AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i284_mjan_pyro_300.orf -o284_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	RMJ12206	155	M_jannaschii_chromosome
#2	RPH00004	159	Pyrococcus_OT3

Motif number 1

AATCTAATGTTTTATAAAATCTTCAATTAA	1	99	0	TTTATAAAAT	    0.961164	-57
TAATGGTTTATTTATGTAATCTAATGTTTT	1	116	0	TTTATGTAAT	    0.777112	-40
ACCCCTCCATTTGTTATAATGGTTTATTTA	1	132	0	TTGTTATAAT	    0.949711	-24
TCAGCGTTCTTTTATAACTTTTTTGTTAAA	2	34	1	TTTATAACTT	    0.782314	-126
TATAACTTTTTTGTTAAATTCCATAACCTT	2	46	1	TTGTTAAATT	    0.957032	-114
TTCCATAACCTTGTTATAATTATGTGTTTA	2	64	1	TTGTTATAAT	    0.949711	-96
ATGTGTTTAGTTGACAAATTTTTGTAAAAT	2	85	1	TTGACAAATT	    0.922179	-75
TTGACAAATTTTTGTAAAATAAATTTTAAA	2	95	1	TTTGTAAAAT	    0.931924	-65
GATTGATTAATTTTTAAAATTTATTTTACA	2	107	0	TTTTTAAAAT	    0.940466	-53
TAATCAATCTTTGACAAAACAAAGGCAATT	2	128	1	TTGACAAAAC	    0.844662	-32
          **********

Masking position 2
Map Score:   12.4914

Number of sites scoring better than the average of aligned sites = 1163
Number in coding regions = 946
Number in noncoding regions = 217
Number of orfs with sites within 600 bp upstream = 179
Fraction of orfs with sites within 600 bp upstream = 0.0287504


Motif number 2

CTTTAGAGAGAATAATTGGGCTACTAAAAA	1	27	0	AATAATTGGG	    0.944395	-129
ATTAATATAAAATAATAAGGTTATAGTTAG	1	74	0	AATAATAAGG	    0.851624	-82
CATTATAACAAATGGAGGGGTGATT     	1	141	1	AATGGAGGGG	    0.995497	-15
AGAGTGGGGTAACGGTGAGGGTA       	2	4	0	AACGGTGAGG	    0.984324	-156
AAGAACGCTGAAGAGTGGGGTAACGGTGAG	2	15	0	AAGAGTGGGG	    0.991609	-145
AACAAAGGCAATTGGAGGGGAAAGG     	2	145	1	ATTGGAGGGG	    0.981996	-15
          **********

Masking position 1
Map Score:   4.81071

Number of sites scoring better than the average of aligned sites = 277
Number in coding regions = 231
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

TTGGGCTACTAAAAAATATTATGGTGATTA	1	12	0	AAAAAATATT	    0.934639	-144
TCTCTAAAGAATTAACTATTTAAGAGCTAA	1	48	1	ATTAACTATT	    0.950585	-108
TTCAATTAATATAAAATAATAAGGTTATAG	1	78	0	ATAAAATAAT	    0.808202	-78
CTAATGTTTTATAAAATCTTCAATTAATAT	1	96	0	ATAAAATCTT	    0.952069	-60
GATTACATAAATAAACCATTATAACAAATG	1	125	1	ATAAACCATT	    0.862551	-31
AGCGTTCTTTTATAACTTTTTTGTTAAATT	2	36	1	TATAACTTTT	    0.693101	-124
ATTTTTGTAAAATAAATTTTAAAAATTAAT	2	102	1	AATAAATTTT	     0.88426	-58
TTTAAAAATTAATCAATCTTTGACAAAACA	2	119	1	AATCAATCTT	    0.841539	-41
          **********

Masking position 5
Map Score:   3.20953

Number of sites scoring better than the average of aligned sites = 1564
Number in coding regions = 1142
Number in noncoding regions = 422
Number of orfs with sites within 600 bp upstream = 365
Fraction of orfs with sites within 600 bp upstream = 0.0586251


Motif number 4

      TTAATCACCATAATATTTTTTAGT	1	5	1	TCACCATAAT	    0.963132	-151
ATTTAAGAGCTAACTATAACCTTATTATTT	1	65	1	TAACTATAAC	    0.982472	-91
CATAAATAAACCATTATAACAAATGGAGGG	1	130	1	CCATTATAAC	    0.961904	-26
     TACCCTCACCGTTACCCCACTCTTC	2	6	1	TCACCGTTAC	    0.949151	-154
ACTAAACACATAATTATAACAAGGTTATGG	2	66	0	TAATTATAAC	    0.961355	-94
          **********

Masking position 7
Map Score:   1.08747

Number of sites scoring better than the average of aligned sites = 175
Number in coding regions = 150
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 5

ATTATAACAAATGGAGGGGTGATT      	1	142	1	ATGGAGGGGT	    0.997183	-14
AGAACGCTGAAGAGTGGGGTAACGGTGAGG	2	14	0	AGAGTGGGGT	    0.984095	-146
ACAAAGGCAATTGGAGGGGAAAGG      	2	146	1	TTGGAGGGGA	    0.991295	-14
          **********

Masking position 6
Map Score:   0.405613

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 27
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

          **********

No masking
Map Score:   4.42969e-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:   4.42969e-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:   4.42969e-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