AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_mjan_reg_300.orf -o00450_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ1260 300 SSU ribosomal protein S6E #2 MJ1261 205 translation initiation factor aIF-2, subunit gamma (aif2G) #3 MJ1262 163 conserved hypothetical protein #4 MJ1263 130 methionyl-tRNA synthetase (metS) #5 MJ1388 300 adenosylhomocysteinase (ahcY) Motif number 1 TAATTTTTGGTTTTAAACTTTCAATGCTAT 1 26 0 TTTTAAACTT 0.711998 -275 GACATAATATTTTAAATAATTTTTGGTTTT 1 42 0 TTTAAATAAT 0.855428 -259 TTAAGGGCATTTTTATAAATATCTTTATTT 1 197 0 TTTTATAAAT 0.828127 -104 TAAAAATGCCCTTAAAAAATCTGTTTTATC 1 212 1 CTTAAAAAAT 0.610809 -89 TAAATTAACTTTTAAGTTTTGATAAAACAG 1 232 0 TTTAAGTTTT 0.639668 -69 TAAAAGTTAATTTAAAAATTAGAAACCAAA 1 248 1 TTTAAAAATT 0.855452 -53 TCCCTCCTATTTTTATTTTTGTTATTTGTT 1 276 0 TTTTATTTTT 0.931848 -25 TAGCTCCTAATTTTATTTTTATTTTATTTA 2 19 1 TTTTATTTTT 0.931848 -187 TTTATTTTTATTTTATTTATCTGTGTTTAA 2 30 1 TTTTATTTAT 0.874747 -176 TTTATCTGTGTTTAAATATTGTAGTGGTGA 2 45 1 TTTAAATATT 0.920542 -161 ATTTTCACATTTTTATAATTTTAGCTTATA 2 118 0 TTTTATAATT 0.9048 -88 ATATTTATTCCTTAATTTTTATTAACTTTG 2 163 0 CTTAATTTTT 0.842985 -43 CCCTACGGGCTTTTATATTTATTCCTTAAT 2 177 0 TTTTATATTT 0.87476 -29 TTTTAATAATATGAGTATCA 3 1 1 TTTTAATAAT 0.886675 -163 CTTAATTAATCTTAATTTTTAAGTGTGTGA 5 13 0 CTTAATTTTT 0.842985 -288 TATTTACTTACTTAATTAATCTTAATTTTT 5 23 0 CTTAATTAAT 0.787142 -278 ATCGGTCTGATTTTAATCTTGTAGTTTCCA 5 126 0 TTTTAATCTT 0.828754 -175 GAAAATAAACCTTAAATTTTTATTCTGAAT 5 154 0 CTTAAATTTT 0.815479 -147 TTTATTTTCTTTTTATTAATTTAATTTATA 5 175 1 TTTTATTAAT 0.903901 -126 GAAGAAAAGCTTTTATTATTTATAAATTCA 5 209 0 TTTTATTATT 0.94899 -92 CCCTACTAATTTTTAAAATTAATTCTTTAA 5 271 1 TTTTAAAATT 0.886688 -30 ********** Masking position 3 Map Score: 25.6926 Number of sites scoring better than the average of aligned sites = 3387 Number in coding regions = 2354 Number in noncoding regions = 1033 Number of orfs with sites within 600 bp upstream = 601 Fraction of orfs with sites within 600 bp upstream = 0.0965307 Motif number 2 CTTTCAATGCTATTGTGATAATATAATA 1 9 0 TATTGTGATA 0.659168 -292 GAAATAAAGATATTTATAAAAATGCCCTTA 1 196 1 TATTTATAAA 0.706921 -105 TTAACTTTTAAGTTTTGATAAAACAGATTT 1 228 0 AGTTTTGATA 0.693236 -73 TTTGGTTTCTAATTTTTAAATTAACTTTTA 1 248 0 AATTTTTAAA 0.953927 -53 TATTCCCTCCTATTTTTATTTTTGTTATTT 1 279 0 TATTTTTATT 0.771972 -22 CTCCTAATTTTATTTTTATTTTATTTATCT 2 22 1 TATTTTTATT 0.771972 -184 TCACCACTACAATATTTAAACACAGATAAA 2 45 0 AATATTTAAA 0.584125 -161 GTTTTTTGACTATTTTGATACTCCGAGTAT 2 83 1 TATTTTGATA 0.90833 -123 AAAATTATAAAAATGTGAAAATACCATAAG 2 126 1 AAATGTGAAA 0.47093 -80 AATTTTTATTAACTTTGAAAAACACTTATG 2 150 0 AACTTTGAAA 0.727928 -56 TTTATTCCTTAATTTTTATTAACTTTGAAA 2 160 0 AATTTTTATT 0.884779 -46 TCGGAGGTGTAAATTTGATACTCATATTAT 3 16 0 AAATTTGATA 0.820182 -148 TTTATTAAGGAAATTTGAATGCCTTCTATA 4 35 1 AAATTTGAAT 0.628601 -96 TATTACAAAATATTTTGAAAGACACTATTA 4 93 1 TATTTTGAAA 0.908345 -38 AATTAATCTTAATTTTTAAGTGTGTGACA 5 10 0 AATTTTTAAG 0.737479 -291 ATAAACCTTAAATTTTTATTCTGAATCGGT 5 150 0 AATTTTTATT 0.884779 -151 TTATTAATTTAATTTATATATTTGAATTTA 5 187 1 AATTTATATA 0.844184 -114 TATATATTTGAATTTATAAATAATAAAAGC 5 201 1 AATTTATAAA 0.845452 -100 AAAAAATAGTAATTTATATATCTCTGCTAC 5 242 1 AATTTATATA 0.844184 -59 CTACCCTACTAATTTTTAAAATTAATTCTT 5 268 1 AATTTTTAAA 0.953927 -33 ********** Masking position 8 Map Score: 18.6725 Number of sites scoring better than the average of aligned sites = 2441 Number in coding regions = 1647 Number in noncoding regions = 794 Number of orfs with sites within 600 bp upstream = 539 Fraction of orfs with sites within 600 bp upstream = 0.0865724 Motif number 3 ACACGTCCCAACTCCATTGGGAGTCAGGACA 1 92 0 ACTCCTTGGG 0.995285 -209 AAGGGGCAGAACTCCACTGGGTCATTGACAC 1 119 0 ACTCCCTGGG 0.98721 -182 TCATTTCACTACCCCTTTGGGGTAAAGGGGC 1 143 0 ACCCCTTGGG 0.996994 -158 TAAATATAAAAGCCCGTAGGGCTTTTATAA 2 186 1 AGCCCTAGGG 0.980593 -20 TATCGCAATCGCCCCGTAGGGGCGAGTAATG 3 71 1 GCCCCTAGGG 0.984858 -93 CGAGTAATGAAATCCTTTAGGATTTCATCTG 3 93 1 AATCCTTAGG 0.862224 -71 ***** ***** Masking position 5 Map Score: 6.35315 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 12 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 AAATATCTTTATTTCACCCTATGCCTCCCCAG 1 179 0 ATTTACCTAT 0.867252 -122 CCTAATTTTATTTTTATTTTATTTATCTGTGT 2 24 1 TTTTATTTAT 0.69857 -182 CATTTTTATAATTTTAGCTTATAAAGTTATAC 2 109 0 ATTTACTTAT 0.971982 -97 ATCCTTTAGGATTTCATCTGATGGAGGCTTCC 3 104 1 ATTTACTGAT 0.867246 -60 CAAAAAAGGTATTAAAGTTTATTAAGGAAATT 4 18 1 ATTAATTTAT 0.818941 -113 TTACTTACTTAATTAATCTTAATTTTTAAGTG 5 18 0 AATTACTTAA 0.923429 -283 ATAAAAAGAAAATAAACCTTAAATTTTTATTC 5 159 0 AATAACTTAA 0.749516 -142 TCTTTTTATTAATTTAATTTATATATTTGAAT 5 182 1 AATTATTTAT 0.914924 -119 TAATTTATATATTTGAATTTATAAATAATAAA 5 196 1 ATTTATTTAT 0.948018 -105 CACCTTAAAGAATTAATTTTAAAAATTAGTAG 5 273 0 AATTATTTAA 0.863772 -28 TCATTTCACCTTAAAGAATTAATT 5 287 0 ATTTACTTAA 0.953389 -14 **** * ***** Masking position 6 Map Score: 8.79498 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 317 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 5 AATGGAGTTGGGACGTGTCAATGACCCAGTGGAG 1 105 1 GGACGGTAGA 0.988387 -196 GCTAACGCTCGGAGGTGTAAATTTGATACTCATA 3 20 0 GGAGGGTATT 0.926637 -144 GCGTTAGCGAGGAGGTGTTAGGGAGTATCGCAAT 3 46 1 GGAGGGTAGA 0.988387 -118 CGCCCCTACGGGGCGATTGCGATACTCCCTAACA 3 61 0 GGGCGTTCTA 0.938619 -103 CGCCCCGTAGGGGCGAGTAATGAAATCCTTTAGG 3 80 1 GGGCGGTAAA 0.923844 -84 TTCATCTGATGGAGGCTTCCTCTATGCTTATTGG 3 116 1 GGAGGTTCTA 0.964291 -48 ATGCTTATTGGAACGATTGAGGGAGAATTATTTT 3 139 1 GAACGTTAGA 0.883852 -25 CCTTCTATAAGAAGGCGTTCATTAATACATTAAT 4 56 1 GAAGGGTCTA 0.94048 -75 ***** ** * ** Masking position 8 Map Score: 1.33393 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 81 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ********** No masking Map Score: -3.14527e-12 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: -3.14527e-12 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: -3.14527e-12 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