AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i289_synecho_ctra_300.orf -o289_synecho_ctra_300.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	RCY23271	201	Synechocystis
#2	RCY11277	49	Synechocystis
#3	RCY18066	196	Synechocystis

Motif number 1

GCTTTTCCAAAGATTTTCTCGGACTAGGTT	1	24	0	AGATTTTCTC	    0.944619	-178
AATGGTACGACGCTTTTCCAAAGATTTTCT	1	35	0	CGCTTTTCCA	    0.978359	-167
GAATTCCGATAGATTTTTCAATGGTACGAC	1	54	0	AGATTTTTCA	    0.956564	-148
TTTGCAAAGGAGAATTTTCACAAAACTTCT	1	85	1	AGAATTTTCA	    0.797848	-117
GTTGAAAGTGAATTTTTCCCTGGGCAGTCA	1	123	1	AATTTTTCCC	    0.949302	-79
GAGTAAAGAAAGTTTTACCCACAAAGTTTC	3	14	1	AGTTTTACCC	     0.96771	-183
TTTTGGCAATCAATTTACCAGAAACTTTGT	3	34	0	CAATTTACCA	    0.820338	-163
GATTGCCAAAAGCTTTTCCCTGCTTTTTAT	3	53	1	AGCTTTTCCC	    0.992165	-144
          **********

Masking position 5
Map Score:   7.08876

Number of sites scoring better than the average of aligned sites = 2104
Number in coding regions = 1828
Number in noncoding regions = 276
Number of orfs with sites within 600 bp upstream = 292
Fraction of orfs with sites within 600 bp upstream = 0.0469001


Motif number 2

          AAACTTGGTCTTTAACCTAG	1	1	1	AAACTTGGTC	    0.871053	-201
ACTTGGTCTTTAACCTAGTCCGAGAAAATC	1	13	1	TAACCTAGTC	    0.942999	-189
ATTCACTTTCAACCCCGGTCAAGAAGTTTT	1	106	0	AACCCCGGTC	    0.971163	-96
AAGTGAATTTTTCCCTGGGCAGTCAGTCTA	1	128	1	TTCCCTGGGC	    0.974153	-74
CTCTCTATCACACCCTAGACTGACTGCCCA	1	143	0	CACCCTAGAC	    0.971882	-59
 AATATCTGCTCCACTGGTCGAGAACTAGA	2	10	1	TCCACTGGTC	    0.932891	-40
AATACACAGTCACCTTGGGCACATCGGGTG	3	112	1	CACCTTGGGC	    0.981852	-85
TTATCCAAATCCCCCTAGCCTGCGGCGCTA	3	167	1	CCCCCTAGCC	    0.971812	-30
          **********

Masking position 8
Map Score:   6.27765

Number of sites scoring better than the average of aligned sites = 2963
Number in coding regions = 2717
Number in noncoding regions = 246
Number of orfs with sites within 600 bp upstream = 259
Fraction of orfs with sites within 600 bp upstream = 0.0415997


Motif number 3

TAGTCCGAGAAAATCTTTGGAAAAGCGTCGT	1	28	1	AAACTTTGGA	    0.905312	-174
CCCCGGTCAAGAAGTTTTGTGAAAATTCTCC	1	93	0	GAATTTTGTG	    0.933883	-109
      GTTGGAATGATTGGGGACAGTCTAG	2	35	0	GAAGATTGGG	    0.979415	-15
CAATTTACCAGAAACTTTGTGGGTAAAACTT	3	23	0	GAACTTTGTG	    0.989165	-174
AAAGCAGGGAAAAGCTTTTGGCAATCAATTT	3	48	0	AAACTTTTGG	    0.905312	-149
CATCAATGGTGAACCAATGGGATTCGCAAAT	3	84	1	GAACAATGGG	    0.977315	-113
      AGGGGAAGCATAGCGCCGCAGGCTA	3	182	0	GAACATAGCG	    0.924446	-15
          *** *******

Masking position 3
Map Score:   3.36893

Number of sites scoring better than the average of aligned sites = 953
Number in coding regions = 861
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 4

GAAAAATCTATCGGAATTCCTTTGCAAAGG	1	65	1	TCGGAATTCC	    0.985673	-137
ACTGTGTATTTGCGAATCCCATTGGTTCAC	3	92	0	TGCGAATCCC	    0.994685	-105
TAATTTGTTATCCAAATCCCCCTAGCCTGC	3	160	1	TCCAAATCCC	    0.992155	-37
          **********

Masking position 5
Map Score:   0.0372895

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 52
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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