AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i323_mixed8_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 
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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	mutA	190	mutA

Motif number 1

ACATGAATAACTCGTTTCCCCAGGCTGGCG	1	33	1	CTCGTTTCCC	     0.97068	-158
TTTCCCCAGGCTGGCGTTTCGTCACACTCC	1	47	1	CTGGCGTTTC	    0.953123	-144
ACACTCCGGCCGCGATTGCCGCACCTGGGC	1	70	1	CGCGATTGCC	    0.984659	-121
TTGCCGCACCTGGGCGTCTATATGGGCGTC	1	85	1	TGGGCGTCTA	    0.931081	-106
GGCGTCTATATGGGCGTCCCGATCAACTAG	1	97	1	TGGGCGTCCC	    0.993112	-94
GGGCTTGCTTCGGGATTGTCACTTAACTAA	1	132	0	CGGGATTGTC	    0.986155	-59
CGATGTTGCTTGGGCTTGCTTCGGGATTGT	1	143	0	TGGGCTTGCT	     0.96435	-48
 CGACTGCTCCTGTTTTCCCAGCAATTAGC	1	172	0	CTGTTTTCCC	    0.912661	-19
          **********

Masking position 7
Map Score:   8.37103

Number of sites scoring better than the average of aligned sites = 9600
Number in coding regions = 8822
Number in noncoding regions = 778
Number of orfs with sites within 600 bp upstream = 598
Fraction of orfs with sites within 600 bp upstream = 0.0960488


Motif number 2

 GTCTTCGGAGCGTACGGGGTCAACATGAA	1	10	1	GCGTACGGGG	    0.970788	-181
TGACGAAACGCCAGCCTGGGGAAACGAGTT	1	41	0	CCAGCCTGGG	    0.988634	-150
TGCGGCAATCGCGGCCGGAGTGTGACGAAA	1	63	0	GCGGCCGGAG	    0.972339	-128
CGCGATTGCCGCACCTGGGCGTCTATATGG	1	80	1	GCACCTGGGC	    0.959025	-111
ACCTGGGCGTCTATATGGGCGTCCCGATCA	1	92	1	CTATATGGGC	     0.81327	-99
AATAAGGCTAGTTGATCGGGACGCCCATAT	1	104	0	GTTGATCGGG	    0.952423	-87
GTTGCTTGGGCTTGCTTCGGGATTGTCACT	1	139	0	CTTGCTTCGG	    0.902484	-52
AATTAGCGATGTTGCTTGGGCTTGCTTCGG	1	149	0	GTTGCTTGGG	    0.989139	-42
          **********

Masking position 9
Map Score:   4.05117

Number of sites scoring better than the average of aligned sites = 23925
Number in coding regions = 22209
Number in noncoding regions = 1716
Number of orfs with sites within 600 bp upstream = 1002
Fraction of orfs with sites within 600 bp upstream = 0.160938


Motif number 3

          **********

No masking
Map Score:   -2.32047e-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 4

          **********

No masking
Map Score:   -2.32047e-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:   -2.32047e-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