AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iaraC_ctra_opreg_300.orf -g0.413 -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 =  	0.413
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	CT663	300	hypothetical protein
#2	CT665	43	hypothetical protein
#3	CT666	26	hypothetical protein
#4	CT670	22	hypothetical protein

Motif number 1

GCACGAACGACTCGTTCTTTTGATTTCTAAA	1	70	0	CTCGTTCTTT	    0.974739	-231
GTCGTTCGTGCCCGATTTTTTTCTAAAATTC	1	90	1	CCCGATTTTT	    0.964195	-211
TCTCTTTCATCCCTTTCAATTTAAAGTACAA	1	123	0	CCCTTTCATT	    0.986706	-178
GATAGAGGAGCCTTTTCTGTTTTCTCTTTCA	1	145	0	CCTTTTCTTT	    0.978967	-156
AATACTCCCTCCCTAGCTATTGGAATGGGCC	1	239	0	CCCTAGCTTT	    0.987142	-62
     AGATACCCTCTCTTTTACCGTTTACA	3	11	0	CCCTCTCTTT	    0.994365	-16
          ******** **

Masking position 10
Map Score:   5.93758

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 104
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 2

TGAATGAGTTGATTTGTGCCGGGAAAATGT	1	25	1	GATTTGTGCC	    0.988403	-276
TCAAAAGAACGAGTCGTTCGTGCCCGATTT	1	78	1	GAGTCGTTCG	    0.974408	-223
GTTCGTGCCCGATTTTTTTCTAAAATTCTT	1	93	1	GATTTTTTTC	    0.911342	-208
ACCTTATGCTGAGTTATGCCAATACCTACT	1	203	0	GAGTTATGCC	    0.988585	-98
GCTAGGGAGGGAGTATTTCGGACCCAGAGC	1	253	1	GAGTATTTCG	    0.943207	-48
         AGATTTATTCCTACCTGGAAG	2	33	0	GATTTATTCC	    0.985174	-11
          **********

Masking position 4
Map Score:   4.37672

Number of sites scoring better than the average of aligned sites = 129
Number in coding regions = 129
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 3

TTAAATTGAAAGGGATGAAAGAGAAAACAG	1	130	1	AGGGATGAAA	    0.969484	-171
TCTCATCTCGATAGAGGAGCCTTTTCTGTT	1	155	0	ATAGAGGAGC	    0.957759	-146
GCTCCTCTATCGAGATGAGAAATCGTTTTT	1	165	1	CGAGATGAGA	    0.969298	-136
TCCAATAGCTAGGGAGGGAGTATTTCGGAC	1	246	1	AGGGAGGGAG	    0.960464	-55
GCTCTCAGTTAGAGATGAGCACGTGAATAC	1	281	1	AGAGATGAGC	    0.989385	-20
AAACGGTAAAAGAGAGGGTATCT       	3	14	1	AGAGAGGGTA	    0.965905	-13
          **********

Masking position 5
Map Score:   2.93392

Number of sites scoring better than the average of aligned sites = 299
Number in coding regions = 299
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 4

GTTGATTTGTGCCGGGAAAATGTGTTTTGG	1	32	1	GCCGGGAAAA	    0.995381	-269
ATTTATTCCTACCTGGAAGAATTAAATAAA	2	22	0	ACCTGGAAGA	    0.981418	-22
      TGTAAACGGTAAAAGAGAGGGTAT	3	5	1	AACGGTAAAA	    0.927823	-22
          GTCTGGAAAATAGTAGGATT	4	1	1	GTCTGGAAAA	    0.980794	-22
          **********

Masking position 7
Map Score:   1.06039

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 47
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 5

ACGAGAGCTGCTCTGAATGAGTTGATTTGT	1	12	1	CTCTGAATGA	    0.973194	-289
AGGCTCCTCTATCGAGATGAGAAATCGTTT	1	163	1	ATCGAGATGA	    0.933926	-138
ACGTGCTCATCTCTAACTGAGAGCTCTGGG	1	275	0	CTCTAACTGA	    0.989663	-26
TTAAATAAACCTCGAACTGC          	2	1	0	CTCGAACTGC	    0.988619	-43
          **********

Masking position 8
Map Score:   0.307212

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 32
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 6

          **********

No masking
Map Score:   2.44017e-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:   2.44017e-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:   2.44017e-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