AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -iphoB_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP016 300 unknown #2 RP018 98 190 KD ANTIGEN PRECURSOR (sca1) #3 RP427 121 PETR PROTEIN (ompR) Motif number 1 AGTGATGTTATGATATTTGCTAAGAAGTTTTAT 1 38 1 TATATTCTAA 0.897173 -263 CTAAGAAGTTTTATATTTTTCTAATAGAAGTTT 1 57 1 TATATTTCTA 0.877812 -244 TACTTTCTATTAATCTTTCTTTTTAGAAACTTC 1 83 0 TATCTTTTTT 0.909338 -218 ATTTTCATTCTAATACTTTCTATTAATCTTTCT 1 96 0 TATATTCTAT 0.949614 -205 AAGTATGATATAATTGTTATTTTTTGCTTGATT 1 133 0 TATTTTTTTT 0.871255 -168 AACAATTATATCATACTTCCAATTATTTAGAGT 1 148 1 TATATTCAAT 0.856234 -153 AATGTGTTTTTAAAACTTTTGATGGAAATTCAA 1 185 0 TAAATTTGAT 0.738819 -116 TAATATTGTTTAATAATTATGTAATTTAATGTG 1 212 0 TATATTTGTA 0.950632 -89 AAAATCTGAATCATAATTTTTTTCATCTTTATT 2 19 0 TATATTTTTT 0.983171 -80 TAAGTTATATTTATATTAGATTAGAAA 3 5 1 TATATTTATT 0.948621 -117 ATTATTAATATCATAGTTGTTTTTGGCTTTCGT 3 57 0 TATATTTTTT 0.983172 -65 ACTATGATATTAATAATTTTGAACCCGTGGTCA 3 73 1 TATATTTGAA 0.924802 -49 TTATACTCATTTTACATCTCGTG 3 109 0 TATATCTTTT 0.902107 -13 * *** ** **** Masking position 3 Map Score: 14.0253 Number of sites scoring better than the average of aligned sites = 944 Number in coding regions = 610 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 2 GTTGGAAATAATTGATTAATTACTGTAAGTGA 1 6 1 AAAAAAATTA 0.961736 -295 GAAAAATATAAAACTTCTTAGCAAATATCATAACATC 1 41 0 AAATAAAATA 0.887191 -260 AGAAGTTTCTAAAAAGAAAGATTAATAGAAAGTATTA 1 82 1 AAAAGTAATA 0.743075 -219 TGAAAATTCAAAATCAAGCAAAAAATAACAATTATAT 1 122 1 AAACAAAATA 0.976214 -179 GATGGAAATTCAACAATACTCTAAATAATTGGAAGTA 1 161 0 CAAATAAATA 0.829726 -140 CAAAAGTTTTAAAAACACATTAAATTACATAATTATT 1 197 1 AAAATAATTA 0.946441 -104 AAGTTAATGAAAAGCAATATATTAATATTGTTTAATA 1 230 0 AAACTTAATA 0.874305 -71 TATAGATATCTCGATTTAAATATAAGTTGTGT 1 279 0 ATACTAAATA 0.780799 -22 TGATTGTAATAAAGATGAAAAAAATTATGATTCAGAT 2 12 1 AAAAAAATTA 0.962772 -87 AAGGAAGAAGAAACAATAGAGCAATTATCCAATTCTG 2 55 1 AAAAAAATTA 0.962772 -44 TTTGACCACGAAAGCCAAAAACAACTATGATATTAAT 3 50 1 AAACAAACTA 0.926626 -72 *** * * ***** Masking position 14 Map Score: 6.6142 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 541 Number in noncoding regions = 283 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 TCGTGGTCAAACCACGGGATGAGTTTCTAA 3 31 0 ACCACGGGAT 0.985435 -91 CCGTGGTTTGACCACGAAAGCCAAAAACAA 3 44 1 ACCACGAAAG 0.978818 -78 TCGTGGTTTGACCACGGGTTCAAAATTATT 3 84 0 ACCACGGGTT 0.982351 -38 CCGTGGTCAAACCACGAGATGTAAAATGAG 3 97 1 ACCACGAGAT 0.984328 -25 ********** Masking position 4 Map Score: 6.44914 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 1 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 TGCTAAGAAGTTTTATATTTTTCTAATAGAA 1 55 1 TTTATATTTT 0.855353 -246 TTTCTATTAATCTTTCTTTTTAGAAACTTCT 1 82 0 TTTTCTTTTT 0.946221 -219 TTTTGCTTGATTTTGAATTTTCATTCTAATA 1 114 0 TTTGAATTTT 0.902897 -187 ATGATATAATTGTTATTTTTTGCTTGATTTT 1 131 0 TTTATTTTTT 0.827579 -170 TTTAGAGTATTGTTGAATTTCCATCAAAAGT 1 173 1 TTTGAATTTC 0.884655 -128 AATATTAATATATTGCTTTTCATTAACTTAT 1 238 1 TTTGCTTTTC 0.958019 -63 AATCATAATTTTTTTCATCTTTATTACAATC 2 13 0 TTTTCATCTT 0.947034 -86 ATTGCTCTATTGTTTCTTCTTCCTTTTGAAA 2 49 0 TTTTCTTCTT 0.935537 -50 TTATACTCATTTTACATCTCGTGGTTTGAC 3 102 0 TTTACATCTC 0.936501 -20 * ********* Masking position 4 Map Score: 7.20508 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 428 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 AGTTTTATATTTTTCTAATAGAAGTTTCTA 1 63 1 TTTTCTAATA 0.934235 -238 TCTAATAGAAGTTTCTAAAAAGAAAGATTA 1 76 1 GTTTCTAAAA 0.948302 -225 CATTCTAATACTTTCTATTAATCTTTCTTT 1 94 0 CTTTCTATTA 0.770406 -207 TTTGAATTTTCATTCTAATACTTTCTATTA 1 104 0 CATTCTAATA 0.959155 -197 AATTTAATGTGTTTTTAAAACTTTTGATGG 1 193 0 GTTTTTAAAA 0.875856 -108 ATAAGTTGTGTATTGTAATAAATAAGTTAA 1 260 0 TATTGTAATA 0.851109 -41 TAGATATCTCGATTTAAATATAAGTTGTGT 1 279 0 GATTTAAATA 0.688184 -22 ATGATTGTAATAAAGATGAAAA 2 3 1 GATTGTAATA 0.962279 -96 CACGGGATGAGTTTCTAATCTAATATAAAT 3 19 0 GTTTCTAATC 0.929183 -103 AAACAACTATGATATTAATAATTTTGAACC 3 68 1 GATATTAATA 0.787176 -54 ********** Masking position 7 Map Score: 8.38036 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 319 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 ********** No masking Map Score: 2.29806e-13 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 7 ********** No masking Map Score: 2.29806e-13 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: 2.29806e-13 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