AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -icysB_synecho_opreg_100.orf -g0.48 -x5 
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 = 	0

Input sequences:
#1	1652528	300	hypothetical protein
#2	cysK	69	cysteine synthase

Motif number 1

ATGGTTAATAACAGATTATAGTTGCTATTTTGGTGATGG	1	30	0	ACGATAGTAT	    0.987125	-271
GCTTCTGCTCACGGAACGATGATGTTGATGGTTAATAAC	1	57	0	ACGACGGTGT	    0.997073	-244
GTAAAGAAAAACCGCCTACAGCTTCTGCTCACGGAACGA	1	77	0	ACGCTAGTGT	    0.994417	-224
CTTTACCAACACTGATTGTGGTCCTGGCTCCCTGAGCTA	1	110	1	ACGATGGGGT	    0.993378	-191
AGCCCGCAAAACAGACCAATGGCCTTGCTTAGCCTAGCA	1	148	1	ACGACAGTGT	    0.997572	-153
ACAATGTGTTACTGAGTATAGGACTTGGTTCCCGTAGTC	1	245	1	ACGATAGTGT	    0.997684	-56
          ** ** **  *    ** *

Masking position 1
Map Score:   7.73681

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 20
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

GTGATGGCTAGGGGCAGGGCCAGTTT      	1	5	0	GGGGCAGCCA	     0.77563	-296
GCCCTGCCCCTAGCCATCACCAAAATAGCAAC	1	17	1	TAGCCACCCA	    0.989174	-284
AATCTGTTATTAACCATCAACATCATCGTTCC	1	52	1	TAACCACACA	    0.949785	-249
CTAGCTCAGGGAGCCAGGACCACAATCAGTGT	1	118	0	GAGCCAGCCA	    0.997739	-183
GATGCTAGGCTAAGCAAGGCCATTGGTCTGTT	1	157	0	TAAGCAGCCA	    0.984631	-144
ATGACTACGGGAACCAAGTCCTATACTCAGTA	1	254	0	GAACCAGCCT	    0.989101	-47
          ****** * ***

Masking position 6
Map Score:   7.00609

Number of sites scoring better than the average of aligned sites = 483
Number in coding regions = 453
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

CCAAAATAGCAACTATAATCTGTTATTAACC	1	36	1	AACTATATCT	    0.906368	-265
GCTAAGCAAGGCCATTGGTCTGTTTTGCGGG	1	150	0	GCCATTGTCT	     0.96305	-151
GCCTTGCTTAGCCTAGCATCTACCATGAATC	1	169	1	GCCTAGATCT	     0.98034	-132
CCTAGCATCTACCATGAATCTAAAGAAAATT	1	180	1	ACCATGATCT	    0.960228	-121
GGGAGAAGTTGACAATTTTCTTTAGATTCAT	1	193	0	GACAATTTCT	     0.94783	-108
CTGAGTATAGGACTTGGTTCCCGTAGTCATT	1	256	1	GACTTGTTCC	    0.871956	-45
TTAACTTTCAAACAAGTGTCTTAAGAAGACG	2	20	0	AACAAGGTCT	    0.965639	-50
          ****** ****

Masking position 9
Map Score:   2.81997

Number of sites scoring better than the average of aligned sites = 444
Number in coding regions = 385
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 4

AAACCGCCTACAGCTTCTGCTCACGGAACG	1	78	0	CAGCTTCTGC	    0.994577	-223
TTGCTTAGCCTAGCATCTACCATGAATCTA	1	172	1	TAGCATCTAC	    0.969385	-129
AGAAAATTGTCAACTTCTCCCACTCTTTCG	1	203	1	CAACTTCTCC	    0.988366	-98
       TTTTAGCTTTTCCTCACACCTAA	1	288	0	TAGCTTTTCC	    0.982119	-13
          **********

Masking position 6
Map Score:   2.11025

Number of sites scoring better than the average of aligned sites = 167
Number in coding regions = 142
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 5

          **********

No masking
Map Score:   1.65857e-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:   1.65857e-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:   1.65857e-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