AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i269_aful_mthe_300.orf -o269_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	RTH00591	27	M.thermo
#2	RTH00127	109	M.thermo
#3	RTH01417	300	M.thermo

Motif number 1

GTTCTATTAATCAAGATGGTGTTTTAA    	1	11	1	TCAAGATGTG	    0.984629	-17
GAATTAAGAATCAAGATAGAGCTGAAATCAG	3	41	1	TCAAGATGAG	    0.991703	-260
ATTAGGCCATTCAAGATTCAGTACAACTACA	3	74	1	TCAAGATCAG	    0.995646	-227
CAGCTGACTTGCAAGTTCCAGGTCAGCTATC	3	136	0	GCAAGTTCAG	    0.982941	-165
CAAGTCAGCTGCATGGTGCAGATGGATTCAA	3	156	1	GCATGGTCAG	    0.954688	-145
ACGGAACTGATCAAGAGCCTG          	3	290	1	TCAAGAGCTG	    0.978173	-11
          ******* ***

Masking position 3
Map Score:   7.29498

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 102
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

ATCAAGATAGAGCTGAAATCAGACATTAGG	3	50	1	AGCTGAAATC	    0.944601	-251
ACATGGTTGTAGTTGTACTGAATCTTGAAT	3	82	0	AGTTGTACTG	     0.88948	-219
ACCGCAGGATAGCTGACCTGGAACTTGCAA	3	129	1	AGCTGACCTG	    0.996302	-172
TGCACCATGCAGCTGACTTGCAAGTTCCAG	3	146	0	AGCTGACTTG	       0.981	-155
CTGCGGGGTATGCTGATCTGTGAGAAGGTG	3	193	0	TGCTGATCTG	    0.989229	-108
AAGTGGAATCTGCCGTCCTCTGAGAGAAGA	3	241	0	TGCCGTCCTC	    0.921185	-60
CCGTGTTTGGTGATGATATGAAGAAGTGGA	3	264	0	TGATGATATG	    0.827611	-37
          **********

Masking position 9
Map Score:   4.50653

Number of sites scoring better than the average of aligned sites = 573
Number in coding regions = 538
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

TATGAAAATTTGTGGGATGTGATGATGAAGCTGT  	2	9	0	TGGGATTGAT	    0.988433	-101
TATTTTAATATGGTTGGAATTATGATTAATATATAT	2	79	0	TGTGGTTGAT	    0.990641	-31
ATTGACATTATGTAGGGGGTATTGAATTAAGAATCA	3	18	1	TGGGGTTGAA	    0.996626	-283
TGGTTGTAGTTGTACTGAATCTTGAATGGCCTAATG	3	73	0	TGCTGTTGAA	    0.965978	-228
AAGGCCTTCCTGCGGGGTATGCTGATCTGTGAGAAG	3	196	0	TGGGGTTGAT	    0.998191	-105
TCTTGATCAGTTCCGTGTTTGGTGATGATATGAAGA	3	270	0	TTGTGTTGAT	    0.966518	-31
          **  ***  *  ****

Masking position 10
Map Score:   5.3094

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 153
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

TGTGGGATGTGATGATGAAGCTGT      	2	5	0	GATGATGAAG	    0.942153	-105
GAATCAAGATAGAGCTGAAATCAGACATTA	3	48	1	AGAGCTGAAA	    0.954973	-253
TCAGCTGCATGGTGCAGATGGATTCAAGTT	3	160	1	GGTGCAGATG	    0.937295	-141
TGATCTGTGAGAAGGTGAAAAACTTGAATC	3	180	0	GAAGGTGAAA	    0.920157	-121
CCGTCCTCTGAGAGAAGAAAGTTCTTGAAG	3	229	0	AGAGAAGAAA	     0.91327	-72
TTCCGTGTTTGGTGATGATATGAAGAAGTG	3	266	0	GGTGATGATA	    0.968904	-35
          **********

Masking position 8
Map Score:   0.818936

Number of sites scoring better than the average of aligned sites = 1779
Number in coding regions = 1665
Number in noncoding regions = 114
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 5

        GTTCTATTAATCAAGATGGTGT	1	3	1	TCTATTAATC	    0.984703	-25
AATTTTCATATTTATAAATCTTTCCATTCA	2	35	1	TTTATAAATC	    0.960902	-75
GGATAACATATATATTAATCATAATTCCAA	2	72	1	TATATTAATC	    0.977399	-38
          **********

Masking position 4
Map Score:   0.283334

Number of sites scoring better than the average of aligned sites = 3
Number in coding regions = 2
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

          **********

No masking
Map Score:   5.42445e-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:   5.42445e-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:   5.42445e-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