AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i229_sel_operon_hpyl_reg_300.orf -o229_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP00892 153 AE000511 #2 RHP00893 226 AE000511 Motif number 1 CTTTTTTTAATCACATTTTTCTTGGTATTT 1 21 1 TCACATTTTT 0.968181 -133 TAATAATACCTTAAATTTGTTTTAGGATTA 1 54 0 TTAAATTTGT 0.921523 -100 AAGGTTATTATTACATTATTCTATTTAATA 1 79 0 TTACATTATT 0.95361 -75 TAAAACTTGACTAAATTTTTAGAAAAAAGT 1 114 1 CTAAATTTTT 0.977581 -40 GCCTTTTTATTTACTTTTTTCTAAAAATTT 1 126 0 TTACTTTTTT 0.986207 -28 TTTGATAAAACTACTTTTTTAAAATCCTTA 2 138 0 CTACTTTTTT 0.985932 -89 ACTAAACCCGCTAAATTTTTGATAAAACTA 2 155 0 CTAAATTTTT 0.977581 -72 GTGCGTTTGATTCCTTTTTTGAGAGTTTAA 2 202 0 TTCCTTTTTT 0.949979 -25 ********** Masking position 6 Map Score: 12.2192 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 237 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 AATGCTAAAACTTTTTTTAA 1 1 1 AATGCTAAAA 0.969002 -153 AGAAAAATGTGATTAAAAAAAGTTTTAGCA 1 13 0 GATTAAAAAA 0.801743 -141 GTATTTTCTTAATCCTAAAACAAATTTAAG 1 45 1 AATCCTAAAA 0.877566 -109 AAATTTAAGGTATTATTAAATAGAATAATG 1 66 1 TATTATTAAA 0.756936 -88 ATAATAACCTTAGGTTTAAAACTTGACTAA 1 98 1 TAGGTTTAAA 0.777464 -56 TTATTTACTTTTTTCTAAAAATTTAGTCAA 1 120 0 TTTTCTAAAA 0.819504 -34 AGTAAATAAAAAGGCTAAAAGAA 1 141 1 AAGGCTAAAA 0.958255 -13 CCATGTTCAAAATTCAAAAAGAAATCCTAA 2 24 0 AATTCAAAAA 0.896463 -203 CGCCAAACTCTATGGAAAAAGTTCCGCTCG 2 83 1 TATGGAAAAA 0.771056 -144 TGCTCTTAAGGATTTTAAAAAAGTAGTTTT 2 132 1 GATTTTAAAA 0.942623 -95 CCGCTAAATTTTTGATAAAACTACTTTTTT 2 148 0 TTTGATAAAA 0.728399 -79 TTAGCGGGTTTAGTTTAAAATAACGCTTAT 2 171 1 TAGTTTAAAA 0.93606 -56 CCTTTTTTGAGAGTTTAAAATAAGCGTTAT 2 190 0 GAGTTTAAAA 0.924115 -37 ********** Masking position 8 Map Score: 10.8925 Number of sites scoring better than the average of aligned sites = 2128 Number in coding regions = 1716 Number in noncoding regions = 412 Number of orfs with sites within 600 bp upstream = 296 Fraction of orfs with sites within 600 bp upstream = 0.0475426 Motif number 3 CACATTTTTCTTGGTATTTTCTTAATCCTAA 1 32 1 TTGGTTTTTC 0.909124 -122 TAAAACAAATTTAAGGTATTATTAAATAGAA 1 60 1 TTAAGTATTA 0.631792 -94 GTTTTAAACCTAAGGTTATTATTACATTATT 1 89 0 TAAGGTATTA 0.8628 -65 GCCTTTTTATTTACTTTTTTCTAAAAATTTA 1 125 0 TTACTTTTTC 0.724068 -29 TTCTTTTAGCCTTTTTATTTACTTTTT 1 137 0 TAGCCTTTTA 0.920059 -17 GCGGTTTCTATAGGGCTTTTTCATGTTTGTT 2 55 0 TAGGGTTTTT 0.916727 -172 TCCATAGAGTTTGGCGGTTTCTATAGGGCTT 2 68 0 TTGGCGTTTC 0.916789 -159 AAGATGCTCTTAAGGATTTTAAAAAAGTAGT 2 128 1 TAAGGTTTTA 0.957393 -99 ATCAAAAATTTAGCGGGTTTAGTTTAAAATA 2 162 1 TAGCGGTTTA 0.958588 -65 GATTCCTTTTTTGAGAGTTTAAAATAAGCGT 2 193 0 TTGAGGTTTA 0.911423 -34 ***** ***** Masking position 9 Map Score: 4.4561 Number of sites scoring better than the average of aligned sites = 3283 Number in coding regions = 2910 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 4 TTAAAAAAAGTTTTAGCATT 1 1 0 TTTTAGCATT 0.875493 -153 CTTAAATTTGTTTTAGGATTAAGAAAATAC 1 45 0 TTTTAGGATT 0.968422 -109 TTTAATAATACCTTAAATTTGTTTTAGGAT 1 56 0 CCTTAAATTT 0.614377 -98 GTAATAATAACCTTAGGTTTAAAACTTGAC 1 95 1 CCTTAGGTTT 0.976513 -59 ATGAAAGGAATCTTAGGATTTCTTTTTGAA 2 12 1 TCTTAGGATT 0.975298 -215 TTGGCGGTTTCTATAGGGCTTTTTCATGTT 2 59 0 CTATAGGGCT 0.843067 -168 GGAACTTTTTCCATAGAGTTTGGCGGTTTC 2 78 0 CCATAGAGTT 0.920453 -149 TTAAGATGCTCTTAAGGATTTTAAAAAAGT 2 126 1 CTTAAGGATT 0.915238 -101 TGATTCCTTTTTTGAGAGTTTAAAATAAGC 2 195 0 TTTGAGAGTT 0.7936 -32 ********** Masking position 5 Map Score: 5.14671 Number of sites scoring better than the average of aligned sites = 1398 Number in coding regions = 1244 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 AATAACCTTAGGTTTAAAACTTGACTAAAT 1 100 1 GGTTTAAAAC 0.868432 -54 TTTTGAACATGGAAACAAACATGAAAAAGC 2 42 1 GGAAACAAAC 0.988602 -185 TCTCAAAAAAGGAATCAAACGCACTCATC 2 208 1 GGAATCAAAC 0.993402 -19 ********** Masking position 7 Map Score: 0.143399 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ********** No masking Map Score: 2.36911e-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: 2.36911e-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: 2.36911e-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