AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -inarL_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 1673774 300 B01_orf116L Protein #2 1673937 300 D02_orf128 Protein Motif number 1 CCAAAATTTTTATTTTTGCCGGTTTAACTGTTGTTA 1 10 1 TTATTTTGTA 0.971295 -291 TTAACTGTTGTTAATTTTTGAGACAAAGTTCTACCAG 1 34 1 TTATTTTGAA 0.915706 -267 ATTTGCACACTAATTTTTGGCGTCTTTTTGTTTTTTG 1 99 1 TAATTTTGTT 0.96161 -202 TGGCGTCTTTTTGTTTTTTGGGTAATTTAAATGATGT 1 116 1 TTGTTTTGTT 0.975577 -185 AAAAAGGTGAAAGTGTTTAAAGAGGTAGGCACCAACA 1 221 0 AAGGTTTGTA 0.881936 -80 AAGGGAAATTTTGCGTTTAATGGCAAAGACCTCCTTT 1 271 0 TTGGTTTGAA 0.890455 -30 GCGAGTCCAATTAATTTTTTAGGGTTTAAAAGAAATT 2 42 1 TTATTTTGTT 0.975124 -259 ACAGGAAAATTTAATTTTTAAGCCTAATGCTAATTTC 2 73 0 TTATTTTGAA 0.913272 -228 AGTGATGGCGTAGAGTTTTTAGTTTTTATTGTTGAAA 2 116 1 TAGGTTTGTT 0.949346 -185 TTTATTGTTGAAACTTTTTAAGCCTTTAATGGGTGTT 2 140 1 AAATTTTGTT 0.917996 -161 ATGGGTGTTGAAAAGTTTGTGGTAGTTTTTCAATTAA 2 168 1 AAAGTTTGTT 0.894903 -133 ACTGTCAGCATTGGTTTTTTAGTTGTTTTAAGTATTT 2 250 1 TTGTTTTGTT 0.975577 -51 GAAAAATATTTGTTTGGAAATAACAAATACTT 2 279 0 ATATTGTGTA 0.711878 -22 *** **** * ** Masking position 8 Map Score: 15.0929 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 177 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 AAAATTAACAACAGTTAAACCGGCAAAAATA 1 21 0 ACAGTTAACC 0.973812 -280 TTTTTGAGACAAAGTTCTACCAGTTAAAAAA 1 48 1 AAAGTTTACC 0.962204 -253 GTTAAAAAAGACACTTTTAAACTCGTAAAAT 1 70 1 ACACTTTAAA 0.929815 -231 TAATAAAATGACAGTTTTAAAAAATCATTTA 1 158 1 ACAGTTTAAA 0.940479 -143 ACCTCTTTAAACACTTTCACCTTTTTCCAAT 1 232 1 ACACTTCACC 0.98001 -69 GCTAATGAAAACGGTTTTAACTCGATAAATC 2 13 0 ACGGTTTAAC 0.923152 -288 TCAACAATAAAAACTAAAAACTCTACGCCAT 2 120 0 AAACTAAAAC 0.850009 -181 AAAGGCTTAAAAAGTTTCAACAATAAAAACT 2 136 0 AAAGTTCAAC 0.963876 -165 TTTAATTGAAAAACTACCACAAACTTTTCAA 2 175 0 AAACTACACA 0.673659 -126 ACCAATGCTGACAGTAGTAACGTTAACGCTA 2 234 0 ACAGTATAAC 0.962133 -67 GAAATAACAAATACTTAAAACAACTAAAAAA 2 264 0 ATACTTAAAC 0.812185 -37 ****** **** Masking position 9 Map Score: 9.81653 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 252 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 TTTTTTGGGTAATTTAAATGATGTATGCGT 1 129 1 AATTTAAATG 0.823138 -172 CTGCCCAAATAAAATAAATGATTTTTTAAA 1 173 0 AAAATAAATG 0.919849 -128 AAACCCTAAAAAATTAATTGGACTCGCTAA 2 39 0 AAATTAATTG 0.766433 -262 TTAGGCTTAAAAATTAAATTTTCCTGTTAT 2 83 1 AAATTAAATT 0.511959 -218 TTGGTTAGGAAATTTAATTGAAAAACTACC 2 188 0 AATTTAATTG 0.754779 -113 GAAAAATATTTGTTTGGAAATA 2 289 0 AAAATATTTG 0.831382 -12 ********** Masking position 5 Map Score: 5.44856 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 49 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 ACCGGCAAAAATAAAAATTTTGG 1 4 0 ATAAAAATTT 0.808522 -297 GGTTTAACTGTTGTTAATTTTTGAGACAAA 1 31 1 TTGTTAATTT 0.673603 -270 TTAATTTTTGAGACAAAGTTCTACCAGTTA 1 44 1 AGACAAAGTT 0.77579 -257 AAAAATTAGTGTGCAAATTTTACGAGTTTA 1 87 0 GTGCAAATTT 0.882726 -214 TTTTGTTTTTTGGGTAATTTAAATGATGTA 1 124 1 TGGGTAATTT 0.898821 -177 AGTAAGGGAAATTTTGCGTTTAAT 1 287 0 AGGGAAATTT 0.957086 -14 TTTAAGCCTAATGCTAATTTCTTTTAAACC 2 64 0 ATGCTAATTT 0.891296 -237 CTGGCATAACAGGAAAATTTAATTTTTAAG 2 88 0 AGGAAAATTT 0.948635 -213 CATTAAAGGCTTAAAAAGTTTCAACAATAA 2 141 0 TTAAAAAGTT 0.725628 -160 TTAATGGGTGTTGAAAAGTTTGTGGTAGTT 2 165 1 TTGAAAAGTT 0.91436 -136 GTATCTTGGTTAGGAAATTTAATTGAAAAA 2 193 0 TAGGAAATTT 0.81038 -108 ********** Masking position 6 Map Score: 6.29412 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 246 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 CAACAGTTAAACCGGCAAAAATAAAAATTT 1 14 0 ACCGGCAAAA 0.95645 -287 GTCTTTTTTAACTGGTAGAACTTTGTCTCA 1 52 0 ACTGGTAGAA 0.850981 -249 ACACTTTTAAACTCGTAAAATTTGCACACT 1 80 1 ACTCGTAAAA 0.955556 -221 TGGGCAGTCAACTCGCTCAGTGACCTGTTG 1 196 1 ACTCGCTCAG 0.846767 -105 TTATTTATTGATTGGAAAAAGGTGAAAGTG 1 243 0 ATTGGAAAAA 0.70596 -58 TTTTGCGTTTAATGGCAAAGACCTCCTTTA 1 270 0 AATGGCAAAG 0.900472 -31 CTTTGCCATTAAACGCAAAATTTCCCTTAC 1 280 1 AAACGCAAAA 0.744762 -21 AACGGTTTTAACTCGATAAATCTA 2 5 0 ACTCGATAAA 0.90685 -296 AATTAATTGGACTCGCTAATGAAAACGGTT 2 28 0 ACTCGCTAAT 0.884016 -273 CTACGCCATCACTGGCATAACAGGAAAATT 2 99 0 ACTGGCATAA 0.943963 -202 ********** Masking position 9 Map Score: 4.7165 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 189 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TCAAAAATTAACAACAGTTAAACCGGCAAA 1 25 0 ACAACAGTTA 0.852409 -276 TTACGAGTTTAAAAGTGTCTTTTTTAACTG 1 68 0 AAAAGTGTCT 0.959268 -233 ATGATTTTTTAAAACTGTCATTTTATTACG 1 156 0 AAAACTGTCA 0.974282 -145 GGAAAAAGGTGAAAGTGTTTAAAGAGGTAG 1 230 0 GAAAGTGTTT 0.798018 -71 TTATCGAGTTAAAACCGTTTTCATTAGCGA 2 16 1 AAAACCGTTT 0.905976 -285 TAAAGGCTTAAAAAGTTTCAACAATAAAAA 2 138 0 AAAAGTTTCA 0.808711 -163 CGATAGATTAACTAGCGTTAACGTTACTAC 2 222 1 ACTAGCGTTA 0.852221 -79 CGTTAACGTTACTACTGTCAGCATTGGTTT 2 237 1 ACTACTGTCA 0.931478 -64 ********** Masking position 4 Map Score: 1.42157 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 200 Number in noncoding regions = 39 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: 1.30983e-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: 1.30983e-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: 1.30983e-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