTCATAAGGCAGTGCTACCGCTTTTTCTT	1	129	0	CAGTGCTACC	    0.958967	-96
TATGAAGATCCCGTGACTTCGGAGTCAATG	1	152	1	CCGTGACTTC	    0.995242	-73
GGCTTAGCTGCATTGACTCCGAAGTCACGG	1	162	0	CATTGACTCC	    0.974062	-63
    TTCAATCCGGTCCTTCTCTGCTTCAG	1	209	0	CCGGTCCTTC	    0.975974	-16
          **********

Masking position 1
Map Score:   5.42624

Number of sites scoring better than the average of aligned sites = 923
Number in coding regions = 863
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 2

         ATGGTTTCAGCCGGAATAGAAG	1	2	1	TGTTTCAGCC	    0.982419	-223
AAGCGATGAATGTCTTTGGCGGAACGGCATA	1	30	1	TGCTTTGGCG	    0.997376	-195
TCTAAGTGTCTGTATTTGGCCAGCTCCATGA	1	69	0	TGATTTGGCC	    0.993079	-156
GAAGATCCCGTGACTTCGGAGTCAATGCAGC	1	155	1	TGCTTCGGAG	    0.993481	-70
          ** ********

Masking position 6
Map Score:   2.17606

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 199
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

TTTCAAATCTCGCAGTATCTAAGTGTCTGT	1	87	0	CGCAGTATCT	     0.98945	-138
GCAGTGCTACCGCTTTTTCTTTCATTAATA	1	120	0	CGCTTTTTCT	     0.98908	-105
TCGGCTTAGCTGCATTGACTCCGAAGTCAC	1	164	0	TGCATTGACT	    0.971779	-61
CGATTATTGATGCTTTATCTGAAGCAGAGA	1	191	1	TGCTTTATCT	    0.990405	-34
          **********

Masking position 6
Map Score:   2.79639

Number of sites scoring better than the average of aligned sites = 219
Number in coding regions = 197
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

          **********

No masking
Map Score:   7.34864e-14

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 5

          **********

No masking
Map Score:   7.34864e-14

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:   7.34864e-14

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