AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -icspA_mgen_opreg_300.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	MG001	300	DNA polymerase III, subunit beta (dnaN)
#2	MG003	84	DNA gyrase subunit B (gyrB)

Motif number 1

TGTACATATGTAATTATTACTGCT       	1	4	0	TAATTATTAT	    0.860581	-297
TGTAAAATATCATTAATTTCTGTTATATATA	1	44	1	CATTAATTTT	    0.964773	-257
TTTTAGAGAGTATTAATTATTACTATAATTA	1	85	1	TATTAATTAT	    0.958096	-216
TTAATTATTACTATAATTAAGCATTTATGCT	1	97	1	CTATAATTAG	    0.904702	-204
CATAAAAAGCTTATAATTAAGCATAAATGCT	1	116	0	TTATAATTAG	    0.913168	-185
ACTAAAATGTCTATAATTTTGTTCATAAAAA	1	139	0	CTATAATTTG	    0.926081	-162
TCTTTAATATCTATTATTTATTATAAGAACT	1	167	0	CTATTATTTT	    0.906867	-134
ATTTCTATTTTTTTATTTTCTTTAATATCTA	1	185	0	TTTTATTTTT	    0.796044	-116
AGGGTTATGATATTTATTTCTATTTTTTTAT	1	200	0	TATTTATTTT	    0.914571	-101
TTTGATTAAGTATTAATTTCTGGGTTATCAA	1	230	0	TATTAATTTT	    0.967858	-71
TTAATTAATATTTTCATTTTTGATTAAGTAT	1	248	0	TTTTCATTTT	    0.938347	-53
AATTCACTTTTATTAATTAATATTTTCATTT	1	260	0	TATTAATTAT	    0.958096	-41
     AAAACCTTTCATTTTTAATGTGTTAT	2	6	1	CTTTCATTTT	    0.932629	-79
TTTTAATGTGTTATAATTATTTGTTATGCCA	2	23	1	TTATAATTAT	    0.958096	-62
          ********* *

Masking position 7
Map Score:   21.0875

Number of sites scoring better than the average of aligned sites = 456
Number in coding regions = 363
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 2

ATGTACTATGTACATATGTAATTATTACTGCT	1	11	0	TAATATTAAT	     0.84923	-290
ATGTACATAGTACATATGTAAAATATCATTAA	1	28	1	TAATATTAAA	    0.948537	-273
TAATTTCTGTTATATATAATAGTATCTATTTT	1	57	1	TAATATATAG	    0.984845	-244
TATATAATAGTATCTATTTTAGAGAGTATTAA	1	69	1	TACTATTTAG	    0.933999	-232
CATAAATGCTTAATTATAGTAATAATTAATAC	1	94	0	TATTATGTAA	    0.788081	-207
AACAAAATTATAGACATTTTAGTTCTTATAAT	1	147	1	TAACATTTAG	    0.925673	-154
TAATATCTATTATTTATTATAAGAACTAAAAT	1	162	0	TATTATATAA	    0.912583	-139
TAATAAATAATAGATATTAAAGAAAATAAAAA	1	175	1	TAATATAAAG	    0.978193	-126
AAAATAGAAATAAATATCATAACCCTTGATAA	1	205	1	TAATATATAA	    0.970673	-96
TATAACACATTAAAAATGAAAGGTTTT     	2	6	0	TAAAATAAAG	    0.876063	-79
          ** **** ****

Masking position 6
Map Score:   9.7006

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 35
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

TATCATTAATTTCTGTTATATATAATAGTAT	1	51	1	TTTGTTATAT	    0.906596	-250
AAGTATTAATTTCTGGGTTATCAAGGGTTAT	1	223	0	TTTGGGTTAT	    0.918018	-78
TTGAATAAAATTTTGGGAAAAA         	1	289	1	TTTGGGAAAA	    0.923594	-12
TTCATTTTTAATGTGTTATAATTATTTGTTA	2	18	1	ATTGTTATAA	    0.816764	-67
CAAACTAAATTTATGGCATAACAAATAATTA	2	36	0	TTTGGCATAA	    0.553308	-49
TAAATTTAGTTTGTGGCAAAAGCTTCTGTAC	2	54	1	TTTGGCAAAA	    0.804916	-31
          ** ********

Masking position 4
Map Score:   2.05061

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 56
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

AATAATTACATATGTACATAGTACATATGT	1	17	1	TATGTACATA	    0.340928	-284
TTAGAGAGTATTAATTATTACTATAATTAA	1	87	1	TTAATTATTA	    0.940268	-214
TAATTAAGCATTTATGCTTAATTATAAGCT	1	110	1	TTTATGCTTA	    0.866714	-191
TGTCTATAATTTTGTTCATAAAAAGCTTAT	1	133	0	TTTGTTCATA	    0.929726	-168
TATAGACATTTTAGTTCTTATAATAAATAA	1	155	1	TTAGTTCTTA	    0.976836	-146
TTAATATCTATTATTTATTATAAGAACTAA	1	165	0	TTATTTATTA	     0.89363	-136
AACCCAGAAATTAATACTTAATCAAAAATG	1	235	1	TTAATACTTA	    0.933345	-66
AATGAAAATATTAATTAATAAAAGTGAATT	1	261	1	TTAATTAATA	    0.892036	-40
TGTGTTATAATTATTTGTTATGCCATAAAT	2	29	1	TTATTTGTTA	    0.831959	-56
          **********

Masking position 5
Map Score:   6.5099

Number of sites scoring better than the average of aligned sites = 217
Number in coding regions = 182
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 5

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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