AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -imalT_mpneu_opreg_100.orf -g0.400 -x5 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 = 0 Input sequences: #1 ugpC 23 sn-glycerol-3-phosphate transport system permease protein; similar to Swiss-Prot Accession Number P10907, from E. coli #2 1673668 300 putative lipoprotein, MG186 homolog, from M. genitalium #3 potA 300 spermidine/putrescine transport ATP-binding prot; similar to Swiss-Prot Accession Number P23858, from E. coli #4 rpsJ 93 ribosomal protein S10; similar to Swiss-Prot Accession Number P38518, from T. maritima #5 1674374 246 VXpSPT7_orf112 Protein Motif number 1 ATCAATTAAATGCTTGATCAAAACCAAGGTGTC 2 39 1 TGTGTCAAAA 0.981768 -262 AAAACTACTTAAATTGCTAAAAATTAACCGTTT 2 116 1 AATGTAAAAA 0.907392 -185 TTGAATTAGTTTTAGGGTCAAAATTAGGCCAAT 2 149 1 TTGGTCAAAA 0.971912 -152 TTAGGTTATTTAGGGGGTAAAAAGTAGAGATTT 2 203 0 TAGGTAAAAA 0.954447 -98 AAAGAGAAGTTGTAGGCTAAAAGAAGGGGAATT 3 17 0 TGGGTAAAAG 0.968574 -284 CTTCTCTTTTTTCTTGTTAAAAGATTCCCTTTC 3 41 1 TTTGTAAAAG 0.972625 -260 AAAAGAGATTTTCTTGATAAAAAGAAAGGGAAT 3 64 0 TTTGTAAAAA 0.979142 -237 GTGGTCTTTATTTTGGTTCAAAATTTAGTCCAA 3 111 1 TTGGTCAAAA 0.963625 -190 TGCAGTTAAATTTGTGCTAAAAATTTGACTGTT 3 145 0 TTTGTAAAAA 0.979142 -156 TTAACTGCAAAAACTGTTCAAAAAATCTCACAA 3 169 1 AATGTCAAAA 0.905643 -132 GGGATAAATTTTCTTGCAAAAAAATGATTGCAA 3 204 0 TTTGAAAAAA 0.88435 -97 TTAGGGGGCAAGCGGGGTCAAAAATTGCTACAA 3 241 1 AGGGTCAAAA 0.933857 -60 AGGGTGAAATTTGATGGTCAAAATGACTACGCT 4 58 0 TTTGTCAAAA 0.978942 -36 AAGACCCATTTAATTGTTAAAAGAAACTTACTA 5 68 0 TATGTAAAAG 0.954447 -179 GCGGCAAACTAGTTTGGAAAAAGATAAGGAATT 5 196 1 AGTGAAAAAG 0.699396 -51 AGTTCAATTGTGACTGCTAAAAGC 5 233 1 TGTGTAAAAG 0.976284 -14 ** ** ****** Masking position 10 Map Score: 29.0138 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 125 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 ATATTTAGAGTAAAACTACTTAAATTGCTAAAAATT 2 105 1 TAAACTTATT 0.732045 -196 AAACTAATTCAAAAACGGTTAATTTTTAGCAATTTA 2 125 0 AAAACGATTT 0.73051 -176 AAGAAAGCGGGAAATTGGCCTAATTTTGACCCTAAA 2 159 0 GAAATGTATT 0.868855 -142 ACTACGGTGAACAATTTAGATAAATTTACATTAATT 2 256 0 ACAATTTATT 0.850172 -45 CTTTACCTAAATTGAACTAACTACGGTGAACAA 2 278 0 TAAATGTATA 0.750303 -23 CTTTTAGCCTACAACTTCTCTTTTTTCTTGTTAAAA 3 27 1 ACAATTTTTT 0.792248 -274 TTTTATCAAGAAAATCTCTTTTTTTATGTCTTAAAA 3 75 1 AAAACTTTTA 0.78987 -226 TTTATGTCTTAAAAGTGGTCTTTATTTTGGTTCAAA 3 97 1 AAAATGTTTT 0.964387 -204 ATTTGTGCTAAAAATTTGACTGTTTTTGGACTAAAT 3 133 0 AAAATTTTTT 0.834846 -168 AAAATCTCACAAAATTGCAATCATTTTTTTGCAAGA 3 190 1 AAAATGTATT 0.976207 -111 CTTGCCCCCTAAAACTGGGATAAATTTTCTTGCAAA 3 217 0 AAAATGTATT 0.976744 -84 TTTTTAAAGAAAAAACGGTATTTATTGTAGCAATTT 3 262 0 AAAACGTTTT 0.968519 -39 GGATACACCGAAAAGCGTAGTCATTTTGACCATCAA 4 45 1 AAAACGTATT 0.978526 -49 AAGATCGCCAAAAAGCGGGGTTACTACTTTTTTGAA 5 116 1 AAAACGTATA 0.945566 -131 TTTAGCAGTCACAATTGAACTGACTAATTCCTTATC 5 218 0 ACAATGTATA 0.871307 -29 **** ** * * ** Masking position 4 Map Score: 15.8989 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 196 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 AATTTCCCGCTTTCTTTTTTTAAAAAATCT 2 179 1 TTTCTTTTTT 0.895579 -122 TTTTAAAAAATCTCTACTTTTTACCCCCTA 2 196 1 TCTCTACTTT 0.906187 -105 TTTGTTAATTCCCCTTCTTTTAGCCTACA 3 10 1 TCCCCTTCTT 0.858686 -291 GCCTACAACTTCTCTTTTTTCTTGTTAAAA 3 33 1 TCTCTTTTTT 0.980242 -268 GTTAAAAGATTCCCTTTCTTTTTATCAAGA 3 56 1 TCCCTTTCTT 0.966818 -245 ATCAAGAAAATCTCTTTTTTTATGTCTTAA 3 79 1 TCTCTTTTTT 0.980242 -222 TTAAAAGTGGTCTTTATTTTGGTTCAAAAT 3 105 1 TCTTTATTTT 0.905545 -196 AAAATTGCAATCATTTTTTTGCAAGAAAAT 3 200 1 TCATTTTTTT 0.814663 -101 ATAAATACCGTTTTTTCTTTAAAAATTAAG 3 273 1 TTTTTTCTTT 0.611466 -28 ACTGACTAATTCCTTATCTTTTTCCAAACT 5 206 0 TCCTTATCTT 0.849178 -41 ********** Masking position 9 Map Score: 8.48719 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 123 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 ATTGCTGGTTTAAACTGCTTTCA 1 5 0 TTAAACTGCT 0.975912 -19 TGATCAAGCATTTAATTGATGTATGGCAAG 2 29 0 TTTAATTGAT 0.86979 -272 GTAAAACTACTTAAATTGCTAAAAATTAAC 2 114 1 TTAAATTGCT 0.940593 -187 GTGCTAAAAATTTGACTGTTTTTGGACTAA 3 135 0 TTTGACTGTT 0.94474 -166 TTAGCACAAATTTAACTGCAAAAACTGTTC 3 158 1 TTTAACTGCA 0.951938 -143 TTTAACTACTTAATTTTTAA 3 291 0 TTTAACTACT 0.925097 -10 AAAAGACCCATTTAATTGTTAAAAGAAACT 5 73 0 TTTAATTGTT 0.921873 -174 TCAGTTCAATTGTGACTGCTAAAAGC 5 231 1 TGTGACTGCT 0.943328 -16 ********** Masking position 5 Map Score: 5.87952 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 242 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 ATTAACCGTTTTTGAATTAGTTTTAGGGTCAAA 2 138 1 TTTGAAATTT 0.913379 -163 TTTACATTAATTGGGAATTAATTGTGTAGTTGT 2 235 0 TTGGGATATT 0.943073 -66 CGGTGAACAATTTAGATAAATTTACATTAATTG 2 255 0 TTTAGAATTT 0.806696 -46 TTTGACTGTTTTTGGACTAAATTTTGAACCAAA 3 122 0 TTTGGAAATT 0.912191 -179 GATTGCAATTTTGTGAGATTTTTTGAACAGTTT 3 179 0 TTGTGATTTT 0.869367 -122 TCTCACAAAATTGCAATCATTTTTTTGCAAGAA 3 194 1 TTGCAAATTT 0.735665 -107 CCCCCTAAAACTGGGATAAATTTTCTTGCAAAA 3 216 0 CTGGGAATTT 0.962442 -85 GCTAAAAGCATTGGGACTTGTTTGCGCTAGTTA 5 17 0 TTGGGATTTT 0.983497 -230 ATGCTTTTAGCTTGGAGCTTTTTTGCTGTTAGT 5 39 1 CTTGGATTTT 0.941414 -208 TTACTACTTTTTTGAAGTTGTTTAATTTCAATG 5 136 1 TTTGAATTTT 0.913379 -111 ****** * *** Masking position 6 Map Score: 5.5329 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 154 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TTGTAATTTTTCGGCGGTCTTGCCATACATC 2 9 1 TTGGCGTCTT 0.994138 -292 ACTCTAAATATACAGGCGCTCTTAGCAATTGTG 2 83 0 TCGGCGTCTT 0.997388 -218 TTAGGCCAATTTCCCGCTTTCTTTTTTTAAAAA 2 172 1 TCCGCTTCTT 0.964685 -129 TAACCCCGCTTTTTGGCGATCTTATTGTGTCAC 5 106 0 TTGGCGTCTT 0.994138 -141 GTTTGCCGCTTGCAGGCCTTATTATTTTCCCAT 5 172 0 TCGGCCTATT 0.964684 -75 * * **** **** Masking position 10 Map Score: 2.06884 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 7 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ATTTAGTGCACAATTGCTAAGAGCGCCTGT 2 75 1 CAATTGCTAA 0.881034 -226 AAAACTACTTAAATTGCTAAAAATTAACCG 2 116 1 AAATTGCTAA 0.960109 -185 ACCTAAATTGAACTAACTACGGTGAACAAT 2 277 0 AACTAACTAC 0.898313 -24 GCGGGGTCAAAAATTGCTACAATAAATACC 3 252 1 AAATTGCTAC 0.966739 -49 TTGATGGTCAAAATGACTACGCTTTTCGGT 4 51 0 AAATGACTAC 0.952275 -43 TGTTAAAAGAAACTTACTAACAGCAAAAAA 5 57 0 AACTTACTAA 0.960109 -190 GTCACAATTGAACTGACTAATTCCTTATCT 5 217 0 AACTGACTAA 0.952275 -30 ********** Masking position 2 Map Score: 5.55785 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 74 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 8 ********** No masking Map Score: 1.77168e-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: 1.77168e-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: 1.77168e-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