AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02060_mpneu_reg_300.orf -o02060_mpneu_300.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 Purged sequences: C12_orf65 21 rpmB; 50S ribosomal protein L28. [SP:RL28_MYCPN] Input sequences: #1 R02_orf694 50 fruA; PTS system, fructose-specific IIABC component (EIIABC-Fru) #2 MPNtRNA-Ser01 300 mptgsb; tRNA-Ser. #3 D09_orf657 182 hypothetical protein. #4 D09_orf508 300 glpK; glycerol kinase (ATP:glycerol 3-phosphotransferase) #5 E09_orf379 300 mtlA; PTS system mannitol-specific component IIA(EIIA-MTL). #6 C12_orf172 134 hypothetical protein. #7 C12_orf141 43 hypothetical protein. #8 C12_orf450 157 deaD; ATP-dependent RNA helicase. #9 C12_orf561 45 hypothetical protein. #10 C12_orf681 30 dnaX; DNA polymerase III subunits gamma and tau. [EC:2.7.7.7] #11 C12_orf132 300 rpsI; 30S ribosomal protein S9. [SP:RS9_MYCPN] #12 GT9_orf940o 51 ptsG; PTS system, glucose-specific IIABC component (EIIABC-Glc) #13 GT9_orf113 54 hypothetical protein. #14 GT9_orf438V 300 hypothetical protein. Motif number 1 GAAAATCCAATATTTATAATAAATTTAGATTCCAGTTC 1 13 0 TATTTATTAG 0.808456 -38 GGTCGCTTGGTTTTTTTACAGAATTTTGCACTTCAGTA 2 113 1 TTTTTATTTG 0.977297 -188 TTTATAAAAATTTTTGCGTTTTCTTTTATTACTGAAGT 2 142 0 TTTTTCTTTA 0.731799 -159 GTGGTCTGCTTTTTTATTGCGCTTTTTGTTAACAAGAA 2 236 0 TTTTTTTTTG 0.902974 -65 AAAAAGTGGTTTTTTAAAAAACATTTAACTCTTATTTA 3 88 1 TTTTTATTAA 0.940506 -95 CAATTAAGCATATTTAATTTTTACTTAAATTTATTAAC 4 36 0 TATTTATTAA 0.678418 -265 GAGAAAAAAATTTTTTTAAATCAATTAAGCATATTTAA 4 57 0 TTTTTATTAA 0.940493 -244 TTTAAAAAAATTTTTTTCTCTGATTGAGGTGGAGCAGA 4 75 1 TTTTTATGAG 0.770316 -226 TAGAATTTGTTTTTTCTTCATCAGTTAAATCTGTTCTA 4 173 0 TTTTTATTAA 0.940506 -128 TACTGATTTTTGACCAACAATTTTTGTAAATGCT 5 277 0 TTTTTATTTT 0.7723 -24 TTTTTCAGCATTTTTCGCTCGTTTTTTACCCAA 6 6 0 TTTTTTTTTA 0.82306 -129 TTTCAGGTATTTTTTTATGCAAAATTTGCCCTAAAAAA 6 55 1 TTTTTATTTG 0.977296 -80 TTGTTTTGGTTTATTTATTATAAGTTTGGGGGCTGATT 8 76 0 TTATTATTTG 0.897287 -82 ACTTTGATAGTTATTAGTAATTAATTAGTTAACAGCCC 8 125 0 TTATTATTAG 0.865203 -33 TCCTGGATTGTTTTTGATATATAGTTTGCTGATAACTC 11 149 1 TTTTTATTTG 0.977297 -152 TTTTTTTCAATAAACTTTGAGCTGTCCAG 11 282 0 TTTTTATTTG 0.977297 -19 AGCTAAGCGATTATTTCTTTTAAGTTAAATCTTAGTTG 13 20 1 TTATTATTAA 0.76236 -35 ATGTGTTCATTTTTTATGTCTTAATTTACTTATGTTAA 14 98 0 TTTTTATTTA 0.955586 -203 CCGCCAAAAATTTTTAATTTAGTTTTTGCTACTTTCTC 14 230 1 TTTTTTTTTG 0.902974 -71 ***** * **** Masking position 5 Map Score: 22.917 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 122 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 AGCGCAATAAAAAAGCAGACCACTGATGGTC 2 251 1 AAAACAGACC 0.934947 -50 AAAATTACACCCTTTCTAAAA 3 172 0 AAAATACACC 0.9146 -11 GAGACTAACTAAAACCACCCCGTGGGGTAGT 4 254 1 AAAACACCCC 0.98532 -47 CTTAAAATTAAAAACTACCCCACGGGGTGGT 4 267 0 AAAATACCCC 0.984115 -34 AAAAGAAGCTAAAAGTCCCCAAGCAATAAAG 5 72 0 AAAATCCCCA 0.839613 -229 TTTTTTATGCAAAATTTGCCCTAAAAAAAGA 6 65 1 AAAATTGCCC 0.932212 -70 ACGGGAAAATTATCCCGGAATGAACA 6 119 0 AAAATATCCC 0.922309 -16 AACAAAATAAGAAATTAGCCCAGTCAAGGGG 8 33 1 GAAATAGCCC 0.941188 -125 TGAACCCCACAAAATCAGCCCCCAAACTTAT 8 64 1 AAAACAGCCC 0.988115 -94 GTTGGGTTTTAAAAACCGCCAAAAATTTTTA 14 215 1 AAAACCGCCA 0.875392 -86 **** ****** Masking position 4 Map Score: 9.53719 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 58 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 CTAAAGTCAGAAAATCCAATATTTATAATAAA 1 28 0 AAAATCAATT 0.915498 -23 AATTCTGTAAAAAAACCAAGCGACCTGAGGCT 2 106 0 AAAAACAAGG 0.865003 -195 ATGTTTTTTAAAAAACCACTTTTTCAGCTCTG 3 80 0 AAAAACACTT 0.890204 -103 AAATACTTTGAAAATCAACGATCTAATAAGTT 3 125 1 AAAATCACGT 0.856909 -58 GAAAATCAAAAGTTCATTAGTTT 4 2 1 AAAATCAAAT 0.87104 -299 CTGATGAAGAAAAAACAAATTCTAGTTGATTA 4 187 1 AAAAACAATC 0.800718 -114 AGATGGAATAAAAAAAGAAGCTAAAAGTCCCC 5 83 0 AAAAAAAAGT 0.710852 -218 AACACCTGATAAAAACCTAGCTTTAATGGTGG 5 120 1 AAAAACTAGT 0.798876 -181 TTACCACCAAAAAAACAATTATGGTCGGAATC 5 170 0 AAAAACATTT 0.748322 -131 TAAACGTTTCAAAATCAAAGATATTTGCGATA 11 199 0 AAAATCAAGT 0.945294 -102 TAGCTAAACAAAAAACAAATTTTTAAAGGAAC 14 43 0 AAAAACAATT 0.958975 -258 GTGGGAGCAGAAAAACGAAAATTTTGTGTTGA 14 171 0 AAAAACAAAT 0.935855 -130 AGAAAGTAGCAAAAACTAAATTAAAAATTTTT 14 235 0 AAAAACAAAT 0.935851 -66 ****** *** * Masking position 4 Map Score: 9.78103 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 102 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 CTCTGATTGAGGTGGAGCAGAAGATAAGCAGA 4 92 1 GTGGAGAGAA 0.991794 -209 AGATTTAACTGATGAAGAAAAAACAAATTCTA 4 179 1 GTGAAGAAAA 0.810475 -122 TGTTCAACCAGATGGAATAAAAAAAGAAGCTA 5 92 0 GTGGAAAAAA 0.941047 -209 TAGCTTTAATGGTGGAATAGGAATCCAATATG 5 137 1 GTGGAAAGGA 0.947383 -164 TCAAATAAGTGTGGGAACAGAAAATCAGGCTT 14 139 1 GGGGAAAGAA 0.986046 -162 AATTTATTTAGTGGGAGCAGAAAAACGAAAAT 14 181 0 GGGGAGAGAA 0.993195 -120 TCGTGAGGGGGAGGGAGGAGAAAGTAGCAAAA 14 253 0 GGGGAGAGAA 0.993195 -48 * ***** **** Masking position 6 Map Score: 6.45922 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 6 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 GAGGTCTCGTCTTACTTGGTTATGTGTTGTTTG 2 62 0 CTTATTTTAT 0.782892 -239 CCTCAGGTCGCTTGGTTTTTTTACAGAATTTTG 2 108 1 CTTGTTTTTA 0.712631 -193 TTCTGTAACTATTAATTAGTTAAGCCTTT 3 7 0 ATTATTTTAA 0.897369 -176 ATTAAATATGCTTAATTGATTTAAAAAAATTTT 4 56 1 CTTATTTTTA 0.948125 -245 TGTTCTACTCATTACTTTATCTACAAAAACAGC 4 147 0 ATTATTTCTA 0.822982 -154 TGAACAACGGATCAATTTCTCAAATTTACTCTT 6 92 0 ATCATTTCAA 0.690842 -43 GGGCTAATTTCTTATTTTGTTATAATTCAACAA 8 21 0 CTTATTTTAT 0.782892 -137 GTTATTAGTAATTAATTAGTTAACAGCCCACTT 8 121 0 ATTATTTTAA 0.897369 -37 CCCTTAGTCTTATTGATTTTAGTACTAGGGT 9 9 1 CTTATGTTTA 0.712631 -37 CTTGGGCTCCATCAGTTGTTCAAGTGACGTACT 11 40 1 ATCATTTCAA 0.690842 -261 GAGCTAAGCGATTATTTCTTTTAAGTTAAATCT 13 19 1 ATTATTTTTA 0.884946 -36 TAAGTTAAATCTTAGTTGCTCAAGA 13 40 1 CTTATTTCAA 0.926248 -15 TTTTTTATGTCTTAATTTACTTATGTTAACGCA 14 94 0 CTTATTCTTA 0.712631 -207 TGTTCCCACACTTATTTGATTAATGTGTTCATT 14 125 0 CTTATTTTAA 0.954081 -176 TAAAACCCAACTCAATTTATTTAGTGGGAGCAG 14 193 0 CTCATTTTTA 0.885422 -108 **** ** **** Masking position 6 Map Score: 10.199 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 107 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 ATTTTTGCGTTTTCTTTTATTACTGAAGTGCAAAATTCTG 2 131 0 TTTTTTTCTG 0.825929 -170 ACGCCGATGCTTTTATCGTTTAAAGTTTTGCAGAGCTGAA 3 50 1 TTTATTTATG 0.86097 -133 TTTACTTAAATTTATTAACCTAAACTAATGAACTTTTGAT 4 15 0 TTTTTCTATG 0.973747 -286 TTTTCTTATTTTTATTCTGCTTATCTTCTGCTCCACCTCA 4 99 0 TTTTTCTATG 0.973747 -202 GAACAAGCTGTTTTTGTAGATAAAGTAATGAGTAGAACAG 4 141 1 TTTTGATATG 0.82519 -160 CGGGGTGGTTTTAGTTAGTCTCAATCATCGTCCAAATAGT 4 236 0 TTATTCTACG 0.587909 -65 AAAGAGTAAATTTGAGAAATTGATCCGTTGTTCATTCCGG 6 91 1 TTTAGTTATG 0.835917 -44 GGGGGCTGATTTTGTGGGGTTCACCCCTTGACTGGGCTAA 8 47 0 TTTTGTTATG 0.957873 -111 AATCCTTAAATTTTTGTTACTTAAACATTGAGGGA 12 6 0 TTTTGCTATG 0.968268 -46 GTTATGAATGTTTGTTCCTTTAAAAATTTGTTTTTTGTTT 14 30 1 TTTTTTTATG 0.965083 -271 AAATTTGTTTTTTGTTTAGCTAAATATGTGCTGAAAGCCA 14 53 1 TTTTTCTATG 0.973747 -248 ATGTCTTAATTTACTTATGTTAACGCAATGGCTTTCAGCA 14 81 0 TTATTTTATG 0.86097 -220 *** ** ** * ** Masking position 11 Map Score: 7.52117 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 23 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CTTGGTTTTTTTACAGAATTTTGCACTTCA 2 118 1 TTACAGAATT 0.892196 -183 TAATTAATAGTTACAGAAATGCCTTGACAC 3 22 1 TTACAGAAAT 0.963221 -161 GATTCATTGCTTTCATCAATGACGATGCCG 5 31 1 TTTCATCAAT 0.862214 -270 CCACCACGTATTTCATAAATCTTTTTACCA 5 196 0 TTTCATAAAT 0.829408 -105 ATGGCAATAATGACAGCAATCACACCACCA 5 220 0 TGACAGCAAT 0.887361 -81 CCAGCAGCTATTACAGCAATGGCAATAATG 5 238 0 TTACAGCAAT 0.971196 -63 ACCGAAGCATTTACAAAAATTGTTGGTCAA 5 272 1 TTACAAAAAT 0.772576 -29 TCAGGTATTTTTTCAGCATTTTTCGCTCGT 6 22 0 TTTCAGCATT 0.896356 -113 AAAGAGTAAATTTGAGAAATTGATCCGTTG 6 91 1 TTTGAGAAAT 0.75542 -44 ********** Masking position 5 Map Score: 4.24438 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 60 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 CATATTTAATTTTTACTTAAATTTATTAAC 4 36 0 TTTTACTTAA 0.801047 -265 AGGTTAGTTCTTAAAATTAAAAACTACCCC 4 277 0 TTAAAATTAA 0.784665 -24 TAGAGTTAAATTAAACTTAAATCCATATAG 7 19 1 TTAAACTTAA 0.920482 -25 ATCAACACAGTAAAACTTAATCTCCTTTAA 11 231 1 TAAAACTTAA 0.880229 -70 CACTTAATCTTTAAACTTAAAGGAGATTAA 11 247 0 TTAAACTTAA 0.920482 -54 GCAACTAAGATTTAACTTAAAAGAAATAAT 13 29 0 TTTAACTTAA 0.939778 -26 ********** Masking position 5 Map Score: 3.20895 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 39 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 TTAATTCCGGAATTTGCTGTTGCAAACAATTT 2 177 0 AATTTTGTTG 0.867918 -124 AGGCTTAACTAATTAATAGTTACAGAAATGCC 3 13 1 AATTAAGTTA 0.538683 -170 CAAAGTATTTAAATAAGAGTTAAATGTTTTTT 3 103 0 AAATAAGTTA 0.716079 -80 AAGAAAAAACAAATTCTAGTTGATTACTATCA 4 193 1 AAATTAGTTG 0.867917 -108 AAGATTTATGAAATACGTGGTGGTGTGATTGC 5 203 1 AAATATGGTG 0.837499 -98 GCCATTGCTGTAATAGCTGCTGGTCAAACCGA 5 245 1 TAATATGCTG 0.752784 -56 GAATTAATACTTGTTGAATTATAACA 8 5 1 TAATATGTTG 0.897766 -153 ATTTCACCGTTATTAACTGTTGCTGATGAATA 11 105 1 TATTATGTTG 0.802664 -196 TTAAATCCTTAAATTTTTGTTACTTAAACATT 12 17 0 AAATTTGTTA 0.738604 -35 CTTTTAAGTTAAATCTTAGTTGCTCAAGA 13 36 1 AAATCAGTTG 0.747485 -19 TTGTTTAGCTAAATATGTGCTGAAAGCCATTG 14 64 1 AAATATGCTG 0.904623 -237 CACATTAATCAAATAAGTGTGGGAACAGAAAA 14 131 1 AAATATGTGG 0.811906 -170 GAAAAACGAAAATTTTGTGTTGAAAGCCTGAT 14 162 0 AATTTTGTTG 0.867918 -139 ***** ***** Masking position 2 Map Score: 3.4817 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 107 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 AATGCCTTGACACGCCGATGCTTTTATCGTTTA 3 39 1 CACCCGGCTT 0.965336 -144 TAACTAAAACCACCCCGTGGGGTAGTTTTTAAT 4 259 1 CACCCGGGGT 0.972622 -42 TGACAGCAATCACACCACCACGTATTTCATAAA 5 207 0 CACCCAACGT 0.937948 -94 AGCTGCTGGTCAAACCGAAGCATTTACAAAAAT 5 259 1 CAACCGGCAT 0.864309 -42 AGTTTAATTTAACTCTAGCGCGCCA 7 3 0 AACCTAGCGC 0.838301 -41 GTTTGCTGATAACTCTACCGCGTTTAATATCGC 11 172 1 AACCTAGCGT 0.951264 -129 ATATGTGCTGAAAGCCATTGCGTTAACATAAGT 14 76 1 AAACCAGCGT 0.951264 -225 CACGAGTGAAAACCCCGGGGCGTGGGCCTTA 14 280 1 AACCCGGCGT 0.992517 -21 *** *** **** Masking position 2 Map Score: 0.641253 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 45 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TTTTTCTCTGATTGAGGTGGAGCAGAAGAT 4 87 1 ATTGAGGTGG 0.912351 -214 GGGTTCACCCCTTGACTGGGCTAATTTCTT 8 41 0 CTTGACTGGG 0.884802 -117 TTGGGGGCTGATTTTGTGGGGTTCACCCCT 8 59 0 ATTTTGTGGG 0.907454 -99 ATTTATTATAAGTTTGGGGGCTGATTTTGT 8 72 0 AGTTTGGGGG 0.798119 -86 AAACAACCACCTTAAGTGGGCTGTTAACTA 8 108 1 CTTAAGTGGG 0.946983 -50 AAGTTTAAAGATTAAGTGGGGAACTGGACA 11 259 1 ATTAAGTGGG 0.95586 -42 AACTCAATTTATTTAGTGGGAGCAGAAAAA 14 188 0 ATTTAGTGGG 0.968779 -113 CACTAAATAAATTGAGTTGGGTTTTAAAAA 14 200 1 ATTGAGTTGG 0.926576 -101 GGTTTTCACTCGTGAGGGGGAGGGAGGAGA 14 264 0 CGTGAGGGGG 0.955183 -37 ********** Masking position 3 Map Score: 6.2198 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 33 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TAATGAAGTCAATCACAAACCATTCAATCA 2 32 1 AATCACAAAC 0.981745 -269 CAAACCATTCAATCACAAACAACACATAAC 2 47 1 AATCACAAAC 0.981745 -254 TTATGGTCGGAATCACATATTGGATTCCTA 5 154 0 AATCACATAT 0.842701 -147 TCTCCATTAAAATCACAATCCTTTATCTTA 11 72 1 AATCACAATC 0.955123 -229 ********** Masking position 5 Map Score: 0.530012 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 6 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 TCAATCACAAACAACACATAACCAAGTAAG 2 55 1 ACAACACATA 0.945699 -246 GGGGAACTGGACAGCTCAAAGTTTATTGAA 11 276 1 ACAGCTCAAA 0.949496 -25 TAACTGCTTTACAACTCAAACTA 14 4 0 ACAACTCAAA 0.945699 -297 GCAATGGCTTTCAGCACATATTTAGCTAAA 14 67 0 TCAGCACATA 0.929181 -234 AATCAGGCTTTCAACACAAAATTTTCGTTT 14 161 1 TCAACACAAA 0.945699 -140 ********** Masking position 3 Map Score: 0.374931 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 32 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 ********** No masking Map Score: 3.15724e-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 15 ********** No masking Map Score: 3.15724e-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