AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_mjan_reg_300.orf -o00550_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 MJ1113 300 N-acetylglucosamine-1-phosphate transferase #2 MJ1345 300 O-linked GlnNAc transferase #3 MJ1346 87 glutamine synthetase (glnA) Motif number 1 ATGAAATATAAAAATATCCTAATTAATATCTT 1 15 1 AAAATATTAA 0.977754 -286 AAAATCAGTAAAAAGATATTAATTAGGATATT 1 27 0 AAAAGATTAA 0.886878 -274 AGATAAGCCAAAAATATCCAAAAAATCAGTAA 1 48 0 AAAATATAAA 0.98618 -253 AATACTTTTCAAAATATTTAAAAACAAATAGA 1 92 0 AAAATATAAA 0.986169 -209 AGGATAACTAAAACTATTAAAAAAATTGCACC 1 147 0 AAACTATAAA 0.883301 -154 GGAAGTAAGGAAAATAATAAAAGAATTTCTAT 1 209 1 AAAATAAAAA 0.978054 -92 TTTTGCTAAAAAATTATAGAAATTCTTTTATT 1 224 0 AAATTATAAA 0.899976 -77 TTTTTAGCAAAAAACATATATATCCTAAACTT 1 244 1 AAAACATATA 0.832051 -57 TAATGAAGATAAAAGAAGTTAAAGTTTAGGAT 1 265 0 AAAAGAATAA 0.898614 -36 GGAAATGCAAAATAAACAAATATTGGGATA 2 9 1 AAAATAAAAA 0.978054 -292 AATATAATTATAAATATAAAAATTTAATTATA 2 62 0 TAAATATAAA 0.894653 -239 ATTATACGCTATAATATAATTATAAATATAAA 2 74 0 ATAATATTTA 0.655716 -227 ATAATGTCATAAAACAATTAATACCCCAATCT 2 101 1 AAAACAAAAT 0.638334 -200 TTATTAACTTTAAATAAACTAATGTGGAAATA 2 132 1 TAAATAATAA 0.768917 -169 TAATGTGGAAATAATATGGAAATAAAAGAAAA 2 151 1 ATAATATAAA 0.928023 -150 ATATGGAAATAAAAGAAAATATCCAGTATTCA 2 164 1 AAAAGAATAT 0.615608 -137 ATTTTAGTGTAAAATATAAATTTTTCTATCTG 2 196 0 AAAATATATT 0.803886 -105 ATTTTACACTAAAATAATTTTAATAAATAATA 2 213 1 AAAATAATTA 0.900506 -88 TATCATAGTAATAATAATTTAACGAAATTCGT 2 243 1 ATAATAATAA 0.834122 -58 AATTTAAATTAAAATATAAAAAT 3 2 0 AAAATATAAA 0.986082 -86 AATATACCGTAAATTATATATATATGGAAGTA 3 35 1 AAATTATATA 0.742301 -53 ******* *** Masking position 6 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 0.964838 -299 AAAGTATTTTATGATGGACTTTAAAAGCATTGGT 1 116 1 ATGATATTAA 0.837868 -185 AATTTCTATAATTTTTTAGCAAAAAACATATATA 1 232 1 ATTTTACAAA 0.908072 -69 TATCCCCTTTATAATGAAGATAAAAGAAGTTAAA 1 274 0 ATAATAAAAA 0.812345 -27 AATTTATGGACTTTTATAATTAAATTTTTATATT 2 48 1 CTTTTATAAA 0.904009 -253 CTATAATATAATTATAAATATAAAAATTTAATTA 2 64 0 ATTATAAAAA 0.893489 -237 TTATAATTATATTATAGCGTATAATGTCATAAAA 2 81 1 ATTATCTTAA 0.776778 -220 ATACCCCAATCTTATTAACTTTAAATAAACTAAT 2 121 1 CTTATATTAA 0.880479 -180 TGTGGAAATAATATGGAAATAAAAGAAAATATCC 2 154 1 ATATGATAAA 0.819082 -147 AAAAATTTATATTTTACACTAAAATAATTTTAAT 2 203 1 ATTTTATAAA 0.972375 -98 TTACTATGATATTATTTATTAAAATTATTTTAGT 2 220 0 ATTATATAAA 0.977922 -81 CATAGTAATAATAATTTAACGAAATTCGTAAAAT 2 246 1 ATAATACAAA 0.870112 -55 GGTTTTAGCAATATGCGATTTTAATCCCCCTATT 2 277 0 ATATGATTAA 0.7348 -24 ATTTTTATATTTTAATTTAAATTGA 3 2 1 TTTTTATTAA 0.673418 -86 AATTTACGGTATATTCAATTTAAATTAAAATATA 3 16 0 ATATTATAAA 0.947728 -72 TACTTCCAGAATTATTCAATCAAA 3 74 1 ATTATATAAA 0.978184 -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 TTAGGATATTTTTATATTTCATAATT 1 5 0 TTTATATCAT 0.965116 -296 TTCAAAATATTTAAAAACAAATAGATAGTATG 1 85 0 TTAAAACAAT 0.790034 -216 CACCAATGCTTTTAAAGTCCATCATAAAATAC 1 119 0 TTTAAATCAT 0.947828 -182 AACTATCCCCTTTATAATGAAGATAAAAGAAG 1 279 0 TTTATATAAG 0.866953 -22 CCAATATTTGTTTATTTTGCATTTCC 2 5 0 TTTATTTCAT 0.736721 -296 TTTATGGACTTTTATAATTAAATTTTTATATT 2 50 1 TTTATATAAA 0.842549 -251 TAATTAAATTTTTATATTTATAATTATATTAT 2 64 1 TTTATATATA 0.618517 -237 CATAAAACAATTAATACCCCAATCTTATTAAC 2 108 1 TTAATACCAA 0.793142 -193 CATTAGTTTATTTAAAGTTAATAAGATTGGGG 2 124 0 TTTAAATAAT 0.941513 -177 AAATTTATATTTTACACTAAAATAATTTTAAT 2 205 1 TTTACATAAA 0.806281 -96 TAAAATAATTTTAATAAATAATATCATAGTAA 2 222 1 TTAATAAAAT 0.596666 -79 AATAGGGGGATTAAAATCGCATATTGCTAAAA 2 277 1 TTAAAACCAT 0.793141 -24 ATTTTTATATTTTAATTTAAATTGA 3 4 1 TTTATATTAA 0.553565 -84 TATATTTTAATTTAAATTGAATATACCGTAAA 3 16 1 TTTAAATAAT 0.941885 -72 ****** * *** Masking position 4 Map Score: 8.75354 Number of sites scoring better than the average of aligned sites = 1133 Number in coding regions = 845 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 4 TATTATTTTCCTTACTTCCCTAAGCAATAA 1 198 0 CTTACTTCCC 0.989201 -103 TTATTTCCATATTATTTCCACATTAGTTTA 2 146 0 ATTATTTCCA 0.957833 -155 GATATTTTCTTTTATTTCCATATTATTTCC 2 157 0 TTTATTTCCA 0.957833 -144 AAGTAAGTTTCCTACTTCCATATATATATA 3 49 0 CCTACTTCCA 0.989201 -39 AAGTAGGAAACTTACTTCCAGAATTATTCA 3 62 1 CTTACTTCCA 0.995106 -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 0.957521 -195 TGATGGACTTTAAAAGCATTGGTGCAATTTT 1 127 1 TAAAACATTG 0.799784 -174 CTAAAACTATTAAAAAAATTGCACCAATGCT 1 141 0 TAAAAAATTG 0.964757 -160 TTGCCATTATTAATCTACTTTTATTGCTTAG 1 178 1 TAATCACTTT 0.786661 -123 AGGAAAATAATAAAAGAATTTCTATAATTTT 1 216 1 TAAAAAATTT 0.979982 -85 ATAATGAAGATAAAAGAAGTTAAAGTTTAGG 1 267 0 TAAAAAAGTT 0.877232 -34 AAATGCAAAATAAACAAATATTGGGATAAAC 2 13 1 TAAACAATAT 0.744518 -288 TAAAAGTCCATAAATTACTTGTTTATCCCAA 2 33 0 TAAATACTTG 0.757644 -268 TGGACTTTTATAATTAAATTTTTATATTTAT 2 54 1 TAATTAATTT 0.766256 -247 TTATACGCTATAATATAATTATAAATATAAA 2 74 0 TAATAAATTA 0.76523 -227 TATAATGTCATAAAACAATTAATACCCCAAT 2 100 1 TAAAAAATTA 0.923457 -201 TAACTTTAAATAAACTAATGTGGAAATAATA 2 136 1 TAAACAATGT 0.812 -165 TATTCACAGATAGAAAAATTTATATTTTACA 2 190 1 TAGAAAATTT 0.877232 -111 TATTTTACACTAAAATAATTTTAATAAATAA 2 212 1 TAAAAAATTT 0.979982 -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