AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icysB_ecoli_bsub_300.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 topA 300 DNA topoisomerase type I, omega protein #2 cysB 209 positive transcriptional regulator for cysteine regulon #3 cysZ 229 required for sulfate transport #4 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A #5 spoIIE 300 serine phosphatase #6 yabS 84 similar to hypothetical proteins #7 yabT 88 yabT #8 yacA 103 similar to cell-cycle protein #9 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #10 yacB 194 similar to hypothetical proteins #11 yacC 85 similar to hypothetical proteins #12 yacD 46 similar to protein secretion PrsA homolog #13 cysK 75 cysteine synthetase A #14 gltC 146 transcriptional regulator (LysR family) #15 ytkP 148 similar to cysteine synthase #16 yvbU 99 similar to transcriptional regulator (LysR family) Motif number 1 CTGCGGATATCAACCCCTTGTCGTGACTCTG 1 190 0 CAACCCCTTT 0.976867 -111 GCCGCTTTCGCGACCCTTTGTTTATAAAAAC 2 27 0 CGACCCTTTT 0.938299 -183 GTCGCGAAAGCGGCCCTTTTTTATTGCATAT 2 44 1 CGGCCCTTTT 0.97641 -166 GCGGCATAAGCCACCCCTGTTTCACACAAAC 4 36 0 CCACCCCTGT 0.89618 -149 GTGGCTTATGCCGCCCCTTATTCCATCTTGC 4 53 1 CCGCCCCTTT 0.991202 -132 GGTTAAGACACCGCCCTTTCACGGCGGTAAC 5 56 1 CCGCCCTTTA 0.972092 -245 AATTCCATTGGCCCCTTTACCAAGCTGTT 7 70 0 TGGCCCCTTA 0.881937 -19 CTAACACTTTCAACCCCTCCAAGCAAAGAAG 8 38 0 CAACCCCTCA 0.881108 -66 AAATCAATTCCAGCCCTTTTAGGGTTAAGAA 11 25 0 CAGCCCTTTA 0.97263 -61 ACCTGCTTTCAGCCCCTTTTCTCAAATTAA 12 27 0 CAGCCCCTTT 0.991375 -20 TCTATCCGCACAGCCTCTTTATTGATAAAAT 15 42 0 CAGCCTCTTA 0.884006 -107 ********* * Masking position 8 Map Score: 13.9479 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 298 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 ACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCAT 1 241 1 AGGTTTTAAG 0.860377 -60 CCTTTAATTCTGTCAGGTTTTTATAAACAAAGGGTCGCG 2 11 1 TGATTTTAAA 0.964871 -199 CCGGTTATTTTGTAAACCGTTTGTGTGAAACAGGGGTGG 4 18 1 TGATTTTTGA 0.739042 -167 CTTCTGCAAGAGAAACCGATTTGTTAGGATGACCCGTAC 5 102 0 AGATTTTAGA 0.922894 -199 GTTTCTGCCTTGATATTCGTTTATGAAAAGAATTTCCGG 5 169 0 TGATTTTAAA 0.964871 -132 GCGAAAGCACAGATAGGATTTTGTCAAAAGAAGGTAACA 5 229 0 AGATTTTAAA 0.95953 -72 TGCCAGCGTCAGCCGGCAGTTTTTTTAGAAAGAAAGCGA 10 12 0 AGGTTTTTAA 0.799348 -183 ATACACGATCAGCGGCTCATTTGTAAACAAATCGATACC 10 105 0 AGGTTTTAAA 0.951231 -90 TGTATGGTATTGTAGAATGTTTGTAAAAAGTAAAGTAGA 10 139 1 TGGTTTTAAA 0.95762 -56 CTAAAAGGGCTGGAATTGATTTATGAAAGAAACCGCGTA 11 34 1 TGATTTTAAG 0.896668 -52 CTTCTTTGACAGCTATTATTTTATCAATAAAGAGGCTGT 15 25 1 AGATTTTAAA 0.95953 -124 TGTCATTCCTTTCTGAATAAAACAAGTGT 15 130 0 TGATTTTAAA 0.964871 -19 ATAAATAAAATGAATCTTTTTTATAAGGAGCATAAGTAA 16 65 1 TGTTTTTAGA 0.686112 -35 ** * *** * ** * Masking position 10 Map Score: 11.2257 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 63 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 AATGTTTGCCGTGGTGGCAAGGTGTTAGAACAA 3 22 0 GGGGGAAGGT 0.972348 -208 CAGAGAATATGCGGAAGTAAGGATTTAGCATAT 4 111 0 GGGAGAAGGA 0.974093 -74 AAATATGGTAGCGGCGGAGGGGATC 5 3 0 GGGGGGGGGA 0.989666 -298 ATAACAGGTGGGAGATGAGAGGA 5 288 1 GAGTGGAGGA 0.943907 -13 CTTACTGTGGGAGGAGGTAAGGA 9 85 1 GGGGGAAGGA 0.994929 -13 TTTGAGAAAAGGGGCTGAAAGCAGGT 12 31 1 GGGTGAAGCA 0.940206 -16 CGGAAATTGATCGGGGGAGAGGAATT 14 4 0 TGGGGGAGGA 0.972032 -143 TATCAATAAAGAGGCTGTGCGGATAGAGGAACA 15 46 1 GGGTGGCGGA 0.978888 -103 * ** ** ***** Masking position 7 Map Score: 6.49476 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 117 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 TACAGTGTGACGCTTTCGTCAATCTGGCAA 1 70 1 CGCTTTCGTC 0.959315 -231 GATATGGACTCGCTCTCTGCGGATATCAAC 1 207 0 CGCTCTCTGC 0.91306 -94 AAAAAAGGGCCGCTTTCGCGACCCTTTGTT 2 36 0 CGCTTTCGCG 0.91326 -174 CCTAACAAATCGGTTTCTCTTGCAGAAGCC 5 113 1 CGGTTTCTCT 0.958121 -188 TGAAAAAAATCGGCTTCTGCAAGAGAAACC 5 124 0 CGGCTTCTGC 0.894499 -177 AAATCTTCGACGGTTTCTGCCTTGATATTC 5 190 0 CGGTTTCTGC 0.973182 -111 ATCCTATCTGTGCTTTCGCTATAATGACAG 5 249 1 TGCTTTCGCT 0.696191 -52 TTCGCTTTCTTTCTAAAAAAAC 10 3 1 CGCTTTCTTT 0.94743 -192 ACTTCCTACGCGGTTTCTTTCATAAATCAA 11 49 0 CGGTTTCTTT 0.93569 -37 ********** Masking position 6 Map Score: 4.98801 Number of sites scoring better than the average of aligned sites = 1032 Number in coding regions = 972 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 GCCTTAGTGTATAGGTGTGAAGAAAAAATA 2 75 0 ATAGGTGTGA 0.663345 -135 TAGTCACCCGCCAGGTGTGACGAAAAAACG 2 157 1 CCAGGTGTGA 0.936525 -53 GCCGTGGTGGCAAGGTGTTAGAACAACAGA 3 18 0 CAAGGTGTTA 0.662415 -212 TAATGACATGCAAGATGGAATAAGGGGCGG 4 63 0 CAAGATGGAA 0.726481 -122 ATATCTATATACAGAAGGGAAATAATGACA 4 85 0 ACAGAAGGGA 0.937036 -100 GATTTTGTCAAAAGAAGGTAACAATACCAA 5 222 0 AAAGAAGGTA 0.66434 -79 TAGCGAAAGCACAGATAGGATTTTGTCAAA 5 240 0 ACAGATAGGA 0.685667 -61 AACGAATATAACAGGTGGGAGATGAGAGGA 5 281 1 ACAGGTGGGA 0.969745 -20 TTCTTCTGGCGAAGATGGGAATATATGAAT 6 31 1 GAAGATGGGA 0.798103 -54 CTCGTATTCTCCAGGAGGAATGAAT 6 70 1 CCAGGAGGAA 0.831582 -15 AATAGCTGTCAAAGAAGGGAGTGTCAGACG 15 12 0 AAAGAAGGGA 0.927782 -137 TTTTATTCAGAAAGGAATGACA 15 137 1 AAAGGAATGA 0.545629 -12 AAAAGTTCTACAAGGAGTGAATGAACA 16 8 0 CAAGGAGTGA 0.916628 -92 ********** Masking position 3 Map Score: 6.27379 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 641 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 6 GCAGAAGCCGATTTTTTTCATTTTTAGACAA 5 134 1 ATTTTTTCAT 0.85036 -167 CATTCCGGAAATTCTTTTCATAAACGAATAT 5 165 1 ATTCTTTCAT 0.897856 -136 GCAATGTATAAGTGTTTCCATTCCACTTGCC 7 36 0 AGTGTTTCAT 0.964053 -53 AGGGGTTGAAAGTGTTAGGATATGAATATCT 8 51 1 AGTGTTAGAT 0.688449 -53 CGAGATGGTTATTGTTTGTATTGGAATGATT 9 26 1 ATTGTTTTAT 0.909795 -72 TGACGCTGGCAGTTTTTTTATGTAAATGATT 10 40 1 AGTTTTTTAT 0.779848 -155 TAAATTATATATTGTTTATATCGTTTTGAAA 14 82 0 ATTGTTTTAT 0.909796 -65 TCATTTTGAGATTCTTTTGATCTAAATTATA 14 104 0 ATTCTTTGAT 0.821248 -43 TTTGTGCGAGAGTGTTTTCATACACTGTTCC 15 73 0 AGTGTTTCAT 0.964054 -76 ******* *** Masking position 6 Map Score: 3.38897 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 60 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 CACAAAGATAGATGAAATCGTGCTTTTTGC 3 114 1 GATGAAATCG 0.717853 -116 TCCTTAACTGTATGAAATTGGGATACAACA 4 159 0 TATGAAATTG 0.914152 -26 CGAAGATTTCTTTGGTATTGTTACCTTCTT 5 211 1 TTTGGTATTG 0.833854 -90 ATCATCCAATTCTGGTATCGATTTGTTTAC 10 92 1 TCTGGTATCG 0.878937 -103 GCTGATCGTGTATGGTATTGTAGAATGTTT 10 131 1 TATGGTATTG 0.877921 -64 CCCTAAAAGGGCTGGAATTGATTTATGAAA 11 32 1 GCTGGAATTG 0.932616 -54 GACAAAAAATTTTGAAATTGATAGATTATA 13 13 1 TTTGAAATTG 0.881397 -63 ATACAAATAGTCGGAAATTGAGGTGTCGAG 13 55 1 TCGGAAATTG 0.914896 -21 ACCGGTATTATCGGAAATTGATCGGGGGAG 14 18 0 TCGGAAATTG 0.914896 -129 ********** Masking position 7 Map Score: 3.10172 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 165 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 TCCATTGCGCAATTACCCGGTAAAATACGCAG 3 169 1 AATTACGGTA 0.855099 -61 TTACCCGGTAAAATACGCAGAATTTTCCTGGG 3 181 1 AAATACAGAA 0.831 -49 ACGGTTTACAAAATAACCGGTAGATTG 4 6 0 AAATACGGTA 0.941589 -179 CCCGCTCAGAGAATATGCGGAAGTAAGGATTT 4 118 0 GAATACGGAA 0.977355 -67 TTTATGAAAAGAATTTCCGGAATGTTGTCTAA 5 157 0 GAATTCGGAA 0.940478 -144 AAGAAATTTGATTTATACGGAAGCG 6 4 0 ATTTACGGAA 0.855099 -81 ATACCAATACAAATAGTCGGAAATTGAGGTGT 13 49 1 AAATACGGAA 0.977794 -27 TTTATGACCGGTATTATCGGAAATTGATCGGG 14 22 0 GTATTCGGAA 0.852601 -125 ***** ***** Masking position 12 Map Score: 2.67172 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 102 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 GAAGGGAAATAATGACATGCAAGATGGAAT 4 72 0 AATGACATGC 0.927696 -113 TCATACAGTTAAGGACAGGCC 4 174 1 AAGGACAGGC 0.985665 -11 CTTTCGCTATAATGACAGGCAACGAATATA 5 261 1 AATGACAGGC 0.988086 -40 CGGGTACGACAATCAAAGGCAAGTGGAATG 7 19 1 AATCAAAGGC 0.916042 -70 AGCAAAGAAGAAGCATAGGCTCTGCAGTTT 8 18 0 AAGCATAGGC 0.941004 -86 TTTTTATGTAAATGATTGGCTCAGCTGCGG 10 54 1 AATGATTGGC 0.900805 -141 ********** Masking position 5 Map Score: 2.598 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 93 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 GGTGACTGAGTTAACAGGTCTTGGCCTACAGG 1 144 0 TTAACGGTTT 0.781882 -157 GTGGTTATAGTTAGCACCTTTTTTATTATTAA 2 118 1 TTAGCCCTTT 0.951762 -92 AATCAGGATGAGCTCCTTTTGACCAATCCC 3 210 0 TGAGCCCTTT 0.976048 -20 GCATATTCTCTGAGCGGGTATGCTACCTGTTG 4 132 1 TGAGCGGTTG 0.946264 -53 CTCCTCACAATGAGCAGGTATTTTAAAGATAT 8 76 0 TGAGCGGTTT 0.985141 -28 TGTTTACAAATGAGCCGCTGATCGTGTATGGT 10 115 1 TGAGCGCTAT 0.922368 -80 GCTCTTTAGCGGGTTTTTAATTTGAGA 12 6 1 TTAGCGGTTT 0.969787 -41 ACCTGCTTTCAGCCCCTTTTCTCAAATTAA 12 27 0 TCAGCCCTTT 0.920468 -20 ***** *** ** Masking position 3 Map Score: 3.692 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 122 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 GTAACTCGTTGCCAGTGGAAGGTTTATCAA 1 238 1 GCCAGTGGAA 0.991896 -63 ATCGGCTTCTGCAAGAGAAACCGATTTGTT 5 116 0 GCAAGAGAAA 0.878996 -185 TCCCATCTTCGCCAGAAGAAATTTGATTTA 6 21 0 GCCAGAAGAA 0.94242 -64 ACAATCAAAGGCAAGTGGAATGGAAACACT 7 27 1 GCAAGTGGAA 0.981923 -62 TGGTAAAGGGGCCAATGGAATT 7 77 1 GCCAATGGAA 0.959104 -12 ********** Masking position 4 Map Score: 1.85303 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 91 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 GATTGACGAAAGCGTCACACTGTACCTGAT 1 64 0 AGCGTCACAC 0.977659 -237 CTTCCAGGAATGCGTCGCACGTTGATAAAC 1 259 0 TGCGTCGCAC 0.956818 -42 ATATTATTTTTTCTTCACACCTATACACTA 2 71 1 TTCTTCACAC 0.893175 -139 TTAAATCGTATTAGTCACCCGCCAGGTGTG 2 146 1 TTAGTCACCC 0.762519 -64 ACATCGTTTTTTCGTCACACCTGGCGGGTG 2 161 0 TTCGTCACAC 0.976991 -49 AAGCCACCCCTGTTTCACACAAACGGTTTA 4 30 0 TGTTTCACAC 0.865251 -155 AAAAACTGCCAGCGTCAGCCGGCAGTTTTT 10 27 0 AGCGTCAGCC 0.866939 -168 GTTTGTCTCACATCCATCTAT 14 136 0 TTTGTCTCAC 0.748389 -11 CAAAGAAGGGAGTGTCAGACGG 15 3 0 AGTGTCAGAC 0.838975 -146 ********** Masking position 5 Map Score: 3.734 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 375 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 ********** No masking Map Score: 2.78065e-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 14 ********** No masking Map Score: 2.78065e-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 15 ********** No masking Map Score: 2.78065e-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