AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i123_aful_mthe_300.orf -o123_aful_mthe_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	RAG50240	202	Archaeoglobus_fulgidus
#2	RTH00401	96	M.thermo

Motif number 1

GGGTTCAAATCCCGTCGAGCCCGTATTTAA	1	27	0	CCCGTCGAGC	    0.997848	-176
GGGCTTTTAACCCGTCGGTCGCGGGTTCAA	1	49	0	CCCGTCGGTC	    0.998845	-154
GGGTTAAAAGCCCGTCGCTCTGCCTGGCTG	1	66	1	CCCGTCGCTC	    0.999373	-137
TGGATGAGGGCTCGTAGCTCAGCCAGGCAG	1	85	0	CTCGTAGCTC	    0.992673	-118
  GCCTTTTCCCCGCAAATCTCGAATGCAC	1	185	0	CCCGCAAATC	    0.975281	-18
          **********

Masking position 4
Map Score:   10.3515

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 44
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

GGCTCGACGGGATTTGAACCCGCGACCGACG	1	36	1	GATTTAACCC	    0.992182	-167
AGAGCGACGGGCTTTTAACCCGTCGGTCGCG	1	56	0	GCTTTAACCC	    0.992401	-147
GCACGAAAAAGATTTAAATCCTCACCATCGC	1	118	0	GATTTAATCC	    0.988463	-85
          GCCTTTTCCCCGCAAATCTCG	1	192	0	GCCTTTCCCC	    0.980666	-11
ATTATGGTTAGATTTTTATCCCTGATAGTAT	2	45	0	GATTTTATCC	    0.990089	-52
          ***** *****

Masking position 5
Map Score:   7.59673

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 38
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

AAATCCCGTCGAGCCCGTATTTAAAAATAGG	1	20	0	GAGCCCGTAT	    0.929987	-183
GACGGGATTTGAACCCGCGACCGACGGGTTA	1	41	1	GAACCCGCGC	    0.994589	-162
GACGGGTTAAAAGCCCGTCGCTCTGCCTGGC	1	63	1	AAGCCCGTCC	    0.986615	-140
GCTGAGCTACGAGCCCTCATCCATTAGCGAT	1	92	1	GAGCCCTCAC	    0.996788	-111
AAAAAGATTTAAATCCTCACCATCGCTAATG	1	113	0	AAATCCTCAC	     0.97167	-90
      TCATGCACCCTCCACAGCATCACTA	2	5	1	GCACCCTCCC	    0.992102	-92
        CCAAATCCTCCGCGACCCTGAAG	2	84	0	AAATCCTCCC	    0.981794	-13
          ********* *

Masking position 6
Map Score:   8.9409

Number of sites scoring better than the average of aligned sites = 543
Number in coding regions = 507
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

TCGAGCCCGTATTTAAAAATAGGAGGATCAA	1	12	0	ATTTAAAATA	    0.874627	-191
CTTTAGAGCACGAAAAAGATTTAAATCCTCA	1	125	0	CGAAAAAATT	    0.851155	-78
CTTTTTCGTGCTCTAAAGATACAAGCAAAGG	1	138	1	CTCTAAAATA	    0.982552	-65
TCGAATGCACCGATAAATATATCTGTCCTTT	1	164	0	CGATAAAATA	      0.9774	-39
CACAGCATCACTATAACAATTTATACTATCA	2	23	1	CTATAACATT	    0.958642	-74
AGGGATAAAAATCTAACCATAATACCCGATG	2	53	1	ATCTAACATA	    0.940388	-44
          ******* ***

Masking position 6
Map Score:   1.27292

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 48
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

CGGGCTTTTAACCCGTCGGTCGCGGGTTCA	1	50	0	ACCCGTCGGT	    0.943044	-153
CAGCCAGGCAGAGCGACGGGCTTTTAACCC	1	66	0	GAGCGACGGG	    0.968523	-137
TTTAAATCCTCACCATCGCTAATGGATGAG	1	107	0	CACCATCGCT	    0.984861	-96
GCACCCTCCACAGCATCACTATAACAATTT	2	15	1	CAGCATCACT	    0.954374	-82
CGCGACCCTGAAGCATCGGGTATTATGGTT	2	67	0	AAGCATCGGG	    0.989122	-30
CCCGATGCTTCAGGGTCGCGGAGGATTTGG	2	77	1	CAGGGTCGCG	    0.986937	-20
          **********

Masking position 7
Map Score:   2.88327

Number of sites scoring better than the average of aligned sites = 546
Number in coding regions = 508
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 6

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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