AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -iaraC_synecho_opreg_100.orf -g0.48 -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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	1653104	300	hypothetical protein
#2	1653417	148	hypothetical protein
#3	1653418	86	hypothetical protein

Motif number 1

AATTTGAATGATAAGTTTTACTATTATTTG	1	45	0	ATAAGTTTTA	    0.977442	-256
CTAAGTAATTTTAAATTTGAATGATAAGTT	1	58	0	TTAAATTTGA	    0.845042	-243
GGATTTACATATAGACTTTAGCTTATAGAT	1	119	1	ATAGACTTTA	      0.9347	-182
ACTTTAGCTTATAGATTTCAAGACATAGGC	1	133	1	ATAGATTTCA	    0.951791	-168
CCCAATCCCCATAAATTTCAACCAAGGAGA	1	270	1	ATAAATTTCA	    0.975092	-31
TTTTCTGGAAATAAATTTGATGAATTATAA	2	18	1	ATAAATTTGA	    0.975092	-131
GGGTAATGGTAAAAGTTTTAAAATTTTATA	2	43	0	AAAAGTTTTA	    0.898364	-106
ACAAAAATCAATAAATTTTAATGAATTAGT	2	96	0	ATAAATTTTA	    0.977967	-53
AATATATCAAAAAAGCTTTATTATTTTTCG	3	36	1	AAAAGCTTTA	    0.851693	-51
          **********

Masking position 7
Map Score:   11.832

Number of sites scoring better than the average of aligned sites = 121
Number in coding regions = 87
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

GATCGCCAGCTTTTTGGGGACTAGATGGTG	1	13	0	TTTTTGGGGA	    0.947317	-288
GTTTTACTATTATTTGGCGATCGCCAGCTT	1	31	0	TATTTGGCGA	    0.905253	-270
ACTTAGCAGATCCAGGGGGACAACTGCAAA	1	82	1	TCCAGGGGGA	    0.994368	-219
CAAGAGTCTATACAGAGCGAAGCCAATGGG	1	180	1	TACAGAGCGA	     0.92396	-121
GCTTGATCTTTCCAGGGGCAATGAACCCCA	1	206	0	TCCAGGGGCA	    0.987668	-95
CTGCCGAAGATTCAGGGCCAAGCTTTACTA	1	239	1	TTCAGGGCCA	    0.982653	-62
TTGGTTGAAATTTATGGGGATTGGGGTAGT	1	265	0	TTTATGGGGA	    0.976377	-36
          **********

Masking position 10
Map Score:   6.54333

Number of sites scoring better than the average of aligned sites = 1265
Number in coding regions = 1089
Number in noncoding regions = 176
Number of orfs with sites within 600 bp upstream = 172
Fraction of orfs with sites within 600 bp upstream = 0.0276261


Motif number 3

GCAGTTGTCCCCCTGGATCTGCTAAGTAATTT	1	77	0	CCCTGATCTC	    0.993936	-224
AGGCATTCAAACCTGCATAGACAAGAGTCTAT	1	159	1	ACCTGATAGC	    0.982879	-142
ATTGGCTTCGCTCTGTATAGACTCTTGTCTAT	1	175	0	CTCTGATAGC	     0.98814	-126
GGTTCATTGCCCCTGGAAAGATCAAGCAAACT	1	209	1	CCCTGAAAGT	    0.935441	-92
TAAAGCTTGGCCCTGAATCTTCGGCAGTTTGC	1	234	0	CCCTGATCTC	    0.993937	-67
AATTGAAGTTGTCTGAAGCGTCTCAATATATC	3	12	1	GTCTGAGCGC	    0.954471	-75
          ***** **** *

Masking position 7
Map Score:   3.54797

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 247
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

CGATCGCCAGCTTTTTGGGGACTAGATGGT	1	14	0	CTTTTTGGGG	    0.967618	-287
AGTTTTACTATTATTTGGCGATCGCCAGCT	1	32	0	TTATTTGGCG	    0.932847	-269
CTTGGTTGAAATTTATGGGGATTGGGGTAG	1	266	0	ATTTATGGGG	    0.913614	-35
     TCTTATTTTTTCTGGAAATAAATTT	2	6	1	TTTTTTCTGG	     0.94944	-143
AAATTTATTGATTTTTGTCGCGAGCACTTT	2	108	1	ATTTTTGTCG	    0.970057	-41
AAGCTTTATTATTTTTCGCACTATTTTCTC	3	48	1	ATTTTTCGCA	    0.868554	-39
TTTTTCGCACTATTTTCTCGACTCATCCCT	3	59	1	TATTTTCTCG	    0.836619	-28
          **********

Masking position 6
Map Score:   2.51483

Number of sites scoring better than the average of aligned sites = 979
Number in coding regions = 823
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 5

TCCAGGGGGACAACTGCAAAATTGGTCGGA	1	92	1	CAACTGCAAA	    0.979643	-209
TACCATTACCCAACTTCACTGGACAAATTA	2	62	1	CAACTTCACT	    0.988353	-87
ACGCTTCAGACAACTTCAATTA        	3	3	0	CAACTTCAAT	    0.990192	-84
          **********

Masking position 3
Map Score:   0.718945

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 30
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 6

          **********

No masking
Map Score:   4.50646e-14

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:   4.50646e-14

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 8

          **********

No masking
Map Score:   4.50646e-14

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