AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_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	yacL	115	similar to hypothetical proteins
#2	gltX	90	glutamyl-tRNA synthetase
#3	ywfO	161	alternate gene name: ipa-93d; similar to hypothetical proteins

Motif number 1

 ACCCCCACCTCCTTTTTTAACATTTTAATTT	1	95	0	TCTTTTTTAC	    0.981232	-21
        CTTGTTTTGATGCCGGGTCTATTT	2	3	1	TTTTTGATGC	    0.964117	-88
AATAGATTCATACATTTTTGCCTGAGGCCATA	2	43	1	TCATTTTTGC	    0.936949	-48
TTCAAATACTTCCTTTCATGTCATGTATGGCC	2	68	0	TCTTTCATGC	    0.985651	-23
   AAACATATTTTTTCTTAGCCTCGGCCCTC	3	8	1	TTTTTCTTAC	    0.944268	-154
ATCGACTCTATTCTTTGAAAACATCCTTGAAT	3	103	0	TCTTTGAAAC	    0.940691	-59
TTAGCCGTGTTTCTATTATATCGACTCTATTC	3	122	0	TCTATTATAC	     0.90356	-40
TCATTCCCTCTTTTTTTTAGCCGTGTTTCTAT	3	138	0	TTTTTTTAGC	    0.922276	-24
          * ******** *

Masking position 6
Map Score:   5.76476

Number of sites scoring better than the average of aligned sites = 1147
Number in coding regions = 984
Number in noncoding regions = 163
Number of orfs with sites within 600 bp upstream = 168
Fraction of orfs with sites within 600 bp upstream = 0.0269836


Motif number 2

AACCAACATTAATATACCCGTATTCATAAG	1	24	0	AATATACCCG	    0.995246	-92
TCTACCACCAAATAGACCCGGCATCAAAAC	2	14	0	AATAGACCCG	    0.996921	-77
AACATCCTTGAATTTGCCCGGCGATTTGTT	3	86	0	AATTTGCCCG	    0.979839	-76
GTTTTCAAAGAATAGAGTCGATATAATAGA	3	113	1	AATAGAGTCG	    0.968158	-49
          **********

Masking position 3
Map Score:   3.86787

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 58
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

TCGGTTAAAACCTTATGAATACGGGTATAT	1	13	1	CCTTATGAAT	    0.981813	-103
TTTCACAAAGTCTTATGCATCCTACGAATA	1	68	0	TCTTATGCAT	    0.940834	-48
ATGCATAAGACTTTGTGAAATTAAAATGTT	1	78	1	CTTTGTGAAA	    0.950373	-38
TCATGTATGGCCTCAGGCAAAAATGTATGA	2	50	0	CCTCAGGCAA	    0.952671	-41
GAAAAACACATCTTGTGAAGCAAAAAAGCC	3	46	0	TCTTGTGAAG	    0.928611	-116
TTTGTTCCATCTTCATGAAAAACACATCTT	3	62	0	CTTCATGAAA	    0.535041	-100
          **********

Masking position 3
Map Score:   1.706

Number of sites scoring better than the average of aligned sites = 728
Number in coding regions = 621
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 4

CACAAAGTCTTATGCATCCTACGAATATCA	1	65	0	TATGCATCCT	    0.936366	-51
     TTTCAAATACTTCCTTTCATGTCAT	2	76	0	AATACTTCCT	    0.970216	-15
CTTGTGAAGCAAAAAAGCCTGACCTGAGGG	3	35	0	AAAAAAGCCT	    0.902691	-127
CTTCATGAAAAACACATCTTGTGAAGCAAA	3	52	0	AACACATCTT	    0.945071	-110
CTATTCTTTGAAAACATCCTTGAATTTGCC	3	98	0	AAAACATCCT	    0.990762	-64
          **********

Masking position 2
Map Score:   1.20882

Number of sites scoring better than the average of aligned sites = 563
Number in coding regions = 451
Number in noncoding regions = 112
Number of orfs with sites within 600 bp upstream = 119
Fraction of orfs with sites within 600 bp upstream = 0.0191134


Motif number 5

          **********

No masking
Map Score:   3.43493e-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:   3.43493e-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:   3.43493e-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