AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_mgen_reg_300.orf -o00460_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #2 MG081 55 ribosomal protein L11 (rpl11) #3 MG087 28 ribosomal protein S12 (rpS12) #4 MG090 51 ribosomal protein S6 (rpS6) #5 MG094 49 replicative DNA helicase (dnaB) #6 MG096 182 conserved hypothetical protein #7 MG097 56 uracil DNA glycosylase (ung) #8 MG098 99 Glu-tRNA amidotransferase subunit gatC-related protein #9 MG395 300 putative lipoprotein Motif number 1 TATTTTATAAAAAAATGATACTAATAACGATTACTAG 1 11 0 AAAATATTAA 0.841898 -223 CATTTTTTTATAAAATAATCAAGAACATCAGCACATG 1 31 1 TAAATAAACA 0.885117 -203 AAACCAAACATAAATTTAGTGATAAAGATCATGTGCT 1 60 0 TAAATAAAAG 0.79921 -174 TTACTAAATAGAAATAAAAAAAGAACCTGTT 1 213 0 TAAAAAAAAA 0.882723 -21 AAAATTTTCCAAAAATGTGGGAGCTAATTAAGCGTTT 2 14 1 AAAATTATAA 0.708036 -42 ACTTTTTGGAAAAACTCATTGAGTAAAGTTATATTTT 4 21 0 AAAATAAAAA 0.978573 -31 TTTTCTTTTCAAAACTGAATGGCTAAAATTG 6 5 0 AAAATAGAAA 0.935796 -178 AAATTAATGGTAAAATTATTCATTAAACTTTCCTTGT 6 46 1 TAAATAAAAA 0.976427 -137 ACGAATTTTTTAAAATGAACTTCGAAATACAAACAGT 6 100 0 TAAATATAAA 0.855009 -83 ATGAAATTAAAAAAGACAATTAAATAACATATTTTAA 6 149 0 AAAAAAATAA 0.871742 -34 ACAATTTATGAAATTAAAAAAGACAAT 6 166 0 ACAATAATAA 0.782335 -17 TTATCTAGGTAAAAGTAACTGATCAAAAATTTCTTAA 7 15 0 AAAATAAAAA 0.978575 -42 AACAACCTTGTAAAATTATTTAACTAAGTGATTATTA 8 57 1 TAAATAATAA 0.971526 -43 TTGACTCAGGTAAACTAACTAAATTAAAACCAAAAAA 9 50 0 TAAATAATAA 0.963627 -251 CAACCATCAAAAAAGTTAAAAATGAAAATAGAACTAC 9 89 0 AAAATAAAAA 0.978575 -212 AGCTAATGAAAAAACTAATGAAAGCAAATGCAACCAT 9 119 0 AAAATAACAA 0.88689 -182 TAGATGCAATTAAAAAGAAGAAGCTAATGAAAAAACT 9 140 0 TAAAAAATAA 0.86103 -161 AATTGCATCTAAAACTAAGCAGAATAAAAATAATTAA 9 166 1 AAAATAGTAA 0.923065 -135 TAAAAATAATTAAATTTATCAGTGAAAAGATGAACTC 9 190 1 TAAATAGAAA 0.930005 -111 CTTTAGCTTCAAAAATAATTGAGTTCATCTTTTCACT 9 210 0 AAAATAATCA 0.874215 -91 AAGTGCTTCTTAACTTCATTAATTAAAGGTTTTGAAA 9 259 1 TAACTAAAAA 0.799112 -42 **** * * * *** Masking position 3 Map Score: 30.6856 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 285 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 CAACTTCATTTGAAACCAAACATAAATTTAG 1 78 0 TGAAACAAAC 0.851509 -156 AACCAGCTTCTAAATCTAAAGCATGATTACA 1 129 0 TAAATCAAAG 0.824108 -105 ACTGGTTACCTGAAACAAAAGTAACCAGCTT 1 151 0 TGAAACAAAG 0.961553 -83 ACTGAGAACCTGAAAAAAACAGGTTCTTTTT 1 196 1 TGAAAAAACA 0.796128 -38 TAAATAGAAATAAAAAAAGAACCTGTTTTTT 1 209 0 TAAAAAAGAA 0.842692 -25 ATACTTAATAAAAATATAACTTTACTCAA 4 9 1 TAAAAAATAA 0.662615 -43 CATTCAGTTTTGAAAAGAAAAGTTTAAATTA 6 21 1 TGAAAAAAAA 0.968546 -162 ACAATTTATGAAATTAAAAAAGACAATTA 6 164 0 TGAAATAAAA 0.884263 -19 TTTACCTAGATAAATTTAAAGTTTATTT 7 39 1 TAAATTAAAG 0.517292 -18 TTAAAAACAAAGCTGTAGTTGA 8 2 1 TAAAAAAAAG 0.941393 -98 ACTTGTTTATTGATTAGAAAAACAACAACCT 8 34 1 TGATTAAAAA 0.656967 -66 CTAACTAAATTAAAACCAAAAAAATTAATCC 9 42 0 TAAAACAAAA 0.958802 -259 AAGTTAAAAATGAAAATAGAACTACTATTGA 9 83 0 TGAAAAAGAA 0.88491 -218 AAGAAGAAGCTAATGAAAAAACTAATGAAAG 9 132 0 TAATGAAAAA 0.590234 -169 TAGATGCAATTAAAAAGAAGAAGCTAATGAA 9 146 0 TAAAAAAAGA 0.731236 -155 CAATTATTTTTGAAGCTAAAGCCTAAGTTTA 9 226 1 TGAAGCAAAG 0.878927 -75 TTTAATACAAAAATATTTCAAAA 9 288 0 TAATACAAAA 0.84334 -13 ****** **** Masking position 8 Map Score: 12.3435 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 535 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 ATTACAATAAAGCAGGATTTATAATCCAACTTC 1 102 0 AGCAATTATA 0.806178 -132 CTAAATCTAAAGCATGATTACAATAAAGCAGGA 1 118 0 AGCAATTCAA 0.860427 -116 TGCTATCATTTGCATATTTAAAA 5 1 0 TGCATTTAAA 0.782153 -49 TGCAAATGATAGCAACATTGAACGTGCTGAAAG 5 20 1 AGCAATTAAC 0.951764 -30 TCGAAATACAAACAGTATTGAAAACTACAACTA 6 83 0 AACAATTAAA 0.954594 -100 ACAATTAAATAACATATTTTAAAGATCTAGAAC 6 138 0 AACATTTAAA 0.947774 -45 CTAATCAATAAACAAGTGTCAACTACAGCTTTG 8 18 0 AACATGTAAC 0.822218 -82 ACAACCTTGTAAAATTATTTAACTAAGTGATTA 8 58 1 AAAAATTAAC 0.573166 -42 CAGGTAAACTAACTAAATTAAAACCAAAAAAAT 9 48 0 AACTATTAAA 0.811105 -253 AAAAAGAAGAAGCTAATGAAAAAACTAATGAAA 9 133 0 AGCTTGAAAA 0.415377 -168 TCTAAAACTAAGCAGAATAAAAATAATTAAATT 9 173 1 AGCAATAAAA 0.888678 -128 GAAGTTAAGAAGCACTTGTTAAACTTAGGCTTT 9 243 0 AGCATGTAAA 0.944543 -58 TTTAATACAAAAATATTTCAAAACCTTTAATT 9 279 0 AAAATTTAAA 0.696612 -22 **** *** *** Masking position 12 Map Score: 5.63765 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 664 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 TGTGCTGATGTTCTTGATTATTTTATAAAA 1 36 0 TTCTTGATTA 0.906391 -198 AGTTATATTTTTATTAAGTAT 4 2 0 TTATTAAGTA 0.909313 -50 TTGGAAAAACTCATTGAGTAAAGTTATATT 4 23 0 TCATTGAGTA 0.910132 -29 AATGGTAAAATTATTCATTAAACTTTCCTT 6 51 1 TTATTCATTA 0.954796 -132 TGACACTTGTTTATTGATTAGAAAAACAAC 8 30 1 TTATTGATTA 0.968116 -70 AACTAAGTGATTATTACTTAATTGCACTTT 8 78 1 TTATTACTTA 0.841611 -22 TTTCATTAGTTTTTTCATTAGCTTCTTCTT 9 133 1 TTTTTCATTA 0.818875 -168 CTTCTTAACTTCATTAATTAAAGGTTTTGA 9 264 1 TCATTAATTA 0.887963 -37 ********** Masking position 10 Map Score: 5.01924 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 29 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 CAGGATTTATAATCCAACTTCATTTGAAAC 1 93 0 AATCCAACTT 0.890714 -141 TTGGATTATAAATCCTGCTTTATTGTAATC 1 106 1 AATCCTGCTT 0.986796 -128 GCTTTATTGTAATCATGCTTTAGATTTAGA 1 122 1 AATCATGCTT 0.899766 -112 GAAACAAAAGTAACCAGCTTCTAAATCTAA 1 141 0 TAACCAGCTT 0.850206 -93 TGTAGTTTTCAATACTGTTTGTATTTCGAA 6 87 1 AATACTGTTT 0.781911 -96 ACAAGTGTCAACTACAGCTTTGTTTTTAA 8 10 0 ACTACAGCTT 0.867307 -90 TAATTATTTTTATTCTGCTTAGTTTTAGAT 9 172 0 TATTCTGCTT 0.872179 -129 ********** Masking position 9 Map Score: 1.10331 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 104 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 CAAGAACATCAGCACATGATCTTTATCACTA 1 50 1 AGCACATGTC 0.938212 -184 CTCAGTTTTTTGGAAATGGTACTGGTTACCT 1 171 0 TGGAAATGTA 0.915345 -63 TTTTAAATATGCAAATGATAGCAACATTGA 5 10 1 TGCAAATGTA 0.982551 -40 ATCAAGCCAATGCAAATTCTAACGGGATTAA 9 18 1 TGCAAATTTA 0.8792 -283 AACTAATGAAAGCAAATGCAACCATCAAAAA 9 113 0 AGCAAATGAA 0.969607 -188 AAAAAGAAGAAGCTAATGAAAAAACTAATGA 9 135 0 AGCTAATGAA 0.868824 -166 GAAGTTAAGAAGCACTTGTTAAACTTAGGCT 9 245 0 AGCACTTGTA 0.911072 -56 ******** ** Masking position 7 Map Score: 1.18544 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 136 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: 2.29038e-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: 2.29038e-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: 2.29038e-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