AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_aful_reg_100.orf -o117_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	RAG45695	300	Archaeoglobus_fulgidus

Motif number 1

ACAAGAAAAAGGAAGAGAGGCTTTAGCATCA	1	39	1	GGAAGAGGGC	    0.999584	-262
AATAATTAACGGAAGAGTGGCACTACACGTT	1	69	0	GGAAGAGGGC	    0.999563	-232
TTATCTGAGGGAAAGAGGGGCACATTGTTGT	1	210	0	GAAAGAGGGC	    0.998869	-91
          ******* ***

Masking position 6
Map Score:   7.13504

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 16
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 2

TCATGAAACAAGAAAAAGGAAGAGAGGCTT	1	32	1	AGAAAAAGGA	    0.952924	-269
TTATTTCTCCCGAAATCGACATGGTTCTTT	1	95	1	CGAAATCGAC	    0.970769	-206
AAAACGATAGTGAAAAAGAACCATGTCGAT	1	109	0	TGAAAAAGAA	    0.927918	-192
TGAGAAGGCTCGAAAACGATAGTGAAAAAG	1	121	0	CGAAAACGAT	    0.986617	-180
AATCTTCAGGCGATAAAGGTACAACAATGT	1	190	1	CGATAAAGGT	    0.957278	-111
CCGGCAGTGACGACATCGGATACGTTTGAG	1	258	0	CGACATCGGA	    0.975671	-43
          **********

Masking position 5
Map Score:   3.29407

Number of sites scoring better than the average of aligned sites = 492
Number in coding regions = 457
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

TTTCGAGCCTTCTCAGAAGTGCCATGAGCT	1	136	1	TCTCAGAAGT	    0.926286	-165
GTGCCATGAGCTTCAAACGTGCATCTGATG	1	154	1	CTTCAAACGT	     0.97977	-147
GATTGTATTTCATCAGATGCACGTTTGAAG	1	164	0	CATCAGATGC	    0.954877	-137
GAAATACAATCTTCAGGCGATAAAGGTACA	1	183	1	CTTCAGGCGA	     0.97338	-118
CCCCTCTTTCCCTCAGATAAATTTTTAAGC	1	221	1	CCTCAGATAA	    0.939301	-80
AAGCCAAACACCTCAAACGTATCCGATGTC	1	247	1	CCTCAAACGT	    0.990919	-54
          **********

Masking position 5
Map Score:   2.9776

Number of sites scoring better than the average of aligned sites = 429
Number in coding regions = 404
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

GATAGTGAAAAAGAACCATGTCGATTTCGG	1	104	0	AAGAACCATG	    0.995426	-197
GCCTTCTCAGAAGTGCCATGAGCTTCAAAC	1	142	1	AAGTGCCATG	     0.99037	-159
         TAAAAACCTTGTTATTATGTA	1	290	0	AAAAACCTTG	    0.978305	-11
          **********

Masking position 2
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 48
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   7.91135e-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 6

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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