AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i307_mixed21_synecho_reg_100.orf -o307_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	RCY40674	143	Synechocystis
#2	RCY52862	204	Synechocystis

Motif number 1

ATTCAAATTCAGAGAAACTTGACTTATATGA	1	29	1	AGAGAACTTG	    0.988549	-115
TTAATTAAGGAAAGATGCTTGTCATTGAAAC	1	103	0	AAAGAGCTTG	    0.972203	-41
AATGAATTCAAAATAAGCTGGTGACGGGATT	2	31	1	AAATAGCTGG	    0.968584	-174
GCTCAGTGGTAGAGCAACTGATTTGTAATCA	2	78	0	AGAGCACTGA	    0.947973	-127
ATTCTGTATCAGAGATGCTGGTGTAGCTCAG	2	103	0	AGAGAGCTGG	    0.998063	-102
AGATTAACCCAGAGGGTCTGGCTAATTTTTG	2	140	1	AGAGGTCTGG	    0.985165	-65
          ***** *****

Masking position 3
Map Score:   6.64868

Number of sites scoring better than the average of aligned sites = 220
Number in coding regions = 189
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

ATGAAGTAAATAGGTTTTGGTCACCATATCCT	1	60	0	TAGGTTTGTC	    0.959931	-84
CTATTTACTTCATCTATTATTCGTGTTTCAAT	1	79	1	CATCTTTATC	    0.945617	-65
CCTTAATTAACAGGTATAGTTCCATACAAA  	1	124	1	CAGGTTAGTC	     0.99334	-20
CAGTCGGTCGCAGGTTCAAATCCCGTCACCAG	2	48	0	CAGGTCAATC	    0.987889	-157
ATCAGAGATGCTGGTGTAGCTCAGTGGTAGAG	2	95	0	CTGGTTAGTC	    0.987877	-110
CTGGGTTAATCTTCTGCTATTCTGTATCAGAG	2	120	0	CTTCTCTATC	    0.885433	-85
          ***** *** **

Masking position 5
Map Score:   1.98774

Number of sites scoring better than the average of aligned sites = 342
Number in coding regions = 298
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 3

GGAAAGATGCTTGTCATTGAAACACGAATA	1	96	0	TTGTCATTGA	    0.966447	-48
ATTCATTAACCTATCATTGATCATCGT   	2	8	0	CTATCATTGA	    0.966448	-197
GGATTTGAACCTGCGACCGACTGATTACAA	2	57	1	CTGCGACCGA	    0.979755	-148
ATCAGTTGCTCTACCACTGAGCTACACCAG	2	87	1	CTACCACTGA	    0.985927	-118
TGGCTAATTTTTGTCCCCGAAAAACTTTTT	2	158	1	TTGTCCCCGA	    0.969272	-47
          **********

Masking position 2
Map Score:   1.65692

Number of sites scoring better than the average of aligned sites = 589
Number in coding regions = 532
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 4

ATTCGTCCATAGAATTCAAATTCAGAGAAA	1	16	1	AGAATTCAAA	    0.974963	-128
CAGGTATAGTTCCATACAAA          	1	134	1	TCCATACAAA	    0.955604	-10
GATAGGTTAATGAATTCAAAATAAGCTGGT	2	23	1	TGAATTCAAA	    0.989938	-182
TGCGACCGACTGATTACAAATCAGTTGCTC	2	68	1	TGATTACAAA	    0.974951	-137
          **********

Masking position 5
Map Score:   1.48532

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 67
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

GAATTCAAATTCAGAGAAACTTGACTTATA	1	27	1	TCAGAGAAAC	    0.985978	-117
AAGATGCTTGTCATTGAAACACGAATAATA	1	93	0	TCATTGAAAC	    0.950755	-51
AATTTTTGTCCCCGAAAAACTTTTTTAACG	2	163	1	CCCGAAAAAC	    0.986997	-42
TTTTTAACGATCCGTAAAACCTAGTAAAAC	2	184	1	TCCGTAAAAC	    0.990172	-21
TCCGTAAAACCTAGTAAAACC         	2	194	1	CTAGTAAAAC	    0.950752	-11
          **********

Masking position 7
Map Score:   4.4027

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 128
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 6

          **********

No masking
Map Score:   -7.8627e-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:   -7.8627e-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:   -7.8627e-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