AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i346_weak7_synecho_reg_300.orf -o346_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY15045	300	Synechocystis
#2	RCY08865	31	Synechocystis

Motif number 1

TTCGATTATTCTTTGTACTGAATACAAAGTG	1	12	1	CTTTGACTGA	    0.987336	-289
GTGATTTTGACTTACCACTGGCTGTTTTCCT	1	84	0	CTTACACTGG	    0.976848	-217
AAATCAAGAGCTCTGTCCTGGGTTCACGGTG	1	119	0	CTCTGCCTGG	    0.992806	-182
GAAAAAATCAGTTTGGCTTGGCAGGTAACCC	1	199	0	GTTTGCTTGG	    0.930381	-102
ACGACATCCCCTTAGGTATGGTGAAAAAATC	1	221	0	CTTAGTATGG	    0.930732	-80
  GTTAGATCCTTTGACCTTAGCCGGAATAT	1	282	0	CTTTGCCTTA	    0.940831	-19
 ACAATCCTCCTTAGTACTGGCAACAATGGC	2	12	0	CTTAGACTGG	    0.995464	-20
          ***** *****

Masking position 9
Map Score:   6.85442

Number of sites scoring better than the average of aligned sites = 1208
Number in coding regions = 1112
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 104
Fraction of orfs with sites within 600 bp upstream = 0.0167041


Motif number 2

TCCTAAATGGAGAAAATTTGACTGATGTCCCGC	1	55	0	AGAATTTGCT	    0.883664	-246
CACGGTGTCGAGTGATTTTGACTTACCACTGGC	1	93	0	AGTATTTGCT	    0.980733	-208
AACCCAGGACAGAGCTCTTGATTTTTCACAGCA	1	126	1	AGACCTTGTT	    0.929148	-175
TTGATTTTTCACAGCATTTGCCCGTTTTATCCT	1	143	1	ACACTTTGCC	    0.982025	-158
ATGGTGAAAAAATCAGTTTGGCTTGGCAGGTAA	1	202	0	AATATTTGCT	    0.933729	-99
       GTTAGATCCTTTGACCTTAGCCGGAA	1	285	0	AGACTTTGCC	    0.994812	-16
          *** * **** **

Masking position 8
Map Score:   3.50532

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 186
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

ACTGATGTCCCGCCGATGACCGATCCACTTT	1	37	0	CGCCGTGACC	    0.993998	-264
GAGAAAATTTGACTGATGTCCCGCCGATGAC	1	48	0	GACTGTGTCC	    0.979158	-253
ACTTACCACTGGCTGTTTTCCTAAATGGAGA	1	75	0	GGCTGTTTCC	    0.967169	-226
AATCACTCGACACCGTGAACCCAGGACAGAG	1	109	1	CACCGGAACC	     0.96224	-192
AGTTTGGCTTGGCAGGTAACCCATCTATGGG	1	190	0	GGCAGTAACC	    0.985129	-111
TTAAAACCATGGACGACATCCCCTTAGGTAT	1	233	0	GGACGCATCC	    0.509512	-68
          ***** *****

Masking position 5
Map Score:   2.47163

Number of sites scoring better than the average of aligned sites = 1095
Number in coding regions = 1029
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 4

TGTACTGAATACAAAGTGGATCGGTCATCG	1	25	1	ACAAAGTGGA	    0.975016	-276
TGGCTGTTTTCCTAAATGGAGAAAATTTGA	1	67	0	CCTAAATGGA	    0.971113	-234
TTTCACCATACCTAAGGGGATGTCGTCCAT	1	226	1	CCTAAGGGGA	     0.99675	-75
TATTTGATGTACTAATGGAAGTTAAAACCA	1	255	0	ACTAATGGAA	    0.933222	-46
TGTTGCCAGTACTAAGGAGGATTGT     	2	17	1	ACTAAGGAGG	    0.959987	-15
          **********

Masking position 5
Map Score:   2.38483

Number of sites scoring better than the average of aligned sites = 536
Number in coding regions = 459
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 5

TTTCCTAAATGGAGAAAATTTGACTGATGT	1	60	0	GGAGAAAATT	    0.957271	-241
GGGCAAATGCTGTGAAAAATCAAGAGCTCT	1	136	0	TGTGAAAAAT	    0.972969	-165
CCCATCTATGGGTTAAAAAAGGATTCAGGA	1	172	0	GGTTAAAAAA	    0.972946	-129
CCTTAGGTATGGTGAAAAAATCAGTTTGGC	1	213	0	GGTGAAAAAA	    0.993055	-88
          **********

Masking position 5
Map Score:   2.51984

Number of sites scoring better than the average of aligned sites = 309
Number in coding regions = 249
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 6

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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