AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i325_not_clear_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	tldD	47	suppresses inhibitory activity of CsrA
#2	BIME161	74	BIME
#3	yhdR	67	orf, hypothetical protein
#4	mreC	65	rod shape-determining protein
#5	mreB	244	regulator of ftsI, penicillin binding protein 3, septation function

Motif number 1

CGTTAGTTACTGCAGTAGAGGATTTTTTACG	1	14	0	TGCAGAGAGG	    0.967561	-34
TGGGCCGCCATCCGGCAAAGGGTTTTTGAGT	3	19	1	TCCGGAAAGG	    0.964644	-49
TCACATTTTTAGCAGACAAGGAGTGACGG  	3	49	1	AGCAGCAAGG	    0.993621	-19
     TCGGATGCAGGCAGGGGAAGTGTCTG	4	6	1	TGCAGCAGGG	    0.997253	-60
CTCGTATCAGACCAGGCAGGGTAAACAGACA	4	31	0	ACCAGCAGGG	     0.99071	-35
CAATCTGGCGAGCAGACAAGCACACTCCCAT	5	58	0	AGCAGCAAGC	    0.990606	-187
CTTACGCGGTTGCAAACAGGCGAGGAATGCT	5	115	1	TGCAACAGGC	    0.985809	-130
TCTGCCTGAGTCCAGAAAGGCTTAATGCATC	5	149	0	TCCAGAAGGC	    0.985603	-96
GGCAGAGATTTGTAACAAAGGAAACGAACTG	5	174	1	TGTAAAAAGG	    0.779037	-71
   ACGCAGCAGCGACAAGGCGCAAAAATCA	5	227	0	AGCGAAAGGC	    0.927503	-18
          ***** *****

Masking position 10
Map Score:   17.1672

Number of sites scoring better than the average of aligned sites = 1427
Number in coding regions = 1319
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 2

TAAAAAATCCTCTACTGCAGTAACTAACGA	1	16	1	TCTACTGCAG	    0.946293	-32
TCACTCCTTGTCTGCTAAAAATGTGACTCA	3	45	0	TCTGCTAAAA	    0.827045	-23
          TCGGATGCAGGCAGGGGAAG	4	1	1	TCGGATGCAG	    0.971685	-65
CCCTGCCTGGTCTGATACGAGAATACGCAT	4	41	1	TCTGATACGA	    0.938682	-25
CATCTGCATATGTGCTGCAACAATCTGGCG	5	79	0	TGTGCTGCAA	    0.955801	-166
ATGACCTTACGCGGTTGCAAACAGGCGAGG	5	110	1	GCGGTTGCAA	    0.902752	-135
GAGGAATGCTGCTGATGCATTAAGCCTTTC	5	136	1	GCTGATGCAT	    0.962573	-109
GCAAAAATCATCTGCTACGGTGAAAATTAG	5	207	0	TCTGCTACGG	     0.97983	-38
GCGCCTTGTCGCTGCTGCGT          	5	235	1	GCTGCTGCGT	    0.981907	-10
          **********

Masking position 6
Map Score:   8.71473

Number of sites scoring better than the average of aligned sites = 4030
Number in coding regions = 3813
Number in noncoding regions = 217
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 3

ATCCTCTACTGCAGTAACTAACGAGTAGCAAA	1	22	1	GCATAACTAC	    0.902875	-26
TTGGCCTTTGGCAACGATTATCCTATGAGATT	2	36	0	GCACGATTTC	    0.964631	-39
GACGCAGCGCGCATTATTCTACGTGAAAACGG	5	24	0	GCATATTCAC	    0.963959	-221
CATATGTGCTGCAACAATCTGGCGAGCAGACA	5	71	0	GCACAATCGG	    0.940408	-174
TAATGCATCAGCAGCATTCCTCGCCTGTTTGC	5	126	0	GCACATTCTC	    0.987109	-119
GAAACGAACTGCACTAATTTTCACCGTAGCAG	5	194	1	GCATAATTTC	    0.982544	-51
GCGACAAGGCGCAAAAATCATCTGCTACGGTG	5	215	0	GCAAAATCTC	    0.978523	-30
          *** ***** **

Masking position 3
Map Score:   3.28238

Number of sites scoring better than the average of aligned sites = 820
Number in coding regions = 763
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 4

TGAGATTGGGGCAATTACGCGCCCTCGTCA	2	13	0	GCAATTACGC	     0.96119	-62
CTGGCTCGTTGGCCTTTGGCAACGATTATC	2	46	0	GGCCTTTGGC	    0.958214	-29
ATGCTGGGCCGCCATCCGGCAAAGGGTTTT	3	15	1	GCCATCCGGC	    0.935185	-53
        TCGGATGCAGGCAGGGGAAGTG	4	3	1	GGATGCAGGC	    0.849422	-63
ATGTGCTGCAACAATCTGGCGAGCAGACAA	5	70	0	ACAATCTGGC	    0.819362	-175
GATTGTTGCAGCACATATGCAGATGAATGA	5	84	1	GCACATATGC	    0.730087	-161
GCAGATGAATGACCTTACGCGGTTGCAAAC	5	102	1	GACCTTACGC	    0.853555	-143
TTACGCGGTTGCAAACAGGCGAGGAATGCT	5	116	1	GCAAACAGGC	    0.721318	-129
AAGCCTTTCTGGACTCAGGCAGAGATTTGT	5	157	1	GGACTCAGGC	    0.987813	-88
TGATTTTTGCGCCTTGTCGCTGCTGCGT  	5	227	1	GCCTTGTCGC	    0.776226	-18
          **********

Masking position 10
Map Score:   5.57197

Number of sites scoring better than the average of aligned sites = 4428
Number in coding regions = 4144
Number in noncoding regions = 284
Number of orfs with sites within 600 bp upstream = 254
Fraction of orfs with sites within 600 bp upstream = 0.0407967


Motif number 5

          **********

No masking
Map Score:   -3.03101e-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:   -3.03101e-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:   -3.03101e-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