AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i331_not_clear6_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	b1775	26	putative transport protein
#2	b1776	300	putative oxidoreductase

Motif number 1

AGATCACAATTACGCAGAAAATGGCTGGGTC	2	166	0	TACCAGAAAA	    0.970666	-135
TGCGTTTTACAACTCAGATCACAATTACGCA	2	181	0	AACCAGATCA	    0.996806	-120
TGAGTTGTAAAACGCAGATCATTATCTGTGT	2	196	1	AACCAGATCA	    0.996829	-105
AAATCTGTAAAACACAGATAATGATCTGCGT	2	207	0	AACCAGATAA	    0.995104	-94
CCATCATACTTACCCACATGATTTTTGAGGT	2	245	0	TACCACATGA	    0.974775	-56
AGCAAAACTAAACACAGAGGATGACGCA   	2	283	1	AACCAGAGGA	    0.992952	-18
          *** *******

Masking position 6
Map Score:   11.2228

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 54
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

        TATCTCGCCATGACCTGGCTAAGTCCC	2	3	1	TCTCAACCTG	    0.984123	-298
CCTGGCTAAGTCCCAGTCCGATCTCTTGCCGTCCC	2	24	1	TCCCCATCTC	    0.994812	-277
TCTCTTGCCGTCCCGTTCACACCTGAATGACTTCT	2	45	1	TCCCCACCTG	     0.99863	-256
TGAACTTAAGTCTCAGACCTATTTGGCCGGTAATC	2	82	1	TCTCCATTTG	    0.992537	-219
TGGCCGGTAATCCCTCTCGAATTTGCTCTTTTTGC	2	105	1	TCCCCATTTG	    0.996674	-196
          ****   *  *****

Masking position 11
Map Score:   3.92649

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 41
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

GACCTGGCTAAGTCCCAGTCCGATCTCTTG	2	22	1	AGTCCCAGTC	    0.997171	-279
GATCTCTTGCCGTCCCGTTCACACCTGAAT	2	43	1	CGTCCCGTTC	    0.970455	-258
CCTGAACTTAAGTCTCAGACCTATTTGGCC	2	80	1	AGTCTCAGAC	    0.974559	-221
TTCGAGAGGGATTACCGGCCAAATAGGTCT	2	96	0	ATTACCGGCC	    0.955778	-205
AACCTGTAACAGACCCAGCCATTTTCTGCG	2	155	1	AGACCCAGCC	    0.994001	-146
          **********

Masking position 6
Map Score:   3.23755

Number of sites scoring better than the average of aligned sites = 467
Number in coding regions = 427
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 4

TCCATCAACCTGTAACAGACCCAGCCATTT	2	149	1	TGTAACAGAC	    0.987959	-152
TGATCTGAGTTGTAAAACGCAGATCATTAT	2	191	1	TGTAAAACGC	    0.993421	-110
ACATTAAATCTGTAAAACACAGATAATGAT	2	213	0	TGTAAAACAC	    0.994464	-88
          **********

Masking position 5
Map Score:   1.81081

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 22
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 5

GCCCCGCCTTCCATCAACCTGTAACAGACC	2	140	1	CCATCAACCT	    0.993701	-161
GCTTAGATGGCCATCATACTTACCCACATG	2	256	0	CCATCATACT	    0.990292	-45
         TGCGTCATCCTCTGTGTTTAG	2	290	0	GCGTCATCCT	     0.99219	-11
          **********

Masking position 6
Map Score:   1.02553

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 57
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 6

      CCACTCTCCTGAAGGAACGTTATC	1	5	1	TCTCCTGAAG	    0.994243	-22
CCCAGTCCGATCTCTTGCCGTCCCGTTCAC	2	35	1	TCTCTTGCCG	    0.990257	-266
CTGAATGACTTCTCCTGAACTTAAGTCTCA	2	67	1	TCTCCTGAAC	    0.984747	-234
AATGGCTGGGTCTGTTACAGGTTGATGGAA	2	148	0	TCTGTTACAG	    0.942099	-153
          **********

Masking position 6
Map Score:   1.26734

Number of sites scoring better than the average of aligned sites = 289
Number in coding regions = 253
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 7

          **********

No masking
Map Score:   -5.58897e-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 8

          **********

No masking
Map Score:   -5.58897e-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 9

          **********

No masking
Map Score:   -5.58897e-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