AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_mpneu_reg_100.orf -o03010_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 Purged sequences: G07_orf139 28 rpsL; 30S ribosomal protein S12. [SP:RS12_MYCPN] C12_orf681 30 dnaX; DNA polymerase III subunits gamma and tau. [EC:2.7.7.7] Input sequences: #1 C09_orf201 89 infC; initiation factor IF-3. [SP:IF3_MYCPN] #2 C09_orf223 300 hypothetical protein. #3 K05_orf425 300 hypothetical protein. #4 K05_orf88 65 rpsP; 30S ribosomal protein S16. [SP:RS16_MYCPN] #5 K05_orf271 300 hypothetical protein. #6 C12_orf65 21 rpmB; 50S ribosomal protein L28. [SP:RL28_MYCPN] #7 C12_orf450 157 deaD; ATP-dependent RNA helicase. #8 C12_orf561 45 hypothetical protein. #9 C12_orf132 300 rpsI; 30S ribosomal protein S9. [SP:RS9_MYCPN] #10 G12_orf122 37 rplL; 50S ribosomal protein L7/L12. [SP:RL7_MYCPN] #11 G12_orf161 117 rplJ; 50S ribosomal protein L10. [SP:RL10_MYCPN] #12 P01_orf354 40 pepP; putative Xaa-Pro aminopeptidase (X-Pro aminopeptidase) #13 P01_orf243 300 hypothetical protein. #14 H08_orf205 60 rpsD, rpS4; 30S ribosomal protein S4. [SP:RS4_MYCPN] #15 H08_orf150 300 hypothetical protein. #16 H91_orf97 44 rpmE; 50S ribosomal protein L31. [SP:RL31_MYCPN] #17 MPNtRNA-Trp02 148 mptgg; tRNA-Trp. #18 F10_orf100b 146 rplU; 50S ribosomal protein L21. [SP:RL21_MYCPN] #19 G07_orf215 56 rpsF; 30S ribosomal protein S6. [SP:RS6_MYCPN] #20 G07_orf688 22 fusA, fus; elongation factor G (EF-G). [SP:EFG_MYCPN] #21 G07_orf155 53 rpsG; 30S ribosomal protein S7. [SP:RS7_MYCPN] #22 G07_orf137 55 rplK; ribosomal protein L11. [SP:RL11_MYCPN] #23 G07_orf389a 275 oppB; oligopeptide transport system permease protein oppB. #24 G07_orf294 300 rpsB; 30S ribosomal protein S2. [SP:RS2_MYCPN] #25 VXpSPT7_orf108 93 rpsJ; 30S ribosomal protein S10. [SP:RS10_MYCPN] #26 VXpSPT7_orf112 246 hypothetical protein. Motif number 1 GAAGGTATGAACTGATACCAAAGAAACTTTGAGTTC 2 235 1 ACAACAAAAA 0.877691 -66 CAAATTGAAAAAGAAAAACATACAAACAATCTTTAG 5 195 1 AAAACATAAA 0.818293 -106 CACGACTAACAATAAAAGCAAGCCAAAATCGGCTTG 5 263 1 AAAACAAGAA 0.975848 -38 ACAAAATAAAAGCAAGCCGATTTTGGCTTG 5 281 0 AAAACAAGGA 0.845726 -20 ATACTTGTTGAATTATAACAAAATAAGAAATTAGCC 7 17 1 AAAACAAAAA 0.980077 -141 AACTTATAATAAATAAACCAAAACAACCACCTTAAG 7 88 1 AAAACAAAAA 0.980077 -70 TATTAACCTGCAATAAACCAAAGAAAATAACGAGTT 11 30 1 CAAACAAAAA 0.954127 -88 TTTAGATCATAAGACAAACAAGTAAACGATAAGTTC 13 142 0 AACACAAGAA 0.845726 -159 GCAAATCTATAACCAGGACAAACTAAAGGATAA 15 8 0 AAAGCAAAAA 0.869699 -293 TCGTGTTATCCATTACACCAAGGGAAG 17 2 0 CAAACAAGAA 0.944699 -147 ATAAGCGTGAAATTATAACAAATTAACCCCTGCTAA 18 56 0 AAAACAAAAA 0.980077 -91 TTTGTTTATACAAAATACCAAAAGAAACGGTTTTAT 18 116 1 CAAACAAAAA 0.954127 -31 TGTTATTGCTAACAAAATCAAAATAAGTTATCAGAT 24 70 0 AAAACAAAAA 0.980077 -231 CAAAATCCACATCTAAAGCAAACCAAAAAGTCACCT 24 107 1 ATAACAAAAA 0.828817 -194 ATTATGCACCAAACAGAGCAAGTTAACTTAATTAAT 24 260 0 AAAACAAGAA 0.975848 -41 ** * * **** ** Masking position 10 Map Score: 17.9776 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 44 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 TTTTACCAGGAAAGTTCTGGGAAAAGCGCAAGATT 2 84 1 AATTTGAAAA 0.977621 -217 ACCATTAGGTAATTTTTCAGAAAAAGCTTCAAAAG 5 117 0 AATTCGAAAA 0.891617 -184 TAAGAAACTTAAGCTTGTAGAAAAAGGTCCAAATT 5 166 1 AATTTGAAAA 0.977621 -135 GGACAGCTCAAAGTTTATTGAAAAAAA 9 284 1 AATTTGAAAA 0.977621 -17 CAGAAATTATTTTTGCAATAGCACAAACGA 11 98 0 ATTTTGAATA 0.688557 -20 CGTAACTTTATGGGAAAACTAAATATAA 19 39 0 AATTTGAAAA 0.977621 -18 GATTGAGTTAATGTTTTTCGTAAAAAAAGGAATTT 21 17 0 ATTTTGAAAA 0.945652 -37 TTTAAAATTTCTAGCAAATTGTGGGAGCT 22 5 1 AATTTGAAAT 0.915532 -51 AGTGGTTCAAAACATTCTACAAAAAAACGATACTA 23 19 0 AATTTCAAAA 0.836105 -257 CCAAAGCCTTAAGATTGTAGCAAATAA 25 3 0 AATTTGAAAT 0.915532 -91 TTTAATTTCAATGATTATGGGAAAATAATAAGGCC 26 156 1 ATTTTGAAAA 0.945652 -91 ** ** * * **** Masking position 12 Map Score: 10.1842 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 21 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 GGAAGCAGAATTAGAAGCCTTTAAGAAACATAACACT 2 184 1 TAGCTTAAAA 0.884628 -117 TAAAAGGTAGTTATTAACACCAAAAAAGCTTTTTAGA 3 149 1 TAACCAAAAA 0.884153 -152 AATTGAAACTAAGAACGCTTCTAAAAAGCTTTTTTGG 3 168 0 ACGCCTAAAA 0.801219 -133 AAGAAGAATATAAGGAACTTTTAAAAAAATGTGAACT 5 75 1 TAACTTAAAA 0.941396 -226 TAATGGTGATTATGAAGTAACTAAGAAACTTAAGCTT 5 145 1 TAGTCTAAAA 0.697043 -156 AAGTGGCTTATAGAGCACGACTAACAATAAAAGCAAG 5 248 1 TCACCTAAAA 0.942725 -53 GGCTGTTAACTAATTAATTACTAATAACTATCAAAGT 7 126 1 TAATCTAAAA 0.809055 -32 TGTTTATTCATCAGCAACAGTTAATAACGGTGAAATC 9 104 0 TAACTTAAAA 0.941323 -197 TAAACCCCTCATAAATAATTAATAAGTAAATATAA 10 9 1 TAATTTAAAA 0.748761 -29 AAATAACGAGTTTTTAACTTTAAAAAAGTTATCGAGG 11 54 1 TAACTAAAAA 0.82461 -64 GATTCCCGTCATCTCCACCATTAACAACGCAAGTTGA 13 249 1 ACACTTAAAA 0.839694 -52 TTGTAGAATGTTTTGAACCACTAACAATGTTTTTAGC 23 32 1 TAACCTAAAA 0.940593 -244 GTCAAACAGCATTTTAGTCGCTAAAAACATTGTTAGT 23 51 0 AAGTCTAAAA 0.470205 -225 ACACTGCCAAACCCAAACGTTTAAGAATATACTTGAA 23 244 0 AAACTTAAAA 0.891707 -32 AGGAGCTTGCAGTTCCACAATTAAAAAGCCACCCGTT 24 149 0 ACACTTAAAA 0.839709 -152 TTGACCATCAAATTTCACCCTTAAGAACTGAGAT 25 70 1 ACACTTAAAA 0.839708 -24 TAAAAGAAACTTACTAACAGCAAAAAAGCTCCAAGCT 26 47 0 TAACCAAAAA 0.883599 -200 TCATTGAAATTAAACAACTTCAAAAAAGTAGTAACCC 26 133 0 TAACCAAAAA 0.886264 -114 * *** **** ** Masking position 13 Map Score: 12.8008 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 163 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 AACCGTTTTAACTCAATTAACCATTAAGGAG 1 16 0 ACCAATTAAC 0.843317 -74 AGTGACAGTAAACCAGCTAACACATAACAAA 2 48 0 AACAGCTAAC 0.911306 -253 AAGATCAGAAAGACAATTAACCAAACGCTTG 2 273 0 AGCAATTAAC 0.745199 -28 ATTATAAAAGAAATAACTAACCTTCGGAGTG 3 36 1 AATAACTAAC 0.891025 -265 GGTTAAGCTTAATTAATTCACTGAGTTTATT 3 206 0 AATAATTCAC 0.781624 -95 AATTAAGCTTAACCAACTAACTTAGGCTTTT 3 223 1 AACAACTAAC 0.918676 -78 CTTCAAAAGAAATTAGTTCACATTTTTTTAA 5 95 0 AATAGTTCAC 0.76501 -206 ATTAGTAATTAATTAGTTAACAGCCCACTTA 7 120 0 AATAGTTAAC 0.918138 -38 GATTAAGTTGAACCAGTTAACCCCGAGCCAT 13 101 0 AACAGTTAAC 0.939377 -200 TATCACAGAGACCTAGTTAACTACTAGGTCT 17 89 1 ACTAGTTAAC 0.779898 -60 AATTAAATTAAAATGATTAACCGCTAA 17 132 1 AATGATTAAC 0.6427 -17 GTGAAATTATAACAAATTAACCCCTGCTAAA 18 55 0 AAAAATTAAC 0.688454 -92 AAATAACTAACTCTATTCTCT 20 12 0 AATAACTAAC 0.891025 -11 ACATTAACTCAATCAATTAACTTTAT 21 38 1 AACAATTAAC 0.944557 -16 ** ******** Masking position 10 Map Score: 10.7619 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 85 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 AAAGATGTGATAAGCCTGGTCCACAGGGTT 2 149 0 TAAGCCTGGT 0.873002 -152 GTTCTAAGCGAAAGCGTAGTTGATACTTGC 13 19 0 AAAGCGTAGT 0.974719 -282 GATTGATGTTTAAGCGTAGTTA 14 49 1 TAAGCGTAGT 0.967331 -12 GCCCAGATTCAAAGCGAAGTTTTCGATCAA 15 118 0 AAAGCGAAGT 0.953841 -183 ACCATCCTTATAAGCGAGGTAGTTCTTTTG 15 259 1 TAAGCGAGGT 0.950408 -42 GATACACCGAAAAGCGTAGTCATTTTGACC 25 46 1 AAAGCGTAGT 0.974719 -48 AGATCGCCAAAAAGCGGGGTTACTACTTTT 26 117 1 AAAGCGGGGT 0.954492 -130 ********** Masking position 3 Map Score: 6.42186 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 21 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TCACCTATCTTTTTATATTTCATATTAACA 5 16 0 TTTTATATTT 0.885233 -285 CAAGCTTAAGTTTCTTAGTTACTTCATAAT 5 153 0 TTTCTTAGTT 0.741864 -148 ACTGGGCTAATTTCTTATTTTGTTATAATT 7 27 0 TTTCTTATTT 0.924815 -131 TTTTATATTTACTTATTAAT 10 28 0 TTTTATATTT 0.885233 -10 CATCAGGTCCTTTCTTATTTGACGAAATTT 15 219 0 TTTCTTATTT 0.924815 -82 ACGGCTTAGATTATATATTTATTGCTTTT 16 10 0 TTATATATTT 0.548723 -35 AAATCTTTACTTTTATATTTAGTTTTCCCA 19 27 1 TTTTATATTT 0.885233 -30 CAGGTTCCTTTTTCTTTTTTATTAGTATTC 23 207 1 TTTCTTTTTT 0.659756 -69 TTTTTCATATTTAGACATAGGT 24 3 1 TTTCATATTT 0.938097 -298 ********** Masking position 6 Map Score: 4.21343 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 13 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TACCTTCGTTCAAAAAACCTTAGTGTTATGTTT 2 209 0 CAAAAACTAG 0.88549 -92 ACTTTGAGTTCTACAAGCGTTTGGTTAATTGTC 2 260 1 CTACAACTTG 0.892777 -41 TAAGCTTAACCAACTAACTTAGGCTTTTTCTTG 3 226 1 CAACTACTGG 0.824431 -75 GGACCTTTTTCTACAAGCTTAAGTTTCTTAGTT 5 163 0 CTACAACTAG 0.975691 -138 AAAAACATACAAACAATCTTTAGAGAATGAAAA 5 208 1 AAACAACTAG 0.705515 -93 TAAACCAAAACAACCACCTTAAGTGGGCTGTTA 7 101 1 CAACCACTAG 0.957659 -57 ATAAAAAACACTACCAGCTTGGGCTCCATCAGT 9 23 1 CTACCACTGG 0.964682 -278 AAAACCTAACAACTTTAGTTGCTAGATC 14 6 1 CTAACACTAG 0.89766 -55 TTATTTGCTACAATCTTAAGGCTTTGGTCG 25 8 1 CTACAACTAG 0.975691 -86 AAGCTCCAAGCTAAAAGCATTGGGACTTGTTTG 26 26 0 CTAAAACTGG 0.903262 -221 ****** * * ** Masking position 6 Map Score: 5.99988 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 30 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 8 TGTTAAAATATTGGCGCTATACAAAGTAGT 1 53 1 TTGGCGCTAT 0.865737 -37 TCAAAAAACCTTAGTGTTATGTTTCTTAAA 2 203 0 TTAGTGTTAT 0.938049 -98 AAAAGCTTTTTTGGTGTTAATAACTACCTT 3 152 0 TTGGTGTTAA 0.7532 -149 CCCTTAGTCTTATTGATTTTAGT 8 4 1 TTAGTCTTAT 0.855036 -42 ATCAAAGATATTTGCGATATTAAACGCGGT 9 188 0 TTTGCGATAT 0.53449 -113 ATTATCATCGTTTGTGCTATTGCAAAAATA 11 91 1 TTTGTGCTAT 0.833315 -27 CGTTTACTTGTTTGTCTTATGATCTAAAGT 13 150 1 TTTGTCTTAT 0.819161 -151 CTTCTACAGTTTAGTCTTATGTTTTAATGT 13 187 0 TTAGTCTTAT 0.855036 -114 CTTCCCTTGGTGTAATGGATAACACG 17 7 1 TTGGTGTAAT 0.753205 -142 GGGAGCTAGTTTAGCGTTATTACCACACCA 22 33 1 TTAGCGTTAT 0.904404 -23 GATGTGGATTTTGGTGTTATTGCTAACAAA 24 90 0 TTGGTGTTAT 0.960031 -211 ********** Masking position 9 Map Score: 4.80487 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 48 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 9 ACTGATACCAAAGAAACTTTGAGTTCTACAAGCGT 2 245 1 AAACTTTAGT 0.980226 -56 TGGTGTTAATAACTACCTTTTAGGTGAGTTTTTTA 3 136 0 AAACTTTAGT 0.980204 -165 TTTAGATTCGAAAAATCCTTTAGATTTAATATCAC 5 42 0 AAACCTTAGT 0.920523 -259 CGTGCTCTATAAGCCACTTTAAGATTTTTTCATTC 5 232 0 AACCTTTAGT 0.929412 -69 TTAATATCGCAAATATCTTTGATTTTGAAACGTTT 9 195 1 AAACTTTATT 0.829345 -106 AGTAAAACTTAATCTCCTTTAAGTTTAAAGATTAA 9 239 1 AATCTTTAGT 0.898823 -62 TTTTTTTCAATAAACTTTGAGCTGTCCAGTTCC 9 278 0 AAACTTTAGT 0.980226 -23 TATATACACAAAAGACCTAGTAGTTAACTAGGTCT 17 97 0 AAACTAGAGT 0.792523 -52 AAGAATTATTAAGGAGCTTGCAGTTCCACAATTAA 24 162 0 AAACTTGAGT 0.960367 -139 ** * **** ** * Masking position 12 Map Score: 4.32796 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 17 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ACCCTCTTTGAACAGGTAGTTTGACCTTACTTAA 4 22 0 ACAGGTTTTA 0.867592 -44 CATAATCACCATTAGGTAATTTTTCAGAAAAAGC 5 125 0 ATAGGTTTTT 0.909529 -176 GCAAGCCAAAATCGGCTTGCTTTTATTTTGT 5 280 1 ACGGCTCTTT 0.776081 -21 ATAAGGTATCATCAGGTCCTTTCTTATTTGACGA 15 224 0 ACAGGTTTTT 0.959219 -77 CTAGTTAACTACTAGGTCTTTTGTGTATATAAAT 17 101 1 ATAGGTTTTT 0.909585 -48 GGACCTGAGAACCAGGTTCCTTTTTCTTTTTTAT 23 195 1 ACAGGTCTTT 0.973075 -81 ACCCGTTAAAAACAGGTGACTTTTTGGTTTGCTT 24 122 0 ACAGGTCTTT 0.974068 -179 ACCTGTTTTTAACGGGTGGCTTTTTAATTGTGGA 24 139 1 ACGGGTCTTT 0.963982 -162 TTTTGCTGTTAGTAAGTTTCTTTTAACAATTAAA 26 59 1 ATAAGTCTTT 0.583611 -188 TTAACAATTAAATGGGTCTTTTAAAGTGACACAA 26 81 1 ATGGGTTTTA 0.665679 -166 * ***** *** * Masking position 7 Map Score: 3.75913 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 29 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 CCTCAGGGATCTTCTTTGCCTTACTGTTTT 2 12 1 CTTCTTTGCC 0.979463 -289 TTATCGTTTACTTGTTTGTCTTATGATCTA 13 146 1 CTTGTTTGTC 0.914873 -155 TCAATGATGCCTTCTTTGCCCAGATTCAAA 15 135 0 CTTCTTTGCC 0.979463 -166 CAGGTCCTTTCTTATTTGACGAAATTTCTA 15 216 0 CTTATTTGAC 0.826686 -85 TAATTTCACGCTTATTTGCGTCTTCTGCGG 18 77 1 CTTATTTGCG 0.928624 -70 AGCATTGGGACTTGTTTGCGCTAGTTAAGC 26 14 0 CTTGTTTGCG 0.967012 -233 TTTTTCCAAACTAGTTTGCCGCTTGCAGGC 26 188 0 CTAGTTTGCC 0.93516 -59 ********** Masking position 5 Map Score: 4.68433 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 ********** No masking Map Score: -3.49344e-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 13 CGAATTGAATACTTTAACCCTGTGGACCAGG 2 134 1 ACTTTAACCT 0.848174 -167 TGAAGTTGATACTTAAACGTTATCTTCAAGA 3 254 0 ACTTAAACTT 0.944336 -47 GTTTGACCTTACTTAAACGCTTCGATT 4 7 0 ACTTAAACCT 0.964169 -59 ACACAGTAAAACTTAATCTCCTTTAAGTTTA 9 235 1 ACTTAATCCC 0.816689 -66 CCAGTTCCCCACTTAATCTTTAAACTTAAAG 9 255 0 ACTTAATCTT 0.913608 -46 AACTGGTTCAACTTAATCCTTAAATTATGAA 13 114 1 ACTTAATCTT 0.913608 -187 TTAAGAATATACTTGAACACTTTCGAATACT 23 230 0 ACTTGAACCT 0.89224 -46 TCAAGTATATTCTTAAACGTTTGGGTTTGGC 23 245 1 TCTTAAACTT 0.752489 -31 ******** ** Masking position 6 Map Score: 1.88783 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 19 Number in noncoding regions = 10 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: -3.49344e-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: -3.49344e-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