AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00590_bsub_reg_300.orf -o00590_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	ggt	184	gamma-glutamyltranspeptidase

Motif number 1

TGCTATATTAGAATCAGCATACGGATTAAG	1	24	0	GAATCAGCAT	    0.937974	-161
TGCTGATTCTAATATAGCACATGGCTCATA	1	35	1	AATATAGCAC	    0.979451	-150
CAATATAATCAATTCTGCACAGAAAAACGG	1	66	1	AATTCTGCAC	     0.94938	-119
TCTGCACAGAAAAACGGCATTATGCACTAT	1	79	1	AAAACGGCAT	    0.976352	-106
TGCACTATATAATATACCATTTGTCACTTG	1	101	1	AATATACCAT	    0.931589	-84
GCGTAAAAAAATTACAGCGTTTTCACAAGT	1	126	0	ATTACAGCGT	     0.95172	-59
AGATTGTAACAATACAGCTTCATATAGGAG	1	158	1	AATACAGCTT	    0.984614	-27
          **********

Masking position 8
Map Score:   5.67903

Number of sites scoring better than the average of aligned sites = 2123
Number in coding regions = 1942
Number in noncoding regions = 181
Number of orfs with sites within 600 bp upstream = 168
Fraction of orfs with sites within 600 bp upstream = 0.0269836


Motif number 2

GTATGCTGATTCTAATATAGCACATGGCTC	1	32	1	TCTAATATAG	    0.983018	-153
GTGCAGAATTGATTATATTGATATGAGCCA	1	56	0	GATTATATTG	    0.981864	-129
ACAAATGGTATATTATATAGTGCATAATGC	1	95	0	TATTATATAG	    0.973823	-90
ATTTTTTTACGCTAAGATTGTAACAATACA	1	144	1	GCTAAGATTG	    0.981317	-41
          **********

Masking position 5
Map Score:   2.36048

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 118
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

ATACGGATTAAGAAGGGACTGCTAT     	1	6	0	AGAAGGGACT	    0.995674	-179
TTTTCTGTGCAGAATTGATTATATTGATAT	1	62	0	AGAATTGATT	    0.932496	-123
CAGCGTTTTCACAAGTGACAAATGGTATAT	1	112	0	ACAAGTGACA	    0.982408	-73
AGCTTCATATAGGAGGGAGAAC        	1	173	1	AGGAGGGAGA	    0.986632	-12
          **********

Masking position 4
Map Score:   0.777713

Number of sites scoring better than the average of aligned sites = 418
Number in coding regions = 303
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 119
Fraction of orfs with sites within 600 bp upstream = 0.0191134


Motif number 4

          **********

No masking
Map Score:   2.227e-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 5

          **********

No masking
Map Score:   2.227e-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:   2.227e-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