AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_hsp60_hsp10_ecoli_reg_100.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	    0.972671	-266
CCCAAATTTTGGGCAACTGCGTAGATTTTCGAT	1	30	1	GGGAACGCGA	     0.99343	-246
ACAAAATCGGGTGAAAACCCTGATTCACCTCAC	1	115	0	GTGAAACCTA	    0.928974	-161
GCCCCTTCAAGGGGGAAAAAGAAAAAAAATTCT	1	155	0	GGGGAAAAGA	    0.963485	-121
CCCCTTGAAGGGGCGAAGCCTCATCCCCATTTC	1	174	1	GGGGAACCTA	    0.993786	-102
GTCACCAGCCGGGAAACCACGTAAGCTCCGGCG	1	211	1	GGGAACACGA	    0.994472	-65
TATCTGTTATGGGTGACGCCGGAGCTTACGTGG	1	227	0	GGGGACCCGA	    0.998817	-49
ACTCTCCTTTGAGAAAGTCCGTATCTGTTATGG	1	248	0	GAGAAGCCGA	    0.962631	-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

GGTTGATGTCCGATTGCGCCCAAATTTTGGG	1	12	1	CGTTGCGCCC	    0.995866	-264
CGAAAATCTACGCAGTTGCCCAAAATTTGGG	1	30	0	CGAGTTGCCC	    0.987882	-246
GGTGAATCAGGGTTTTCACCCGATTTTGTGC	1	119	1	GGTTTCACCC	    0.965434	-157
AATTTTTTTTCTTTTTCCCCCTTGAAGGGGC	1	157	1	CTTTTCCCCC	    0.932388	-119
AATGGGGATGAGGCTTCGCCCCTTCAAGGGG	1	174	0	AGCTTCGCCC	    0.972692	-102
GTGGTTTCCCGGCTGGTGACCAGAGAAATGG	1	200	0	GGTGGTGACC	    0.873787	-76
CCGGAGCTTACGTGGTTTCCCGGCTGGTGAC	1	211	0	CGGGTTTCCC	    0.958664	-65
ACGTAAGCTCCGGCGTCACCCATAACAGATA	1	229	1	CGCGTCACCC	    0.796668	-47
          ** ********

Masking position 10
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

TCCGATTGCGCCCAAATTTTGGGCAACTGC	1	20	1	CCCAAATTTT	    0.932414	-256
CACATTTCATCGCAATTTCTTCATCGCCGT	1	88	0	CGCAATTTCT	    0.988197	-188
GGGTTTTCACCCGATTTTGTGCTGATCAGA	1	128	1	CCGATTTTGT	    0.934548	-148
TTGTGCTGATCAGAATTTTTTTTCTTTTTC	1	144	1	CAGAATTTTT	    0.933622	-132
GAAGCCTCATCCCCATTTCTCTGGTCACCA	1	188	1	CCCCATTTCT	    0.978753	-88
ATAACAGATACGGACTTTCTCAAAGGAGAG	1	250	1	CGGACTTTCT	    0.974963	-26
          **********

Masking position 7
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	     0.93191	-275
CATCGCAATTTCTTCATCGCCGTCATAAGC	1	81	0	TCTTCATCGC	    0.992737	-195
TTCACCTCACATTTCATCGCAATTTCTTCA	1	95	0	ATTTCATCGC	    0.936547	-181
GAATTTTTTTTCTTTTTCCCCCTTGAAGGG	1	156	1	TCTTTTTCCC	    0.956148	-120
AAGGGGCGAAGCCTCATCCCCATTTCTCTG	1	181	1	GCCTCATCCC	    0.985736	-95
        TATCTTTATTCCTTAAATTCGT	2	32	0	TCTTTATTCC	    0.931842	-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