AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00930_aful_reg_100.orf -o00930_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0373 300 transcription initiation factor IID #2 AF1975 99 glutamyl-tRNA reductase (hemA) #3 AF1976 93 26S protease regulatory subunit 4 Motif number 1 AGAATGTAACCGAGAAGCAGAATCAGGCCGCT 1 17 0 CGAGACAGAA 0.864496 -284 GCCATCACAACGAAACCAACCAATAGCTAGAA 1 45 0 CGAAAAACCA 0.960274 -256 AAACGAGGGGCAGAAGCCATCACAACGAAACC 1 60 0 CAGAACATCA 0.96561 -241 CGGAGATTTTCAGAACTCTCCATTTTTGAGGT 1 173 1 CAGAACTCCA 0.99006 -128 TAGGTAAAAGCGAGAACCTCAAAAATGGAGAG 1 188 0 CGAGACTCAA 0.964204 -113 TCGTGATTAACAAAATAAATCAAAGTTAAGAG 1 228 1 CAAAAAATCA 0.737818 -73 CCGTTCCGGGAGTCTCCACCATTTTATC 2 7 1 CGGGACTCCA 0.993837 -93 CTTATAGTTCAGAATTCACAAGTGCTTTTTA 2 79 0 CAGAACACAA 0.975748 -21 CTCTACGTTCCGGAAGCCTCCAAATACATATA 3 41 0 CGGAACTCCA 0.9948 -53 ***** ***** Masking position 5 Map Score: 10.8157 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 559 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 GATTAGGGATAAAACGTAGGCAACAGCGCA 1 94 0 AAAACGTAGG 0.912537 -207 TGCCTAACCGAAAAGGGTGTTGACACTGCG 1 145 1 AAAAGGGTGT 0.956096 -156 GAGAACCTCAAAAATGGAGAGTTCTGAAAA 1 179 0 AAAATGGAGA 0.983696 -122 AGAAGTAGGTAAAAGCGAGAACCTCAAAAA 1 195 0 AAAAGCGAGA 0.919802 -106 TAAGTCTTTAAAAATGGTGGTGTT 1 287 1 AAAATGGTGG 0.99276 -14 TTAAAATGATAAAATGGTGGAGACTCCCGG 2 16 0 AAAATGGTGG 0.99276 -84 AGCAAAAAATAAAATTGAGGGATAAAAT 3 76 1 AAAATTGAGG 0.965064 -18 ********** Masking position 4 Map Score: 10.2988 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 246 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 GGGAGTGATGATTAGGGATAAAACGTAGGC 1 103 0 ATTAGGGATA 0.940098 -198 TTATAATCGCGGGAGTGATGATTAGGGATA 1 113 0 GGGAGTGATG 0.948839 -188 AATCAAAGTTAAGAGGGATGGCAAAGGTAT 1 245 1 AAGAGGGATG 0.991097 -56 TTCTTATATGATGAGTGATATATATGTATT 3 21 1 ATGAGTGATA 0.971655 -73 TTCCGGAACGTAGAGGGAAGCAAAAAATAA 3 58 1 TAGAGGGAAG 0.950414 -36 AAAAATAAAATTGAGGGATAAAAT 3 80 1 TTGAGGGATA 0.986072 -14 ********** Masking position 4 Map Score: 4.58273 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 409 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TTAACTTTGATTTATTTTGTTAATCACGAT 1 227 0 TTTATTTTGT 0.89459 -74 TTATATGGTATATAAGTCTTTAAAAATGGT 1 275 1 TATAAGTCTT 0.898045 -26 ATTTTATCATTTTAATTTTTGCTTTTCAGC 2 31 1 TTTAATTTTT 0.95867 -69 ACAAGTGCTTTTTAAGTTTTTTATTCAGCA 2 63 0 TTTAAGTTTT 0.973329 -37 ATGAGTGATATATATGTATTTGGAGGCTTC 3 31 1 TATATGTATT 0.855952 -63 ATCCCTCAATTTTATTTTTTGCTTCCCTCT 3 69 0 TTTATTTTTT 0.958693 -25 ********** Masking position 4 Map Score: 2.91236 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 81 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 5 GAATGTAACCGAGAAGCAGAATCAGGCCGC 1 18 0 GAGAAGCAGA 0.990803 -283 CGCAGGAAACGAGGGGCAGAAGCCATCACA 1 68 0 GAGGGGCAGA 0.987065 -233 ACCCTTTTCGGTTAGGCAGATTATAATCGC 1 133 0 GTTAGGCAGA 0.944051 -168 AAGTTAAGAGGGATGGCAAAGGTATTTATA 1 250 1 GGATGGCAAA 0.940074 -51 CAGCAATGCTGAAAAGCAAAAATTAAAATG 2 38 0 GAAAAGCAAA 0.968159 -62 GGAACGTAGAGGGAAGCAAAAAATAAAATT 3 62 1 GGGAAGCAAA 0.986659 -32 ********** Masking position 8 Map Score: 5.66891 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 372 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ********** No masking Map Score: 1.44541e-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: 1.44541e-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: 1.44541e-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