AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_aful_reg_300.orf -o070_aful_300.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	RAG01314	41	Archaeoglobus_fulgidus
#2	RAG01312	300	Archaeoglobus_fulgidus
#3	RAG03096	48	Archaeoglobus_fulgidus

Motif number 1

GCAAGAAATATAAATCTTGCTGAG       	1	4	0	TAATCTTGCT	    0.989334	-38
GCAAGATTTATATTTCTTGCTTAGGGCAGGA	1	15	1	TATTCTTGCT	    0.986156	-27
        CCTATTTCCTGCCCTAAGCAAGA	1	29	0	TATTCCTGCC	    0.963595	-13
CTATCATTGCTCAAGCTTGCTAAATTCAAAT	2	57	0	TCAGCTTGCT	    0.971804	-244
AGTGCTGATACCTCTGCTGCTCCCCATAGCC	2	89	1	CCTTGCTGCT	    0.967209	-212
CTCGTTCATCCCAGTCTTGCTTTTTGCCCCG	2	134	1	CCATCTTGCT	    0.986906	-167
ATGAAAGTTATAAATGCCGCTAAAATTTACT	2	274	1	TAATGCCGCT	    0.935664	-27
          *** *******

Masking position 9
Map Score:   6.21201

Number of sites scoring better than the average of aligned sites = 290
Number in coding regions = 272
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

TTTACTGACCTCATGAGCATTATCATAACGCTTAAA	2	13	0	TCAAGTTCAT	    0.963996	-288
AGCAGAGGTATCAGCACTCCTATCATTGCTCAAGCT	2	71	0	TCAACTTCAT	    0.984411	-230
CATAGCCCTCTTAGAACTCGTCTCGTTCATCCCAGT	2	113	1	TTAACTTCGT	      0.9911	-188
CCGATGTACCTTCTGGGAAGTGTCGTTTCGCAAAGT	2	162	1	TTCGGTTCGT	    0.907744	-139
CCTATGAGGCTCACGGCCAATTCCGTAGAACTTTGC	2	191	0	TCAGCTCCGT	    0.990594	-110
TTAGCGGCATTTATAACTTTCATCGTACCCGCTTTA	2	261	0	TTAACCTCGT	    0.971952	-40
TTATAAATCTTCAAAACAATTCCCGTC         	3	2	0	TCAACTCCGT	    0.993632	-47
          ***  **   * ****

Masking position 1
Map Score:   4.04838

Number of sites scoring better than the average of aligned sites = 214
Number in coding regions = 201
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

TTTCTTGCTTAGGGCAGGAAATAGG     	1	27	1	AGGGCAGGAA	    0.952085	-15
CAATGATAGGAGTGCTGATACCTCTGCTGC	2	79	1	AGTGCTGATA	    0.826455	-222
AGGGCTATGGGGAGCAGCAGAGGTATCAGC	2	92	0	GGAGCAGCAG	    0.929142	-209
GAGTTCTAAGAGGGCTATGGGGAGCAGCAG	2	102	0	AGGGCTATGG	    0.887185	-199
AAGGTACATCGGGGCAAAAAGCAAGACTGG	2	144	0	GGGGCAAAAA	    0.977832	-157
TAGGATTCGTGGGGCTGATGTACTACTTTT	2	223	1	GGGGCTGATG	    0.992442	-78
TACTTTTTGAGGGGCTAAAGCGGGTACGAT	2	246	1	GGGGCTAAAG	     0.99164	-55
          **********

Masking position 5
Map Score:   3.87459

Number of sites scoring better than the average of aligned sites = 1604
Number in coding regions = 1529
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 4

TCTTGCTTAGGGCAGGAAATAGG       	1	29	1	GGCAGGAAAT	    0.987757	-13
TGCTCATGAGGTCAGTAAAGATTAAATATT	2	30	1	GTCAGTAAAG	    0.989689	-271
       AACCTCAGTAAATTTTAGCGGCA	2	288	0	CTCAGTAAAT	    0.983883	-13
       GCTGCCAGTAAATCACGCACTTT	3	36	0	GCCAGTAAAT	    0.992782	-13
          **********

Masking position 4
Map Score:   3.30253

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 6
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

TTTGCGAAACGACACTTCCCAGAAGGTACA	2	166	0	GACACTTCCC	    0.994746	-135
GAGGCTCACGGCCAATTCCGTAGAACTTTG	2	192	0	GCCAATTCCG	    0.990991	-109
AAATCTTCAAAACAATTCCCGTC       	3	4	0	AACAATTCCC	    0.988955	-45
          **********

Masking position 4
Map Score:   0.528377

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 22
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:   -6.79689e-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:   -6.79689e-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 8

          **********

No masking
Map Score:   -6.79689e-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