AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_aful_reg_100.orf -o070_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	RAG01314	41	Archaeoglobus_fulgidus
#2	RAG01312	300	Archaeoglobus_fulgidus
#3	RAG03096	48	Archaeoglobus_fulgidus

Motif number 1

GCAAGAAATATAAATCTTGCTGAG       	1	4	0	TAATCTTGCT	    0.989153	-38
GCAAGATTTATATTTCTTGCTTAGGGCAGGA	1	15	1	TATTCTTGCT	    0.985923	-27
        CCTATTTCCTGCCCTAAGCAAGA	1	29	0	TATTCCTGCC	    0.962995	-13
CTATCATTGCTCAAGCTTGCTAAATTCAAAT	2	57	0	TCAGCTTGCT	    0.971335	-244
AGTGCTGATACCTCTGCTGCTCCCCATAGCC	2	89	1	CCTTGCTGCT	    0.966667	-212
CTCGTTCATCCCAGTCTTGCTTTTTGCCCCG	2	134	1	CCATCTTGCT	    0.986685	-167
ATGAAAGTTATAAATGCCGCTAAAATTTACT	2	274	1	TAATGCCGCT	    0.934635	-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

TTACTGACCTCATGAGCATTATCATAACGC	2	18	0	CATGAGCATT	    0.944803	-283
ATTTAGCAAGCTTGAGCAATGATAGGAGTG	2	63	1	CTTGAGCAAT	    0.906681	-238
GCAGCAGAGGTATCAGCACTCCTATCATTG	2	79	0	TATCAGCACT	    0.904761	-222
CCAGTCTTGCTTTTTGCCCCGATGTACCTT	2	144	1	TTTTTGCCCC	    0.844695	-157
CGGAATTGGCCGTGAGCCTCATAGGATTCG	2	202	1	CGTGAGCCTC	    0.977206	-99
AAAAGTAGTACATCAGCCCCACGAATCCTA	2	223	0	CATCAGCCCC	    0.993313	-78
ATCGTACCCGCTTTAGCCCCTCAAAAAGTA	2	246	0	CTTTAGCCCC	    0.989695	-55
          **********

Masking position 3
Map Score:   4.02772

Number of sites scoring better than the average of aligned sites = 1155
Number in coding regions = 1090
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

TAAGCAAGAAATATAAATCTTGCTGAG   	1	8	0	ATATAAATCT	    0.873266	-34
ATGAGCATTATCATAACGCTTAAACC    	2	7	0	TCATAACGCT	    0.936742	-294
ATATTTGAATTTAGCAAGCTTGAGCAATGA	2	55	1	TTAGCAAGCT	    0.830437	-246
ATAGGAGTGCTGATACCTCTGCTGCTCCCC	2	84	1	TGATACCTCT	    0.874009	-217
CATAGCCCTCTTAGAACTCGTCTCGTTCAT	2	113	1	TTAGAACTCG	    0.956756	-188
GGCCAATTCCGTAGAACTTTGCGAAACGAC	2	183	0	GTAGAACTTT	    0.854285	-118
TTAGCGGCATTTATAACTTTCATCGTACCC	2	267	0	TTATAACTTT	    0.951073	-34
ATCACGCACTTTATAAATCTTCAAAACAAT	3	18	0	TTATAAATCT	    0.970773	-31
          **********

Masking position 3
Map Score:   1.71301

Number of sites scoring better than the average of aligned sites = 409
Number in coding regions = 355
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 4

       CCTATTTCCTGCCCTAAGCAAGA	1	29	0	ATTTCCTGCC	    0.987391	-13
AATATTTAATCTTTACTGACCTCATGAGCA	2	30	0	CTTTACTGAC	     0.98938	-271
TGCCGCTAAAATTTACTGAGGTT       	2	288	1	ATTTACTGAG	    0.983402	-13
AAAGTGCGTGATTTACTGGCAGC       	3	36	1	ATTTACTGGC	    0.992565	-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

TGTACCTTCTGGGAAGTGTCGTTTCGCAAA	2	166	1	GGGAAGTGTC	    0.994407	-135
CAAAGTTCTACGGAATTGGCCGTGAGCCTC	2	192	1	CGGAATTGGC	    0.990322	-109
       GACGGGAATTGTTTTGAAGATTT	3	4	1	GGGAATTGTT	    0.988113	-45
          **********

Masking position 5
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