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

Motif number 1

GCACGAACGACTCGTTCTTTTGATTTCTAAA	1	70	0	CTCGTTCTTT	    0.975858	-231
GTCGTTCGTGCCCGATTTTTTTCTAAAATTC	1	90	1	CCCGATTTTT	    0.965764	-211
TCTCTTTCATCCCTTTCAATTTAAAGTACAA	1	123	0	CCCTTTCATT	    0.987302	-178
GATAGAGGAGCCTTTTCTGTTTTCTCTTTCA	1	145	0	CCTTTTCTTT	    0.979902	-156
AATACTCCCTCCCTAGCTATTGGAATGGGCC	1	239	0	CCCTAGCTTT	    0.987718	-62
     AGATACCCTCTCTTTTACCGTTTACA	3	11	0	CCCTCTCTTT	     0.99462	-16
          ******** **

Masking position 10
Map Score:   6.1517

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

AGAGCTGCTCTGAATGAGTTGATTTGTGCCGGG	1	15	1	TGAAGGTGAT	    0.894958	-286
ATTTGTGCCGGGAAAATGTGTTTTGGGAGATGT	1	36	1	GGAAAGTTTT	     0.98569	-265
AATGTGTTTTGGGAGATGTCTTTAGAAATCAAA	1	50	1	GGGAAGTTTT	    0.954956	-251
AGAAATCAAAAGAACGAGTCGTTCGTGCCCGAT	1	73	1	AGAAGGTGTT	    0.988668	-228
TATCGAGATGAGAAATCGTTTTTCTTTTTAAAG	1	172	1	AGAATGTTTT	    0.959875	-129
CAATAGCTAGGGAGGGAGTATTTCGGACCCAGA	1	248	1	GGAGGGTTTT	    0.992765	-53
AAACGGTAAAAGAGAGGGTATCT          	3	14	1	AGAGGGTTCT	    0.966416	-13
          **** * ** ***

Masking position 9
Map Score:   3.38486

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

ACATTTTCCCGGCACAAATCAACTCATTCA	1	25	0	GGCACAAATC	    0.993372	-276
AAGAATTTTAGAAAAAAATCGGGCACGAAC	1	93	0	GAAAAAAATC	    0.942661	-208
AGTAGGTATTGGCATAACTCAGCATAAGGT	1	203	1	GGCATAACTC	     0.99041	-98
CTTCCAGGTAGGAATAAATCT         	2	33	1	GGAATAAATC	    0.991278	-11
          **********

Masking position 6
Map Score:   3.36175

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	    0.979264	-295
TCATCTCGATAGAGGAGCCTTTTCTGTTTT	1	153	0	AGAGGAGCCT	    0.983883	-148
TCCTCTATCGAGATGAGAAATCGTTTTTCT	1	167	1	AGATGAGAAA	    0.818393	-134
GCATAAGGTCAGCGGGGCCCATTCCAATAG	1	224	1	AGCGGGGCCC	    0.989752	-77
TCTCAGTTAGAGATGAGCACGTGAATAC  	1	283	1	AGATGAGCAC	    0.985835	-18
ACGGTAAAAGAGAGGGTATCT         	3	16	1	AGAGGGTATC	    0.899255	-11
          **********

Masking position 1
Map Score:   2.3695

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

          **********

No masking
Map Score:   2.36911e-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:   2.36911e-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:   2.36911e-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