AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irhaS_pyro_opreg_300.orf -g0.419 -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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH0864	300	208aa long hypothetical transcription initiation factor IIB

Motif number 1

TTTCGAAGTGATAGCCTTGGGAGATATGTGTTC	1	13	0	ATACTTGGAG	    0.989372	-288
TTATTATCTTCCACTTTTCGAAGTGATAGCCTT	1	28	0	CCATTTGAAG	    0.982425	-273
CCCATATTATATATACTTGGAAGGTAAACTTTA	1	113	0	ATACTTGAAG	    0.992823	-188
AACTGGACACCTAATCTTGGATCCCCCATATTA	1	137	0	CTACTTGATC	    0.961584	-164
GGGGTCATAAATAATTTTTGAAGAACCACAAAC	1	167	0	ATATTTGAAG	    0.988762	-134
TCCTTTGATACTAGGGTTAGAACATTTTCTTCT	1	245	1	CTAGTTGAAC	     0.97825	-56
TCTTCTCCCCCTAAGTTTAGGAGTAAGGGAACT	1	272	1	CTATTTGGAG	    0.991886	-29
          ***  *** ****

Masking position 3
Map Score:   8.34306

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 134
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

 CCGAACACATATCTCCCAAGGCTATCACTT	1	10	1	TATCTCCAAG	    0.978804	-291
CCCAAGGCTATCACTTCGAAAAGTGGAAGAT	1	25	1	TCACTTCAAA	     0.89211	-276
AAAACAACAGTTTCCTTGAAGTTTAAATTTC	1	60	1	TTTCCTTAAG	    0.895314	-241
TTTAAATACCTTTCTCTAAAAAATTTGAAAT	1	86	0	TTTCTCTAAA	    0.938582	-215
ATTTAAAGTTTACCTTCCAAGTATATATAAT	1	110	1	TACCTTCAAG	     0.96022	-191
CCAGTTTGTGGTTCTTCAAAAATTATTTATG	1	164	1	GTTCTTCAAA	     0.92848	-137
ACATTTTCTTCTCCCCCTAAGTTTAGGAGTA	1	266	1	CTCCCCCAAG	     0.93878	-35
CGAAGTTCCCTTACTCCTAAACTTAGGGGGA	1	277	0	TTACTCCAAA	    0.972875	-24
          ******* ***

Masking position 9
Map Score:   3.66806

Number of sites scoring better than the average of aligned sites = 971
Number in coding regions = 886
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 3

   CCGAACACATATCTCCCAAGGCTATCA	1	8	1	CATATCTCCC	    0.955172	-293
TGTTGTTTTTATTATCTTCCACTTTTCGAA	1	39	0	ATTATCTTCC	    0.991419	-262
GTAAACTTTAAATACCTTTCTCTAAAAAAT	1	93	0	AATACCTTTC	    0.943436	-208
GTATTTAAAGTTTACCTTCCAAGTATATAT	1	108	1	TTTACCTTCC	    0.980145	-193
GGGTTAGAACATTTTCTTCTCCCCCTAAGT	1	258	1	ATTTTCTTCT	    0.870626	-43
          **********

Masking position 7
Map Score:   1.10057

Number of sites scoring better than the average of aligned sites = 628
Number in coding regions = 575
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

AAAAGTGGAAGATAATAAAAACAACAGTTT	1	43	1	GATAATAAAA	    0.892801	-258
TAAAAAATTTGAAATTTAAACTTCAAGGAA	1	71	0	GAAATTTAAA	    0.950318	-230
TTTAGAGAAAGGTATTTAAAGTTTACCTTC	1	97	1	GGTATTTAAA	    0.984025	-204
ATATATACTTGGAAGGTAAACTTTAAATAC	1	108	0	GGAAGGTAAA	     0.94226	-193
AGTGCGGCCACGTAATTAAATCCTTTGATA	1	225	1	CGTAATTAAA	    0.945525	-76
          **********

Masking position 4
Map Score:   0.575766

Number of sites scoring better than the average of aligned sites = 282
Number in coding regions = 243
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


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


Motif number 7

          **********

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