AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i147_bsub_mtub_100.orf -o147_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	cysH	300	phosphoadenosine phosphosulfate
#2	nirA	300	nirA

Motif number 1

ATAGGTCCAGTCCCTCAGCCGCTCTTGATAAG	1	46	0	TCTCAGCCGC	    0.988291	-255
TACAAACTATGCAGGTTGCCGGGCTTCATAGG	1	73	0	GCGTTGCCGG	    0.987514	-228
AAAATGGAATTCATTTTGCTGGAAGTAGCACC	1	106	0	TCTTTGCTGG	    0.966889	-195
TTCCTGTCTTTCTTTCCGCCGGATTGAAAGTT	1	160	1	TCTCCGCCGG	    0.997075	-141
ACAAACAGTAGCTTTCTGCCGGTTGTCTTTTC	1	253	0	GCTCTGCCGG	     0.98922	-48
TTTGACCAGGTCGCGCAGCTGCACGCCATCCA	2	72	1	TCGCAGCTGC	     0.98134	-229
GGGCGCGGGTTCTTGGCGGCGGTCACGGTGAC	2	113	0	TCGGCGGCGG	    0.995284	-188
GATTCGCAGATCGGGGCGCGGGTTCTTGGCGG	2	126	0	TCGGCGCGGG	    0.994455	-175
GATCTGCGAATCGCGCTGGTGGCTCGGCGGCA	2	146	1	TCGCTGGTGG	    0.982844	-155
CCGCTTGAGGTCGATGTGCCGCCGAGCCACCA	2	162	0	TCTGTGCCGC	    0.990937	-139
GAGGGGCAGATCCGGTCGCCGGCTGCAGATAC	2	242	0	TCGTCGCCGG	    0.996589	-59
CGCCGCTTGTTCCGGGAGGGGCAGATCCGGTC	2	257	0	TCGGAGGGGC	    0.940628	-44
          **  ********

Masking position 2
Map Score:   25.4363

Number of sites scoring better than the average of aligned sites = 1249
Number in coding regions = 1185
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 2

GTCCAGTCCCTCAGCCGCTCTTGATAAGTT	1	44	0	TCAGCCGCTC	    0.956391	-257
GGACTGGACCTATGAAGCCCGGCAACCTGC	1	65	1	TATGAAGCCC	    0.934409	-236
ACAGGAACAGCATGCAGCCCTTATCTTTCA	1	137	0	CATGCAGCCC	      0.9868	-164
TCCTGTCTTTCTTTCCGCCGGATTGAAAGT	1	161	1	CTTTCCGCCG	    0.894471	-140
TATCTGTATATCAGCAGCCGCGAATCACAT	1	216	1	TCAGCAGCCG	    0.991359	-85
CCATGGATGGCGTGCAGCTGCGCGACCTGG	2	77	0	CGTGCAGCTG	    0.980724	-224
TGACCGCCGCCAAGAACCCGCGCCCCGATC	2	120	1	CAAGAACCCG	    0.711374	-181
TTGAGGTCGATGTGCCGCCGAGCCACCAGC	2	160	0	TGTGCCGCCG	      0.9937	-141
CTCAAGCGGGTCTGCAGCTGTGGCTGTCGG	2	185	1	TCTGCAGCTG	    0.990484	-116
GGCTGTCGGCCTTGACGCCGTAAACCCAGC	2	206	1	CTTGACGCCG	    0.963069	-95
CCCACCTGTATCTGCAGCCGGCGACCGGAT	2	235	1	TCTGCAGCCG	    0.996911	-66
GGCGACCGGATCTGCCCCTCCCGGAACAAG	2	254	1	TCTGCCCCTC	     0.92986	-47
          **********

Masking position 8
Map Score:   21.1464

Number of sites scoring better than the average of aligned sites = 3012
Number in coding regions = 2833
Number in noncoding regions = 179
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 3

TAAGGGCTGCATGCTGTTCCTGTCTTTCTTTC	1	144	1	ATGCGTTCCG	    0.857258	-157
ACTTTCAATCCGGCGGAAAGAAAGACAGGAAC	1	159	0	CGGCGAAAGA	    0.844881	-142
TGATTCGCGGCTGCTGATATACAGATAGCCTT	1	211	0	CTGCGATATC	    0.822576	-90
AAAAGACAACCGGCAGAAAGCTACTGTTTGTT	1	254	1	CGGCGAAAGT	    0.844881	-47
ATGGATGGATAGGCCGACCCGG          	2	1	0	AGGCGACCCG	     0.97779	-300
GGGTTCTTGGCGGCGGTCACGGTGACATTCTG	2	107	0	CGGCGTCACG	    0.978872	-194
GCGCCCCGATCTGCGAATCGCGCTGGTGGCTC	2	139	1	CTGCAATCGG	    0.869711	-162
GGTGGCTCGGCGGCACATCGACCTCAAGCGGG	2	163	1	CGGCCATCGC	    0.935536	-138
ACAGCCACAGCTGCAGACCCGCTTGAGGTCGA	2	180	0	CTGCGACCCC	    0.978805	-121
TACGGCGTCAAGGCCGACAGCCACAGCTGCAG	2	196	0	AGGCGACAGC	      0.9489	-105
CGGTCGCCGGCTGCAGATACAGGTGGGCTGGG	2	230	0	CTGCGATACG	     0.98387	-71
GTTCCGGGAGGGGCAGATCCGGTCGCCGGCTG	2	249	0	GGGCGATCCG	    0.965048	-52
CCGGAACAAGCGGCGTTTAGCGCGTCCTAGGT	2	274	1	CGGCTTTAGG	    0.796024	-27
          **** ***** *

Masking position 4
Map Score:   12.478

Number of sites scoring better than the average of aligned sites = 3021
Number in coding regions = 2852
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 119
Fraction of orfs with sites within 600 bp upstream = 0.0191134


Motif number 4

          **********

No masking
Map Score:   1.30983e-12

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:   1.30983e-12

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:   1.30983e-12

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