AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iaraC_ctra_opreg_100.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

TTTAGAAATCAAAAGAACGAGTCGTTCGTGC	1	70	1	AAAAGACGAG	    0.971369	-231
GAATTTTAGAAAAAAATCGGGCACGAACGAC	1	90	0	AAAAAACGGG	    0.971369	-211
TTGTACTTTAAATTGAAAGGGATGAAAGAGA	1	123	1	AATTGAAGGG	    0.978515	-178
TGAAAGAGAAAACAGAAAAGGCTCCTCTATC	1	145	1	AACAGAAAGG	    0.960008	-156
GGCCCATTCCAATAGCTAGGGAGGGAGTATT	1	239	1	AATAGCAGGG	    0.985402	-62
TGTAAACGGTAAAAGAGAGGGTATCT     	3	11	1	AAAAGAAGGG	    0.996234	-16
          ****** ****

Masking position 2
Map Score:   5.93758

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 84
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

CCCGGCACAAATCAACTCATTCAGAGCAGCTCT	1	15	0	ATCACCTTCA	    0.879787	-286
ACATCTCCCAAAACACATTTTCCCGGCACAAAT	1	36	0	AAAACTTTCC	    0.983381	-265
TTTGATTTCTAAAGACATCTCCCAAAACACATT	1	50	0	AAAACTTCCC	    0.947947	-251
ATCGGGCACGAACGACTCGTTCTTTTGATTTCT	1	73	0	AACACCTTCT	    0.986833	-228
CTTTAAAAAGAAAAACGATTTCTCATCTCGATA	1	172	0	AAAACATTCT	    0.954019	-129
TCTGGGTCCGAAATACTCCCTCCCTAGCTATTG	1	248	0	AAAACCCTCC	    0.991587	-53
          AGATACCCTCTCTTTTACCGTTT	3	14	0	AGAACCCTCT	    0.962065	-13
          *** ** * ****

Masking position 5
Map Score:   3.17221

Number of sites scoring better than the average of aligned sites = 170
Number in coding regions = 170
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

TGAATGAGTTGATTTGTGCCGGGAAAATGT	1	25	1	GATTTGTGCC	    0.993216	-276
GTTCGTGCCCGATTTTTTTCTAAAATTCTT	1	93	1	GATTTTTTTC	    0.941385	-208
ACCTTATGCTGAGTTATGCCAATACCTACT	1	203	0	GAGTTATGCC	     0.99019	-98
         AGATTTATTCCTACCTGGAAG	2	33	0	GATTTATTCC	    0.991079	-11
          **********

Masking position 5
Map Score:   3.20879

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 44
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

CAACTCATTCAGAGCAGCTCTCGTA     	1	6	0	AGAGCAGCTC	    0.979683	-295
TCATCTCGATAGAGGAGCCTTTTCTGTTTT	1	153	0	AGAGGAGCCT	     0.98421	-148
TCCTCTATCGAGATGAGAAATCGTTTTTCT	1	167	1	AGATGAGAAA	    0.821465	-134
GCATAAGGTCAGCGGGGCCCATTCCAATAG	1	224	1	AGCGGGGCCC	     0.98996	-77
TCTCAGTTAGAGATGAGCACGTGAATAC  	1	283	1	AGATGAGCAC	    0.986123	-18
ACGGTAAAAGAGAGGGTATCT         	3	16	1	AGAGGGTATC	    0.901125	-11
          **********

Masking position 1
Map Score:   2.13992

Number of sites scoring better than the average of aligned sites = 281
Number in coding regions = 280
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

GTTGATTTGTGCCGGGAAAATGTGTTTTGG	1	32	1	GCCGGGAAAA	    0.996062	-269
ATTTATTCCTACCTGGAAGAATTAAATAAA	2	22	0	ACCTGGAAGA	    0.984125	-22
      TGTAAACGGTAAAAGAGAGGGTAT	3	5	1	AACGGTAAAA	    0.937848	-22
          GTCTGGAAAATAGTAGGATT	4	1	1	GTCTGGAAAA	     0.98359	-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 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