AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ioxyR_ecoli_bsub_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dps 298 global regulator, starvation conditions #2 yhiR 202 orf, hypothetical protein #3 gor 71 glutathione oxidoreductase #4 katG 300 catalase; hydroperoxidase HPI(I) #5 oxyR 266 activator, hydrogen peroxide-inducible genes #6 ycgK 192 similar to transcriptional regulator (LysR family) #7 gltC 146 transcriptional regulator (LysR family) #8 dps 262 alternate gene name: ytkB; stress- and starvation-induced gene controlled by sigma-B #9 yvbU 99 similar to transcriptional regulator (LysR family) #10 ywqM 122 similar to transcriptional regulator (LysR family) #11 ywbI 105 alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family) #12 yybE 228 similar to transcriptional regulator (LysR family) Motif number 1 TTTCCTCTACACCGTCTTTATATATCGAATTATGCAAAAGCA 1 61 1 ACCTCTATGA 0.980125 -238 AATTTCATATCCTCTTGATGTTATGTCCCAGTAATTAACG 1 269 0 ATCTCGATGA 0.933862 -30 GATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGA 4 189 0 ATCTATATGA 0.902533 -112 CTACAGTGTTACCGTTACGATACACAGCGTTAGAGAGAAGTT 4 255 0 ACCTTGATGA 0.963786 -46 TATCATTTTCATCATTTTTATATCTTGGACGAATCATAACAG 6 139 0 ATCTTTATGA 0.981014 -54 GACTATGTATACCCTTAATATCGTACGCTAAAACCTCTTTTT 8 210 0 ACCTTTATGA 0.985784 -53 AATAAAATGAATCTTTTTTATAAGGAGCATAAGTAAATTGTT 9 68 1 ATCTTTATGA 0.981014 -32 GATGAAGAAAATCATTCGTAAACAAAGGAGCAGATGCATC 10 9 0 ATCTTTAAGA 0.86782 -114 AATCGAAATAATCATCTGTATTGATTGATGAATCCATTATAT 10 51 0 ATCTCTATGA 0.973444 -72 GCGCTTCACCCTTTCTATAGACAAAAGGAATACTTCTTA 11 77 0 ACCTTTATAA 0.845194 -29 TTATCTTAGCACCGTTGATATATGTTGTATAATGCATATAAA 12 114 1 ACCTTTATGA 0.985784 -115 *** ** *** * * Masking position 10 Map Score: 11.555 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 47 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GACGGTGTAGAGGAAAAGTAGCGAGAAATT 1 47 0 AGGAAAAGTA 0.854979 -252 GTAATTAACGAGATTAAGTATAGCACCGGC 1 249 0 AGATTAAGTA 0.807496 -50 TAACATCAAGAGGATATGAAATT 1 286 1 AGGATATGAA 0.887373 -13 CTGGTTAAAGAGGTTAAGGAAGCGCTCAAC 2 21 1 AGGTTAAGGA 0.819161 -182 CATGCTACACACATTATGTAAAGCGCCTGT 2 49 0 ACATTATGTA 0.625724 -154 GCGGTAATCAACGATAAGGACACTTTGTC 3 53 1 ACGATAAGGA 0.923935 -19 CATTACTTGAAGGATATGAAGCTAAAACCC 4 95 1 AGGATATGAA 0.887373 -206 TCTTTAACCAACAATATGTAAGATCTCAAC 4 197 1 ACAATATGTA 0.838902 -104 ATCATCATTTACGAAAAGAAGGAGCTGGTT 6 89 0 ACGAAAAGAA 0.749535 -104 GCTTCTCATTACGATAAGTATTTTGATTGT 8 110 0 ACGATAAGTA 0.961316 -153 TTTTATAAGGAGCATAAGTAAATTGTT 9 83 1 AGCATAAGTA 0.826912 -17 GACCTTATGTACAATAAGTATATAAGGGAG 11 19 0 ACAATAAGTA 0.918357 -87 ATATATATTAAGAATAAGAAGTATTCCTTT 11 63 1 AGAATAAGAA 0.885105 -43 ********** Masking position 6 Map Score: 9.83817 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 118 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 ATTTACATTTCTGCATGGTTATGCATAACCAT 1 10 1 TCTCATGTTT 0.893661 -289 AGCGAGAAATTCTGCATGGTTATGCATAACCAT 1 25 0 TCTCATGTTT 0.893661 -274 CTACTTTTCCTCTACACCGTCTTTATATATCGA 1 56 1 TCTCACCTCT 0.941157 -243 TTAGTTTTGTTTTTCACGCTTGTTACCACTATT 1 180 1 TTTCACGTTT 0.893661 -119 ATCAGCCTTGTTTTCTCCCTCATTACTTGAAGG 4 75 1 TTTCTCCTCT 0.853703 -226 ATCAATTTGATCTACATCTCTTTAACCAACAAT 4 179 1 TCTCATCCTT 0.857654 -122 GGCAAATACCTTTTCATCCCGATACATCTCGGC 6 23 1 TTTCATCCGT 0.596643 -170 GAACCTATCATTTTCATCATTTTTATATCTTGG 6 153 0 TTTCATCTTT 0.940823 -40 TTATATATTGTTTATATCGTTTTGAAAACCTAC 7 76 0 TTTTATCTTT 0.72572 -71 TAAAACCTCTTTTTTACCCTTATCTGTCACGAT 8 191 0 TTTTACCTTT 0.788814 -72 GGTATCTCCTCCTTGTTATATGACTAT 8 246 0 TCTCTCCTGT 0.849745 -17 GATGCATCTGCTCCTTTGTTTACGAATGA 10 7 1 TCTCTCCTTT 0.942256 -116 TTACGAATGATTTTCTTCATCATATAATGGATT 10 30 1 TTTCTTCTCT 0.805207 -93 TTGTTCTCTTCCTTTCTAAATCGGTTT 10 106 0 TCTTTCCTTT 0.730872 -17 TAAAATATCCTTTTCATGCTTATATGTAATAAG 12 152 1 TTTCATGTTT 0.856179 -77 *** **** ** * Masking position 3 Map Score: 9.68398 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 695 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 AAATTCACTACACTTAACCCCATGCTACACACA 2 66 0 CACTTAACCT 0.927895 -137 AAGGATATGAAGCTAAAACCCTTTTTTATAAAG 4 104 1 AGCTAAACCT 0.927895 -197 TAGCAATGAACGATTATCCCTATCAAGCATTCT 5 200 0 CGATTATCCT 0.942826 -67 GATCAATTTCCGATAATACCGGTCATAAAATCT 7 25 1 CGATAATCCT 0.942826 -122 TAATATCGTACGCTAAAACCTCTTTTTTACCCT 8 204 0 CGCTAAACCT 0.991397 -59 ATGATTATTTCGATTAATCCAATCGCTAAAACC 10 78 1 CGATTAACCT 0.978282 -45 TTAATCCAATCGCTAAAACCGATTTAGAAAGGA 10 91 1 CGCTAAACCT 0.991397 -32 GCGCTTCACCCTTTCTATAGACAA 11 92 0 CGCTTCACCT 0.968362 -14 ******* ** * Masking position 4 Map Score: 7.25085 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 186 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 ATTCCGAAAATTCCTGGCGAGCAGATAAATA 1 108 1 TTCTGGCGAG 0.934404 -191 TAATGTGTGTAGCATGGGGTTAAGTGTAGTG 2 63 1 AGCTGGGGTT 0.877241 -140 GCCATAAAAAAGCCCGGCGATAAGCCAGGCT 5 34 0 AGCCGGCGAT 0.956061 -233 AAAAAAGCGGATCCTGGAGATCCGCAAAAGT 5 67 1 ATCTGGAGAT 0.932198 -200 GCCACGATAGTTCATGGCGATAGGTAGAATA 5 231 0 TTCTGGCGAT 0.978778 -36 GCCATGAACTATCGTGGCGATGGAGGATGGA 5 244 1 ATCTGGCGAT 0.945657 -23 ATCCCGATACATCTCGGCGTTTTTAGAAAAC 6 38 1 ATCCGGCGTT 0.952902 -155 *** ******* Masking position 6 Map Score: 3.6278 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 584 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 TTACATTTCTGCATGGTTATGCATAACCATG 1 13 1 GCATGTTATG 0.959136 -286 GAGAAATTCTGCATGGTTATGCATAACCATG 1 24 0 GCATGTTATG 0.959136 -275 TTATGCAAAAGCATATTTATTCCGAAAATTC 1 90 1 GCATTTTATT 0.941867 -209 CTAACTCATTGAATCTTTATTAGTTTTGTTT 1 161 1 GAATTTTATT 0.863633 -138 TTATCGCCGGGCTTTTTTATGGCAAAAAAAA 5 42 1 GCTTTTTATG 0.962738 -225 TCCAGGATCCGCTTTTTTTTGCCATAAAAAA 5 54 0 GCTTTTTTTG 0.904386 -213 TAAATAAAATGAATCTTTTTTATAAGGAGCA 9 66 1 GAATTTTTTT 0.698656 -34 AATAAAGGATGATTGTTTATGAATGGCAGTG 12 45 0 GATTTTTATG 0.909906 -184 **** ****** Masking position 7 Map Score: 3.14028 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 213 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 AATTTCATATCCTCTTGATGTTATGTCCCA 1 279 0 CCTCTTGATG 0.724765 -20 GCGGCGGCGGCCTCTTTTCGGTATACTGTC 2 121 1 CCTCTTTTCG 0.971519 -82 ATTTTCCCGCCCTCATTTCGAGGCAGCATT 4 39 0 CCTCATTTCG 0.980366 -262 TTGTTTTCTCCCTCATTACTTGAAGGATAT 4 82 1 CCTCATTACT 0.855005 -219 TTCGAGAGTTTCTCAACTCGAATAACTAAA 5 108 0 TCTCAACTCG 0.492175 -159 GAACCAGCTCCTTCTTTTCGTAAATGATGA 6 88 1 CTTCTTTTCG 0.748759 -105 CATCCATCTATCTCATTTTGAGATTCTTTT 7 117 0 TCTCATTTTG 0.857418 -30 TCATGACGCTTCTCATTACGATAAGTATTT 8 117 0 TCTCATTACG 0.905879 -146 TACGCTAAAACCTCTTTTTTACCCTTATCT 8 199 0 CCTCTTTTTT 0.71563 -64 TTTATCGGTCCCTCATCATGTTGTGGAGCA 12 17 1 CCTCATCATG 0.876688 -212 ********** Masking position 3 Map Score: 3.67115 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 369 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 CGAATTATGCAAAAGCATATTTATTCCGAA 1 86 1 AAAAGCATAT 0.875456 -213 GAACAGCCAGAATAGCGGAACACATAGCCG 1 223 1 AATAGCGGAA 0.798089 -76 CCGCCGCCGCGAAAGCGTAACGTTTCTCAT 2 101 0 GAAAGCGTAA 0.896969 -102 CGGGGCGCACAAAAGCGTATCAGGACAGTA 2 144 0 AAAAGCGTAT 0.973051 -59 ACATAATCAAAAAAGCTTAATTAAGATCAA 4 154 1 AAAAGCTTAA 0.843754 -147 TATGGCAAAAAAAAGCGGATCCTGGAGATC 5 59 1 AAAAGCGGAT 0.961202 -208 GGACGACTGTAAAAGCCTATAATGTAAAGC 8 54 0 AAAAGCCTAT 0.912275 -209 ********** Masking position 4 Map Score: 2.12684 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 88 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 AACCCTTTTTTATAAAGCATTTGTCCGAAT 4 120 1 TATAAAGCAT 0.958546 -181 CGATTATCCCTATCAAGCATTCTGACTGAT 5 193 0 TATCAAGCAT 0.876771 -74 AAGCCTATAATGTAAAGCATACCATTGATC 8 42 0 TGTAAAGCAT 0.939613 -221 TTCTTCATCATATAATGGATTCATCAATCA 10 42 1 TATAATGGAT 0.884506 -81 ATTCGTAAGAAATAAAGGATGATTGTTTAT 12 56 0 AATAAAGGAT 0.785168 -173 ATATATGTTGTATAATGCATATAAAATATC 12 131 1 TATAATGCAT 0.909578 -98 CATATAAGCATGAAAAGGATATTTTATATG 12 148 0 TGAAAAGGAT 0.710929 -81 ********** Masking position 5 Map Score: 1.33588 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 19 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TGCTATACTTAATCTCGTTAATTACTGGGACAT 1 254 1 AACTCGTAAT 0.718606 -45 GCGCTTCCTTAACCTCTTTAACCAGGACTGCGC 2 13 0 AACTCTTAAC 0.976221 -190 CTCGCGCTACAATCGCGGTAATCAACGATAAGG 3 39 1 AACGCGTAAC 0.954153 -33 ATTTGATCTACATCTCTTTAACCAACAATATGT 4 183 1 CACTCTTAAC 0.978011 -118 GAGAGTTTCTCAACTCGAATAACTAAAGCCAAC 5 102 0 CACTCGATAC 0.735576 -165 TCGAGTTGAGAAACTCTCGAAACGGGCAGTGAC 5 117 1 AACTCTGAAC 0.915994 -150 AACGGAGCGGCACCTCTTTTAACCCTTGAAGTC 5 147 0 CACTCTTTAC 0.925171 -120 TAAAATCTAACAACTCTATAATCATTGTAGGTT 7 50 1 CACTCTTAAC 0.978011 -97 TAGGTTTTCAAAACGATATAAACAATATATAAT 7 77 1 AACGATTAAC 0.718606 -70 CGATTAATCCAATCGCTAAAACCGATTTAGAAA 10 88 1 AACGCTAAAC 0.902313 -35 ** **** *** * Masking position 11 Map Score: 4.5565 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 258 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 CGAATACGGGCCGATTTTTACTTACCGGAA 2 172 1 CCGATTTTTA 0.933468 -31 GAAGCTAAAACCCTTTTTTATAAAGCATTT 4 112 1 CCCTTTTTTA 0.96941 -189 AAATGAAACACCGTTTTCTAAAAACGCCGA 6 51 0 CCGTTTTCTA 0.954117 -142 ATTCCACCTCCCGTTTTTTAACAATTGTAG 8 148 1 CCGTTTTTTA 0.978796 -115 ACGCTAAAACCTCTTTTTTACCCTTATCTG 8 198 0 CTCTTTTTTA 0.85861 -65 ********** Masking position 5 Map Score: 1.63344 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 25 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 TTCTTATTTATCTGCTCGCCAGGAATTTTC 1 113 0 TCTGCTCGCC 0.945018 -186 GCACCGGCTATGTGTTCCGCTATTCTGGCT 1 227 0 TGTGTTCCGC 0.938404 -72 GATACGCTTTTGTGCGCCCCGAATACGGGC 2 153 1 TGTGCGCCCC 0.98903 -50 CAATGTGCTCCCCTCTACAGTGT 4 288 0 TGTGCTCCCC 0.9953 -13 TATGAATGGCAGTGCTCCACAACATGATGA 12 29 0 AGTGCTCCAC 0.94221 -200 ********** Masking position 3 Map Score: 0.586329 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 39 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: -2.32047e-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 14 ********** No masking Map Score: -2.32047e-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 15 ********** No masking Map Score: -2.32047e-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