AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ifruR_rpxx_opreg_300.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP264 300 unknown #2 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #3 RP492 300 PYRUVATE,PHOSPHATE DIKINASE PRECURSOR (ppdK) #4 RP707 194 unknown #5 RP708 300 INTEGRATION HOST FACTOR ALPHA-SUBUNIT (himA) Motif number 1 TGCTGTGCAAATAATTAACAATATATAATAA 1 6 0 ATAATCATAT 0.955663 -295 TCTAAGATAAATAACATTAAGTAATTTGTCTATAAT 1 130 0 ATAACAATTT 0.913356 -171 AATCCAAAAAATAATTAAAAATGCTTTTTAAAAAGA 1 209 1 ATAATAATTT 0.985258 -92 TGCAAGCAATATACTAAGCAATCTTTTTAAAAAGCA 1 230 0 ATACTCATTT 0.914229 -71 ACCTAACAAGCTAATTGAAATTCTTTTAACATATTA 3 96 0 CTAATAATTT 0.913356 -205 TGTGTGTACAATAATTACAATAAATTTTCCCCTCAG 3 133 0 ATAATAAATT 0.876732 -168 ATTTGTTATTATAATTGTAATTATATTGTGTGTACA 3 159 0 ATAATAATAT 0.977043 -142 AACAAATTCCATAATGTCAATTCTTTAAAGAAAGAT 3 188 1 ATAATAATTT 0.985256 -113 TTACGGTATAATAATATTAACTCAATTCACATCTAT 4 40 0 ATAATAATAT 0.977049 -155 ATACTCTAAAATACATGTGTTATTAC 4 179 0 ATACTAATAT 0.930996 -16 AGGATTTTTAATAATTTTCAATTTTTACTTTTTACA 5 166 0 ATAATCATTT 0.96864 -135 AATAAATTACATAATAATATTTATTTGCACTTCAGG 5 199 0 ATAATATTTT 0.876725 -102 AAATAATACCAATTTTATATATTATGTT 5 283 0 ATAATAATAT 0.977036 -18 ***** ** * ** Masking position 3 Map Score: 17.7847 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 121 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 CACAGCATTCAATTTATGTTAAGTTAGAAGATTA 1 35 1 ATTTAGTAAT 0.862031 -266 TAGAAGATTAACACTATGTTATATGAGGTGCTGA 1 59 1 AACTAGTATT 0.955358 -242 AAGATAAATAACATTAAGTAATTTGTCTATAATT 1 129 0 AATTAGAATT 0.825299 -172 ATCTCTTATTAATCTAAGATAAATAACATTAAGT 1 144 0 ATCTAGTAAT 0.829015 -157 TGCAAGCAATATACTAAGCAATCTTTTTAAAAAG 1 232 0 AACTAGAATT 0.920594 -69 TTGTATAAGTAGACTATGCAAAAAATAAACAATG 2 37 1 AACTAGAAAA 0.842109 -66 TGCAAAAAATAAACAATGGTAATTTAACATTGGT 2 53 1 AACAAGTAAT 0.695111 -50 ACGACCATTTAGATTATGGTAGCTTTTCTTAAAT 3 55 1 AATTAGTAGT 0.850985 -246 AAATTAGTCAATAATATGTTAAAAGAATTTCAAT 3 85 1 AAATAGTAAA 0.739477 -216 TAAAGAATTGACATTATGGAATTTGTTATTATAA 3 181 0 AATTAGAATT 0.93699 -120 TAGCAATGTTAAATTAAGATATCTTTCTTTAAAG 3 210 0 AATTAGTATT 0.967701 -91 CATTATTTATACATTAGGAAAAAAATAGTAGCAA 3 238 0 AATTAGAAAA 0.876891 -63 ACTCGATTAAAGTTTACGGTATAATAATATTAAC 4 55 0 ATTTAGTATA 0.854764 -140 CAGATCTGATACAATAAGTTATATAGATCACTCG 4 84 0 AAATAGTATT 0.86064 -111 TATCTAGGTGATTTTATGTAATAACACATGTATT 4 162 1 ATTTAGAATA 0.750162 -33 TTTACTTTTTACATAAAGCTATAACCTATAAATT 5 145 0 AATAAGTATA 0.735166 -156 TAACAGTAGAATATTACGTTAATAAATTACATAA 5 221 0 AATTAGTAAA 0.922639 -80 CCAATTTTATATATTATGTTGTTTAAATATCCAG 5 269 0 AATTAGTGTT 0.760007 -32 * **** * *** * Masking position 6 Map Score: 20.4763 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 208 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 TTATTATATATTGTTAATTATTTGCAC 1 5 1 TAATTTTTAA 0.946407 -296 TAATCTAAGATAAATAACATTAAGTAATTTGTC 1 136 0 TAATACTTAA 0.484403 -165 CTTACAATGACATCTCTTATTAATCTAAGATAA 1 156 0 CACTTTTTAA 0.970278 -145 AAAATACTCTCATCTTTTCGTAAACCAATGTTA 2 77 0 CACTTTGTAA 0.948053 -26 TAGATTATGGTAGCTTTTCTTAAATTAGTCAAT 3 64 1 TACTTTTTAA 0.978 -237 TAAATTAAGATATCTTTCTTTAAAGAATTGACA 3 202 0 TACTTCTTAA 0.939052 -99 GCTAATAGTGTATATGTTTTTAAGTACTACATT 3 268 0 TAATTTTTAA 0.946421 -33 TGCACTTCACTATCTTTTGTTTAGTTCT 5 6 0 TACTTTTTTA 0.825501 -295 TTGGTGCCACCACCTGATAGTAAGTATCGTTTT 5 56 0 CACTATGTAA 0.788428 -245 CTATAACCTATAAATTTTGCTAATGCTTCAACT 5 128 0 TAATTTCTAA 0.786516 -173 TTATAGGTTATAGCTTTATGTAAAAAGTAAAAA 5 148 1 TACTTAGTAA 0.759496 -153 GAAGTGCAAATAAATATTATTATGTAATTTATT 5 202 1 TAATTTTTAT 0.651896 -99 ACGTAATATTCTACTGTTATTAATATTTTAGTT 5 236 1 CTCTTTTTAA 0.77504 -65 ** ** ** **** Masking position 5 Map Score: 7.51828 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 360 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 AAGTAATTTGTCTATAATTAAAAACTGCAC 1 118 0 TCTATAATTA 0.840159 -183 TTAAAAAGCATTTTTAATTATTTTTTGGAT 1 210 0 TTTTTAATTA 0.799226 -91 AAAAATGCTTTTTAAAAAGATTGCTTAGTA 1 225 1 TTTAAAAAGA 0.544384 -76 CTGTTTAAGCTCTATAAGGATCAAAG 1 285 1 TCTATAAGGA 0.788509 -16 CCAAGTTGATTGTATAAGTAGACTATGCAA 2 28 1 TGTATAAGTA 0.883962 -75 CGTAAACCAATGTTAAATTACCATTGTTTA 2 62 0 TGTTAAATTA 0.886 -41 TGGTAGCTTTTCTTAAATTAGTCAATAATA 3 71 1 TCTTAAATTA 0.840159 -230 GTCAATAATATGTTAAAAGAATTTCAATTA 3 91 1 TGTTAAAAGA 0.845548 -210 TAATGTCAATTCTTTAAAGAAAGATATCTT 3 199 1 TCTTTAAAGA 0.489928 -102 ATAGTAGCAATGTTAAATTAAGATATCTTT 3 218 0 TGTTAAATTA 0.886 -83 TTTTTCCTAATGTATAAATAATGTAGTACT 3 249 1 TGTATAAATA 0.885749 -52 AGTGTATATGTTTTTAAGTACTACATTATT 3 265 0 TTTTTAAGTA 0.795998 -36 TATATTATGTTGTTTAAATATCCAGAACTA 5 264 0 TGTTTAAATA 0.912835 -37 ********** Masking position 6 Map Score: 11.3643 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 203 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 TTGTTAATTATTTGCACAGCATTCAATTTAT 1 21 1 TTTGCACACA 0.979903 -280 CCGCAGTGACTTAGCAATCCAAAAAATAATT 1 194 1 TTAGCAATCA 0.95583 -107 CACCACGTGTGTTGCAATCCAGATCTGATAC 4 106 0 GTTGCAATCA 0.969764 -89 TTATATCTAGTTTGCACTTCACTATCTTTTG 5 20 0 TTTGCACTCA 0.993805 -281 ATAATATTTATTTGCACTTCAGGATTTTTAA 5 191 0 TTTGCACTCA 0.993805 -110 ******** ** Masking position 6 Map Score: 4.4877 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 CTAACTTAACATAAATTGAATGCTGTGCAA 1 32 0 ATAAATTGAA 0.762629 -269 GTCTATAATTAAAAACTGCACCTTTACCAT 1 109 0 AAAAACTGCA 0.933743 -192 TAGACTATGCAAAAAATAAACAATGGTAAT 2 46 1 AAAAAATAAA 0.705377 -57 TGGTGACGAAAAAAACTGAATATGTGCTTT 4 132 1 AAAAACTGAA 0.978633 -63 AACTAGATATAAAACCTAAAACGATACTTA 5 39 1 AAAACCTAAA 0.893701 -262 TGTAAAAAGTAAAAATTGAAAATTATTAAA 5 166 1 AAAAATTGAA 0.939305 -135 AAATTATTAAAAATCCTGAAGTGCAAATAA 5 185 1 AAATCCTGAA 0.864835 -116 ********** Masking position 3 Map Score: 2.06667 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 200 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 ********** No masking Map Score: -2.10077e-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: -2.10077e-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 9 ********** No masking Map Score: -2.10077e-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