AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i206_nucleases_bbur_reg_100.orf -o206_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00127	300	3615

Motif number 1

TATTTTTGTTAAAATTTTAATTATCAAGCT	1	45	0	AAAATTTTAA	     0.87453	-256
AAATTTTAACAAAAATAAATCAAAATAATT	1	58	1	AAAAATAAAT	    0.700556	-243
AAACAATTTGAAAAATTATTTTGATTTATT	1	71	0	AAAAATTATT	    0.617697	-230
AAATTGTTTTAAGAATTTAATAAAAATGCA	1	92	1	AAGAATTTAA	    0.970872	-209
TAAGCTTTGGAAGGATTTTTTATCTGCATT	1	116	0	AAGGATTTTT	    0.888436	-185
AAAGCACACGAGAGATTTTTAAAAACTAGC	1	156	1	AGAGATTTTT	     0.75847	-145
GATTACTATAACAGATTTAAAGACACTCAT	1	201	1	ACAGATTTAA	    0.936907	-100
CAAGTTAGACAAAAATTTATTAATATTGAT	1	236	1	AAAAATTTAT	    0.652661	-65
ATATTGATAGAAAAATTTTACATTAAATTC	1	258	1	AAAAATTTTA	    0.681698	-43
TTTTGTCCTTACGAATTTAATGTAAAATTT	1	270	0	ACGAATTTAA	    0.936893	-31
CGTAAGGACAAAAAATTAAAATTC      	1	287	1	AAAAATTAAA	    0.955495	-14
          **********

Masking position 1
Map Score:   14.2588

Number of sites scoring better than the average of aligned sites = 2454
Number in coding regions = 1711
Number in noncoding regions = 743
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 2

TTTTTGTTAAAATTTTAATTATCAAGCTTT	1	43	0	AATTTTAATT	    0.737049	-258
AAATTATTTTGATTTATTTTTGTTAAAATT	1	59	0	GATTTATTTT	    0.862132	-242
TTCTTAAAACAATTTGAAAAATTATTTTGA	1	77	0	AATTTGAAAA	    0.822648	-224
TTGTTTTAAGAATTTAATAAAAATGCAGAT	1	95	1	AATTTAATAA	    0.914185	-206
GCTTTGGAAGGATTTTTTATCTGCATTTTT	1	113	0	GATTTTTTAT	    0.890867	-188
GCACACGAGAGATTTTTAAAAACTAGCGAA	1	159	1	GATTTTTAAA	    0.890866	-142
TACTATAACAGATTTAAAGACACTCATGAT	1	204	1	GATTTAAAGA	    0.942977	-97
AGACACTCATGATTTCAAGTTAGACAAAAA	1	221	1	GATTTCAAGT	    0.878697	-80
GTTAGACAAAAATTTATTAATATTGATAGA	1	239	1	AATTTATTAA	    0.863128	-62
TGTCCTTACGAATTTAATGTAAAATTTTTC	1	267	0	AATTTAATGT	    0.919245	-34
         GAATTTTAATTTTTTGTCCTT	1	290	0	AATTTTAATT	    0.737049	-11
          **********

Masking position 2
Map Score:   9.23802

Number of sites scoring better than the average of aligned sites = 2784
Number in coding regions = 1821
Number in noncoding regions = 963
Number of orfs with sites within 600 bp upstream = 152
Fraction of orfs with sites within 600 bp upstream = 0.0244137


Motif number 3

TGGAGTTGGATAGCTTGATATGTAT     	1	6	0	TAGCTTGATA	    0.974826	-295
CAATTTACCAAAGCTTGATAATTAAAATTT	1	34	1	AAGCTTGATA	    0.991448	-267
AATTTTTGTCTAACTTGAAATCATGAGTGT	1	223	0	TAACTTGAAA	    0.951019	-78
AAAATTTATTAATATTGATAGAAAAATTTT	1	247	1	AATATTGATA	    0.926203	-54
          **********

Masking position 5
Map Score:   2.74331

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 105
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

TTTGTTAAAATTTTAATTATCAAGCTTTGG	1	41	0	TTTTAATTAT	    0.955402	-260
ATAATTAAAATTTTAACAAAAATAAATCAA	1	51	1	TTTTAACAAA	    0.921592	-250
TGAAAAATTATTTTGATTTATTTTTGTTAA	1	63	0	TTTTGATTTA	     0.82143	-238
TTTCAAATTGTTTTAAGAATTTAATAAAAA	1	88	1	TTTTAAGAAT	    0.886634	-213
TTTATCTGCATTTTTATTAAATTCTTAAAA	1	98	0	TTTTTATTAA	    0.932553	-203
ACACGAGAGATTTTTAAAAACTAGCGAAAT	1	161	1	TTTTTAAAAA	    0.477258	-140
TTTCTATCAATATTAATAAATTTTTGTCTA	1	241	0	TATTAATAAA	    0.858718	-60
       GAATTTTAATTTTTTGTCCTTAC	1	288	0	TTTTAATTTT	    0.886923	-13
          **********

Masking position 6
Map Score:   4.88093

Number of sites scoring better than the average of aligned sites = 2779
Number in coding regions = 1711
Number in noncoding regions = 1068
Number of orfs with sites within 600 bp upstream = 164
Fraction of orfs with sites within 600 bp upstream = 0.0263412


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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