AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i206_nucleases_mtub_reg_100.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	recC	276	recC

Motif number 1

CCAAAGCAACCGCGTCACCCACCAC     	1	6	0	CGCGTCACCC	    0.998955	-271
TTTGGGCAACCGCCTCACACCTACACCGCC	1	31	1	CGCCTCACAC	    0.996293	-246
ACACCTACACCGCCTCCTCCATCTCGAAGT	1	47	1	CGCCTCCTCC	    0.992326	-230
CATGACGAGCCGCCTCGGACGTGACACACT	1	74	0	CGCCTCGGAC	    0.979549	-203
TCCGAGGCGGCTCGTCATGCCGACATCGCG	1	85	1	CTCGTCATGC	    0.973817	-192
ATGCCGACATCGCGGCACGCCCCAGCGCGT	1	101	1	CGCGGCACGC	    0.998176	-176
CATGCATGTCGGCGGCCGGCCGCTCGACTA	1	245	1	GGCGGCCGGC	     0.60061	-32
        CGGGCGTCACCCTAGTCGAGCG	1	265	0	GGCGTCACCC	     0.99578	-12
          **********

Masking position 6
Map Score:   19.2557

Number of sites scoring better than the average of aligned sites = 3928
Number in coding regions = 3568
Number in noncoding regions = 360
Number of orfs with sites within 600 bp upstream = 304
Fraction of orfs with sites within 600 bp upstream = 0.0488275


Motif number 2

GTTGCCCAAAGCAACCGCGTCACCCACCAC	1	11	0	GCAACCGCGT	    0.995839	-266
GTTGCTTTGGGCAACCGCCTCACACCTACA	1	26	1	GCAACCGCCT	    0.993865	-251
GCCTCACACCTACACCGCCTCCTCCATCTC	1	42	1	TACACCGCCT	    0.941165	-235
GTCGGCATGACGAGCCGCCTCGGACGTGAC	1	79	0	CGAGCCGCCT	    0.951349	-198
TCGTCATGCCGACATCGCGGCACGCCCCAG	1	96	1	GACATCGCGG	     0.98066	-181
CGCGGCACGCCCCAGCGCGTTGATGAAATC	1	111	1	CCCAGCGCGT	    0.980667	-166
GCGCGTTGATGAAATCCCGGAACGGTTCGA	1	125	1	GAAATCCCGG	    0.932584	-152
AGGTCGACAAGAAGGCCCGTACCGACTGGT	1	171	1	GAAGGCCCGT	    0.945349	-106
GTCGTTCGGTGATCTCGCGTCTGTTTATGC	1	208	1	GATCTCGCGT	     0.84652	-69
AGTCGAGCGGCCGGCCGCCGACATGCATGC	1	244	0	CCGGCCGCCG	     0.94164	-33
          **********

Masking position 6
Map Score:   10.5352

Number of sites scoring better than the average of aligned sites = 23377
Number in coding regions = 21972
Number in noncoding regions = 1405
Number of orfs with sites within 600 bp upstream = 826
Fraction of orfs with sites within 600 bp upstream = 0.132669


Motif number 3

CCGCCTCCTCCATCTCGAAGTGTGTCACGTCCGA	1	56	1	CTTCGAAGTG	    0.967677	-221
GTCGGCATGACGAGCCGCCTCGGACGTGACACAC	1	75	0	CACCGCCGGA	    0.945115	-202
GGCGGCTCGTCATGCCGACATCGCGGCACGCCCC	1	90	1	CTCCGACCGC	    0.987568	-187
AATCCCGGAACGGTTCGATATCTGACCCAGTTCC	1	137	1	CGTCGATCTG	    0.937755	-140
TACGGGCCTTCTTGTCGACCTGGAACTGGGTCAG	1	158	0	CTTCGACGGA	    0.996284	-119
CAAGAAGGCCCGTACCGACTGGTAGCCCTTGTCG	1	178	1	CTCCGACGTA	    0.990359	-99
CGCGAGATCACCGAACGACAAGGGCTACCAGTCG	1	193	0	CGACGACGGG	    0.993945	-84
CGCCAGCATGCATGTCGGCGGCCGGCCGCTCGAC	1	239	1	CTTCGGCCCG	    0.955585	-38
CGGCGGCCGGCCGCTCGACTAGGGTGACGCCCG 	1	254	1	CGTCGACGGG	      0.9985	-23
          * * *****  ***

Masking position 6
Map Score:   10.4571

Number of sites scoring better than the average of aligned sites = 7579
Number in coding regions = 7097
Number in noncoding regions = 482
Number of orfs with sites within 600 bp upstream = 370
Fraction of orfs with sites within 600 bp upstream = 0.0594282


Motif number 4

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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