AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -itorR_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 RP069 266 DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (dcd) #2 RP070 196 PROTEIN-EXPORT PROTEIN SECB (secB) #3 RP071 196 TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR) #4 RP427 121 PETR PROTEIN (ompR) Motif number 1 AAATAATATGGAATTATTAAA 1 2 0 GAATTATTAA 0.902505 -265 TAATAATTCCATATTATTTAAATAATAAAT 1 13 1 ATATTATTTA 0.80344 -254 TTTGTATAGTAAATTTATTATTTAAATAAT 1 25 0 AAATTTATTA 0.744406 -242 TATACAAAATAAACTTTTAGATTAGTTAAT 1 47 1 AAACTTTTAG 0.586698 -220 TGACAATAAGAAACTATTAAATTCTTAATT 1 116 1 AAACTATTAA 0.952199 -151 TATATACTTAAAATTAAGAATTTAATAGTT 1 127 0 AAATTAAGAA 0.915851 -140 TTTTAAAGAAAAATTTTGTATTGTAAATAA 1 201 1 AAATTTTGTA 0.835031 -66 TTATAACGCATAATTATTTACAATACAAAA 1 214 0 TAATTATTTA 0.876097 -53 AAACTTTATTTAATTAATAAACTAATGATT 1 242 0 TAATTAATAA 0.675254 -25 ATTAGCTTTAAAATTAAGATCGCGAATAGG 2 30 0 AAATTAAGAT 0.664205 -167 TTTAAGTGAGAAATTATGAAGTTTTTTGAA 2 69 1 AAATTATGAA 0.974401 -128 TTTAAAGCAAAAATTAATAAGATGTTTATC 2 102 0 AAATTAATAA 0.882206 -95 TAATAATTAAAAATTTTTAAAGCAAAAATT 2 117 0 AAATTTTTAA 0.965951 -80 TAAAAATTTTTAATTATTAGGCAAAATAAA 2 128 1 TAATTATTAG 0.854297 -69 CAGGCTCTAAAAATTATGTTAAATTTTTAA 2 166 1 AAATTATGTT 0.714902 -31 AAATTATGTTAAATTTTTAATAAGGATTTT 2 176 1 AAATTTTTAA 0.965951 -21 TATAAAATTTTTACTATTAAATTCTACCTT 3 53 0 TTACTATTAA 0.556462 -144 ATATTTAATCAAATTATAAAATTTTTACTA 3 67 0 AAATTATAAA 0.854909 -130 TTCTTTACTTATATTATTAATGAACGTATA 3 96 1 ATATTATTAA 0.923345 -101 AACTAAATTATAATTTTTTATCTAGTGCTT 3 126 0 TAATTTTTTA 0.799609 -71 ATTTAGTTAATAATTATTAACTAAATTATT 3 148 1 TAATTATTAA 0.960326 -49 ATTATTAACTAAATTATTATCAAAATTGAA 3 160 1 AAATTATTAT 0.930243 -37 CACGGGTTCAAAATTATTAATATCATAGTT 4 72 0 AAATTATTAA 0.985911 -50 ********** Masking position 5 Map Score: 33.2747 Number of sites scoring better than the average of aligned sites = 1783 Number in coding regions = 1143 Number in noncoding regions = 640 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 2 GTTTATTTTGTATAGTAAATTTATTATTTA 1 31 0 TATAGTAAAT 0.767076 -236 TAACTAATCTAAAAGTTTATTTTGTATAGT 1 45 0 AAAAGTTTAT 0.863985 -222 AAACTTTTAGATTAGTTAATTAAATCAACT 1 57 1 ATTAGTTAAT 0.874407 -210 TTCTGCAAAGTATATTATATTTTAGCGTAG 1 85 0 TATATTATAT 0.564096 -182 CTTAAAATTAAGAATTTAATAGTTTCTTAT 1 121 0 AGAATTTAAT 0.804574 -146 ATTCTTAATTTTAAGTATATAGCGTTGTAT 1 136 1 TTAAGTATAT 0.685554 -131 CGTTATAATCATTAGTTTATTAATTAAATA 1 236 1 ATTAGTTTAT 0.872177 -31 AATCAAAACTTTATTTAATTAATAAACTA 1 248 0 TTTATTTAAT 0.912094 -19 ATCTTAATTTTAAAGCTAATTAAAATCTTT 2 40 1 TAAAGCTAAT 0.715281 -157 TAATAAGATGTTTATCTTATTCAAAAAACT 2 88 0 TTTATCTTAT 0.644908 -109 TTATTGGATAATTAGGTAATTTT 3 4 0 ATTAGGTAAT 0.644724 -193 AATTAAAGGTAGAATTTAATAGTAAAAATT 3 48 1 AGAATTTAAT 0.804574 -149 TTTAATAGTAAAAATTTTATAATTTGATTA 3 62 1 AAAATTTTAT 0.779715 -135 ATAAGTAAAGAATATTTAATCAAATTATAA 3 78 0 AATATTTAAT 0.875553 -119 AAAATTATAATTTAGTTAATAATTATTAAC 3 139 1 TTTAGTTAAT 0.947904 -58 TTGATAATAATTTAGTTAATAATTATTAAC 3 153 0 TTTAGTTAAT 0.947904 -44 TTATCAAAATTGAATTTTATGGAGAAAAAT 3 176 1 TGAATTTTAT 0.765912 -21 ********** Masking position 4 Map Score: 15.028 Number of sites scoring better than the average of aligned sites = 1330 Number in coding regions = 859 Number in noncoding regions = 471 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 3 ACTTCCATAAATATAGTGGTAATAATACAA 1 160 0 ATATAGTGGT 0.946527 -107 ATAATTTTTTATCTAGTGCTTTATACGTTC 3 117 0 ATCTAGTGCT 0.954855 -80 TTAGAAACTCATCCCGTGGTTTGACCACGA 4 31 1 ATCCCGTGGT 0.99356 -91 TTGTTTTTGGCTTTCGTGGTCAAACCACGG 4 44 0 CTTTCGTGGT 0.950382 -78 AATAATTTTGAACCCGTGGTCAAACCACGA 4 84 1 AACCCGTGGT 0.98041 -38 CTCATTTTACATCTCGTGGTTTGACCACGG 4 97 0 ATCTCGTGGT 0.994307 -25 ********** Masking position 7 Map Score: 7.41989 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 17 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 GTATAGTAAATTTATTATTTAAATAATATGGAA 1 19 0 TTTATTTAAA 0.902516 -248 AACTATTAAATTCTTAATTTTAAGTATATAGCG 1 127 1 TTCTTTTTAA 0.726483 -140 CAATACAAAATTTTTCTTTAAAAAATCTAAAAC 1 191 0 TTTTTTAAAA 0.90943 -76 TAATCATTAGTTTATTAATTAAATAAAGTTTTG 1 241 1 TTTATTTAAA 0.902516 -26 CGCGAATAGGTTCCTACATAAAAAAGAAG 2 7 0 TTCCTTAAAA 0.87851 -190 AACTTCATAATTTCTCACTTAAAAAGATTTTAA 2 59 0 TTTCTTTAAA 0.967622 -138 ATTATGAAGTTTTTTGAATAAGATAAACATCTT 2 81 1 TTTTTTAAGA 0.886788 -116 ATCTTATTAATTTTTGCTTTAAAAATTTTTAAT 2 109 1 TTTTTTTAAA 0.965195 -88 AATATTGTTGTTTTTCAATTAAAGGTAGAATTT 3 32 1 TTTTTTTAAA 0.965195 -165 ATTATAAAATTTTTACTATTAAATTCTACCTTT 3 52 0 TTTTATTAAA 0.611141 -145 TGATTAAATATTCTTTACTTATATTATTAATGA 3 86 1 TTCTTTTATA 0.760244 -111 TATTTTTCTCCATAAAATTCAATTTTG 3 180 0 TTTCTTAAAA 0.931012 -17 TAAGTTATATTTATATTAGATTAGAAACTC 4 8 1 TATTTTTAGA 0.645801 -114 ***** ***** Masking position 13 Map Score: 15.3839 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 342 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 GTATAGTAAATTTATTATTTAAATAATATGGA 1 20 0 TTTATATTAA 0.602606 -247 AATCTAAAACTACTTCCATAAATATAGTGGTA 1 169 0 TACTTCTAAA 0.721667 -98 ACAATACAAAATTTTTCTTTAAAAAATCTAAA 1 193 0 ATTTTCTTAA 0.824121 -74 AATCATTAGTTTATTAATTAAATAAAGTTTTG 1 242 1 TTATTATAAA 0.888116 -25 CGCGAATAGGTTCCTACATAAAAAAGAAG 2 8 0 TTCCTCTAAA 0.906578 -189 AACTTCATAATTTCTCACTTAAAAAGATTTTA 2 60 0 TTTCTATTAA 0.892008 -137 ATTATGAAGTTTTTTGAATAAGATAAACATCT 2 81 1 TTTTTATAAG 0.764187 -116 ATCTTATTAATTTTTGCTTTAAAAATTTTTAA 2 109 1 TTTTTCTTAA 0.930193 -88 TCGCAATTTTATTTTGCCTAATAATTAAAAAT 2 133 0 ATTTTCTAAT 0.570632 -64 AAAAATCCTTATTAAAAATTTAACAT 2 181 0 ATCCTATAAA 0.776287 -16 AATATTGTTGTTTTTCAATTAAAGGTAGAATT 3 32 1 TTTTTATTAA 0.931329 -165 AAAATTTTATAATTTGATTAAATATTCTTTAC 3 72 1 AATTTATAAA 0.557923 -125 TGATTAAATATTCTTTACTTATATTATTAATG 3 86 1 TTCTTATTAT 0.635256 -111 TAGTTAATAATTATTAACTAAATTATAATTTT 3 139 0 TTATTATAAA 0.888116 -58 TAGTTAATAATTATTAACTAAATTATTATCAA 3 151 1 TTATTATAAA 0.888116 -46 TATTTTTCTCCATAAAATTCAATTTT 3 181 0 TTTCTCTAAA 0.928315 -16 ***** * **** Masking position 5 Map Score: 12.0802 Number of sites scoring better than the average of aligned sites = 1391 Number in coding regions = 908 Number in noncoding regions = 483 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 6 TATTTTAGCGTAGTTGATTTAATTAACTAA 1 68 0 TAGTTGATTT 0.966005 -199 ATATTTATGGAAGTAGTTTTAGATTTTTTA 1 176 1 AAGTAGTTTT 0.918358 -91 TCCAATAATATTGTTGTTTTTCAATTAAAG 3 26 1 TTGTTGTTTT 0.966016 -171 ATTAATATCATAGTTGTTTTTGGCTTTCGT 4 57 0 TAGTTGTTTT 0.986267 -65 ********** Masking position 4 Map Score: 1.55606 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 10 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: -3.17312e-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: -3.17312e-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: -3.17312e-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