AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i296_mixed11_aful_reg_100.orf -o296_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	RAG05258	41	Archaeoglobus_fulgidus
#2	RAG05274	111	Archaeoglobus_fulgidus
#3	RAG26611	137	Archaeoglobus_fulgidus

Motif number 1

      AAAACCAAAGCTTTTTAATCATAAAGTT	1	5	1	CCAACTTTTA	    0.992423	-37
 CCTTCTCCTCCTAAACTTTATGATTAAAAAGCT	1	19	0	CCAACTTATA	    0.991365	-23
ATGGTCATTAGCTAAAAGCTTTAATATAGCGTAA	2	30	0	GCAAACTTTA	    0.967809	-82
AGCTAATGACCATAATAGTTATAAGGCAACCTTT	2	51	1	CAAAATTATA	    0.965609	-61
GCAACCTTTTGAAAAGCGTTTTTAAACTTGAAAT	2	76	1	GAAACTTTTA	    0.936897	-36
GAAGTTCATTCCAAATAATTTTAAATAAGTTGGC	3	25	0	CCAAATTTTA	    0.995744	-113
CGGAATTAATCCGAAAAATTTTTACCTATATGAC	3	97	1	CCAAATTTTA	    0.995487	-41
          ** ** * **** *

Masking position 5
Map Score:   11.6609

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 75
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 2

        CCAACTCCCTTAAAAGTAATTA	2	3	1	AACTCCCTTA	    0.985798	-109
CCTTAAAAGTAATTACGCTATATTAAAGCT	2	18	1	AATTACGCTA	    0.978202	-94
TTTTCGGATTAATTCCGCTAAATGCCTTCT	3	84	0	AATTCCGCTA	    0.994422	-54
ATATGACAACTACTCCCCTACGGG      	3	124	1	TACTCCCCTA	    0.990912	-14
          **********

Masking position 4
Map Score:   3.86627

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 26
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

CCTAAACTTTATGATTAAAAAGCTTTGGTTT	1	12	0	ATGTTAAAAA	    0.972785	-30
CATTAGCTAAAAGCTTTAATATAGCGTAATT	2	28	0	AAGTTTAATA	    0.972799	-84
TTTCGATTTCAAGTTTAAAAACGCTTTTCAA	2	84	0	AAGTTAAAAA	    0.988818	-28
CATTCCAAATAATTTTAAATAAGTTGGCTCG	3	22	0	AATTTAAATA	    0.949919	-116
          *** *******

Masking position 6
Map Score:   1.35962

Number of sites scoring better than the average of aligned sites = 40
Number in coding regions = 13
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 4

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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