AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_mjan_reg_100.orf -o00030_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 MJ0406 154 ribokinase (rbsK) #2 MJ0679 39 transketolase'' #3 MJ0680 23 pentose-5-phosphate-3-epimerase #4 MJ0681 156 transketolase' #5 MJ1368 122 sulfate transport system permease protein (cysT) #6 MJ1603 300 ribose 5-phosphate isomerase #7 MJ1605 37 glucose-6-phosphate isomerase #8 MJ1606 167 glycogen synthase (glgA) Motif number 1 AGTAACTTTAAAGTTAAAATTATTGAACTACTA 1 26 0 AATAAAATAT 0.97275 -129 CTAATACTTAATGTTCAATTTATTCAAATCATT 1 114 1 ATTCAATTAT 0.747909 -41 AAACAAAAATAATAAATTAATTA 2 1 1 AAAAAAATAT 0.958517 -39 TAAAACTTACACCTAAAAATAATAGATAGTAAA 4 21 0 ACAAAAATAT 0.888974 -136 TAATGATGTTATGCTAAAATAATTGTTAGTCAT 4 57 0 ATTAAAATAT 0.95616 -100 TAAAAAAAGCAAAAACAAAAAATCCATAATGAT 4 83 0 AAACAAAAAT 0.758093 -74 TAAGATTTAAAAAATAATATCATTACTCAATGA 4 121 0 AATAATATAT 0.961624 -36 TAAATTTTTAATGAAAATATTATACTATCAAAT 5 16 1 ATAAATATAT 0.831644 -107 AATTTGTGTTAAACAAAATTGATGACATTTGAT 5 42 0 AAAAAATTAT 0.902136 -81 ATTTTGTTTAACACAAATTTTATATAATTAGGT 5 56 1 ACAAATTTAT 0.720263 -67 AATCATTTTTAAGGTAATTAAATTACCTAATTA 5 80 0 AATAATTAAT 0.820926 -43 GAAATAATTGTAATATAATCATCGAAACT 6 7 1 ATTAATATAT 0.939851 -294 ATAAAACACAAAAATAATATTATTTTCTTTTTC 6 80 1 AATAATATAT 0.961624 -221 AGATTTAAATATATAAATATAATGAAGAAAAAG 6 106 0 ATAAATATAT 0.879599 -195 TCAAAATTCCAAACTCAATATATAGACTGTGAA 6 181 0 AATCAATAAT 0.659211 -120 GATATTATTTAATGTAAAAAGATGCCTTTGGCA 6 214 0 AATAAAAAAT 0.934478 -87 TAAATTAGATAATATAAAAACATTGTGATATAT 8 82 1 AATAAAAAAT 0.934385 -86 ATATATGTACATCATAATATAATATTTATTGTT 8 109 1 ATTAATATAT 0.771281 -59 ** ****** ** Masking position 13 Map Score: 21.5588 Number of sites scoring better than the average of aligned sites = 1317 Number in coding regions = 883 Number in noncoding regions = 434 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 2 TTAAAATTATTGAACTACTACTTAAAGATTTTTAG 1 10 0 TAATATTAAA 0.941757 -145 AGTAGTTCAATAATTTTAACTTTAAAGTTACTCTAT 1 27 1 TATTTTTAAA 0.96897 -128 CAATTTTTGCTAATCTACTATATAAAGGGTTCAAAC 1 68 1 TATTAATAAA 0.918015 -87 ATTCAAATCATTAAGTTATTCTTAAAAATT 1 135 1 TAATTTTAAA 0.9365 -20 AATAAATTAATTATTTTGGGTGAAAAATC 2 21 1 TATTTGAAAA 0.860305 -19 GGTGTAAGTTTTAAATATGACTAACAATTATTTTAG 4 41 1 TAATATAACA 0.778572 -116 AAATCCATAATGATGTTATGCTAAAATAATTGTTAG 4 61 0 TATTTTAAAA 0.958233 -96 CATTACTCAATGAATTAATAAAAAAAGCAAAAACAA 4 98 0 TAATAAAAAA 0.78128 -59 CATTGAGTAATGATATTATTTTTTAAATCTTAAAAA 4 122 1 TATTTTTTAA 0.899392 -35 TTTGATAGTATAATATTTTCATTAAAAATTTATTAA 5 12 0 TATTTTTAAA 0.968931 -111 CCTAATTATATAAAATTTGTGTTAAACAAAATTGAT 5 52 0 TAATTTTAAA 0.936697 -71 ATTAGGTAATTTAATTACCTTAAAAATGATTAAGAT 5 82 1 TAATAAAAAA 0.795048 -41 AAAGTTTTTGTAATTTATAGATTTAAATATATAAAT 6 121 0 TATTATTTAA 0.926939 -180 GGATAAGATATTATTTAATGTAAAAAGATGCCTTTG 6 217 0 TATTAAAAAA 0.891609 -84 GAAAGTCCTGTAATATTTCAATAACAACCACAAAGC 6 258 1 TATTTTAACA 0.877561 -43 AATATCATCATTTAGATTTTTAAATATAGTATA 8 8 1 TATTATTTAA 0.927273 -160 AAAAACTATCTAATAGATACTTTAAATTAGATAATA 8 60 1 TATGATTAAA 0.785729 -108 TATTATATTATGATGTACATATATCACAATGTTTTT 8 97 0 TATTATATCA 0.705338 -71 CATCATAATATAATATTTATTGTTAAAATCTGAAAT 8 118 1 TATTTGTTAA 0.755651 -50 * ** ** ***** Masking position 1 Map Score: 19.8858 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 977 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 334 Fraction of orfs with sites within 600 bp upstream = 0.053646 Motif number 3 AATTATTGAACTACTACTTAAAGATTTTTAG 1 10 0 CTATCTTAAA 0.709866 -145 TAGAGTAACTTTAAAGTTAAAATTATTGAACT 1 30 0 TTAATTAAAA 0.93129 -125 TTTTGCTAATCTACTATATAAAGGGTTCAAAC 1 72 1 CTATTATAAA 0.870574 -83 AATCATTAAGTTATTCTTAAAAATT 1 140 1 TTATTTAAAA 0.961957 -15 TATTTAAAACTTACACCTAAAAATAATAGATA 4 26 0 TTAACTAAAA 0.838308 -131 TAATTGTTAGTCATATTTAAAACTTACACCTA 4 39 0 TCAATTAAAA 0.643837 -118 ACTCAATGAATTAATAAAAAAAGCAAAAACAA 4 98 0 TTATAAAAAA 0.689222 -59 AGTAATGATATTATTTTTTAAATCTTAAAAAG 4 127 1 TTATTTTAAA 0.927517 -30 AGTATAATATTTTCATTAAAAATTTATTAAA 5 10 0 TTTATAAAAA 0.516678 -113 TTAAATTACCTAATTATATAAAATTTGTGTTA 5 64 0 TAATTATAAA 0.66363 -59 GGTAATTTAATTACCTTAAAAATGATTAAGAT 5 86 1 TTACTAAAAA 0.814345 -37 ACCATAATCCCTATAATTAAAATCAGACCAAT 6 43 1 CTAATTAAAA 0.879564 -258 TTTATAGATTTAAATATATAAATATAATGAAG 6 112 0 TAATTATAAA 0.663809 -189 AAGATATTATTTAATGTAAAAAGATGCCTTTG 6 217 0 TTATTAAAAA 0.956536 -84 CCCAAATCTTTTATTACATAAAGTGGAAAG 7 9 0 TTATCATAAA 0.801268 -29 AAGATTTATACTATATTTAAAAATCTAAATGA 8 18 0 CTAATTAAAA 0.879811 -150 TTTAAATTAGATAATATAAAAACATTGTGATA 8 80 1 ATATTAAAAA 0.715288 -88 AATATAATATTTATTGTTAAAATCTGAAATTG 8 124 1 TTATTTAAAA 0.95603 -44 *** * ****** Masking position 10 Map Score: 16.2157 Number of sites scoring better than the average of aligned sites = 1316 Number in coding regions = 870 Number in noncoding regions = 446 Number of orfs with sites within 600 bp upstream = 344 Fraction of orfs with sites within 600 bp upstream = 0.0552522 Motif number 4 TAGATTAGCAAAAATTGTTTATATAGAGTA 1 55 0 AAAATTGTTT 0.845755 -100 TTAATTTATTATTTTTGTTT 2 1 0 ATTTTTGTTT 0.962276 -39 AATTTTATTTTTTGGTGATT 3 1 1 AATTTTATTT 0.903313 -23 TCATTATGGATTTTTTGTTTTTGCTTTTTT 4 84 1 TTTTTTGTTT 0.82051 -73 AAATGTCATCAATTTTGTTTAACACAAATT 5 45 1 AATTTTGTTT 0.976138 -78 TAATTATATAAAATTTGTGTTAAACAAAAT 5 56 0 AAATTTGTGT 0.894539 -67 AAATAATATTATTTTTGTGTTTTATCCCGA 6 75 0 ATTTTTGTGT 0.935254 -226 ACACAAAAATAATATTATTTTCTTTTTCTT 6 85 1 AATATTATTT 0.774071 -216 ********** Masking position 5 Map Score: 6.27215 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 361 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 5 CTAAAAATCTTTAAGTAGTAGTTCAA 1 7 1 ATCTTTAAGT 0.454358 -148 TATATAGAGTAACTTTAAAGTTAAAATTAT 1 36 0 AACTTTAAAG 0.519613 -119 TAAGTATTAGAACAATAACTGTTTGAACCC 1 94 0 AACAATAACT 0.927235 -61 GAATAAATTGAACATTAAGTATTAGAACAA 1 109 0 AACATTAAGT 0.833046 -46 ACTTAATGATTTGAATAAATTGAACATTAA 1 121 0 TTGAATAAAT 0.543608 -34 AATTTTTAAGAATAACTTAATGATTTG 1 138 0 AAGAATAACT 0.799568 -17 AAACAAAAATAATAAATTAATTATTTT 2 8 1 AATAATAAAT 0.642211 -32 AAAAAGCAAAAACAAAAAATCCATAATGAT 4 83 0 AACAAAAAAT 0.81051 -74 ATATATTTAAATCTATAAATTACAAAAACT 6 125 1 ATCTATAAAT 0.786807 -176 ATCTATAAATTACAAAAACTTTTTATAACA 6 135 1 TACAAAAACT 0.576964 -166 GGCATCTTTTTACATTAAATAATATCTTAT 6 221 1 TACATTAAAT 0.881165 -80 TTTTTAAATATAGTATAAATCTTAGAAAGG 8 27 1 TAGTATAAAT 0.698909 -141 ATCTAATAGATACTTTAAATTAGATAATAT 8 67 1 TACTTTAAAT 0.808765 -101 TTCAGATTTTAACAATAAATATTATATTAT 8 122 0 AACAATAAAT 0.957968 -46 ********** Masking position 7 Map Score: 6.92356 Number of sites scoring better than the average of aligned sites = 1432 Number in coding regions = 1205 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 6 TATAGAGTAACTTTAAAGTTAAAATTATTG 1 34 0 CTTTAAAGTT 0.813107 -121 TTAAGTTATTCTTAAAAATT 1 145 1 CTTAAAAATT 0.884833 -10 TTTTTTAAATCTTAAAAAGGTGAAACT 4 140 1 CTTAAAAAGG 0.968918 -17 ATTTAATTACCTTAAAAATGATTAAGATTG 5 90 1 CTTAAAAATG 0.924161 -33 AATATATAGACTGTGAAAGTCCTGTATTAA 6 168 0 CTGTGAAAGT 0.916034 -133 ATCTTATCCTCTGTGAAAGTCCTGTAATAT 6 244 1 CTGTGAAAGT 0.916034 -57 TAGTATAAATCTTAGAAAGGTATAAAAACT 8 37 1 CTTAGAAAGG 0.968309 -131 ATTGAAATTGCTTTAAAGGGGTAATT 8 152 1 CTTTAAAGGG 0.946388 -16 ********** Masking position 6 Map Score: 6.86743 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 134 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 AAACAAAAATAATAAATTAATTA 2 4 1 CAAAAATAAT 0.844496 -36 TATCCCTAATCAATCTTAATCATTTTTAAG 5 100 0 CAATCTTAAT 0.952171 -23 ATCGAAACTCCAACCATAATCCCTATAATT 6 31 1 CAACCATAAT 0.955537 -270 GGATAAAACACAAAAATAATATTATTTTCT 6 78 1 CAAAAATAAT 0.844496 -223 CTTTTTATAACATTCTTAATACAGGACTTT 6 153 1 CATTCTTAAT 0.781066 -148 ATCAAAATTCCAAACTCAATATATAGACTG 6 185 0 CAAACTCAAT 0.951251 -116 ATTTCAATAACAACCACAAAGCCAGAAAAG 6 272 1 CAACCACAAA 0.790571 -29 CCCTTTAAAGCAATTTCAATTTCAGATTTT 8 142 0 CAATTTCAAT 0.751164 -26 ********** Masking position 8 Map Score: 3.03239 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 142 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 AACAATAACTGTTTGAACCCTTTATATAGT 1 84 0 GTTTGAACCC 0.940097 -71 GATTTTTCACCCAAAATAATTA 2 28 0 TTTTTCACCC 0.915897 -12 ATGATATTATTTTTTAAATCTTAAAAAGGT 4 131 1 TTTTTAAATC 0.775013 -26 TTATTTTTGTGTTTTATCCCGAATTGGTCT 6 67 0 GTTTTATCCC 0.968615 -234 TTACAAAAACTTTTTATAACATTCTTAATA 6 144 1 TTTTTATAAC 0.817291 -157 GAGTTTGGAATTTTGATGCCAAAGGCATCT 6 198 1 TTTTGATGCC 0.920499 -103 TATTAGATAGTTTTTATACCTTTCTAAGAT 8 45 0 TTTTTATACC 0.966926 -123 ********** Masking position 4 Map Score: 1.00014 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 288 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ********** No masking Map Score: -9.92328e-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 10 ********** No masking Map Score: -9.92328e-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 11 ********** No masking Map Score: -9.92328e-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