AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i203_dna_repair_mtub_reg_300.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	    0.963477	-287
CGGCCACCGACTAGTCGTGGGATACCAGCGGA	1	59	0	CAGCGTGGGA	     0.99417	-242
CGACTAGTCGGTGGCCGGGGGAAATGCCGAAT	1	74	1	GGGCGGGGGA	    0.997261	-227
TCACGATCCACCGGATGCGGGATTCGGCATTT	1	95	0	CGGTGCGGGA	    0.998347	-206
GTGAAGTCCACCAATCGGGGGACGATCGGCCC	1	123	1	CAACGGGGGA	    0.974135	-178
GGGGGACGATCGGCCCGCGGTGCCCCCCTACC	1	139	1	CGCCGCGGTG	    0.951594	-162
GCGCGTTAACCGGGTAGGGGGGCACCGCGGGC	1	151	0	CGGAGGGGGG	    0.997368	-150
GCGACAACAACGAGAAGCGGGAG         	1	288	1	CAGAGCGGGA	    0.995924	-13
    TAGTTACGGGGCGCAGCAACCCCCGTAA	2	7	1	CGGCGCAGCA	    0.969727	-32
    TCGGTAGAGGTTACGGGGGTTGCTGCGC	2	21	0	GGGTACGGGG	    0.909523	-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

         CGTTGTAGTCGATTTCCACTT	1	2	1	GTTGTAGTCG	    0.937866	-299
TTCCTGACTTATCTTTGGCGGGTTTGGACT	1	30	1	ATCTTTGGCG	    0.903002	-271
GTGGGATACCAGCGGAGTCCAAACCCGCCA	1	45	0	AGCGGAGTCC	    0.956852	-256
CCCACGACTAGTCGGTGGCCGGGGGAAATG	1	70	1	GTCGGTGGCC	    0.994027	-231
TTCACGATCCACCGGATGCGGGATTCGGCA	1	98	0	ACCGGATGCG	    0.791955	-203
TCGTCCCCCGATTGGTGGACTTCACGATCC	1	118	0	ATTGGTGGAC	    0.903003	-183
ACGATCGGCCCGCGGTGCCCCCCTACCCGG	1	144	1	CGCGGTGCCC	    0.936892	-157
GAACGTGACTCTTGTTGGCCACTGTTGTCG	1	236	1	CTTGTTGGCC	    0.978241	-65
CTTGTTGGCCACTGTTGTCGAGGTGCCTTA	1	246	1	ACTGTTGTCG	    0.950638	-55
CCCGCTTCTCGTTGTTGTCGCACTTGCGTC	1	279	0	GTTGTTGTCG	    0.970876	-22
          **********

Masking position 9
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

ACTTATCTTTGGCGGGTTTGGACTCCGCTGG	1	36	1	GGCGGTTTGG	    0.818605	-265
CCCGGCCACCGACTAGTCGTGGGATACCAGC	1	62	0	GACTATCGTG	    0.804742	-239
ACGACTAGTCGGTGGCCGGGGGAAATGCCGA	1	73	1	GGTGGCGGGG	    0.876427	-228
CCACCGGATGCGGGATTCGGCATTTCCCCCG	1	89	0	CGGGATCGGC	    0.892234	-212
TCCCGCATCCGGTGGATCGTGAAGTCCACCA	1	105	1	GGTGGTCGTG	    0.984861	-196
TCGTGAAGTCCACCAATCGGGGGACGATCGG	1	121	1	CACCATCGGG	    0.652178	-180
GGGCACCGCGGGCCGATCGTCCCCCGATTGG	1	133	0	GGCCGTCGTC	    0.941346	-168
AATGTGTGCGCGTTAACCGGGTAGGGGGGCA	1	159	0	CGTTACCGGG	    0.900073	-142
TGCACACTAACGCGTTTCGTGTGGAATGTGT	1	183	0	CGCGTTCGTG	    0.955037	-118
GTGCTGTGAACGTGACTCTTGTTGGCCACTG	1	229	1	CGTGATCTTG	    0.937412	-72
GACTCTTGTTGGCCACTGTTGTCGAGGTGCC	1	242	1	GGCCATGTTG	    0.834134	-59
      CTCCCGCTTCTCGTTGTTGTCGCAC	1	286	0	CGCTTTCGTT	    0.661517	-15
          ***** *****

Masking position 7
Map Score:   6.92637

Number of sites scoring better than the average of aligned sites = 27717
Number in coding regions = 25368
Number in noncoding regions = 2349
Number of orfs with sites within 600 bp upstream = 1159
Fraction of orfs with sites within 600 bp upstream = 0.186155


Motif number 4

          **********

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 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