AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_hsp60_hsp10_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	mopB	275	GroES, 10 Kd chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity
#2	mopA	43	GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein

Motif number 1

CCCAAAATTTGGGCGCAATCGGACATCAACCC 	1	10	0	GGGGCATCGA	    0.975568	-266
CCCAAATTTTGGGCAACTGCGTAGATTTTCGAT	1	30	1	GGGAACGCGA	     0.99414	-246
ACAAAATCGGGTGAAAACCCTGATTCACCTCAC	1	115	0	GTGAAACCTA	    0.936201	-161
GCCCCTTCAAGGGGGAAAAAGAAAAAAAATTCT	1	155	0	GGGGAAAAGA	    0.967324	-121
CCCCTTGAAGGGGCGAAGCCTCATCCCCATTTC	1	174	1	GGGGAACCTA	    0.994458	-102
GTCACCAGCCGGGAAACCACGTAAGCTCCGGCG	1	211	1	GGGAACACGA	     0.99507	-65
TATCTGTTATGGGTGACGCCGGAGCTTACGTGG	1	227	0	GGGGACCCGA	    0.998945	-49
ACTCTCCTTTGAGAAAGTCCGTATCTGTTATGG	1	248	0	GAGAAGCCGA	    0.966557	-28
          *** *** *** *

Masking position 13
Map Score:   10.9093

Number of sites scoring better than the average of aligned sites = 467
Number in coding regions = 423
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

CCCAAAATTTGGGCGCAATCGGACATCAACC	1	12	0	GGGCGCAACG	    0.995236	-264
CCCAAATTTTGGGCAACTGCGTAGATTTTCG	1	30	1	GGGCAACTCG	    0.985995	-246
GCACAAAATCGGGTGAAAACCCTGATTCACC	1	119	0	GGGTGAAACC	    0.965476	-157
GCCCCTTCAAGGGGGAAAAAGAAAAAAAATT	1	157	0	GGGGGAAAAG	    0.922447	-119
CCCCTTGAAGGGGCGAAGCCTCATCCCCATT	1	174	1	GGGCGAAGCT	    0.971275	-102
CCATTTCTCTGGTCACCAGCCGGGAAACCAC	1	200	1	GGTCACCACC	     0.85767	-76
GTCACCAGCCGGGAAACCACGTAAGCTCCGG	1	211	1	GGGAAACCCG	    0.952428	-65
TATCTGTTATGGGTGACGCCGGAGCTTACGT	1	229	0	GGGTGACGCG	    0.813343	-47
          ******** **

Masking position 2
Map Score:   6.83167

Number of sites scoring better than the average of aligned sites = 1902
Number in coding regions = 1795
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 106
Fraction of orfs with sites within 600 bp upstream = 0.0170254


Motif number 3

GCAGTTGCCCAAAATTTGGGCGCAATCGGA	1	20	0	AAAATTTGGG	    0.940759	-256
ACGGCGATGAAGAAATTGCGATGAAATGTG	1	88	1	AGAAATTGCG	    0.989625	-188
TCTGATCAGCACAAAATCGGGTGAAAACCC	1	128	0	ACAAAATCGG	    0.942636	-148
GAAAAAGAAAAAAAATTCTGATCAGCACAA	1	144	0	AAAAATTCTG	    0.941815	-132
TGGTGACCAGAGAAATGGGGATGAGGCTTC	1	188	0	AGAAATGGGG	     0.98149	-88
CTCTCCTTTGAGAAAGTCCGTATCTGTTAT	1	250	0	AGAAAGTCCG	    0.978173	-26
          **********

Masking position 4
Map Score:   3.48061

Number of sites scoring better than the average of aligned sites = 320
Number in coding regions = 282
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 4

GCGCAATCGGACATCAACCC          	1	1	0	ACATCAACCC	    0.932336	-275
CATCGCAATTTCTTCATCGCCGTCATAAGC	1	81	0	TCTTCATCGC	    0.992785	-195
TTCACCTCACATTTCATCGCAATTTCTTCA	1	95	0	ATTTCATCGC	    0.936946	-181
GAATTTTTTTTCTTTTTCCCCCTTGAAGGG	1	156	1	TCTTTTTCCC	    0.956429	-120
AAGGGGCGAAGCCTCATCCCCATTTCTCTG	1	181	1	GCCTCATCCC	     0.98583	-95
        TATCTTTATTCCTTAAATTCGT	2	32	0	TCTTTATTCC	    0.932269	-12
          **********

Masking position 4
Map Score:   3.25999

Number of sites scoring better than the average of aligned sites = 1132
Number in coding regions = 1026
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 125
Fraction of orfs with sites within 600 bp upstream = 0.0200771


Motif number 5

          **********

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 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