AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -iphoB_rpxx_opreg_300.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 0.901672 -263 CTAAGAAGTTTTATATTTTTCTAATAGAAGTTT 1 57 1 TATATTTCTA 0.883047 -244 TACTTTCTATTAATCTTTCTTTTTAGAAACTTC 1 83 0 TATCTTTTTT 0.913356 -218 ATTTTCATTCTAATACTTTCTATTAATCTTTCT 1 96 0 TATATTCTAT 0.951942 -205 AAGTATGATATAATTGTTATTTTTTGCTTGATT 1 133 0 TATTTTTTTT 0.876732 -168 AACAATTATATCATACTTCCAATTATTTAGAGT 1 148 1 TATATTCAAT 0.862249 -153 AATGTGTTTTTAAAACTTTTGATGGAAATTCAA 1 185 0 TAAATTTGAT 0.748302 -116 TAATATTGTTTAATAATTATGTAATTTAATGTG 1 212 0 TATATTTGTA 0.952914 -89 AAAATCTGAATCATAATTTTTTTCATCTTTATT 2 19 0 TATATTTTTT 0.983974 -80 TAAGTTATATTTATATTAGATTAGAAA 3 5 1 TATATTTATT 0.950991 -117 ATTATTAATATCATAGTTGTTTTTGGCTTTCGT 3 57 0 TATATTTTTT 0.983976 -65 ACTATGATATTAATAATTTTGAACCCGTGGTCA 3 73 1 TATATTTGAA 0.928184 -49 TTATACTCATTTTACATCTCGTG 3 109 0 TATATCTTTT 0.906412 -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 TCGTGGTCAAACCACGGGATGAGTTTCTAA 3 31 0 ACCACGGGAT 0.984535 -91 CCGTGGTTTGACCACGAAAGCCAAAAACAA 3 44 1 ACCACGAAAG 0.98048 -78 TCGTGGTTTGACCACGGGTTCAAAATTATT 3 84 0 ACCACGGGTT 0.981699 -38 CCGTGGTCAAACCACGAGATGTAAAATGAG 3 97 1 ACCACGAGAT 0.983517 -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 3 GTTGGAAATAATTGATTAATTACTGTAAGTGA 1 6 1 AAAAAAATTA 0.965954 -295 GAAAAATATAAAACTTCTTAGCAAATATCATAACATC 1 41 0 AAATAAAATA 0.899507 -260 AGAAGTTTCTAAAAAGAAAGATTAATAGAAAGTATTA 1 82 1 AAAAGTAATA 0.766994 -219 TGAAAATTCAAAATCAAGCAAAAAATAACAATTATAT 1 122 1 AAACAAAATA 0.979041 -179 GATGGAAATTCAACAATACTCTAAATAATTGGAAGTA 1 161 0 CAAATAAATA 0.847237 -140 CAAAAGTTTTAAAAACACATTAAATTACATAATTATT 1 197 1 AAAATAATTA 0.952632 -104 AAGTTAATGAAAAGCAATATATTAATATTGTTTAATA 1 230 0 AAACTTAATA 0.887851 -71 TATAGATATCTCGATTTAAATATAAGTTGTGT 1 279 0 ATACTAAATA 0.802141 -22 TGATTGTAATAAAGATGAAAAAAATTATGATTCAGAT 2 12 1 AAAAAAATTA 0.967137 -87 AAGGAAGAAGAAACAATAGAGCAATTATCCAATTCTG 2 55 1 AAAAAAATTA 0.967137 -44 TTTGACCACGAAAGCCAAAAACAACTATGATATTAAT 3 50 1 AAACAAACTA 0.934953 -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 4 TTCTATTAGAAAAATATAAAACTTCTTAGCA 1 55 0 AAAATATAAA 0.879935 -246 AGAAGTTTCTAAAAAGAAAGATTAATAGAAA 1 82 1 AAAAAGAAAA 0.956152 -219 TATTAGAATGAAAATTCAAAATCAAGCAAAA 1 114 1 AAAATTCAAA 0.920154 -187 AAAATCAAGCAAAAAATAACAATTATATCAT 1 131 1 AAAAAATAAA 0.856087 -170 ACTTTTGATGGAAATTCAACAATACTCTAAA 1 173 0 GAAATTCAAA 0.904812 -128 ATAAGTTAATGAAAAGCAATATATTAATATT 1 238 0 GAAAAGCAAA 0.96585 -63 GATTGTAATAAAGATGAAAAAAATTATGATT 2 13 1 AAGATGAAAA 0.956822 -86 TTTCAAAAGGAAGAAGAAACAATAGAGCAAT 2 49 1 AAGAAGAAAA 0.947331 -50 GTCAAACCACGAGATGTAAAATGAGTATAA 3 102 1 GAGATGTAAA 0.948128 -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 TTTTATATTTTTCTAATAGAAGTTTCTAAA 1 65 1 TTCTAATAGA 0.970356 -236 TTCTAATACTTTCTATTAATCTTTCTTTTT 1 92 0 TTCTATTAAT 0.880645 -209 TGAATTTTCATTCTAATACTTTCTATTAAT 1 102 0 TTCTAATACT 0.946074 -199 AAGTTGTGTATTGTAATAAATAAGTTAATG 1 258 0 TTGTAATAAA 0.966825 -43 ATGATTGTAATAAAGATGAAAAAA 2 5 1 TTGTAATAAA 0.966825 -94 CGGGATGAGTTTCTAATCTAATATAAATAT 3 17 0 TTCTAATCTA 0.889811 -105 ********** Masking position 5 Map Score: 2.95571 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 139 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 ATTTTTTGCTTGATTTTGAATTTTCATTCT 1 118 0 TGATTTTGAA 0.905563 -183 TTATTTAGAGTATTGTTGAATTTCCATCAA 1 170 1 TATTGTTGAA 0.965517 -131 TATTGTTTAATAATTATGTAATTTAATGTG 1 212 0 TAATTATGTA 0.854636 -89 AATATATTAATATTGTTTAATAATTATGTA 1 222 0 TATTGTTTAA 0.784105 -79 ATGATTGTAATAAAGATGAAAAAAATTATG 2 11 1 TAAAGATGAA 0.853171 -88 TTTAATGTCGTACCAATCAGAA 2 87 0 TAATGTCGTA 0.896002 -12 ATGATATTAATAATTTTGAACCCGTGGTCA 3 76 1 TAATTTTGAA 0.968907 -46 ********** Masking position 10 Map Score: 2.74408 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 338 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 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 Motif number 9 ********** 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