AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i203_dna_repair_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	lprJ	300	lprJ
#2	Rv1691	38	hypothetical protein Rv1691

Motif number 1

AAAGATAAGTCAGGAAGTGGAAATCGACTACA	1	14	0	CGGAGTGGAA	    0.956692	-287
CGGCCACCGACTAGTCGTGGGATACCAGCGGA	1	59	0	CAGCGTGGGA	    0.993045	-242
CGACTAGTCGGTGGCCGGGGGAAATGCCGAAT	1	74	1	GGGCGGGGGA	    0.996731	-227
TCACGATCCACCGGATGCGGGATTCGGCATTT	1	95	0	CGGTGCGGGA	    0.998027	-206
GTGAAGTCCACCAATCGGGGGACGATCGGCCC	1	123	1	CAACGGGGGA	    0.969268	-178
GGGGGACGATCGGCCCGCGGTGCCCCCCTACC	1	139	1	CGCCGCGGTG	    0.946407	-162
GCGCGTTAACCGGGTAGGGGGGCACCGCGGGC	1	151	0	CGGAGGGGGG	    0.996859	-150
GCGACAACAACGAGAAGCGGGAG         	1	288	1	CAGAGCGGGA	    0.995136	-13
    TAGTTACGGGGCGCAGCAACCCCCGTAA	2	7	1	CGGCGCAGCA	     0.96406	-32
    TCGGTAGAGGTTACGGGGGTTGCTGCGC	2	21	0	GGGTACGGGG	    0.893819	-18
          * ** *******

Masking position 10
Map Score:   16.8189

Number of sites scoring better than the average of aligned sites = 6330
Number in coding regions = 5840
Number in noncoding regions = 490
Number of orfs with sites within 600 bp upstream = 410
Fraction of orfs with sites within 600 bp upstream = 0.0658529


Motif number 2

AAGTGGAAATCGACTACAACG         	1	2	0	CGACTACAAC	    0.935991	-299
AGTCCAAACCCGCCAAAGATAAGTCAGGAA	1	30	0	CGCCAAAGAT	    0.900186	-271
TGGCGGGTTTGGACTCCGCTGGTATCCCAC	1	45	1	GGACTCCGCT	    0.955523	-256
CATTTCCCCCGGCCACCGACTAGTCGTGGG	1	70	0	GGCCACCGAC	    0.993835	-231
TGCCGAATCCCGCATCCGGTGGATCGTGAA	1	98	1	CGCATCCGGT	    0.786678	-203
GGATCGTGAAGTCCACCAATCGGGGGACGA	1	118	1	GTCCACCAAT	    0.900188	-183
CCGGGTAGGGGGGCACCGCGGGCCGATCGT	1	144	0	GGGCACCGCG	     0.93499	-157
CGACAACAGTGGCCAACAAGAGTCACGTTC	1	236	0	GGCCAACAAG	    0.977556	-65
TAAGGCACCTCGACAACAGTGGCCAACAAG	1	246	0	CGACAACAGT	    0.949128	-55
GACGCAAGTGCGACAACAACGAGAAGCGGG	1	279	1	CGACAACAAC	    0.969965	-22
          **********

Masking position 4
Map Score:   7.5085

Number of sites scoring better than the average of aligned sites = 32338
Number in coding regions = 30704
Number in noncoding regions = 1634
Number of orfs with sites within 600 bp upstream = 961
Fraction of orfs with sites within 600 bp upstream = 0.154353


Motif number 3

TCCACTTCCTGACTTATCTTTGGCGGGTTTG	1	25	1	GACTTTCTTT	    0.718086	-276
CCCGGCCACCGACTAGTCGTGGGATACCAGC	1	62	0	GACTATCGTG	    0.815307	-239
TCCCGCATCCGGTGGATCGTGAAGTCCACCA	1	105	1	GGTGGTCGTG	    0.971554	-196
TCGTGAAGTCCACCAATCGGGGGACGATCGG	1	121	1	CACCATCGGG	    0.654651	-180
GGGCACCGCGGGCCGATCGTCCCCCGATTGG	1	133	0	GGCCGTCGTC	    0.968959	-168
TGCACACTAACGCGTTTCGTGTGGAATGTGT	1	183	0	CGCGTTCGTG	    0.931723	-118
GTGCTGTGAACGTGACTCTTGTTGGCCACTG	1	229	1	CGTGATCTTG	    0.915532	-72
GACTCTTGTTGGCCACTGTTGTCGAGGTGCC	1	242	1	GGCCATGTTG	    0.908581	-59
      CTCCCGCTTCTCGTTGTTGTCGCAC	1	286	0	CGCTTTCGTT	    0.950291	-15
          ***** *****

Masking position 7
Map Score:   4.25036

Number of sites scoring better than the average of aligned sites = 7704
Number in coding regions = 6939
Number in noncoding regions = 765
Number of orfs with sites within 600 bp upstream = 559
Fraction of orfs with sites within 600 bp upstream = 0.0897848


Motif number 4

CGTTAACCGGGTAGGGGGGCACCGCGGGCCGAT	1	147	0	GTAGGGCACC	    0.984523	-154
CCCCTACCCGGTTAACGCGCACACATTCCACAC	1	163	1	GTTAGGCACA	    0.997931	-138
CACGAAACGCGTTAGTGTGCAAACCTTTATCCC	1	193	1	GTTAGGCAAA	    0.991705	-108
        TAGTTACGGGGCGCAGCAACCCCCG	2	3	1	GTTAGGCGCA	    0.996474	-36
          ****  * *****

Masking position 2
Map Score:   0.985217

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 28
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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:   7.2008e-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