AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i274_hypothetical19_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1739	300	transcriptional activator (metR)

Motif number 1

CCAGGTTATCAAATAAAAAATCTAAATATA	1	66	1	AAATAAAAAA	    0.947538	-235
TATCTATCTTAGATAGATTTATATTTAGAT	1	85	0	AGATAGATTT	    0.757363	-216
AATCTATCTAAGATAGATAAAATTAAATTA	1	96	1	AGATAGATAA	    0.938431	-205
AGATAGATAAAATTAAATTAAGTTAAGTAA	1	106	1	AATTAAATTA	     0.91308	-195
AATTAAATTAAGTTAAGTAAAAACAGAATT	1	116	1	AGTTAAGTAA	    0.911814	-185
GAATTAAACAAATTAGATAAAGAATAAATA	1	141	1	AATTAGATAA	    0.960072	-160
ATTAGATAAAGAATAAATATAGAACCCCAG	1	152	1	GAATAAATAT	    0.740182	-149
TAATTATTTTAGTTAAAATACAAAACCCCA	1	191	0	AGTTAAAATA	    0.831447	-110
ATTTTAACTAAAATAATTATCTAAATAATT	1	202	1	AAATAATTAT	    0.877967	-99
ATAATTATCTAAATAATTAATTTTATTAAT	1	214	1	AAATAATTAA	    0.918431	-87
GAAATATGCTAATTAATAAAATTAATTATT	1	225	0	AATTAATAAA	    0.892876	-76
AATACATTAAAATTAGAAATATGCTAATTA	1	240	0	AATTAGAAAT	    0.907464	-61
ATTCATATAAAATTAAGAATTAGGGAACCA	1	274	0	AATTAAGAAT	    0.851836	-27
          **********

Masking position 5
Map Score:   14.5743

Number of sites scoring better than the average of aligned sites = 1561
Number in coding regions = 1105
Number in noncoding regions = 456
Number of orfs with sites within 600 bp upstream = 300
Fraction of orfs with sites within 600 bp upstream = 0.048185


Motif number 2

ATGGTAGTGTGGGGTTTCCCCATGTGAGAGTAG	1	26	1	GGGTTCCCCT	    0.985535	-275
TGATAACCTGGCGGTGCCCTACTCTCACATGGG	1	44	0	GGGTGCCTAT	    0.993445	-257
AGGGCACCGCCAGGTTATCAAATAAAAAATCTA	1	57	1	CGGTTTCAAT	    0.976679	-244
TCCTTAAACTGGGGTTCTATATTTATTCTTTAT	1	157	0	GGGTTTATAT	    0.980589	-144
TTTAAGGACTGGGGTTTTGTATTTTAACTAAAA	1	182	1	GGGTTTGTAT	     0.98682	-119
ATGTATTATACTGGTTCCCTAATTCTTAATTTT	1	263	1	CGGTTCCTAT	    0.995406	-38
          * **** **** *

Masking position 5
Map Score:   4.20798

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 42
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

ATGCCGATGGTAGTGTGGGGTTTCCCCATG	1	20	1	TAGTGTGGGG	    0.977604	-281
TTCCCCATGTGAGAGTAGGGCACCGCCAGG	1	41	1	GAGAGTAGGG	    0.981676	-260
CCCCAGTCCTTAAACTGGGGTTCTATATTT	1	166	0	TAAACTGGGG	    0.984553	-135
CCCCAGTTTAAGGACTGGGGTTTTGTATTT	1	176	1	AGGACTGGGG	    0.993591	-125
TATAAAATTAAGAATTAGGGAACCAGTATA	1	269	0	AGAATTAGGG	    0.918005	-32
          **********

Masking position 6
Map Score:   2.67212

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 100
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

ATAGATTTATATTTAGATTTTTTATTTGATA	1	72	0	ATTTAATTTT	    0.894799	-229
GATAGATAAAATTAAATTAAGTTAAGTAAAA	1	107	1	ATTAATTAAG	    0.503342	-194
TCTTTATCTAATTTGTTTAATTCTGTTTTTA	1	133	0	ATTTGTTAAT	    0.915952	-168
AACTGGGGTTCTATATTTATTCTTTATCTAA	1	153	0	CTATATTATT	    0.575327	-148
AGGACTGGGGTTTTGTATTTTAACTAAAATA	1	186	1	TTTTGATTTT	    0.592687	-115
AAAATTAATTATTTAGATAATTATTTTAGTT	1	207	0	ATTTAATAAT	    0.937542	-94
ATGCTAATTAATAAAATTAATTATTTAGATA	1	219	0	ATAAATTAAT	    0.479798	-82
AATTTTATTAATTAGCATATTTCTAATTTTA	1	232	1	ATTAGATATT	    0.932126	-69
AGTATAATACATTAAAATTAGAAATATGCTA	1	244	0	ATTAAATTAG	    0.685089	-57
TCTTAATTTTATATGAATATTATTA      	1	286	1	ATATGATATT	    0.902242	-15
          ***** *****

Masking position 8
Map Score:   2.30711

Number of sites scoring better than the average of aligned sites = 1638
Number in coding regions = 1276
Number in noncoding regions = 362
Number of orfs with sites within 600 bp upstream = 229
Fraction of orfs with sites within 600 bp upstream = 0.0367812


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