AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_mgen_reg_100.orf -o00030_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 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 MG058 85 ribose-phosphate pyrophosphokinase (prs) #5 MG064 255 conserved hypothetical protein #6 MG109 59 serine/threonine protein kinase, putative #7 MG211 189 conserved hypothetical protein #8 MG406 140 conserved hypothetical protein Motif number 1 AAATAATCTATTTGAAATAATTCTTCATAAAACCTTT 1 68 0 TTTAATCTTA 0.886344 -121 AATGGGAATGTTTTCAAATCTTCTTAAATAATCTATT 1 93 0 TTTATTCTTA 0.978225 -96 AAAAGCGCAATTTGATTCTTATCTTTAATGGGAATGT 1 119 0 TTTTTTCTTA 0.96823 -70 AATTGCGCTTTTTAAAACTGTTTTTGATGATTACAAA 1 144 1 TTTATTTTTA 0.975704 -45 AAGCACGTTATTTTTAGTTTATCTAAAAGCAAAACAC 4 15 1 TTTATTCTAA 0.908724 -71 TATTTAGTTTTTTGCAGATATTTTCAACCAGTGTTTT 4 45 0 TTTATTTTCA 0.954373 -41 ATATTTTAACTATCCAGATTGTTTTAACAATCTTTAG 5 61 1 TATATTTTTA 0.877947 -195 CTTTGCTATCTTTAATCTTGTTTTTGAGTTTGCAAAG 5 115 1 TTTTTTTTTA 0.965616 -141 GTTCCACAGCTTTATTTCTGTTTTCAACTAAAGCTGT 5 162 0 TTTTTTTTCA 0.934119 -94 AAGAACTGATTTTTAAATTTGTCTCTGACTAATTTAT 5 225 1 TTTATTCTCG 0.754908 -31 AGCTTTTCAATTTGATACTTATTTTCAACAATATCAC 6 17 0 TTTTTTTTTA 0.965631 -43 CCCACCCCTATTTAAAAGCTTTTCAATTTGATACT 6 35 0 TATAATTTTA 0.555282 -25 AGTGATATCCTTTTAAACTTTTTTAAAGCTAGCTCTA 7 41 0 TTTATTTTAA 0.875229 -149 CTGTGCTATCTTTTGTTTTTCTCTTAACCGCATCCCT 7 123 0 TTTTTTCTTA 0.968218 -67 TAGCTTGGTTATTTGTACTAATTTTAATAGCAGTTGT 8 71 1 ATTTTTTTTA 0.720047 -70 *** * * **** * Masking position 12 Map Score: 18.5518 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 247 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 CTCAAAAAACTAATACATCAAAC 1 3 1 CAAAAAACAA 0.946009 -186 GCTTGTTCATAAAAAAGTAAACGGTTGAAGT 1 32 0 AAAAAAGTAA 0.890718 -157 AAAACAGTTTTAAAAAGCGCAATTTGATTCT 1 137 0 TAAAAAGCCA 0.862763 -52 TTTAGTTTATCTAAAAGCAAAACACTGGTTG 4 27 1 CTAAAAGCAA 0.829633 -59 AAAATATCTGCAAAAAACTAAATATTTCAGA 4 58 1 CAAAAAACAA 0.946009 -28 TGATGGTAAAAAGAAAGCGAAAGCCTAAGCT 5 19 1 AAGAAAGCAA 0.972284 -237 GCAAAGTAAGAAAAAAGATCATACTAAAGAT 5 90 0 AAAAAAGACA 0.885637 -166 AACAAGATTAAAGATAGCAAAGTAAGAAAAA 5 106 0 AAGATAGCAA 0.936164 -150 AGTTCTTTTAAAAAAAGACAATGTTATCTAC 5 201 0 AAAAAAGAAA 0.921129 -55 ATGCGGTTAAGAGAAAAACAAAAGATAGCAC 7 127 1 GAGAAAAAAA 0.572745 -63 AGAAAAACAAAAGATAGCACAGAAAAAGCGC 7 138 1 AAGATAGCCA 0.906752 -52 AGATAGCACAGAAAAAGCGCAGGAAGTTTCG 7 149 1 GAAAAAGCCA 0.944896 -41 CCAAGCTACAAAAATAATTAAGGTAATAATT 8 48 0 AAAATAATAA 0.546823 -93 AAAATTAGTACAAATAACCAAGCTACAAAAA 8 65 0 CAAATAACAA 0.879877 -76 ******** ** Masking position 6 Map Score: 10.7371 Number of sites scoring better than the average of aligned sites = 593 Number in coding regions = 531 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TTAATGGGAATGTTTTCAAATCTTCTTAAA 1 102 0 TGTTTTCAAA 0.833513 -87 CATCAAAAACAGTTTTAAAAAGCGCAATTT 1 143 0 AGTTTTAAAA 0.881833 -46 ATGGTTTTGTAATCATCAAAAACAGTTTTA 1 156 0 AATCATCAAA 0.459746 -33 AGCAAAACACTGGTTGAAAATATCTGCAAA 4 42 1 TGGTTGAAAA 0.886151 -44 TGGTTGAAAATATCTGCAAAAAACTAAATA 4 52 1 TATCTGCAAA 0.717839 -34 CTTGTTTTTGAGTTTGCAAAGTAATTTAGC 5 131 1 AGTTTGCAAA 0.941425 -125 GCTACAGCTTTAGTTGAAAACAGAAATAAA 5 159 1 TAGTTGAAAA 0.864946 -97 GTCAGAGACAAATTTAAAAATCAGTTCTTT 5 224 0 AATTTAAAAA 0.763079 -32 TGTTGAAAATAAGTATCAAATTGAAAAGCT 6 24 1 AAGTATCAAA 0.774667 -36 CCTAAGATTGAAGTTAAAAATGATGATTTA 7 13 1 AAGTTAAAAA 0.856907 -177 ATTTAGAGCTAGCTTTAAAAAAGTTTAAAA 7 38 1 AGCTTTAAAA 0.696632 -152 AGCTTTAAAAAAGTTTAAAAGGATATCACT 7 48 1 AAGTTTAAAA 0.919459 -142 AACAATAGAAAGGTTGCAAAAATTATTACC 8 28 1 AGGTTGCAAA 0.967617 -113 ACAAATAACCAAGCTACAAAAATAATTAAG 8 57 0 AAGCTACAAA 0.815585 -84 ********** Masking position 8 Map Score: 10.1179 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 520 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 AAAGCACGTTATTTTTAGTTTATCTAAAAG 4 14 1 ATTTTTAGTT 0.939766 -72 GCCCTCTGAAATATTTAGTTTTTTGCAGAT 4 63 0 ATATTTAGTT 0.939689 -23 TGTTTTAACAATCTTTAGTATGATCTTTTT 5 80 1 ATCTTTAGTA 0.952563 -176 ATTTAGCTACAGCTTTAGTTGAAAACAGAA 5 154 1 AGCTTTAGTT 0.984724 -102 CAAGTTCCACAGCTTTATTTCTGTTTTCAA 5 172 0 AGCTTTATTT 0.912518 -84 TTTCTGTGCTATCTTTTGTTTTTCTCTTAA 7 133 0 ATCTTTTGTT 0.952563 -57 ********** Masking position 5 Map Score: 4.49259 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 73 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TTCTGCTAAATCAATGGTTTTGTA 1 175 0 GCTAAATCAA 0.955716 -14 ACTAAAGATTGTTAAAACAATCTGGATAGT 5 69 0 GTTAAAACAA 0.931192 -187 AGATAGCAAAGTAAGAAAAAAGATCATACT 5 96 0 GTAAGAAAAA 0.689745 -160 AAATTACTTTGCAAACTCAAAAACAAGATT 5 128 0 GCAAACTCAA 0.897753 -128 CTTTTTTAAAGCTAGCTCTAAATCATCATT 7 31 0 GCTAGCTCTA 0.874173 -159 AAGTACGCAGGTTAGCACAACGCCATGAAT 7 80 1 GTTAGCACAA 0.965072 -110 CTTAATGGCTAGCTAAACTGCGAAACT 7 173 0 GCTAGCTAAA 0.935073 -17 AAATAACCAAGCTACAAAAATAATTAAGGT 8 55 0 GCTACAAAAA 0.796979 -86 ATTGCCTTTTGTTAAAACAACAACTGCTAT 8 97 0 GTTAAAACAA 0.931192 -44 ********** Masking position 4 Map Score: 5.0623 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 177 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 AGAAGATTTGAAAACATTCCCATTAAAGATA 1 106 1 AAAACATTCC 0.957785 -83 ACACTGGTTGAAAATATCTGCAAAAAACTAA 4 48 1 AAAATATCGC 0.921844 -38 CTGGATAGTTAAAATATTACGCGAATTAAGC 5 47 0 AAAATATTCG 0.934328 -209 CTTATTTTCAACAATATCACCTATCT 6 6 0 ACAATATCCC 0.949519 -54 AAGGTTGCAAAAATTATTACCTTAATTATTT 8 37 1 AAATTATTCC 0.970808 -104 TAAAATGTCCAAATTATTGCCTTTTGTTAAA 8 111 0 AAATTATTCC 0.970808 -30 ******** ** Masking position 6 Map Score: 1.41036 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 36 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 7 ********** No masking Map Score: -1.13444e-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: -1.13444e-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: -1.13444e-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