AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1260	193	acetyl-CoA carboxylase carboxyl transferase subunit beta  (accD)
#2	HI1394	221	conserved hypothetical protein

Motif number 1

TCTCCTCTTATTGAACATTTTTTTTATTTTTTTG	1	52	0	TTGAATTTTT	    0.981518	-142
TTTGCTACTTGTAAGACCGTTTTTGTACTGCTCC	1	113	0	GTAAGTTTTT	    0.931017	-81
          TTTTTGACCTTTTTATTGACTAGA	1	180	0	TTTTTTTTTT	    0.856362	-14
     ATAAGTTTAGATAATTTATTTCTTGTTTT	2	6	1	TTTAGTTTAT	     0.94636	-216
TTGTCATATTGTGATGAAATTTTTATTTATGATA	2	38	1	GTGATTTTTT	    0.947698	-184
GGCATTGCGCTTGAATTGATTTTTCAACTAAAAG	2	77	1	TTGAATTTTT	    0.981518	-145
CATTACTCAATTTAGTGAATTTTTACCAAGCTGG	2	118	1	TTTAGTTTTT	    0.991144	-104
TATCAATTGATTTAATACTTTTTTACACCAGCTT	2	145	0	TTTAATTTTT	    0.981878	-77
GCGGTTAGGTTTTAGAAAGTTTTTACAAATCCTA	2	183	0	TTTAGTTTTT	    0.991144	-39
          *****    *****

Masking position 10
Map Score:   11.4495

Number of sites scoring better than the average of aligned sites = 553
Number in coding regions = 419
Number in noncoding regions = 134
Number of orfs with sites within 600 bp upstream = 134
Fraction of orfs with sites within 600 bp upstream = 0.0215226


Motif number 2

TATCTGAAATTTATTTTGGAGTATTT       	1	4	0	TATTTGAGTA	    0.863092	-190
TAATTTGCTCTCCTCTTATTGAACATTTTTTTT	1	61	0	TCCTTTTGAA	    0.797131	-133
GGAGAGCAAATTATCTTGTTTAAAAGGAAATCG	1	81	1	TACTTTTTAA	    0.868611	-113
TATTAGAACATAAATTTATAGAATTTGCTACTT	1	137	0	TATTTTAGAA	    0.981326	-57
TTTGACCTTTTTATTGACTAGAAAATTGCGCGT	1	169	0	TATGATAGAA	    0.819072	-25
         ATAAGTTTAGATAATTTATTTCTT	2	2	1	TATTTGATAA	    0.947402	-220
GATGAAATTTTTATTTATGATAACTCTGGCATT	2	50	1	TATTAGATAA	    0.883257	-172
AATGCAGTTATCTTTTAGTTGAAAAATCAATTC	2	89	0	TTTTATTGAA	    0.741317	-133
ACTGCATTACTCAATTTAGTGAATTTTTACCAA	2	114	1	TATTTGTGAA	    0.975944	-108
CCTAGATTTATCAATTGATTTAATACTTTTTTA	2	154	0	TATTGTTTAA	    0.814416	-68
TAAAGAGCGGTTAGGTTTTAGAAAGTTTTTACA	2	190	0	TAGTTTAGAA	    0.925856	-32
          * * *** *****

Masking position 13
Map Score:   4.03087

Number of sites scoring better than the average of aligned sites = 945
Number in coding regions = 758
Number in noncoding regions = 187
Number of orfs with sites within 600 bp upstream = 170
Fraction of orfs with sites within 600 bp upstream = 0.0273049


Motif number 3

    AAATACTCCAAAATAAATTTCAGATAA	1	7	1	TCAAAATAAA	    0.928748	-187
TCTGTAAGACAAAAAAATAAAAAAAATGTTC	1	43	1	AAAAAATAAA	    0.945985	-151
GATTTCCTTTTAAACAAGATAATTTGCTCTC	1	82	0	TAACAAGATA	    0.812739	-112
ACAAGTAGCAAATTCTATAAATTTATGTTCT	1	135	1	AATCTATAAA	    0.735654	-59
TTGCGCGTATTAGAACATAAATTTATAGAAT	1	146	0	TAAACATAAA	    0.812739	-48
CGCAATTTTCTAGTCAATAAAAAGGTCAAAA	1	172	1	TATCAATAAA	    0.959188	-22
ACAATATGACAAAACAAGAAATAAATTATCT	2	19	0	AAACAAGAAA	    0.936387	-203
GCCAGAGTTATCATAAATAAAAATTTCATCA	2	49	0	TCTAAATAAA	    0.916451	-173
TGATTTTTCAACTAAAAGATAACTGCATTAC	2	93	1	ACAAAAGATA	    0.630261	-129
GCTTGGTAAAAATTCACTAAATTGAGTAATG	2	118	0	AATCACTAAA	     0.78834	-104
TGTAAAAAAGTATTAAATCAATTGATAAATC	2	152	1	TATAAATCAA	    0.767338	-70
          ** ********

Masking position 11
Map Score:   4.81229

Number of sites scoring better than the average of aligned sites = 1118
Number in coding regions = 828
Number in noncoding regions = 290
Number of orfs with sites within 600 bp upstream = 235
Fraction of orfs with sites within 600 bp upstream = 0.0377449


Motif number 4

TTTTTTATTTTTTTGTCTTACAGACCACGT	1	37	0	TTTTGTCTTA	     0.97363	-157
TTCTATAAATTTATGTTCTAATACGCGCAA	1	147	1	TTATGTTCTA	    0.966392	-47
TTATTTCTTGTTTTGTCATATTGTGATGAA	2	26	1	TTTTGTCATA	     0.93596	-196
AGTAATGCAGTTATCTTTTAGTTGAAAAAT	2	95	0	TTATCTTTTA	    0.932986	-127
TAAAGAGCGGTTAGGTTTTAGAAAGTTTTT	2	193	0	TTAGGTTTTA	    0.956646	-29
          **********

Masking position 6
Map Score:   1.75824

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 100
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 5

          **********

No masking
Map Score:   -6.44162e-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:   -6.44162e-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:   -6.44162e-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