AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_aful_reg_100.orf -o057_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -x5 -e 
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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG18637	262	Archaeoglobus_fulgidus
#2	RAG33372	69	Archaeoglobus_fulgidus
#3	RAG33427	35	Archaeoglobus_fulgidus
#4	RAG19353	73	Archaeoglobus_fulgidus
#5	RAG27692	75	Archaeoglobus_fulgidus

Motif number 1

AGGAAGGTTTAGCAGCATGTATTTAAGCTTTTCCA	1	64	0	AGCGCGTTTA	    0.996057	-199
TGTAGCCAAAACCAGGGTGTTTGGATTTTATTTTA	1	110	1	ACCGGGTTGA	    0.994116	-153
GCTTCTAATTAGCGGGAGGTGTTCTGCAGTGGCTC	1	169	1	AGCGGGTTTT	    0.995463	-94
TTAAAAAAAGAGCCGGATGTATTTAAAGCTTGTTC	4	13	1	AGCGGGTTTA	    0.998877	-61
AAGGTATTATAGCAGGTTGTGTGAAGAATTAAC  	4	51	1	AGCGGGTTGA	    0.998645	-23
GGGTTTTCGGAGCGGTAAGTATTTATCCAAAGCGG	5	24	0	AGCGTGTTTA	    0.994167	-52
          *** **  ** ** *

Masking position 10
Map Score:   11.1976

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 11
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

ATTGGAGGAAGGTTTAGCAGCATGTATTTAA	1	73	0	GGTTTAGCAC	    0.965719	-190
AAACACCCTGGTTTTGGCTACACCATGCATT	1	101	0	GTTTTGGCTC	    0.990959	-162
TTTAGGTTTAGCTTTGGCTACTGGTTTAGCT	1	141	1	GCTTTGGCTC	    0.998174	-122
TTTGGCTACTGGTTTAGCTTCTAATTAGCGG	1	153	1	GGTTTAGCTC	    0.993191	-110
GAGGTGTTCTGCAGTGGCTCCGTGCTTGTGT	1	184	1	GCAGTGGCTC	    0.969003	-79
TTCTGAACAAGCTTTAAATACATCCGGCTCT	4	21	0	GCTTTAAATC	    0.901482	-53
ATACTCTGCCGCTTTGGATAAATACTTACCG	5	16	1	GCTTTGGATA	    0.953406	-60
          ********* *

Masking position 5
Map Score:   8.04248

Number of sites scoring better than the average of aligned sites = 270
Number in coding regions = 245
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

ACAATTTTTAAAACTTAAAAAATTTTCGATAG	1	19	1	AAACTTAAAA	    0.981124	-244
TTTTCGATAGATAAATCAAAAATTGGAAAAGC	1	41	1	ATAAATAAAA	    0.866872	-222
AAAAATTGGAAAAGCTTAAATACATGCTGCTA	1	58	1	AAAGCTAAAA	    0.928815	-205
AGCCAAAGCTAAACCTAAAATAAAATCCAAAC	1	128	0	AAACCTAAAA	    0.972205	-135
TTTATGCTCTAAAAATATAAGAGGTGTTTTAT	1	220	1	AAAAATTAAA	    0.743552	-43
CTTTTACCTAACATATAAAACACCTCTTATAT	1	234	0	ACATATAAAA	    0.845513	-29
          AAATTTGAAACATGTCGCAAAA	2	1	1	AAATTTAAAA	    0.970637	-69
AACATGTCGCAAAATTTAAATACTTTGCTATT	2	19	1	AAAATTAAAA	    0.970637	-51
CTATTGAAACATATTTCAAATAGGAGGTGAGA	2	46	1	ATATTTAAAA	    0.912633	-24
CTTTCTGAACAAGCTTTAAATACATCCGGCTC	4	22	0	AAGCTTAAAA	    0.915541	-52
          ****** *** *

Masking position 6
Map Score:   8.83933

Number of sites scoring better than the average of aligned sites = 322
Number in coding regions = 155
Number in noncoding regions = 167
Number of orfs with sites within 600 bp upstream = 176
Fraction of orfs with sites within 600 bp upstream = 0.0282686


Motif number 4

CATGCATTGGAGGAAGGTTTAGCAGCATGTA	1	78	0	AGGAAGTTTA	    0.900516	-185
TAAAAATATAAGAGGTGTTTTATATGTTAGG	1	229	1	AGAGGGTTTT	    0.960937	-34
ATGTTTCAATAGCAAAGTATTTAAATTTTGC	2	27	0	AGCAAGTATT	    0.951599	-43
          AAAAACGTTTTATTACCCAAT	3	1	1	AAAAAGTTTT	    0.912763	-35
AAGCTTGTTCAGAAAGGTATTATAGCAGGTT	4	38	1	AGAAAGTATT	    0.977398	-36
CATGCAGTAAAAAAGGGTTTTCGGAGCGGTA	5	42	0	AAAAGGTTTT	    0.906232	-34
          ***** *****

Masking position 8
Map Score:   1.66332

Number of sites scoring better than the average of aligned sites = 195
Number in coding regions = 173
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 5

CTCTAAAAATATAAGAGGTGTTTTATATGT	1	226	1	ATAAGAGGTG	    0.990184	-37
CATATTTCAAATAGGAGGTGAGAAT     	2	55	1	ATAGGAGGTG	    0.996379	-15
GAAAGGTATTATAGCAGGTTGTGTGAAGAA	4	49	1	ATAGCAGGTT	    0.982083	-25
          **********

Masking position 6
Map Score:   1.30751

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 7
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 6

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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