AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_mjan_reg_100.orf -o00550_mjan_100.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 MJ1113 300 N-acetylglucosamine-1-phosphate transferase #2 MJ1345 300 O-linked GlnNAc transferase #3 MJ1346 87 glutamine synthetase (glnA) Motif number 1 AAGATATTAATTAGGATATTTTTATATTTCAT 1 15 0 TTAATATTTT 0.976941 -286 AATATCCTAATTAATATCTTTTTACTGATTTT 1 27 1 TTAATCTTTT 0.886223 -274 TTACTGATTTTTTGGATATTTTTGGCTTATCT 1 48 1 TTTATATTTT 0.985656 -253 TCTATTTGTTTTTAAATATTTTGAAAAGTATT 1 92 1 TTTATATTTT 0.985646 -209 GGTGCAATTTTTTTAATAGTTTTAGTTATCCT 1 147 1 TTTATAGTTT 0.879356 -154 ATAGAAATTCTTTTATTATTTTCCTTACTTCC 1 209 0 TTTTTATTTT 0.977229 -92 AATAAAAGAATTTCTATAATTTTTTAGCAAAA 1 224 1 TTTATAATTT 0.896534 -77 AAGTTTAGGATATATATGTTTTTTGCTAAAAA 1 244 0 TATATGTTTT 0.82697 -57 ATCCTAAACTTTAACTTCTTTTATCTTCATTA 1 265 1 TTATTCTTTT 0.895137 -36 TATCCCAATATTTGTTTATTTTGCATTTCC 2 9 0 TTTTTATTTT 0.977229 -292 TATAATTAAATTTTTATATTTATAATTATATT 2 62 1 TTTATATTTA 0.891081 -239 TTTATATTTATAATTATATTATAGCGTATAAT 2 74 1 TAAATATTAT 0.650874 -227 AGATTGGGGTATTAATTGTTTTATGACATTAT 2 101 0 ATTTTGTTTT 0.62958 -200 TATTTCCACATTAGTTTATTTAAAGTTAATAA 2 132 0 TTATTATTTA 0.76215 -169 TTTTCTTTTATTTCCATATTATTTCCACATTA 2 151 0 TTTATATTAT 0.925466 -150 TGAATACTGGATATTTTCTTTTATTTCCATAT 2 164 0 ATATTCTTTT 0.606674 -137 CAGATAGAAAAATTTATATTTTACACTAAAAT 2 196 1 AATATATTTT 0.798127 -105 TATTATTTATTAAAATTATTTTAGTGTAAAAT 2 213 0 TAATTATTTT 0.89708 -88 ACGAATTTCGTTAAATTATTATTACTATGATA 2 243 0 TTATTATTAT 0.828839 -58 ATTTTTATATTTTAATTTAAATT 3 2 1 TTTATATTTT 0.985562 -86 TACTTCCATATATATATAATTTACGGTATATT 3 35 0 TATATAATTT 0.735235 -53 *** ******* Masking position 7 Map Score: 32.1393 Number of sites scoring better than the average of aligned sites = 2845 Number in coding regions = 2049 Number in noncoding regions = 796 Number of orfs with sites within 600 bp upstream = 536 Fraction of orfs with sites within 600 bp upstream = 0.0860906 Motif number 2 AATTATGAAATATAAAAATATCCTA 1 2 1 ATTATATTAA 0.9612 -299 AAAGTATTTTATGATGGACTTTAAAAGCATTGGT 1 116 1 ATGATATTAA 0.823495 -185 AATTTCTATAATTTTTTAGCAAAAAACATATATA 1 232 1 ATTTTACAAA 0.899708 -69 TATCCCCTTTATAATGAAGATAAAAGAAGTTAAA 1 274 0 ATAATAAAAA 0.796287 -27 AATTTATGGACTTTTATAATTAAATTTTTATATT 2 48 1 CTTTTATAAA 0.894821 -253 CTATAATATAATTATAAATATAAAAATTTAATTA 2 64 0 ATTATAAAAA 0.883414 -237 TTATAATTATATTATAGCGTATAATGTCATAAAA 2 81 1 ATTATCTTAA 0.758551 -220 ATACCCCAATCTTATTAACTTTAAATAAACTAAT 2 121 1 CTTATATTAA 0.869294 -180 TGTGGAAATAATATGGAAATAAAAGAAAATATCC 2 154 1 ATATGATAAA 0.803435 -147 AAAAATTTATATTTTACACTAAAATAATTTTAAT 2 203 1 ATTTTATAAA 0.969492 -98 TTACTATGATATTATTTATTAAAATTATTTTAGT 2 220 0 ATTATATAAA 0.975656 -81 CATAGTAATAATAATTTAACGAAATTCGTAAAAT 2 246 1 ATAATACAAA 0.858125 -55 GGTTTTAGCAATATGCGATTTTAATCCCCCTATT 2 277 0 ATATGATTAA 0.714406 -24 ATTTTTATATTTTAATTTAAATTGA 3 2 1 TTTTTATTAA 0.651528 -86 AATTTACGGTATATTCAATTTAAATTAAAATATA 3 16 0 ATATTATAAA 0.942425 -72 TACTTCCAGAATTATTCAATCAAA 3 74 1 ATTATATAAA 0.975892 -14 ***** * * *** Masking position 2 Map Score: 16.4453 Number of sites scoring better than the average of aligned sites = 1079 Number in coding regions = 776 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 3 AATTATGAAATATAAAAATATCCTAA 1 5 1 ATGATATAAA 0.953522 -296 CATACTATCTATTTGTTTTTAAATATTTTGAA 1 85 1 ATTGTTTTAA 0.776449 -216 GTATTTTATGATGGACTTTAAAAGCATTGGTG 1 119 1 ATGATTTAAA 0.937547 -182 TATATATGTTTTTTGCTAAAAAATTATAGAAA 1 234 0 TTTGTAAAAA 0.6131 -67 CTTCTTTTATCTTCATTATAAAGGGGATAGTT 1 279 1 CTTATATAAA 0.861872 -22 GGAAATGCAAAATAAACAAATATTGG 2 5 1 ATGAAATAAA 0.687443 -296 AATATAAAAATTTAATTATAAAAGTCCATAAA 2 50 0 TTTATATAAA 0.908068 -251 ATAATATAATTATAAATATAAAAATTTAATTA 2 64 0 TATATATAAA 0.675796 -237 GTTAATAAGATTGGGGTATTAATTGTTTTATG 2 108 0 TTGGTATTAA 0.829714 -193 CCCCAATCTTATTAACTTTAAATAAACTAATG 2 124 1 ATTATTTAAA 0.928492 -177 ATTAAAATTATTTTAGTGTAAAATATAAATTT 2 205 0 TTTATGTAAA 0.842333 -96 TTTTAGCAATATGCGATTTTAATCCCCCTATT 2 277 0 ATGGTTTTAA 0.779705 -24 ATTTTTATATTTTAATTTAAATTGAATATAC 3 10 1 TTTATTTAAA 0.590337 -78 *** * ****** Masking position 11 Map Score: 7.48278 Number of sites scoring better than the average of aligned sites = 1134 Number in coding regions = 856 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 4 TATTATTTTCCTTACTTCCCTAAGCAATAA 1 198 0 CTTACTTCCC 0.988128 -103 TTATTTCCATATTATTTCCACATTAGTTTA 2 146 0 ATTATTTCCA 0.953788 -155 GATATTTTCTTTTATTTCCATATTATTTCC 2 157 0 TTTATTTCCA 0.953787 -144 AAGTAAGTTTCCTACTTCCATATATATATA 3 49 0 CCTACTTCCA 0.988128 -39 AAGTAGGAAACTTACTTCCAGAATTATTCA 3 62 1 CTTACTTCCA 0.994617 -26 ********** Masking position 6 Map Score: 6.18975 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 20 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 AAGTCCATCATAAAATACTTTTCAAAATATT 1 106 0 TAAAAACTTT 0.951438 -195 TGATGGACTTTAAAAGCATTGGTGCAATTTT 1 127 1 TAAAACATTG 0.776386 -174 CTAAAACTATTAAAAAAATTGCACCAATGCT 1 141 0 TAAAAAATTG 0.95967 -160 TTGCCATTATTAATCTACTTTTATTGCTTAG 1 178 1 TAATCACTTT 0.762193 -123 AGGAAAATAATAAAAGAATTTCTATAATTTT 1 216 1 TAAAAAATTT 0.977041 -85 ATAATGAAGATAAAAGAAGTTAAAGTTTAGG 1 267 0 TAAAAAAGTT 0.861315 -34 AAATGCAAAATAAACAAATATTGGGATAAAC 2 13 1 TAAACAATAT 0.716946 -288 TAAAAGTCCATAAATTACTTGTTTATCCCAA 2 33 0 TAAATACTTG 0.730986 -268 TGGACTTTTATAATTAAATTTTTATATTTAT 2 54 1 TAATTAATTT 0.743507 -247 TTATACGCTATAATATAATTATAAATATAAA 2 74 0 TAATAAATTA 0.742635 -227 TATAATGTCATAAAACAATTAATACCCCAAT 2 100 1 TAAAAAATTA 0.913076 -201 TAACTTTAAATAAACTAATGTGGAAATAATA 2 136 1 TAAACAATGT 0.789653 -165 TATTCACAGATAGAAAAATTTATATTTTACA 2 190 1 TAGAAAATTT 0.861315 -111 TATTTTACACTAAAATAATTTTAATAAATAA 2 212 1 TAAAAAATTT 0.977041 -89 ***** ***** Masking position 2 Map Score: 15.8959 Number of sites scoring better than the average of aligned sites = 746 Number in coding regions = 585 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 6 ********** No masking Map Score: 2.93755e-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: 2.93755e-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: 2.93755e-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