AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_mgen_reg_300.orf -o00271_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 MG014 239 ABC transporter, ATP-binding protein #2 MG015 46 ABC transporter, ATP-binding protein #3 MG017 65 ATP-dependent RNA helicase, putative #4 MG018 188 ATP-dependent RNA helicase, putative #5 MG019 41 heat shock protein (dnaJ) #6 MG040 158 lipoprotein, putative #7 MG042 197 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #8 MG364 63 conserved hypothetical protein Motif number 1 ATCCTAAGGGTATTTAACTAATTATTATAACAAT 1 154 1 TATTTAATTA 0.604761 -86 TATTTTGGTTAAATTAAAATTGTTATAATAATTA 1 172 0 AAATTAAATT 0.964142 -68 TACCCCTCGAATTTTAACAGTTTTTATAATCAAA 1 204 1 ATTTTAAATT 0.794245 -36 TGAAGTAATTAATCTCTTTAAAATCTTTC 2 28 0 TAATTAACTT 0.962365 -19 ATAAATTTAATAGTGTTGAAAGACAAA 3 4 1 AATTTAAATT 0.957475 -62 AGCTGATCAAAAATTAATAATGTTTGTCTTTCAA 3 26 0 AAATTAAATT 0.963607 -40 TTAAATAATCTATTTGAAATAATTCTTCATAAAA 4 73 0 TATTTGAATT 0.806379 -116 TCAAATAGATTATTTAAGAAGATTTGAAAACATT 4 90 1 TATTTAAATT 0.957341 -99 CAAATTGCGCTTTTTAAAACTGTTTTTGATGATT 4 142 1 TTTTTAAATT 0.794245 -47 GCAAGAATTATAATTAACACTCTAAGGATGCAAG 5 12 1 TAATTAAATA 0.912299 -30 TAATTAATCTTCTAGTATTTAGTT 6 1 1 TAATTAACTA 0.90836 -158 CACAACTATAAAACTAATCCTTTTTTGCAAAATA 6 38 0 AAACTAACTT 0.709513 -121 ATATGACGGTATTTTAGCTAATTATTTTTAGTA 6 136 0 TATTTTACTT 0.592631 -23 CTTAGCATATTTTAATCAATTAAATCTGTTTA 7 9 1 ATTTTAACTA 0.579958 -189 TTACTATTAAAAAATAAACAGATTTAATTGATTA 7 23 0 AAAATAACTT 0.622383 -175 GTAAAAACACAATTTAACCTTGTTTCTATTTAAC 7 53 1 AATTTAACTT 0.955477 -145 ACCTTGTTTCTATTTAACAAAATTGGTTTGAAAA 7 69 1 TATTTAAATT 0.956011 -129 TTTTACAGCAAAATTGATAGCCTTTTTCAAACCA 7 92 0 AAATTGAATT 0.83264 -106 TTGCTGTAAAAAATTAAGATATTTTTTATCAAAA 7 115 1 AAATTAAATT 0.964079 -83 ATTGTTATACTAATTAACGTTTTTTATTGAAAAT 7 162 1 TAATTAAGTT 0.809192 -36 TTTTTATTGAAAATTAAGTATTTAAA 7 182 1 AAATTAATTA 0.658294 -16 ACTCTAAAACTAATTAATAACCTAA 8 2 0 TAATTAAATA 0.912253 -62 ******* * ** Masking position 5 Map Score: 26.7029 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 354 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 ATTTAACTAATTATTATAACAATTTTAATTTA 1 165 1 TTTATAACAA 0.631177 -75 TTAGCTGTTTTGATTATAAAAACTGTTAAAAT 1 214 0 TGTATAAAAA 0.838291 -26 TTGTAGTGCTTGTTCATAAAAAAGTAAACGGT 4 38 0 TGTATAAAAA 0.830215 -151 TTTGAAAACATTCCCATTAAAGATAAGAATCA 4 112 1 TTCATTAAAG 0.749609 -77 AAACTGTTTTTGATGATTACAAAACCATTGAT 4 158 1 TGTATTACAA 0.853629 -31 AGCAAGAATTATAATTAACACTCTAAGGAT 5 9 1 TTTATTAACA 0.621756 -33 CTTTTTGGTATCTCTATAAAAAGTAGTATCAA 6 77 1 TCCATAAAAA 0.864691 -82 AGCTAATTATTTTTAGTAAAAAGAAATCAAAA 6 122 0 TTTGTAAAAA 0.728445 -37 AATTGTGTTTTTACTATTAAAAAATAAACAGA 7 35 0 TTCATTAAAA 0.93534 -163 GCTATCAATTTTGCTGTAAAAAATTAAGATAT 7 105 1 TTCGTAAAAA 0.938017 -93 TTATGCTAATTTTTGATAAAAAATATCTTAAT 7 127 0 TTTATAAAAA 0.629756 -71 TTATCAAAAATTAGCATAAAAAATTGTTATAC 7 140 1 TTGATAAAAA 0.946922 -58 AAAACGTTAATTAGTATAACAATTTTTTATGC 7 153 0 TTGATAACAA 0.895778 -45 AATACTTAATTTTCAATAAAAAACGTTAATTA 7 172 0 TTCATAAAAA 0.75015 -26 ATATGGTTCTAGTTACAATATAATCAAG 8 46 0 TTTGTTACAA 0.837039 -18 ** * ******* Masking position 9 Map Score: 18.0391 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 238 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 CTATACTTCCAAGCATAATCCTAAGGGTAT 1 137 1 AAGCATAATC 0.703502 -103 CCTCGAATTTTAACAGTTTTTATAATCAAA 1 208 1 TAACAGTTTT 0.783499 -32 GTTGAAAGACAAACATTATTAATTTTTGAT 3 25 1 AAACATTATT 0.911481 -41 AGGTTTTATGAAGAATTATTTCAAATAGAT 4 70 1 AAGAATTATT 0.719286 -119 TAGATTATTTAAGAAGATTTGAAAACATTC 4 95 1 AAGAAGATTT 0.800382 -94 TAATCATCAAAAACAGTTTTAAAAAGCGCA 4 147 0 AAACAGTTTT 0.930938 -42 AAGTAGTATCAAACATTTTTTTATCTTTTG 6 97 1 AAACATTTTT 0.801736 -62 TCTTTTTACTAAAAATAATTAGCTAAAATA 6 130 1 AAAAATAATT 0.759539 -29 CTTAGCATATTTTAATCAATTA 7 3 1 TAGCATATTT 0.787885 -195 ATTAAAAAATAAACAGATTTAATTGATTAA 7 22 0 AAACAGATTT 0.945017 -176 TTAATAGTAAAAACACAATTTAACCTTGTT 7 47 1 AAACACAATT 0.805636 -151 ********** Masking position 5 Map Score: 6.77341 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 314 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 GTTATAATAATTAGTTAAATACCCTTAGGA 1 155 0 TTAGTTAAAT 0.862517 -85 TATAATCAAAACAGCTAATTTT 1 228 1 ACAGCTAATT 0.893355 -12 TAATTTTTGATCAGCTAAATAAAACAAAGC 3 44 1 TCAGCTAAAT 0.980596 -22 TTCTGCTAAATCAATGGTTTT 4 178 0 TCTGCTAAAT 0.9762 -11 CTAATCCTTTTTTGCAAAATAACTAACTAA 6 29 0 TTTGCAAAAT 0.890969 -130 TGACGGTATTTTAGCTAATTATTTTTAGTA 6 136 0 TTAGCTAATT 0.943543 -23 TCAAACCAATTTTGTTAAATAGAAACAAGG 7 70 0 TTTGTTAAAT 0.835853 -128 TTAATTTTTTACAGCAAAATTGATAGCCTT 7 102 0 ACAGCAAAAT 0.834611 -96 AACAATTTTTTATGCTAATTTTTGATAAAA 7 138 0 TATGCTAATT 0.804804 -60 ********** Masking position 7 Map Score: 8.64172 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 124 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 AAGTCCATTTACTTCCACCAATAATGGGGAT 1 59 0 ACTTCCACCA 0.957504 -181 AAGTAAATGGACTTGAACCATCGACCTCACC 1 76 1 ACTTGAACCT 0.991004 -164 TGAACCATCGACCTCACCCTTATCAGGGGTG 1 89 1 ACCTCACCCT 0.936421 -151 AATACATCAAACTTCAACCGTTTACTTTTTT 4 22 1 ACTTCAACCT 0.991004 -167 TTATCACTTGCATCCTTAGAGTGTTA 5 26 0 ACTTGCATCT 0.933901 -16 TTATATTGTAACTAGAACCATAT 8 51 1 ACTAGAACCT 0.964511 -13 ********* * Masking position 1 Map Score: 2.47312 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 13 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ACAATTTTAATTTAACCAAAATACCCCTCG 1 183 1 TTTAACCAAA 0.851062 -57 TAACAGTTTTTATAATCAAAACAGCTAATT 1 218 1 TATAATCAAA 0.947873 -22 TGTAAAACCAAGTTCTTGAAAG 2 3 1 TAAAACCAAG 0.819448 -44 CATTAAAGATAAGAATCAAATTGCGCTTTT 4 126 1 AAGAATCAAA 0.822004 -63 CTATAAAAAGTAGTATCAAACATTTTTTTA 6 90 1 TAGTATCAAA 0.902486 -69 TTTTGTTAAATAGAAACAAGGTTAAATTGT 7 61 0 TAGAAACAAG 0.856349 -137 TTAAGATATTTTTTATCAAAAATTAGCATA 7 128 1 TTTTATCAAA 0.64515 -70 CTAGTTACAATATAATCAAGATAATAATAT 8 36 0 TATAATCAAG 0.938374 -28 ATATTGTAACTAGAACCATAT 8 53 1 TAGAACCATA 0.819055 -11 ********** Masking position 5 Map Score: 3.68286 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 167 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AGTTGAGCTACATCCCCATTATTGGTGGAA 1 48 1 CATCCCCATT 0.961844 -192 GTCGATGGTTCAAGTCCATTTACTTCCACC 1 71 0 CAAGTCCATT 0.744647 -169 AACTAATTATTATAACAATTTTAATTTAAC 1 169 1 TATAACAATT 0.754367 -71 GTTTGTCTTTCAACACTATTAAATTTAT 3 9 0 CAACACTATT 0.858596 -57 GATTTGAAAACATTCCCATTAAAGATAAGA 4 110 1 CATTCCCATT 0.863828 -79 TTGATGATTACAAAACCATTGATTTAGCAG 4 167 1 CAAAACCATT 0.963288 -22 TTAATAGTAAAAACACAATTTAACCTTGTT 7 47 1 AAACACAATT 0.721543 -151 TAGCCTTTTTCAAACCAATTTTGTTAAATA 7 79 0 CAAACCAATT 0.941911 -119 CGTTAATTAGTATAACAATTTTTTATGCTA 7 151 0 TATAACAATT 0.754367 -47 ********** Masking position 8 Map Score: 2.5067 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 198 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: -3.16659e-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: -3.16659e-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 10 ********** No masking Map Score: -3.16659e-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