AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i232_mjan_pyro_300.orf -o232_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00277	70	Pyrococcus_OT3
#2	RPH00276	300	Pyrococcus_OT3

Motif number 1

CTCAACAATAAAAAATAGAGATAGA      	1	5	0	AAAAATAGGA	    0.938107	-66
AATCTCTTTTAAATTCAACGTTTTATCTCAA	1	31	0	AAATTCAAGT	    0.923464	-40
        CGAAATATAATCCCTTAAAAATC	1	58	0	AAATATAACC	    0.863711	-13
CTTTCGACGAAAATTCCAAGACTGAAAGAAA	2	58	1	AAATTCCAGA	    0.888448	-243
AAGACTGAAAGAAAATAAAGACAAACTGATA	2	75	1	GAAAATAAGA	    0.880257	-226
TAACCCTAAGAAAAATAAGGTAGCTCTTTTC	2	104	1	AAAAATAAGT	    0.917622	-197
CTAGAAGCTTAAATTCAAGGATATTAAGTAG	2	154	0	AAATTCAAGA	    0.974483	-147
AGGATTTGTAAAATTTAGTCAGGCAACTTAA	2	195	0	AAATTTAGCA	    0.911186	-106
CAAATATGTCAAAAACAAACATTTATATTGA	2	252	1	AAAAACAACA	    0.962757	-49
TTTTCACGGTAAAATTAATCAATATAAATGT	2	270	0	AAAATTAACA	    0.959775	-31
          ******** **

Masking position 3
Map Score:   7.93478

Number of sites scoring better than the average of aligned sites = 1433
Number in coding regions = 1260
Number in noncoding regions = 173
Number of orfs with sites within 600 bp upstream = 161
Fraction of orfs with sites within 600 bp upstream = 0.0258593


Motif number 2

        TCTATCTCTATTTTTTATTGTT	1	3	1	TATCTCTATT	    0.977029	-68
TTCAACGTTTTATCTCAACAATAAAAAATA	1	19	0	TATCTCAACA	    0.838668	-52
ATCCCTTAAAAATCTCTTTTAAATTCAACG	1	42	0	AATCTCTTTT	    0.942803	-29
TATACCCTCATATCTCTTTACGTAGGAATT	2	12	0	TATCTCTTTA	    0.983861	-289
AAAAATAAGGTAGCTCTTTTCCACTAGCTC	2	114	1	TAGCTCTTTT	    0.989678	-187
TCTTTTCCACTAGCTCAGTTGTGTGGCTAC	2	128	1	TAGCTCAGTT	     0.94947	-173
TTCTAGCCCCTAGCTCTTAAGTTGCCTGAC	2	179	1	TAGCTCTTAA	    0.947825	-122
          **********

Masking position 2
Map Score:   7.76733

Number of sites scoring better than the average of aligned sites = 417
Number in coding regions = 374
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 3

AAAGAGATATGAGGGTATAAGATAAAATAACTT	2	23	1	GAGGTATAGT	    0.996042	-278
TATTTTTCTTAGGGTTATCAGTTTGTCTTTATT	2	88	0	AGGGTATAGT	    0.991773	-213
GCTTAAATTCAAGGATATTAAGTAGCCACACAA	2	146	0	AAGGTATAAT	    0.955361	-155
TTAAGAGCTAGGGGCTAGAAGCTTAAATTCAAG	2	166	0	GGGGTAGAGT	    0.991895	-135
CTCAAATGATGAGCCTTTTAGATTTCTACAAAT	2	224	1	GAGCTTTAGT	    0.955991	-77
          **** *** ** *

Masking position 6
Map Score:   0.934829

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 70
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

CTAAGAAAAATAAGGTAGCTCTTTTCCACT	2	109	1	TAAGGTAGCT	     0.96489	-192
TTCAAGGATATTAAGTAGCCACACAACTGA	2	142	0	TTAAGTAGCC	    0.993681	-159
CCCCTAGCTCTTAAGTTGCCTGACTAAATT	2	185	1	TTAAGTTGCC	    0.988911	-116
          **********

Masking position 3
Map Score:   0.220967

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 9
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   -1.25466e-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:   -1.25466e-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:   -1.25466e-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