AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ityrR_mjan_opreg_100.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0611 300 conserved hypothetical integral membrane protein #2 MJ0612 94 chorismate mutase/prephenate dehydratase (tyrA) #3 MJ1393 247 conserved hypothetical protein Motif number 1 AAAGCTCCCATTATTCCAAATATTGCCCCAGAAG 1 42 0 TTATTATATT 0.92271 -259 AATAATGGGAGCTTTAGCTATTTTAGCTCCACAT 1 61 1 GCTTTATTTT 0.966288 -240 TATAAGAGTGGCAGTAATCATATTTGCACTTATA 1 133 1 GCAGTATATT 0.93007 -168 CTATATAGTAGTTTTCCAAATATTAATCCAGTTA 1 234 0 GTTTTATATT 0.974691 -67 TTATAGGATTGTAGTATATATATTTTGATGAAAC 2 59 0 GTAGTATATT 0.955026 -36 TATTTTTGCTTATTTTAAAATGTTTT 3 3 1 TTTTTATTTT 0.960098 -245 GTTTTATTAGGTATTGATAATTTTAATATCAAAA 3 32 1 GTATTATTTT 0.964263 -216 TTATATATCGGCTGTTATTATTTTCAAATTGAAA 3 69 1 GCTGTATTTT 0.964036 -179 TTTTGGGTTCTTTTTCTAAATTTTTGAAAAATCA 3 113 1 TTTTTATTTT 0.960098 -135 TATGGAACATTTTTTAGACATTTTTGATTTTTCA 3 137 0 TTTTTATTTT 0.960098 -111 ATGTCTTCCGTTTGTATAAATAATTTATGGAACA 3 162 0 TTTGTATAAT 0.7064 -86 ***** ***** Masking position 10 Map Score: 12.4359 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 560 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 2 AACTTTTTCTAAAAGTTTCATTGTTAGGTTT 2 31 0 AAAGTTTCAT 0.993163 -64 AACTTTTAGAAAAAGTTTCATCAAAATATAT 2 45 1 AAAGTTTCAT 0.993163 -50 GCTTATTTTAAAATGTTTTATTAGGTATTGA 3 18 1 AAAGTTTTAT 0.984729 -230 TTTTAATATCAAAAGGTTTATATATCGGCTG 3 52 1 AAAGGTTTAT 0.966694 -196 AATGTCTAAAAAATGTTCCATAAATTATTTA 3 149 1 AAAGTTCCAT 0.984954 -99 *** ******* Masking position 7 Map Score: 6.8105 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 17 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 GGGGCAATATTTGGAATAATGGGAGCTTTA 1 47 1 TTGGAATAAT 0.908344 -254 TCCCTTACTCTTTAAAAACTGGAATTGCAC 1 180 1 TTTAAAAACT 0.893314 -121 GGATTAATATTTGGAAAACTACTATATAGG 1 239 1 TTGGAAAACT 0.962781 -62 AATGAAACTTTTAGAAAAAGTTTCATCAAA 2 40 1 TTAGAAAAAG 0.942697 -55 ATAAAACATTTTAAAATAAGCAAAAATA 3 9 0 TTAAAATAAG 0.725728 -239 TATTTTCAAATTGAAAACCTTGGACTTTTT 3 87 1 TTGAAAACCT 0.754677 -161 TTTCAAAAATTTAGAAAAAGAACCCAAAAA 3 112 0 TTAGAAAAAG 0.942697 -136 TTTCTAAATTTTTGAAAAATCAAAAATGTC 3 125 1 TTTGAAAAAT 0.952255 -123 ATCAAAAATGTCTAAAAAATGTTCCATAAA 3 143 1 TCTAAAAAAT 0.703425 -105 ********** Masking position 5 Map Score: 5.15492 Number of sites scoring better than the average of aligned sites = 1140 Number in coding regions = 976 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 4 TTCACTGGGGATTACAACCCATCAGTCGGAG 1 11 1 ATTACAACCA 0.985555 -290 TGCAAATATGATTACTGCCACTCTTATATTT 1 130 0 ATTACTGCCC 0.953878 -171 TTCATGGAAAATAAAAACCTAACAATGAAAC 2 17 1 ATAAAAACCA 0.941482 -78 TATTAAAATTATCAATACCTAATAAAACATT 3 29 0 ATCAATACCA 0.931143 -219 TTTGAAAATAATAACAGCCGATATATAAACC 3 66 0 ATAACAGCCA 0.975293 -182 ACATTACATTATTACTACCTACTTAAGAATG 3 192 1 ATTACTACCA 0.985555 -56 ********* * Masking position 4 Map Score: 3.74897 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 74 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TAATCATATTTGCACTTATAGATTTAATTC 1 147 1 TGCACTTATA 0.933526 -154 CACACTTAGCTGGGCTTATAACTGGATTAA 1 216 1 TGGGCTTATA 0.980688 -85 GGCTTATAACTGGATTAATATTTGGAAAAC 1 228 1 TGGATTAATA 0.90575 -73 TTTTCACCATTGGATTTTTAATAGTATCTT 1 280 0 TGGATTTTTA 0.974967 -21 GTTTCATTGTTAGGTTTTTATTTTCCATGA 2 18 0 TAGGTTTTTA 0.833218 -77 TTGAAAACCTTGGACTTTTTGGGTTCTTTT 3 97 1 TGGACTTTTT 0.937931 -151 ********** Masking position 6 Map Score: 2.04818 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 256 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 TCGGAGCTTCTGGGGCAATATTTGGAATAA 1 36 1 TGGGGCAATA 0.984824 -265 TGGGATTGGTAAGGGAAATACAACAACTCT 1 98 0 AAGGGAAATA 0.939234 -203 TAAATATAAGAGTGGCAGTAATCATATTTG 1 129 1 AGTGGCAGTA 0.913235 -172 TTTTAAAGAGTAAGGGAGTAGAATTAAATC 1 167 0 TAAGGGAGTA 0.907024 -134 AATCCTATAAAGGGGGAATATT 2 83 1 AGGGGGAATA 0.98975 -12 TTGTGTGAAATAGGGGAACATTCTTAAGTA 3 211 0 TAGGGGAACA 0.957325 -37 ********** Masking position 7 Map Score: 2.13662 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 117 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 ********** No masking Map Score: -1.1836e-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: -1.1836e-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 9 ********** No masking Map Score: -1.1836e-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