AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i320_mixed5_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ndk	115	nucleoside diphosphate kinase
#2	hisS	300	histidyl-tRNA synthetase

Motif number 1

AGAAATTTCTCCGCCCCGGATTGATTAATTATCA	1	26	1	CCGCCCCGGA	    0.996251	-90
     ATTCTCCACCCCATCATTATGTATGTATA	1	97	0	CCACCCCTTA	    0.992514	-19
AGAGAGGAACCCGCCCCAGGCTGAAAGCGGATCC	2	31	1	CCGCCCCGGA	    0.982449	-270
ACCCGTGGTGCCACCCTAGTTGGAATACGTTCAT	2	170	0	CCACCCTGGA	    0.995536	-131
AAAAAAACTCCCGCCCCTACTATACATGATAGTA	2	218	0	CCGCCCCATA	    0.996664	-83
          ******* *   **

Masking position 14
Map Score:   9.09057

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 31
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

ATTAATCAATCCGGGGCGGAGAAATTTCTT	1	25	0	CCGGGGCGGA	     0.99459	-91
ATACATAATGATGGGGTGGAGAAT      	1	102	1	ATGGGGTGGA	    0.987919	-14
CGCTTTCAGCCTGGGGCGGGTTCCTCTCTA	2	30	0	CTGGGGCGGG	     0.99902	-271
GCGTTAAAGGATCGAGCGGGAATATGAACG	2	147	1	ATCGAGCGGG	    0.959623	-154
CGTATTCCAACTAGGGTGGCACCACGGGTA	2	175	1	CTAGGGTGGC	    0.967401	-126
TCATGTATAGTAGGGGCGGGAGTTTTTTTC	2	223	1	TAGGGGCGGG	    0.989399	-78
          **********

Masking position 6
Map Score:   8.36991

Number of sites scoring better than the average of aligned sites = 230
Number in coding regions = 190
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

GCATGATTAGAGAGGAACCCGCCCCAGGCT	2	23	1	AGAGGAACCC	    0.965105	-278
CCAGGCTGAAAGCGGATCCCATTGCGTCTT	2	46	1	AGCGGATCCC	    0.949063	-255
ACAACACTCCGGAGGTTTCCTGCTGAACGC	2	83	1	GGAGGTTTCC	     0.98735	-218
ACTGCCTAATGGCGTTATTCACGCGTTCAG	2	105	0	GGCGTTATTC	    0.834107	-196
ATCCTTTAACGCAGGTTCACGTTCACTGCC	2	129	0	GCAGGTTCAC	    0.941427	-172
AGTAGGGACGAGAGTTATACCCGTGGTGCC	2	192	0	AGAGTTATAC	    0.901404	-109
GAATACATAAGGAGGTCTACCT        	2	289	1	GGAGGTCTAC	    0.971914	-12
          **********

Masking position 4
Map Score:   2.62816

Number of sites scoring better than the average of aligned sites = 842
Number in coding regions = 612
Number in noncoding regions = 230
Number of orfs with sites within 600 bp upstream = 200
Fraction of orfs with sites within 600 bp upstream = 0.0321234


Motif number 4

AACATCTTTCTGATAATTAATCAATCCGGG	1	40	0	TGATAATTAA	    0.932851	-76
CATTAGGCAGTGAACGTGAACCTGCGTTAA	2	124	1	TGAACGTGAA	    0.982782	-177
GGATCGAGCGGGAATATGAACGTATTCCAA	2	155	1	GGAATATGAA	      0.9198	-146
TCGTTAATGATGAAAATGAAAAAAACTCCC	2	240	0	TGAAAATGAA	    0.978103	-61
AAATATCCAATGATCGTTAATGATGAAAAT	2	253	0	TGATCGTTAA	      0.9548	-48
          **********

Masking position 7
Map Score:   1.93567

Number of sites scoring better than the average of aligned sites = 446
Number in coding regions = 394
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 5

          **********

No masking
Map Score:   -8.99957e-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:   -8.99957e-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:   -8.99957e-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