AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i144_Electron_Transport_1_synecho_reg_100.orf -o144_synecho_100.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	RCY15025	300	Synechocystis
#2	RCY34156	134	Synechocystis

Motif number 1

GCAGACTATTCCCCCAAAGCTCCGTGCGATAATGG	1	18	0	CCCCCAGCGT	    0.998782	-283
TTGCTAATCCCTCCCTAATCCTGGTTCTCAAAACT	1	57	0	CTCCCATCGT	    0.963431	-244
GGGATTTCTACCCCTGCAGCAACGAATGTTTTCTG	1	92	0	CCCCTAGCGA	    0.998656	-209
GGGTAGAAATCCCCTTTATCAGCGAAGACAATGAT	1	114	1	CCCCTATCGA	    0.996176	-187
GTAAAGCAATTCTCCAGAGCGGGGTCAAGCTCCAG	1	226	0	TCTCCAGCGT	    0.939408	-75
AAATTACAATCCCCTACAGGGTAAAGCAATTCTCC	1	246	0	CCCCTAGGAA	    0.959605	-55
    AGCAAACCTCTATCTCTCGGAAAACAACAAA	1	280	0	CCTCTCTCGA	    0.931682	-21
AGCTAGCCATCCCCCTAAGCACAGAAAGTTAAAGA	2	13	0	CCCCCAGCGA	    0.999355	-122
CTAATGACCTCCCCCATGGGCCCGACCGCCAGAGA	2	55	1	CCCCCGGGGA	    0.992154	-80
          *****  ***   **

Masking position 4
Map Score:   16.0107

Number of sites scoring better than the average of aligned sites = 1035
Number in coding regions = 951
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

GATAAATTTGTTCTATGGCAATCATTGTCTTCG	1	136	0	TTCTTGCATC	    0.995615	-165
TGCCGTCTCCTTCTGTGCCTGTTTTTATGATAA	1	164	0	TTCTTGCGTT	     0.97886	-137
TTCTTCAGAGTTCTTTAACAATCTTGCCGTCTC	1	188	0	TTCTTACATC	    0.990986	-113
         TTTCTTTAACTTTCTGTGCTTAGG	2	2	1	TTCTTACTTC	    0.977534	-133
TTTGCCAAAAATCTCTGGCGGTCGGGCCCATGG	2	68	0	ATCTTGCGTC	    0.986689	-67
ATTCTAGAAATTCAGCAACGATCCAGCGATTAA	2	101	1	TTCACACATC	    0.936372	-34
GATCCAGCGATTAATTGTCAGTCCT        	2	120	1	TTAATGCGTC	    0.952712	-15
          **** ** * ***

Masking position 2
Map Score:   6.08162

Number of sites scoring better than the average of aligned sites = 374
Number in coding regions = 331
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 3

TGCTGCAGGGGTAGAAATCCCCTTTATCAGC	1	106	1	GTAGAATCCC	     0.88257	-195
TATGGCAATCATTGTCTTCGCTGATAAAGGG	1	125	0	ATTGTCTCGC	    0.957144	-176
CTTTAACAATCTTGCCGTCTCCTTCTGTGCC	1	178	0	CTTGCCTCTC	    0.980826	-123
TTGGCTGGAGCTTGACCCCGCTCTGGAGAAT	1	222	1	CTTGACCCGC	    0.964669	-79
AACAACAAAAATTACAATCCCCTACAGGGTA	1	258	0	ATTACATCCC	    0.857289	-43
GGTCATTAAGCTAGCCATCCCCCTAAGCACA	2	25	0	CTAGCCTCCC	    0.991463	-110
TTAATGACCTAATGACCTCCCCCATGGGCCC	2	47	1	AATGACTCCC	    0.957292	-88
          ****** ****

Masking position 9
Map Score:   1.5453

Number of sites scoring better than the average of aligned sites = 1044
Number in coding regions = 931
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 4

ATTTGTTCTATGGCAATCATTGTCTTCGCT	1	134	0	TGGCAATCAT	    0.961934	-167
CAGAAGGAGACGGCAAGATTGTTAAAGAAC	1	182	1	CGGCAAGATT	     0.98508	-119
CTTAGGGGGATGGCTAGCTTAATGACCTAA	2	29	1	TGGCTAGCTT	    0.983765	-106
CAGAGATTTTTGGCAAAATTCTAGAAATTC	2	84	1	TGGCAAAATT	    0.976351	-51
          **********

Masking position 6
Map Score:   1.03812

Number of sites scoring better than the average of aligned sites = 191
Number in coding regions = 161
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 5

GGGAGGGATTAGCAACAGAAAACATTCGTT	1	77	1	AGCAACAGAA	    0.971847	-224
CTACCCCTGCAGCAACGAATGTTTTCTGTT	1	90	0	AGCAACGAAT	    0.985577	-211
TCTCTCGGAAAACAACAAAAATTACAATCC	1	269	0	AACAACAAAA	     0.93624	-32
CATCCCCCTAAGCACAGAAAGTTAAAGAAA	2	11	0	AGCACAGAAA	    0.937123	-124
CTAGAAATTCAGCAACGATCCAGCGATTAA	2	104	1	AGCAACGATC	    0.968536	-31
          **********

Masking position 4
Map Score:   0.631336

Number of sites scoring better than the average of aligned sites = 446
Number in coding regions = 386
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 6

          **********

No masking
Map Score:   -5.09159e-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:   -5.09159e-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:   -5.09159e-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