AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_mgen_reg_100.orf -o00710_mgen_100.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 Purged sequences: MG301 30 glyceraldehyde-3-phosphate dehydrogenase (gap) Input sequences: #1 MG018 188 ATP-dependent RNA helicase, putative #2 MG019 41 heat shock protein (dnaJ) #3 MG022 29 DNA-directed RNA polymerase, subunit delta (rpoE) #4 MG064 255 conserved hypothetical protein #5 MG211 189 conserved hypothetical protein #6 MG304 176 ABC transporter, ATP binding protein #7 MG406 140 conserved hypothetical protein #8 MG431 59 triosephosphate isomerase (tpiA) #9 MG432 85 conserved hypothetical protein Motif number 1 CCGTTTACTTTTTTATGAACAAGCACTACAA 1 39 1 TTTTATGAAA 0.814977 -150 ACTACAAAGGTTTTATGAAGAATTATTTCAA 1 63 1 TTTTATGAAA 0.814977 -126 TGAAGAATTATTTCAAATAGATTATTTAAGA 1 78 1 TTTCAAATAA 0.833913 -111 CAAATAGATTATTTAAGAAGATTTGAAAACA 1 91 1 ATTTAAGAAA 0.740203 -98 TCAAAAACAGTTTTAAAAAGCGCAATTTGAT 1 140 0 TTTTAAAAAC 0.970191 -49 TCGCGTAATATTTTAACTATCCAGATTGTTT 4 54 1 TTTTAACTAC 0.951027 -202 ATCCAGATTGTTTTAACAATCTTTAGTATGA 4 72 1 TTTTAACAAC 0.974161 -184 TTATTTCTGTTTTCAACTAAAGCTGTAGCTA 4 157 0 TTTCAACTAA 0.853288 -99 AAATCAGTTCTTTTAAAAAAAGACAATGTTA 4 206 0 TTTTAAAAAA 0.953385 -50 TCAGAGACAAATTTAAAAATCAGTTCTTTTA 4 222 0 ATTTAAAAAC 0.849603 -34 CTTTTTTGTTTTTTATCTACCAAAAAACAGA 6 61 1 TTTTATCTAC 0.839271 -116 TATTTATAAATTTTAAAAATAAGTCAGAGCT 6 97 0 TTTTAAAAAA 0.958329 -80 AAAACCTCAGTTTTAAATACCCAAAACACCA 6 149 1 TTTTAAATAC 0.943707 -28 GCAGTTGTTGTTTTAACAAAAGGCAATAATT 7 100 1 TTTTAACAAA 0.958835 -41 TTTTATAAGTTTTCAAAAACCATTTTCTTTT 8 31 0 TTTCAAAAAC 0.932259 -29 ********* * Masking position 5 Map Score: 20.4046 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 289 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 CTCAAAAAACTAATACATCAAACTTCAACCG 1 6 1 AAAATATAAA 0.972452 -183 CATTCCCATTAAAGATAAGAATCAAATTGCGCTTTT 1 120 1 AAAGTAGAAA 0.888589 -69 AGCAAGAATTATAATTAACACTCTAAGGATGCAAGT 2 11 1 ATAATACAAA 0.857397 -31 GAAAAGTAGTATTAGAATTTTATTGAT 3 2 1 AAAATATAAA 0.972452 -28 TCTGGATAGTTAAAATATTACGCGAATTAAGCTTAG 4 43 0 TAAATATAAA 0.789763 -213 CAAAGTAAGAAAAAAGATCATACTAAAGATTGTTAA 4 84 0 AAAAGACAAA 0.946949 -172 AAACAAGATTAAAGATAGCAAAGTAAGAAAAAAGAT 4 102 0 AAAGTACAAA 0.976464 -154 AAAAGTTTAAAAGGATATCACTGGAAGTACGCAGGT 5 56 1 AAGGTACAAA 0.867436 -134 GAGAAAAACAAAAGATAGCACAGAAAAAGCGCAGGA 5 137 1 AAAGTACAAA 0.976464 -53 ATTCCAAATAAAAAAGAGCAGCACAACAGCTGCTTT 6 29 1 AAAAGACAAA 0.946949 -148 AAAGGTTGCAAAAATTATTACCTTAATTATTTTTGT 7 36 1 AAAATATAAA 0.972452 -105 AACTGCTATTAAAATTAGTACAAATAACCAAGCTAC 7 70 0 AAAATATATA 0.789763 -71 ATTAATTACCAAAATTATTAAAATAATTGTTCTTAA 9 58 1 AAAATATAAA 0.972452 -28 **** ** ** ** Masking position 7 Map Score: 17.2291 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 89 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 AATTCTTCATAAAACCTTTGTAGTGCTTGTTCAT 1 53 0 AAACCTTAGT 0.797407 -136 AGAAGATTTGAAAACATTCCCATTAAAGATAAGA 1 106 1 AAACATCATT 0.944114 -83 TTCTGCTAAATCAATGGTTTTGTAATCATCA 1 168 0 AAACATTTTT 0.548806 -21 AAATCAATAAAATTCTAATACTAC 3 16 0 AAACATAATT 0.85057 -14 GAACTTGTAGATAACATTGTCTTTTTTTAAAAGA 4 195 1 ATACATCTTT 0.928293 -61 ACAAATTTAAAAATCAGTTCTTTTAAAAAAAGAC 4 213 0 AAACATTTTT 0.905043 -43 AGCTAGCTCTAAATCATCATTTTTAACTTCAATC 5 18 0 AAACACTTTT 0.957515 -172 GTTTAAAAGGATATCACTGGAAGTACGCAGGTTA 5 60 1 ATACATAAGT 0.548615 -130 AAAAAACAAAAAAGCAGCTGTTGTGCTGCTCTTT 6 41 0 AAACACTTGT 0.69427 -136 CTACAAGTTAAAAACCTCAGTTTTAAATACCCAA 6 139 1 AAACCCTTTT 0.840348 -38 ACTAATTTTAATAGCAGTTGTTGTTTTAACAAAA 7 87 1 ATACATTTGT 0.897907 -54 TAAAATGTCCAAATTATTGCCTTTTGTTAAAACA 7 108 0 AAATATCTTT 0.709905 -33 AAGTTTTCAAAAACCATTTTCTTTTCCAACTAAT 8 22 0 AAACATCTTT 0.975151 -38 AGTTAAGAACAATTATTTTAATAATTTTG 9 67 0 AGACATTTTT 0.834241 -19 *** ** * **** Masking position 3 Map Score: 12.2959 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 451 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ACTTCAACCGTTTACTTTTTTATGAACAAG 1 32 1 TTTACTTTTT 0.582414 -157 TAGGCTTTCGCTTTCTTTTTACCATCAAAT 4 16 0 CTTTCTTTTT 0.879032 -240 TATCTTTAATCTTGTTTTTGAGTTTGCAAA 4 121 1 CTTGTTTTTG 0.770086 -135 CACAGCTTTATTTCTGTTTTCAACTAAAGC 4 165 0 TTTCTGTTTT 0.847126 -91 GTAGATAACATTGTCTTTTTTTAAAAGAAC 4 201 1 TTGTCTTTTT 0.90564 -55 TCTGTGCTATCTTTTGTTTTTCTCTTAACC 5 131 0 CTTTTGTTTT 0.879032 -59 TGTGCTGCTCTTTTTTATTTGGAATATGTT 6 24 0 TTTTTTATTT 0.804114 -153 AACAGCTGCTTTTTTGTTTTTTATCTACCA 6 53 1 TTTTTGTTTT 0.898451 -124 AGCTAAAAATCTGTTTTTTGGTAGATAAAA 6 71 0 CTGTTTTTTG 0.852969 -106 ATTGTTTTGGTGTTTTGGGTATTTAA 6 161 0 TTGGTGTTTT 0.857372 -16 TTTTTGCAACCTTTCTATTGTTTCAATTGA 7 20 0 CTTTCTATTG 0.626003 -121 TTTTTGTAGCTTGGTTATTTGTACTAATTT 7 65 1 TTGGTTATTT 0.736084 -76 TTAATAGCAGTTGTTGTTTTAACAAAAGGC 7 94 1 TTGTTGTTTT 0.90564 -47 GTCCAAATTATTGCCTTTTGTTAAAACAAC 7 106 0 TTGCCTTTTG 0.784179 -35 TAATTAATAATTTCTTATTTACTATCTTAT 9 36 0 TTTCTTATTT 0.719971 -50 ********** Masking position 8 Map Score: 9.05368 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 887 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 GTAATCATCAAAAACAGTTTTAAAAAGCGC 1 148 0 AAAACAGTTT 0.808496 -41 ATATTACGCGAATTAAGCTTAGGCTTTCGC 4 35 0 AATTAAGCTT 0.722797 -221 AAAAGATCATACTAAAGATTGTTAAAACAA 4 79 0 ACTAAAGATT 0.861784 -177 GCAAAGTAAGAAAAAAGATCATACTAAAGA 4 91 0 AAAAAAGATC 0.778298 -165 GCAAACTCAAAAACAAGATTAAAGATAGCA 4 118 0 AAACAAGATT 0.713113 -138 TCTGTTTTCAACTAAAGCTGTAGCTAAATT 4 153 0 ACTAAAGCTG 0.91729 -103 TGAAAACAGAAATAAAGCTGTGGAACTTGT 4 173 1 AATAAAGCTG 0.915851 -83 AGCTAGCTTTAAAAAAGTTTAAAAGGATAT 5 44 1 AAAAAAGTTT 0.851838 -146 TAAGAGAAAAACAAAAGATAGCACAGAAAA 5 134 1 ACAAAAGATA 0.707055 -56 AAAGAGCAGCACAACAGCTGCTTTTTTGTT 6 41 1 ACAACAGCTG 0.946211 -136 TATCTACCAAAAAACAGATTTTTAGCTCTG 6 74 1 AAAACAGATT 0.906583 -103 TAAAATTTATAAATAAGCTTAGTTTGCTAC 6 113 1 AAATAAGCTT 0.849224 -64 TTTTGTTAAAACAACAACTGCTATTAAAAT 7 91 0 ACAACAACTG 0.536749 -50 ********** Masking position 6 Map Score: 6.19217 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 459 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 CTCAAAAAACTAATACATCAAACTTCAA 1 8 1 AACTAATAAT 0.46002 -181 AATCTATTTGAAATAATTCTTCATAAAACCT 1 70 0 AAATAATTTT 0.899474 -119 AAATCTTCTTAAATAATCTATTTGAAATAAT 1 84 0 AAATAATCAT 0.870223 -105 TGAGTTTGCAAAGTAATTTAGCTACAGCTTT 4 139 1 AAGTAATTAG 0.834288 -117 ACTAATAAATTAGTCAGAGACAAATTT 4 239 0 AAATTAGTAG 0.654265 -17 TAAATTTTAAAAATAAGTCAGAGCTAAAAAT 6 91 0 AAATAAGTAG 0.902585 -86 ATAATTAAGGTAATAATTTTTGCAACCTTTC 7 35 0 TAATAATTTT 0.64658 -106 CAAGCTACAAAAATAATTAAGGTAATAATTT 7 47 0 AAATAATTAG 0.963944 -94 AAATTAGTACAAATAACCAAGCTACAAAAAT 7 64 0 AAATAACCAG 0.635681 -77 TTTCTTTTCCAACTAATTGATCATTAAG 8 8 0 AACTAATTAT 0.870231 -52 AGTAAATAAGAAATTATTAATTACCAAAATT 9 43 1 AAATTATTAT 0.798069 -43 ACAATTATTTTAATAATTTTGGTAATTAATA 9 57 0 TAATAATTTG 0.716538 -29 AAAATTATTAAAATAATTGTTCTTAACT 9 68 1 AAATAATTTT 0.899387 -18 ******** ** Masking position 6 Map Score: 5.85911 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 197 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 ********** No masking Map Score: -1.40444e-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: -1.40444e-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: -1.40444e-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