AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i201_excinuclease_abc_bsub_reg_300.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)
#2	csbA	300	putative membrane protein

Motif number 1

GACATAATGAATATAAAGACTGAATACCTGCT	1	15	1	ATATAAAGCG	    0.838119	-171
TGCTTTTAAAACGTAAAAGCAGGTATTCAGTC	1	32	0	ACGTAAAACG	    0.904963	-154
GTTTTTGTGTATAAAAAACCTGCTTTTAAAAC	1	52	0	ATAAAAAACG	    0.982904	-134
GGTTTTTTATACACAAAAACAGCTGGAAATAA	1	64	1	ACACAAAACG	    0.947919	-122
ACAGCTGGAAATAAAAAACCACCGAACTTTAG	1	82	1	ATAAAAAACC	     0.96712	-104
ACACAATGGAAAGCAAAATCACTAAAAATACG	1	116	0	AAGCAAAACC	    0.737423	-70
CTTCCTATAGATATAGTAACACAATGGAAAGC	1	134	0	ATATAGTACC	    0.800183	-52
GAAGATTTCGTTAAAGAAACGGAGGCTTATTT	1	162	1	TTAAAGAACG	    0.885243	-24
GAAAATAGGCATACAGTACCAGTACGGCCGCA	2	48	0	ATACAGTACG	    0.924859	-253
TGATGATGTAATAAAAAAAGTGCCGCTGATTA	2	108	1	ATAAAAAAGG	    0.859435	-193
ATAGTAAAAAATGAAGAATCGGACAATCGTGC	2	241	0	ATGAAGAACG	    0.982075	-60
ATCAGATCAGATGAAGAATCCCTGAGGAGGGT	2	274	1	ATGAAGAACC	    0.965553	-27
          ******** * *

Masking position 5
Map Score:   12.179

Number of sites scoring better than the average of aligned sites = 2333
Number in coding regions = 1962
Number in noncoding regions = 371
Number of orfs with sites within 600 bp upstream = 326
Fraction of orfs with sites within 600 bp upstream = 0.0523611


Motif number 2

       AAAAATAAGCCTCCGTTTCTTTAACGAA	1	168	0	AAGCTCCGTT	    0.922989	-18
ATTATCCTGAAAAATGCGGCCGTACTGGTACTGTA	2	34	1	ATGCGCCGAC	    0.996224	-267
TTATTCTCGGAATCTGGCGGCGGACTTGATGATGT	2	82	1	ATGGGGCGAC	    0.950337	-219
TGTAATAAAAAAAGTGCCGCTGATTAGAACAGCGG	2	114	1	ATGCGCTGTT	    0.960632	-187
AACTTATTCCATGGTGCCGCTGTTCTAATCAGCGG	2	130	0	ATGCGCTGTC	    0.996319	-171
CCATATTTGCATTTTGGTGCCGGTCAAAACTTATT	2	157	0	ATGGGCCGTC	    0.996333	-144
GAATCGGACAATCGTGCATTCGCTCCCTCTACTTA	2	223	0	ATGCTTCGTC	    0.974983	-78
CTCCTCAGGGATTCTTCATCTGATCTGATTATAGT	2	268	0	ATTCTCTGTC	    0.929141	-33
          *   *** **** **

Masking position 1
Map Score:   8.41727

Number of sites scoring better than the average of aligned sites = 877
Number in coding regions = 822
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

TAAAGACTGAATACCTGCTTTTACGTTTTAA	1	28	1	ATACCGCTTT	    0.944073	-158
TGTGTATAAAAAACCTGCTTTTAAAACGTAA	1	48	0	AAACCGCTTT	    0.895917	-138
TGGAAATAAAAAACCACCGAACTTTAGTTCG	1	87	1	AAACCCCGAA	    0.836354	-99
    AAAAATAAGCCTCCGTTTCTTTAACGA	1	169	0	AAGCCCCGTT	    0.990148	-17
ATCCTGAAAAATGCGGCCGTACTGGTACTGT	2	37	1	ATGCGCCGTA	    0.897977	-264
CTGGTACTGTATGCCTATTTTCTTTTATTCT	2	58	1	ATGCCATTTT	    0.865615	-243
AATAAAAAAAGTGCCGCTGATTAGAACAGCG	2	117	1	GTGCCCTGAT	    0.937776	-184
TTATTCCATGGTGCCGCTGTTCTAATCAGCG	2	131	0	GTGCCCTGTT	    0.979463	-170
TACTTACACCATACCCCTTTTCAGCCAAAAT	2	198	0	ATACCCTTTT	    0.961635	-103
          ***** *****

Masking position 4
Map Score:   4.97789

Number of sites scoring better than the average of aligned sites = 1741
Number in coding regions = 1485
Number in noncoding regions = 256
Number of orfs with sites within 600 bp upstream = 228
Fraction of orfs with sites within 600 bp upstream = 0.0366206


Motif number 4

          **********

No masking
Map Score:   5.21128e-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 5

          **********

No masking
Map Score:   5.21128e-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:   5.21128e-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