AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -iphoB_mgen_opreg_100.orf -g0.317 -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 =  	0.317
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MG289	300	high affinity transport system protein P37

Motif number 1

TTTAGTTTTAAACAAATTCAATTTCGTTTGTAAC	1	13	0	ACAATTAATT	    0.992762	-288
GAGTTAGAATATAATGTTAAATTTTCCCTGTCTG	1	48	0	AAATTTAATT	     0.96088	-253
ATATTTTTTAATAAAGATTAATTGCCAGCAACTT	1	141	1	AAAAATAATG	    0.980131	-160
ATTAATTGCCAGCAACTTGAATCTAAGTAATAAA	1	157	1	ACAATTAATT	    0.992762	-144
TAAGTTTTTAATAAAAATAAATATTCACTTTATT	1	185	0	AAAAATAATT	    0.987867	-116
AAAATAGACTACAAATTTGAATATAAGTTTTTAA	1	208	0	AAAATTAATT	    0.992876	-93
AACTAATATAAAAAAGTTGAATATTTAAAAACAA	1	243	1	AAAATTAATT	    0.992876	-58
ATTATTAATTATCAAAATTAATTGTTTTTAAATA	1	264	0	ACAAATAATG	    0.979766	-37
          * *** ** *** *

Masking position 10
Map Score:   16.8656

Number of sites scoring better than the average of aligned sites = 106
Number in coding regions = 89
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

TTCAATTTCGTTTGTAACTT          	1	1	0	TTTGTAACTT	    0.817781	-300
TCTGTTTTAGTTTTAAACAAATTCAATTTC	1	22	0	TTTTAAACAA	    0.935862	-279
TAGAATATAATGTTAAATTTTCCCTGTCTG	1	48	0	TGTTAAATTT	    0.764406	-253
CGAATTACTTTTTTGAATTAAAGCTATTCT	1	100	0	TTTTGAATTA	      0.9531	-201
TAAAAAATATTTTTTAAGATCCGAATTACT	1	121	0	TTTTTAAGAT	    0.924434	-180
TAAAAAATATTTTTTAATAAAGATTAATTG	1	135	1	TTTTTAATAA	    0.820298	-166
TGAATATAAGTTTTTAATAAAAATAAATAT	1	195	0	TTTTTAATAA	    0.820298	-106
TAGACTACAAATTTGAATATAAGTTTTTAA	1	208	0	ATTTGAATAT	    0.764289	-93
TTGTAGTCTATTTTTAACTAATATAAAAAA	1	228	1	TTTTTAACTA	    0.961613	-73
AATATTCAACTTTTTTATATTAGTTAAAAA	1	238	0	TTTTTTATAT	    0.858366	-63
AATTAATTGTTTTTAAATATTCAACTTTTT	1	253	0	TTTTAAATAT	    0.959803	-48
TAATCCTGGATTATTAATTATCAAAATTAA	1	277	0	TTATTAATTA	    0.720838	-24
          **********

Masking position 7
Map Score:   15.1242

Number of sites scoring better than the average of aligned sites = 848
Number in coding regions = 729
Number in noncoding regions = 119
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 3

TGAATTTGTTTAAAACTAAAACAGACAGGG	1	27	1	TAAAACTAAA	    0.959414	-274
TCTGAATAGCAAAAAATATAAGAATAGCTT	1	80	1	AAAAAATATA	    0.926677	-221
TTTTTTGAATTAAAGCTATTCTTATATTTT	1	92	0	TAAAGCTATT	    0.768602	-209
CTTTAATTCAAAAAAGTAATTCGGATCTTA	1	107	1	AAAAAGTAAT	      0.9201	-194
TTCGGATCTTAAAAAATATTTTTTAATAAA	1	126	1	AAAAAATATT	    0.914124	-175
TATTTTTTAATAAAGATTAATTGCCAGCAA	1	142	1	TAAAGATTAA	     0.81084	-159
AAGTTTTTAATAAAAATAAATATTCACTTT	1	188	0	TAAAAATAAA	    0.966344	-113
TATTTTTATTAAAAACTTATATTCAAATTT	1	200	1	AAAAACTTAT	    0.867921	-101
TTATATTAGTTAAAAATAGACTACAAATTT	1	224	0	TAAAAATAGA	    0.942064	-77
AACTAATATAAAAAAGTTGAATATTTAAAA	1	243	1	AAAAAGTTGA	    0.755137	-58
GTTGAATATTTAAAAACAATTAATTTTGAT	1	258	1	TAAAAACAAT	    0.819859	-43
          **********

Masking position 4
Map Score:   11.1627

Number of sites scoring better than the average of aligned sites = 967
Number in coding regions = 817
Number in noncoding regions = 150
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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