AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_mpneu_reg_100.orf -o00530_mpneu_100.ace -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 R02_orf694 50 fruA; PTS system, fructose-specific IIABC component (EIIABC-Fru) #2 MPNtRNA-Ser01 300 mptgsb; tRNA-Ser. #3 E09_orf379 300 mtlA; PTS system mannitol-specific component IIA(EIIA-MTL). #4 P02_orf305 138 yjfW; #5 GT9_orf940o 51 ptsG; PTS system, glucose-specific IIABC component (EIIABC-Glc) #6 GT9_orf113 54 hypothetical protein. #7 GT9_orf438V 300 hypothetical protein. Motif number 1 AGGAACTGGAATCTAAATTTATTATAAA 1 8 1 GGAATCAAAT 0.843397 -43 TCTAATGAAGTCAATCACAAACCATTCAATC 2 30 1 TCAATCCAAA 0.844547 -271 CACAAACCATTCAATCACAAACAACACATAA 2 45 1 TCAATCCAAA 0.844547 -256 TAAATTGTTTGCAACAGCAAATTCCGGAATT 2 176 1 GCAACACAAA 0.953485 -125 AACAAAAAGCGCAATAAAAAAGCAGACCACT 2 244 1 GCAATAAAAA 0.973441 -57 TAAAAATTTCTCAATATAAATTGTAAGCAGA 2 280 0 TCAATAAAAT 0.708934 -21 TCAACCAGATGGAATAAAAAAAGAAGCTAAA 3 90 0 GGAATAAAAA 0.969282 -211 TGGTGGAATAGGAATCCAATATGTGATTCCG 3 146 1 GGAATCAATA 0.738541 -155 TATGAATGGCGGAACCCAAAAAGGGTCACAC 4 50 0 GGAACCAAAA 0.972129 -89 GTATTCTTTAGCAATAAAAAACTCCCGGTTT 4 93 0 GCAATAAAAA 0.973441 -46 CATATTTAGCTAAACAAAAAACAAATTTTTA 7 50 0 TAAACAAAAA 0.637884 -251 AATAAGTGTGGGAACAGAAAATCAGGCTTTC 7 142 1 GGAACAAAAA 0.974586 -159 AATCAGGCTTTCAACACAAAATTTTCGTTTT 7 161 1 TCAACAAAAA 0.940386 -140 TTATTTAGTGGGAGCAGAAAAACGAAAATTT 7 179 0 GGAGCAAAAA 0.848348 -122 ****** **** Masking position 3 Map Score: 15.9816 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 122 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 CCTAAAGTCAGAAAATCCAATATTTATAATAAAT 1 27 0 GAAATCAAAT 0.751487 -24 GTAATAAAAGAAAACGCAAAAATTTTTATAAATT 2 148 1 AAACGCAAAT 0.95633 -153 CCAAGCAATAAAGATGCCAATAATCGGCATCGTC 3 51 0 AAGTGCAAAT 0.92411 -250 GGAATAAAAAAAGAAGCTAAAAGTCCCCAAGCAA 3 77 0 AAGAGCAAAT 0.98722 -224 CTCAATGTTTAAGTAACAAAAATTTAAGGATTTA 5 14 1 AAGAACAAAT 0.982924 -38 TCTTGAGCAACTAAGATTTAACTTAAAA 6 37 0 GAGAACAAAT 0.96986 -18 CAAATTTTTAAAGGAACAAACATTCATAACTGCT 7 26 0 AAGAACAAAT 0.982924 -275 TTAGCTAAACAAAAAACAAATTTTTAAAGGAACA 7 42 0 AAAAACAATT 0.751104 -259 TAAGTAAATTAAGACATAAAAAATGAACACATTA 7 104 1 AAGCATAAAT 0.721196 -197 AGTGGGAGCAGAAAAACGAAAATTTTGTGTTGAA 7 170 0 GAAAACAAAT 0.935756 -131 TGGGTTTTAAAAACCGCCAAAAATTTTTAATTTA 7 217 1 AAACGCAAAT 0.95633 -84 AGGGAGGAGAAAGTAGCAAAAACTAAATTAAAAA 7 240 0 AAGAGCAAAT 0.98722 -61 *** *** ** * * Masking position 9 Map Score: 15.0541 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 73 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 ACTTGGTTATGTGTTGTTTGTGATTGAATGGTTT 2 48 0 GTTTGTGTGT 0.824652 -253 CTGTGAGGTCTCGTCTTACTTGGTTATGTGTTGT 2 65 0 TCTCTTTTGT 0.860306 -236 CGAGCCTCAGGTCGCTTGGTTTTTTTACAGAATT 2 104 1 GTGCTTTTTT 0.827425 -197 AAAAATTTTTGCGTTTTCTTTTATTACTGAAGTG 2 141 0 GCTTTTTTTT 0.922106 -160 TAAAAATTCCGTTTCTTTCTTGTTAACAAAAAGC 2 220 1 GTTCTTTTGT 0.974906 -81 TCAGTGGTCTGCTTTTTTATTGCGCTTTTTGTTA 2 243 0 GCTTTTTTGG 0.9099 -58 CCAATAATCGGCATCGTCATTGATGAAAGCAATG 3 35 0 GCTCGTTTGT 0.979585 -266 CCGATTATTGGCATCTTTATTGCTTGGGGACTTT 3 58 1 GCTCTTTTGT 0.988483 -243 GGGACTTTTAGCTTCTTTTTTTATTCCATCTGGT 3 84 1 GCTCTTTTTT 0.949868 -217 GACCATAATTGTTTTTTTGGTGGTAAAAAGATTT 3 176 1 GTTTTTGTGT 0.893758 -125 GAAATACGTGGTGGTGTGATTGCTGTCATTATTG 3 212 1 GTGTGTTTGT 0.883535 -89 TGCCTAAAAAGCCGTTTACTTGTATTCTTTAGCA 4 111 0 GCGTTTTTGA 0.792065 -28 ** **** *** * Masking position 7 Map Score: 9.45425 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 219 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 AATTTTTGCGTTTTCTTTTATTACTGAAGTGCAAAA 2 136 0 TTTCTTATTG 0.832887 -165 ACGCAAAAATTTTTATAAATTGTTTGCAACAGCAAA 2 161 1 TTTATATTTG 0.716729 -140 AGCTCGCTTAATTCCGGAATTTGCTGTTGCAAACAA 2 180 0 ATTCGATTTG 0.853047 -121 CTTTGGATTCATTGCTTTCATCAATGACGATGCCGA 3 26 1 ATTCTCATTG 0.974476 -275 CCAATATGTGATTCCGACCATAATTGTTTTTTTGGT 3 161 1 ATTCGCATTG 0.936115 -140 TGGTAAAAAGATTTATGAAATACGTGGTGGTGTGAT 3 196 1 ATTATAATTG 0.951601 -105 TGGTGGTGTGATTGCTGTCATTATTGCCATTGCTGT 3 220 1 ATTCTCATTG 0.974476 -81 CATTATTGCCATTGCTGTAATAGCTGCTGGTCAAAC 3 238 1 ATTCTAATTG 0.98386 -63 AACCGAAGCATTTACAAAAATTGTTGGTCAAAAATC 3 271 1 TTTCAAATTG 0.816468 -30 ACCTTTTTTAAATCCTTAAATTTTTGTTACTTAAAC 5 20 0 AATCTAATTG 0.875939 -32 AAATGAACACATTAATCAAATAAGTGTGGGAACAGA 7 124 1 ATTATAATTG 0.951601 -177 GCCAAAAATTTTTAATTTAGTTTTTGCTACTTTCTC 7 232 1 TTTATAGTTG 0.680169 -69 *** ** *** ** Masking position 11 Map Score: 8.77422 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 72 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TCGTCATTGATGAAAGCAATGAATCCAAAG 3 26 0 TGAAAGCAAT 0.986011 -275 ATGGCAATAATGACAGCAATCACACCACCA 3 220 0 TGACAGCAAT 0.990911 -81 CCAGCAGCTATTACAGCAATGGCAATAATG 3 238 0 TTACAGCAAT 0.964839 -63 AAATATGTGCTGAAAGCCATTGCGTTAACA 7 74 1 TGAAAGCCAT 0.976384 -227 ********** Masking position 5 Map Score: 2.88719 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 AATCTAAATTTATTATAAATATTGGATTTT 1 20 1 TATTATAAAT 0.884412 -31 ACGCAAAAATTTTTATAAATTGTTTGCAAC 2 161 1 TTTTATAAAT 0.904904 -140 GATTCATTGCTTTCATCAATGACGATGCCG 3 31 1 TTTCATCAAT 0.906411 -270 CCACCACGTATTTCATAAATCTTTTTACCA 3 196 0 TTTCATAAAT 0.959427 -105 GACCAACAATTTTTGTAAATGCTTCGGTTT 3 270 0 TTTTGTAAAT 0.931717 -31 AAATGAACCTTTTTTAAATCCTTAAATTT 5 33 0 TTTTTTAAAT 0.90351 -19 ********** Masking position 6 Map Score: 3.02359 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 19 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TTCCATCTGGTTGAACACCTGATAAAAACC 3 107 1 TTGAACACCT 0.938518 -194 CATAAATCTTTTTACCACCAAAAAAACAAT 3 183 0 TTTACCACCA 0.943347 -118 ATGCTTCGGTTTGACCAGCAGCTATTACAG 3 252 0 TTGACCAGCA 0.979262 -49 TACTGATTTTTGACCAACAATTTTTGTAA 3 282 0 TTGACCAACA 0.982511 -19 TCTTGAGCAACTAAGATTTAAC 6 43 0 TTGAGCAACT 0.936004 -12 ********** Masking position 4 Map Score: 1.38444 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 47 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GGAACTGGAATCTAAATTTATTATAAATAT 1 12 1 TCTAAATTTA 0.844737 -39 TATTGGATTTTCTGACTTTAGG 1 39 1 TCTGACTTTA 0.878838 -12 TATTTTGCGCTGTTAATTAAC 4 2 0 TGTTAATTAA 0.886311 -137 CTTAAATTTTTGTTACTTAAACATTGAGGG 5 12 0 TGTTACTTAA 0.925181 -40 GCAACTAAGATTTAACTTAAAAGAAATAAT 6 29 0 TTTAACTTAA 0.704793 -26 TATGAATGTTTGTTCCTTTAAAAATTTGTT 7 32 1 TGTTCCTTTA 0.840482 -269 ATTTTTTATGTCTTAATTTACTTATGTTAA 7 98 0 TCTTAATTTA 0.925962 -203 CGCCAAAAATTTTTAATTTAGTTTTTGCTA 7 231 1 TTTTAATTTA 0.847345 -70 ********** Masking position 10 Map Score: 1.40728 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 80 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 TGGTTTTTTTACAGAATTTTGCACTTCAGT 2 120 1 ACAGAATTTT 0.956813 -181 CAAGAAAGAAACGGAATTTTTAGAAGAGCT 2 212 0 ACGGAATTTT 0.959885 -89 CCATCAGTGGTCTGCTTTTTTATTGCGCTT 2 250 0 TCTGCTTTTT 0.737811 -51 TACTGATTTTTGACCAACAAT 3 290 0 ACTGATTTTT 0.952689 -11 ATACAAGTAAACGGCTTTTTAGGCAAAAG 4 120 1 ACGGCTTTTT 0.954475 -19 TAAACAAAAAACAAATTTTTAAAGGAACAA 7 41 0 ACAAATTTTT 0.879623 -260 GGCTTTCAACACAAAATTTTCGTTTTTCTG 7 166 1 ACAAAATTTT 0.857652 -135 ********** Masking position 7 Map Score: 4.05153 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 70 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 ********** No masking Map Score: 8.83505e-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: 8.83505e-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 12 ********** No masking Map Score: 8.83505e-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