AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i105_Manganese_Transport_synecho_reg_100.orf -o105_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	RCY20071	98	Synechocystis
#2	RCY34291	164	Synechocystis

Motif number 1

     AAACAACTTTGTGTTTTGACACGTTGA	1	6	1	ACTTGGTTTT	    0.970815	-93
GTGTTTTGACACGTTGAGTTTTTCTGTAATCA	1	21	1	ACTTGGTTTT	    0.970815	-78
CTGGACTTAATCTTGACGATTTACCACTACCT	1	54	1	TCTGAGATTT	    0.970811	-45
ACTGGTAAGCTCGTGGGCTTTTTCTGA     	2	6	0	TCTGGCTTTT	    0.991822	-159
GAGTTAAAATTTCTTAACTTTTACCAACTGGT	2	32	0	TTTTACTTTT	    0.915167	-133
ATCTCATTTTTCATTATCTTCTCATAATTGCA	2	75	0	TCTTACTTCT	    0.982443	-90
TAATGGTCTTTCATGATCATCTCATTTTTCAT	2	93	0	TCTGACATCT	    0.965713	-72
          ** *** *****

Masking position 4
Map Score:   5.94677

Number of sites scoring better than the average of aligned sites = 447
Number in coding regions = 381
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 2

TCTTGACGATTTACCACTACCTAAAATCTG	1	64	1	TTACCACTAC	    0.982179	-35
AGTTAAGAAATTTTAACTCCCCGTTTTCAC	2	45	1	TTTTAACTCC	    0.951711	-120
TAACTCCCCGTTTTCACTGCAATTATGAGA	2	58	1	TTTTCACTGC	    0.990371	-107
ATCATCTCATTTTTCATTATCTTCTCATAA	2	80	0	TTTTCATTAT	    0.937154	-85
TGAAAGACCATTATCACTATGGCAACATCA	2	112	1	TTATCACTAT	    0.981916	-53
          **********

Masking position 6
Map Score:   3.33548

Number of sites scoring better than the average of aligned sites = 261
Number in coding regions = 223
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

CAAGATTAAGTCCAGTTGATTACAGAAAAA	1	39	0	TCCAGTTGAT	    0.926867	-60
CCACGAGCTTACCAGTTGGTAAAAGTTAAG	2	22	1	ACCAGTTGGT	     0.62181	-143
CACTGCAATTATGAGAAGATAATGAAAAAT	2	72	1	ATGAGAAGAT	    0.958341	-93
ATAATGAAAAATGAGATGATCATGAAAGAC	2	90	1	ATGAGATGAT	     0.97052	-75
CTCCCCGGGAAGCAAATGATGTTGCCATAG	2	128	0	AGCAAATGAT	    0.788398	-37
          **********

Masking position 4
Map Score:   1.3844

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 292
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 4

AGTTGATTACAGAAAAACTCAACGTGTCAA	1	26	0	AGAAAAACTC	    0.987438	-73
TAAATCGTCAAGATTAAGTCCAGTTGATTA	1	47	0	AGATTAAGTC	    0.978855	-52
        TCAGAAAAAGCCCACGAGCTTA	2	3	1	AGAAAAAGCC	    0.991827	-162
          **********

Masking position 6
Map Score:   0.523319

Number of sites scoring better than the average of aligned sites = 71
Number in coding regions = 61
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 5

          **********

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 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