AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i319_mixed4_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	comGB	52	probably part of the DNA transport machinery
#2	comGA	300	late competence gene

Motif number 1

CTCTTTAATAACCTGGCTTGATCCTTTAACAACCAG	1	17	0	ACCGTTGTTT	     0.99484	-36
       TTCACCGAGCCTCTTTAATAACCTGGCTT	1	34	0	ACCGCTCTAT	    0.993864	-19
TGACCAAATGACCGGTATTGTTGCATTAGGCGATCT	2	20	1	ACCTTTGTAT	    0.984888	-281
AGACATGGTCACCATGCCTGCTAGATTCCATTTTCA	2	99	0	ACCGCTGTAT	    0.998072	-202
AGGCATGGTGACCATGTCTGCTTTTTTATTTATAGG	2	116	1	ACCGCTGTTT	    0.998251	-185
CTGTTTGATTACCTTTTCTTCTTTTTCTACAATATG	2	252	1	ACCTCTTTTT	    0.973655	-49
          ***  * *** *  **

Masking position 9
Map Score:   7.79922

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 56
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

GTCAATAAGCGAAAACAGCATAATGAAAATG	2	76	1	GAAAAAGCAT	    0.967353	-225
ACAGCATAATGAAAATGGAATCTAGCAGGCA	2	90	1	GAAAAGGAAT	    0.995848	-211
TTTCTGGCAAGAAAAAAGACTTTCAACTGAA	2	176	0	GAAAAAGACT	    0.961442	-125
GTTATATGCTGAAAAACCAATTCTTTCTGGC	2	199	0	GAAAACCAAT	    0.950847	-102
ATCAAACAGGGAAAACGTGATTTTGTGAGAT	2	230	0	GAAAAGTGAT	    0.967353	-71
AGAAAAAGAAGAAAAGGTAATCAAACAGGGA	2	249	0	GAAAAGTAAT	     0.98781	-52
TGCGTTGAAAGGAGAGGGAATCAAA      	2	286	1	GGAGAGGAAT	    0.957817	-15
          ***** *****

Masking position 5
Map Score:   6.45906

Number of sites scoring better than the average of aligned sites = 747
Number in coding regions = 661
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 3

CTTGATCCTTTAACAACCAGACTTTT       	1	4	0	TAACAACCGT	    0.987578	-49
CGAGCCTCTTTAATAACCTGGCTTGATCCTTTA	1	25	0	TAATAACCGT	    0.994366	-28
GAAAATGACCAAATGACCGGTATTGTTGCATTA	2	15	1	AAATGACCGT	    0.991793	-286
TGTTTTCGCTTATTGACCAGTATCTTTCTCAAC	2	60	0	TATTGACCGT	    0.991794	-241
GGGAAAATTATAATGACAGGGGTACATTCAGTT	2	150	1	TAATGACAGT	    0.987046	-151
          ******** *  *

Masking position 6
Map Score:   4.83583

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 43
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

AACGGAAAGATCGCCTAATGCAACAATACC	2	33	0	TCGCCTAATG	     0.99241	-268
TATGCTGTTTTCGCTTATTGACCAGTATCT	2	68	0	TCGCTTATTG	    0.988791	-233
TAAGCGAAAACAGCATAATGAAAATGGAAT	2	81	1	CAGCATAATG	    0.969876	-220
TCTCCTTTCAACGCATATTGTAGAAAAAGA	2	271	0	ACGCATATTG	    0.988789	-30
          **********

Masking position 6
Map Score:   2.33926

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 123
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

AGGCGATCTTTCCGTTGAGAAAGATACTGG	2	47	1	TCCGTTGAGA	    0.994945	-254
AGGGGTACATTCAGTTGAAAGTCTTTTTTC	2	167	1	TCAGTTGAAA	    0.988596	-134
TTCTACAATATGCGTTGAAAGGAGAGGGAA	2	276	1	TGCGTTGAAA	    0.992279	-25
          **********

Masking position 8
Map Score:   1.95462

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 13
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 6

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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