AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ihipB_ecoli_hinf_100.orf -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	hipB	222	persistence to inhibition of murein or DNA biosynthesis; regulatory protein
#2	HI0666.1	199	H. influenzae predicted coding region HI0666.1

Motif number 1

AATCCTCCTTTTTATCCGCGATCGCGGATATCGCAGCGTT	1	87	1	TTTTCGGGAA	    0.994577	-136
TATCGCAGCGTTTATCCCGTAGAGCGGATAAGATGTGTTT	1	115	1	TTTTCTGGAA	    0.997579	-108
TATTATAAGTTTTATCCTTTAGTGAGGATAAGTCAATCTG	1	156	0	TTTTCTGGAA	    0.997579	-67
CCACAGCAAGTTTATCCGCTTAAGGGGATATTATAAGTTT	1	184	0	TTTTCTGGAA	    0.998605	-39
CCATTTGTAATTTGTCCCATTTTTTGGAGAGCAGATTAAA	2	36	0	TTTTCTGGAA	    0.998656	-164
GAATATCTTTTTTGATTTTTTTTAGGGAAAAATTTGAGGA	2	110	0	TTTATTGGAA	    0.976494	-90
  ATTTGATATTTTTTTCTTTTTATGGAAATATTTTATAT	2	172	0	TTTTTTGGAA	    0.994759	-28
          *** * *  *     *** *

Masking position 18
Map Score:   17.3484

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 10
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

AATCCTCCTTTTTATCCGCGATCGCGGATATCGCAGC	1	87	1	TTTATCCGGG	    0.999364	-136
TATCGCAGCGTTTATCCCGTAGAGCGGATAAGATGTG	1	115	1	TTTATCCGGG	    0.999364	-108
TATTATAAGTTTTATCCTTTAGTGAGGATAAGTCAAT	1	159	0	TTTATCCGGG	    0.999364	-64
CCACAGCAAGTTTATCCGCTTAAGGGGATATTATAAG	1	187	0	TTTATCCGGG	    0.999364	-36
CCATTTGTAATTTGTCCCATTTTTTGGAGAGCAGATT	2	39	0	TTTGTCCTGG	    0.992684	-161
          *******      * **

Masking position 5
Map Score:   11.7792

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 11
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

      ACCGTATAAGCCGCATGTCGAGAT	1	5	1	TATAAGCCGC	    0.989823	-218
AGTCGGCAATATTAAGCCGCATGCCATCTC	1	30	0	ATTAAGCCGC	     0.96547	-193
AACGCCTTATTTAAATCCTCCTTTTTATCC	1	74	1	TTAAATCCTC	    0.906781	-149
AAATCCTCCTTTTTATCCGCGATCGCGGAT	1	86	1	TTTTATCCGC	    0.990022	-137
CTCTACGGGATAAACGCTGCGATATCCGCG	1	109	0	TAAACGCTGC	    0.796194	-114
TGGAAACACATCTTATCCGCTCTACGGGAT	1	128	0	TCTTATCCGC	    0.973176	-95
TCCACAGCAAGTTTATCCGCTTAAGGGGAT	1	195	0	GTTTATCCGC	    0.963442	-28
TTTCAATTAATTTAATCTGCTCTCCAAAAA	2	26	1	TTTAATCTGC	    0.984125	-174
AAATGATACTTAAAATCTGCTCTGTCCATT	2	71	0	TAAAATCTGC	    0.952982	-129
          **********

Masking position 7
Map Score:   12.8024

Number of sites scoring better than the average of aligned sites = 987
Number in coding regions = 829
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 135
Fraction of orfs with sites within 600 bp upstream = 0.0216833


Motif number 4

AGTCAATCTGGAAACACATCTTATCCGCTC	1	136	0	GAAACACATC	    0.895441	-87
ACTAAAGGATAAAACTTATAATATCCCCTT	1	173	1	AAAACTTATA	    0.919626	-50
GGAATTATTCAAAAATGATACTTAAAATCT	2	83	0	AAAAATGATA	    0.963372	-117
ATTTTTCCCTAAAAAAAATCAAAAAAGATA	2	117	1	AAAAAAAATC	    0.938133	-83
AAAAAAAATCAAAAAAGATATTCTAAAAAC	2	127	1	AAAAAAGATA	    0.971632	-73
TCTAAAAACAAAAAATCATATATGATATAA	2	148	1	AAAAATCATA	    0.963372	-52
CATAAAAAGAAAAAAATATCAAAT      	2	186	1	AAAAAATATC	    0.963913	-14
          **********

Masking position 4
Map Score:   5.53539

Number of sites scoring better than the average of aligned sites = 473
Number in coding regions = 343
Number in noncoding regions = 130
Number of orfs with sites within 600 bp upstream = 149
Fraction of orfs with sites within 600 bp upstream = 0.0239319


Motif number 5

          **********

No masking
Map Score:   -7.57849e-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:   -7.57849e-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:   -7.57849e-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