AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i201_excinuclease_abc_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	uvrB	185	excinuclease ABC (subunit B)

Motif number 1

AGCAGGTATTCAGTCTTTATATTCATTATGTC	1	15	0	CAGCTTTTAT	    0.985264	-171
GACTGAATACCTGCTTTTACGTTTTAAAAGCA	1	32	1	CTGTTTTCGT	    0.989471	-154
GTTTTAAAAGCAGGTTTTTTATACACAAAAAC	1	52	1	CAGTTTTTAT	    0.990036	-134
TTATTTCCAGCTGTTTTTGTGTATAAAAAACC	1	64	0	CTGTTTTTGT	    0.992891	-122
CTAAAGTTCGGTGGTTTTTTATTTCCAGCTGT	1	82	0	GTGTTTTTAT	     0.98995	-104
CGTATTTTTAGTGATTTTGCTTTCCATTGTGT	1	116	1	GTGTTTTCTT	    0.978836	-70
TAAAGAAACGGAGGCTTATTTTT         	1	173	1	GAGCTTATTT	    0.880598	-13
          *** **** ***

Masking position 6
Map Score:   9.37514

Number of sites scoring better than the average of aligned sites = 1017
Number in coding regions = 829
Number in noncoding regions = 188
Number of orfs with sites within 600 bp upstream = 160
Fraction of orfs with sites within 600 bp upstream = 0.0256987


Motif number 2

ATAATGAATATAAAGACTGAATACCTGCTT	1	18	1	TAAAGACTGA	    0.887552	-168
TTTTAAAACGTAAAAGCAGGTATTCAGTCT	1	31	0	TAAAAGCAGG	    0.978683	-155
TTTTACGTTTTAAAAGCAGGTTTTTTATAC	1	46	1	TAAAAGCAGG	    0.978683	-140
CAGCTGGAAATAAAAAACCACCGAACTTTA	1	83	1	TAAAAAACCA	    0.879891	-103
AAATACGAACTAAAGTTCGGTGGTTTTTTA	1	93	0	TAAAGTTCGG	    0.909598	-93
GCAAAATCACTAAAAATACGAACTAAAGTT	1	106	0	TAAAAATACG	    0.931612	-80
TTCCTATAGATATAGTAACACAATGGAAAG	1	135	0	TATAGTAACA	    0.811487	-51
TTACTATATCTATAGGAAGATTTCGTTAAA	1	147	1	TATAGGAAGA	    0.923161	-39
AAGATTTCGTTAAAGAAACGGAGGCTTATT	1	163	1	TAAAGAAACG	    0.980368	-23
          **********

Masking position 4
Map Score:   8.99947

Number of sites scoring better than the average of aligned sites = 1710
Number in coding regions = 1392
Number in noncoding regions = 318
Number of orfs with sites within 600 bp upstream = 316
Fraction of orfs with sites within 600 bp upstream = 0.0507549


Motif number 3

          **********

No masking
Map Score:   2.37484e-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 4

          **********

No masking
Map Score:   2.37484e-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:   2.37484e-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