AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i262_synecho_ctra_100.orf -o262_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -x5 -e 
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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY35276	173	Synechocystis
#2	RCT00511	62	Chlamydia_trachomatis
#3	RCT00512	300	Chlamydia_trachomatis

Motif number 1

GGCAATGCTGACCCCTAGGCCTACCAAAATT	1	99	0	ACCCCTAGCC	    0.948032	-75
TTGCCAAGGCGGCCCCATCCCCATAAAACTC	1	125	1	GGCCCCACCC	    0.997379	-49
GGGTTGGTCGGGACCTAACTCTTGGT     	2	47	1	GGACCTACTC	    0.983939	-16
TTTTCCGTTAGGCACAAGCTCATTACGTTTT	3	69	0	GGCACAACTC	    0.968795	-232
GATTCAGGATGCCCCTACCCCTAGAGCATGG	3	118	1	GCCCCTACCC	    0.998628	-183
AAGCAAAACAGGCCTAACCTCCCCATGCTCT	3	140	0	GGCCTAACTC	    0.973901	-161
AAGCCTTTCCGCCCATATCCCTGTTCTCTAC	3	206	0	GCCCATACCC	    0.991255	-95
          ******* ***

Masking position 7
Map Score:   8.83112

Number of sites scoring better than the average of aligned sites = 1127
Number in coding regions = 1056
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 2

CAGTCCAGGCGTTCATCCTTTCCCTACTCC	1	17	0	GTTCATCCTT	     0.92618	-157
ACCAAAATTTGTTAAGCTTTGTATCTAATT	1	78	0	GTTAAGCTTT	    0.846779	-96
AACAAATTTTGGTAGGCCTAGGGGTCAGCA	1	95	1	GGTAGGCCTA	    0.938587	-79
TAGGCCTAGGGGTCAGCATTGCCAAGGCGG	1	107	1	GGTCAGCATT	    0.955966	-67
TATGGGGATGGGGCCGCCTTGGCAATGCTG	1	120	0	GGGCCGCCTT	    0.985142	-54
        ATGGGAAACGTTTTAAGAATAT	1	162	0	GGGAAACGTT	     0.80671	-12
CTAGGGGTAGGGGCATCCTGAATCGACTAC	3	112	0	GGGCATCCTG	    0.965408	-189
GCATGGGGAGGTTAGGCCTGTTTTGCTTTT	3	143	1	GTTAGGCCTG	    0.931798	-158
TCCTTCTAAAGGGAAGCCTTTCCGCCCATA	3	220	0	GGGAAGCCTT	    0.994061	-81
          **********

Masking position 9
Map Score:   7.88633

Number of sites scoring better than the average of aligned sites = 1103
Number in coding regions = 1013
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 104
Fraction of orfs with sites within 600 bp upstream = 0.0167041


Motif number 3

CACAAGCTCATTACGTTTTTCAATAAGACTTT	3	56	0	TTACTTTTCA	    0.961758	-245
TATCATGATTTTCCGTTAGGCACAAGCTCATT	3	76	0	TTCCTTAGCA	    0.985845	-225
AGGCCTGTTTTGCTTTTTGTAAAAATACTTTT	3	156	1	TGCTTTTTAA	    0.790474	-145
GCGGAAAGGCTTCCCTTTAGAAGGAGGCTGGT	3	225	1	TTCCTTTGAA	    0.967104	-76
AAACTGATTCTTCTTTTAATCACCAGCCTCCT	3	246	0	TTCTTTATCA	     0.94881	-55
AGAATCAGTTTGCCATTAAGCAACTGAAAAAA	3	267	1	TGCCTTAGCA	    0.949276	-34
  ACTTATCCTTACTTTTTTCAGTTGCTTAAT	3	281	0	TTACTTTTCA	    0.961554	-20
          **** *** ***

Masking position 12
Map Score:   4.35923

Number of sites scoring better than the average of aligned sites = 432
Number in coding regions = 368
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

        AGAAATGATTTTCTTGCTCGACA	3	3	1	AATGATTTTC	    0.965073	-298
TGCTCGACATAGAAGTTTTTCATTTGAATTC	3	25	1	AAAGTTTTTC	     0.95737	-276
CACAAGCTCATTACGTTTTTCAATAAGACTT	3	57	0	TACGTTTTTC	    0.988738	-244
CTACATGCTATCATGATTTTCCGTTAGGCAC	3	85	0	TATGATTTTC	    0.975376	-216
  ACTTATCCTTACTTTTTTCAGTTGCTTAA	3	282	0	TACTTTTTTC	    0.943896	-19
          * *********

Masking position 7
Map Score:   2.1299

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 122
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 5

    AATGGCGGAGTAGGGAAAGGATGAAC	1	7	1	GGAGTAGGGA	      0.9905	-167
GAAAATCATGATAGCATGTAGTCGATTCAG	3	95	1	ATAGCATGTA	    0.777427	-206
CCATGCTCTAGGGGTAGGGGCATCCTGAAT	3	119	0	GGGGTAGGGG	     0.96933	-182
CCCTACCCCTAGAGCATGGGGAGGTTAGGC	3	130	1	AGAGCATGGG	    0.982268	-171
CAAGGAAGTGAGAGTAGGTAGAGAACAGGG	3	189	1	AGAGTAGGTA	    0.977008	-112
GAGTAGGTAGAGAACAGGGATATGGGCGGA	3	200	1	AGAACAGGGA	    0.968346	-101
          **********

Masking position 6
Map Score:   3.50875

Number of sites scoring better than the average of aligned sites = 921
Number in coding regions = 816
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 6

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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