AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iarcA_ecoli_hinf_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 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #2 gltA_sdhC 600 gltA: citrate synthase, sdhC: succinate dehydrogenase, cytochrome b556 #3 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #4 focA 300 probable formate transporter (formate channel 1) #5 icdA 201 isocitrate dehydrogenase, specific for NADP+ #6 hrpA 257 helicase, ATP-dependent #7 ydcF 271 orf, hypothetical protein #8 aldA 196 aldehyde dehydrogenase, NAD-linked #9 glcD_glcC 250 glcD: glycolate oxidase subunit D, glcC: transcriptional activator for glc operon #10 lldP 300 L-lactate permease #11 sodA 284 superoxide dismutase, manganese #12 HI0181 300 formate transporter #13 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) #14 HI1088 248 superoxide dismutase (sodA) #15 HI1218 279 L-lactate permease (lctP) #16 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #17 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #18 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) Motif number 1 ACTGTTCAGGATAAAACCCGACAAACTATATGTAG 2 165 0 ATAAACAAAA 0.880098 -436 ATTAGATGATTAAAAATTAAATAAATGTTGTTATC 2 212 0 TAAAATAAAA 0.808307 -389 AAAATAAATTTTAAAAATTAACAAATGAGTTGAAT 4 126 0 TTAAAAAAAA 0.744403 -175 TAACGTTATGACAGAACAACAAAAATTGACCTTTA 6 204 1 ACAAACAAAA 0.839388 -54 TATTCACCGAAAACAAACATATAAATCACAGGAGT 8 167 1 AAAAAAAAAA 0.909059 -30 ATCAGCTGCCACACAACACAACAAAGCGAAGCCTA 9 223 1 ACAAACAAAA 0.839388 -28 CTTTCATTGCAAAGAAAAGCAAAAATTATTTCAAC 12 168 0 AAAAAAAAAA 0.909059 -133 AGTCAATTAAATAAAATATAACAAATAAGCCCTAT 13 25 1 ATAAATAAAA 0.899218 -276 CACATTTTTGATATAAATACAAAAATAGGGCTTAT 13 49 0 ATAAAAAAAA 0.886989 -252 ACATAAGGATAAAAAATAGTAAAAAATGCTATATA 13 87 0 AAAAATAAAA 0.919117 -214 TTGATTTAAAACAAAATTTAATAAATTCACTTTTT 14 109 1 ACAAATAAAA 0.863997 -140 AATTCACTTTTTAAAAAAGGAAAAACATTTAATGA 14 132 1 TTAAAAAAAA 0.744403 -117 AAAATTGAGCAAATAATAGCAAAAAAATTGATTTA 14 169 0 AAAAATAAAA 0.919117 -80 ATAGAAGAATATAGAATATGATAAAGATTTTTA 15 94 0 ATAAATAAAA 0.899218 -186 CAAATAGTAATAAAAATGTAAGAAATGGAANCAAA 15 147 1 TAAAATAAAA 0.808307 -133 TATGCTTTGCATATAAATCCATAAAATAATCACAT 15 228 1 ATAAAAAAAA 0.886989 -52 TTTTACCTCGTAAAAACGTTAAAAATATTGACCGC 16 89 0 TAAAACAAAA 0.776231 -25 TCCTTTTTGAAAAAAATCTGAAAAAACTTTAAAAC 18 18 1 AAAAATAAAA 0.919117 -282 TTTAGCGAACAAAAAAACACAAAAAAATTACCGCA 18 87 1 AAAAAAAAAA 0.909059 -213 *** *** * *** Masking position 6 Map Score: 17.2604 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 135 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 2 TACAAAATTGTTAACAATTTTTAAACAACAAACGGCAA 1 68 0 TTACTTTACA 0.949529 -233 ATCATCTAATTTGACAATCATTCAACAAAGTTGTTACA 2 237 1 TTGCTATACA 0.975465 -364 AGGCGGTAATTTAGCTATAAATTGATCACCGTCGAAAA 3 42 1 TTACTATATA 0.601062 -259 CCGTTGCTTGTTGACACTTTATTCACAATCCTGCCACA 6 46 1 TTGCTTTACA 0.967708 -212 AAATTGCCCGTTTGTGAACCACTTGTTTGCA 8 4 1 TTGCTTTACA 0.96795 -193 TTGATGTTAATTAACAATGTATTCACCGAAAACAAACA 8 148 1 TTACTTTACG 0.732997 -49 TTACATCAATTTAACATTGAGTTAACCAAGACAAGGTC 9 89 1 TTACTATACA 0.961217 -162 CTGATGAGGATTGCCCTTTTCTTTACCAGACATCTCCC 10 50 1 TTGCTTTACA 0.96795 -251 TTGCCAATACATAACATTTAGTTAACCATTCATTGTCA 10 167 1 ATACTATACA 0.823036 -134 AATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAAC 11 94 0 TTGCTATACA 0.962035 -191 ATCATTTTCAATATCATTTAATTAACTATAATGAACCA 11 206 1 ATACTATACA 0.823036 -79 TATGGGAATTTTGTCTTTAATTAAACAAACCTTGCAAA 12 118 1 TTGCTATACA 0.975276 -183 ATAATCCAAATTGGCGGCTATTCTACTACTAAACATAA 13 116 0 TTGCCATACA 0.852984 -185 GTATTCGTGTTTAGCCTTGTCTAAACTAATATTCACTC 18 251 1 TTACTTTACA 0.949545 -49 *** * * * * ** * Masking position 15 Map Score: 15.7997 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 11 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 GGTATTTTACAAAATTGTTAACAATTTTTAAACAACA 1 76 0 AATTGTATTT 0.860574 -225 TATATGTAGGTTAATTGTAATGATTTTGTGAACAGCC 2 137 0 TTTTGTATTT 0.834375 -464 TCACGATAACAACATTTATTTAATTTTTAATCATCTA 2 208 1 AATTTAATTT 0.724244 -393 TTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGAT 2 253 0 ATTTGTATTT 0.922888 -348 TAAACAGGTTTTTGTTGAAGCAAATTTGCATTTTTCG 3 74 0 TTTTGAATTT 0.87271 -227 CAAAAACCTGTTTATTGTAAGGATTTTGCGGCGTAAT 3 97 1 TTTTGTATTT 0.834377 -204 TGCGATACGGATGCTTTAGAGCAATTTTTTGTTAATG 5 110 0 ATTTTAATTT 0.808998 -92 CGATGCCCCGTTGCTTGTTGACACTTTATTCACAATC 6 39 1 TTTTGTATTT 0.834377 -219 CGTCTCTCTGATGATTGATGTTAATTAACAATGTATT 8 134 1 ATTTGAATTA 0.665564 -63 ATGTATTGGCAACATTGATGTGAGTTTTAATTGGGAA 10 142 0 AATTGAATTT 0.912176 -159 TTAATATGGGAATTTTGTCTTTAATTAAACAAACCTT 12 114 1 AATTGTATTA 0.477237 -187 AATATCAAAGTTTGTTGAAATAATTTTTGCTTTTCTT 12 155 1 TTTTGAATTT 0.872715 -146 AAATACTTCTATAATTGGTGCTATTTTACTCTCCTCC 12 204 0 ATTTGGATTT 0.840097 -97 TGAAAATTTAATACTTTTAACAAGTTTACGACTACAA 12 239 0 ATTTTTATTT 0.69001 -62 TGACATTGAAAAAGTTGATGAAAATTTAATACTTTTA 12 257 0 AATTGAATTT 0.854781 -44 CAGTATTCTAATATTTGATGAAATTTTCGCAACTCAA 14 37 1 ATTTGAATTT 0.942305 -212 TTTTTTTGCTATTATTTGCTCAATTTTGGTTATAGAC 14 177 1 ATTTTGATTT 0.571059 -72 AAACGTTAAAAATATTGACCGCACTTTTACGGTCTTT 16 74 0 AATTGAATTT 0.912169 -40 AAACACAATGTTTTTTGACCGCAGTTTTCATCAA 17 8 0 TTTTGAATTT 0.872717 -55 CTTTGTTTTAAAGTTTTTTCAGATTTTTTTCAAAAAG 18 20 0 AATTTTATTT 0.660094 -280 CAAATCTTGTAAATTTTAGAAGATTTTTTGAGATAAA 18 185 0 AATTTAATTT 0.706392 -115 ** **** * *** Masking position 6 Map Score: 16.1719 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 141 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TGCTACCTTGCTGCACCCAGAAATCCATAGG 1 159 0 CTGCCCCAGA 0.980316 -142 GCTAACGCCGCTGCGGCCTGAAAGACGACGG 1 245 1 CTGCGCCTGA 0.934482 -56 ATGCAAAACACTGCTTCCAGATGCGAAAACG 2 44 1 CTGCTCCAGA 0.926119 -557 ACAGCCTATACTGCCGCCAGGTCTCCGGAAC 2 112 0 CTGCGCCAGG 0.989287 -489 GCCCAGAGCTCTGTACCCAGGTTTTCCCCTC 2 472 1 CTGTCCCAGG 0.746179 -129 GTTTGCTCGTCTGCCACCACGTTGCATATGC 5 157 0 CTGCACCACG 0.840657 -45 AATCCAGCCGCTGCTGCAAGGCCGTAAAGGT 6 232 0 CTGCGCAAGG 0.95324 -26 ATACAATTCTCTGCTGCAAGATGAATAATGT 7 113 1 CTGCGCAAGA 0.96121 -159 GCGCAAAAATCAGCTGCCACACAACACAACA 9 215 1 CAGCGCCACA 0.889877 -36 TACCAGACATCTCCCCCCACAAGAATTGGCC 10 73 1 CTCCCCCACA 0.730431 -228 AAATCGACAACGGCGGCAACAGGCGAAAGGT 11 83 0 CGGCGCAACA 0.829514 -202 CATTAACAATCGGCCGCCCGACAATACTGGA 11 257 1 CGGCGCCCGA 0.89027 -28 **** ****** Masking position 7 Map Score: 8.24964 Number of sites scoring better than the average of aligned sites = 1345 Number in coding regions = 1307 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 TCAACCTGGCTTTACCCGTTTTTTATTTGG 2 520 0 TTTACCCGTT 0.76513 -81 ATTACCGATATTTAACCTTATAATTAC 4 8 0 TTTAACCTTA 0.712757 -293 AACAACAAAAATTGACCTTTACGGCCTTGC 6 218 1 ATTGACCTTT 0.884119 -40 TTCCTGAATTTTTACCCTTACCGTTTTAGA 7 74 0 TTTACCCTTA 0.829792 -198 AAATTGCCCGTTTGTGAACCAC 8 3 1 ATTGCCCGTT 0.838581 -194 CCTTCACAGAATTGTCCTTTCACGATTCCG 8 106 1 ATTGTCCTTT 0.854213 -91 TCATCAGAGAATTGCCCTTAGGTTGTTGAT 10 27 0 ATTGCCCTTA 0.886033 -274 TCTGATGAGGATTGCCCTTTTCTTTACCAG 10 49 1 ATTGCCCTTT 0.93746 -252 CGTGCTGTCGATTAACCTTTCGCCTGTTGC 11 69 1 ATTAACCTTT 0.868183 -216 TTTACTATTTTTTATCCTTATGTTTAGTAG 13 99 1 TTTATCCTTA 0.655843 -202 CTGGTGTTTTTTTAACCTTTAAAAATAATT 13 165 1 TTTAACCTTT 0.827118 -136 TCCCATACAAATTATCCTTTCATTCTCCAA 15 11 1 ATTATCCTTT 0.834933 -269 ********** Masking position 3 Map Score: 7.54834 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 101 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TGACCTGGATCACTGTTCAGGATAAAACCCGACAA 2 176 0 CATGTGATAA 0.864592 -425 AGATAAATTGTTCTCGATCAAATTGGCTGA 3 6 1 AATGTGATCA 0.970735 -295 ATAGATGAGAAATTGATATAGATCATATCTCGCCT 4 228 0 AATGTGATCA 0.970735 -73 TCTTTTAAGGAAATGCTGTAGATAAACATTATTCA 7 134 0 AATGTGATAA 0.968371 -138 ACGCGACGAAAAATGATGAGGATAAGAAG 11 5 0 AATGTGATAA 0.968371 -280 ATAGTTAATTAAATGATATTGAAAATGATTATCAA 11 200 0 AATGTGAAAA 0.932721 -85 TTGACATTGAAAAAGTTGATGAAAATTTAATACTT 12 260 0 AAAGTGAAAA 0.661099 -41 TATTTTATTTAATTGACTTAGATCAAATTGAC 13 8 0 AATGCGATCA 0.8737 -293 ATAGCAAAAAAATTGATTTAGATCATTAAATGTTT 14 154 0 AATGTGATCA 0.970735 -95 AAGATTTGTTAAATGTTTGTGAAAAGCAAATATTG 18 214 1 AATGTGAAAA 0.932721 -86 ** ** * ***** Masking position 12 Map Score: 6.69029 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 35 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ATACTGCCGCCAGGTCTCCGGAACACCCTG 2 106 0 CAGGTCTCCG 0.867116 -495 TTGTTAGTATCTCGTCGCCGACTTAATAAA 4 269 1 CTCGTCGCCG 0.874088 -32 TCACCTCTCCTTCGAGCGCTA 5 191 0 CACCTCTCCT 0.88388 -11 TATAGAGTACCACATCGCGGCTTTCTATGC 6 131 0 CACATCGCGG 0.905987 -127 GCAAAACACGCACATCACGTAAGTGATTAT 9 58 1 CACATCACGT 0.724725 -193 GAGTCTGTTGCTCATCTCCTTGTCACACGT 10 246 0 CTCATCTCCT 0.944125 -55 TGCAGGTCTCCTGGAGTCCACG 10 289 0 CAGGTCTCCT 0.829425 -12 TTCGTCGCGTCACATCTCCGACGAGATGAG 11 30 1 CACATCTCCG 0.974657 -255 GATTTTTACACTCATCTCGTCGGAGATGTG 11 40 0 CTCATCTCGT 0.907807 -245 TGATTTGCTTCACATCTCGGGCATTTTCCT 11 139 1 CACATCTCGG 0.957287 -146 TCTCAACTCCTTTGTATAAAC 13 290 0 CTCAACTCCT 0.682233 -11 ********** Masking position 6 Map Score: 6.80966 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 252 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TTTAATTGGGAAATTGTGAACCAGAGGTCAG 10 123 0 AAATGTGAAC 0.775077 -178 ATTTATATCAAAAATGTGATCTATATAGCAT 13 66 1 AAATGTGATC 0.943177 -235 CTATTTTAAGAAAATGTGATCAATATCTCAT 15 194 0 AAATGTGATC 0.943177 -86 AAAGACCGTAAAAGTGCGGTCAATATTTTTA 16 74 1 AAATGCGGTC 0.986073 -40 TTGATGAAAACTGCGGTCAAAAAACATT 17 8 1 AAATGCGGTC 0.986073 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACACA 17 38 0 AAATGCGGTC 0.986073 -25 TAATTATTTGAAAGTGCGGTAATTTTTTTGT 18 105 0 AAATGCGGTA 0.901806 -195 *** ******* Masking position 3 Map Score: 5.53798 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 15 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ACTGTCCCGAATGAATTGGTCAATACTTCCA 2 353 0 ATGAATTGGC 0.767426 -248 ATCATTAACAAAAAATTGCTCTAAAGCATCC 5 108 1 AAAAATTGCC 0.838046 -94 ACAGAACAACAAAAATTGACCTTTACGGCCT 6 214 1 AAAAATTGAC 0.65483 -44 TTAAGAACAGAAAAATTGGTCCTACCTGTGC 9 24 0 AAAAATTGGC 0.950864 -227 AGAGCTGGAAAAAAAATGGTCTGACCGGTAG 9 129 1 AAAAAATGGC 0.919418 -122 ATGTCTGGTAAAGAAAAGGGCAATCCTCATC 10 52 0 AAGAAAAGGC 0.791629 -249 CTCCCCCCACAAGAATTGGCCCTACCAATTC 10 83 1 AAGAATTGGC 0.962921 -218 CAGATAAGCGAAGAATTGGTAGGGCCAATTC 10 95 0 AAGAATTGGA 0.865461 -206 ATATAAATACAAAAATAGGGCTTATTTGTTA 13 43 0 AAAAATAGGC 0.827631 -258 AAAAAATAGTAAAAAATGCTATATAGATCAC 13 81 0 AAAAAATGCA 0.43044 -220 ATAAAAATGTAAGAAATGGAANCAAAATGTT 15 156 1 AAGAAATGGA 0.791353 -124 ********* * Masking position 5 Map Score: 3.67946 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 188 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 TATAGGCTGTTCACAAAATCATTACAATTAAC 2 133 1 TCAAAATCAT 0.751617 -468 GATTAAAAATTAAATAAATGTTGTTATCGTGA 2 208 0 TAAAAATGTT 0.88556 -393 CACTGTTACATAAGTTAATCTTAGGTGAAATA 2 321 0 TAATAATCTT 0.539685 -280 TTTATTTGGATAATCAAATATTTACTCCGTAT 4 159 1 TAAAAATATT 0.678554 -142 ACATATCTTTTAAGGAAATGCTGTAGATAAAC 7 142 0 TAAAAATGCT 0.549651 -130 AATGAATGGTTAACTAAATGTTATGTATTGGC 10 169 0 TAAAAATGTT 0.88556 -132 TCATTATAGTTAATTAAATGATATTGAAAATG 11 208 0 TAAAAATGAT 0.675399 -77 TGTCTTTAATTAAACAAACCTTGCAAAATATC 12 129 1 TAAAAACCTT 0.634727 -172 TGCGAAAATTTCATCAAATATTAGAATACTGT 14 36 0 TCAAAATATT 0.634206 -213 TTGATTTAGATCATTAAATGTTTTTCCTTTTT 14 145 0 TCAAAATGTT 0.864049 -104 AATATGGCATTAAASSAATCTTTATCATATTC 15 84 1 TAASAATCTT 0.931983 -196 ATCCATAAAATAATCACATCTTTTAATCTAAC 15 244 1 TAAACATCTT 0.634727 -36 GCCCACCGATTAATGAAATCTTTGGTGGGCAG 16 29 1 TAAAAATCTT 0.931983 -85 TAGTGAATTTTCATCAAATCATCATATCAAAT 18 151 0 TCAAAATCAT 0.751617 -149 TATCTTTATCTCAAAAAATCTTCTAAAATTTA 18 181 1 TCAAAATCTT 0.918394 -119 TCACAAACATTTAACAAATCTTGTAAATTTTA 18 204 0 TTAAAATCTT 0.635171 -96 *** ******* Masking position 8 Map Score: 8.67718 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 66 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 TATAGTTTGTCGGGTTTTATCCTGAACAGTGAT 2 170 1 CGGGTTTACT 0.795191 -431 GTTATGAAGTCGGTATTTCACCTAAGATTAACT 2 308 1 CGGTTTTCCT 0.782384 -293 CTGGCTTTACCCGTTTTTTATTTGGCTCGCCGC 2 512 0 CCGTTTTTTT 0.662207 -89 GGCTGAAAGGCGGTAATTTAGCTATAAATTGAT 3 35 1 CGGTATTTCT 0.92605 -266 GGTTAAATATCGGTAATTTGTATTTAATAAATA 4 21 1 CGGTATTTAT 0.705857 -280 AAATGCTTACCGGGTTTTTTCTTTATCAGGCAA 7 20 0 CGGGTTTTTT 0.967218 -252 CATTTAGCGCCGGGTTTTTTATTAATTCTAAAA 7 48 1 CGGGTTTTTT 0.967218 -224 AGTTATTAAGCGGGCTTTTCGTTTTCGTCTATC 9 167 0 CGGGTTTTTT 0.967218 -84 GGCATTAAGTGGGTGATTTGCTTCACATCTCGG 11 126 1 GGGTATTTTT 0.587465 -159 CTTCACATCTCGGGCATTTTCCTGCAAAACCAT 11 146 1 CGGGATTTCT 0.952478 -139 TGCATTCCATCGGGCTTTGTTTTAAAGTTTTTT 18 38 0 CGGGTTTGTT 0.860202 -262 TTTGAAAGTGCGGTAATTTTTTTGTGTTTTTTT 18 97 0 CGGTATTTTT 0.930511 -203 **** **** ** Masking position 7 Map Score: 4.46648 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 258 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 12 AGTGTTTTGCATGACGCGCAGTTATAGAAA 2 26 0 ATGACGCGCA 0.935345 -575 GGAAAAGCATATAATGCGTAAAAGTTATGA 2 285 1 ATAATGCGTA 0.798264 -316 GTCTTACGCAATAAGGCGCTAAGGAGACCT 2 578 1 ATAAGGCGCT 0.954965 -23 TTATAGCCTAATAACGCGCATCTTTCATGA 5 40 1 ATAACGCGCA 0.975348 -162 AGATAAGGCGCTCTGGATCAAC 10 3 1 ATAAGGCGCT 0.954965 -298 AATTCTCACTATAATGCGCAAAATTTGGAG 15 35 0 ATAATGCGCA 0.962375 -245 ********** Masking position 4 Map Score: 1.71266 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 90 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 TATTTATCTCCGGCGGTCATACCCGTCGTCTTT 1 265 0 CGGCTCATCC 0.879884 -36 GGAGACCTGGCGGCAGTATAGGCTGTTCACAAA 2 117 1 CGGCTATAGC 0.985334 -484 ATTTAAGTTCCGGCAGTCTTACGCAATAAGGCG 2 563 1 CGGCTCTTCG 0.771068 -38 ATGCGAGTTACGGGCCTATAAGCCAGGCGAGAT 4 204 1 CGGGTATAGC 0.907081 -97 TTATGAATTGCCGCATTATAGCCTAATAACGCG 5 25 1 CCGCTATACC 0.834186 -177 TACCACATCGCGGCTTTCTATGCGTTGTTCAAT 6 121 0 CGGCTCTAGC 0.982275 -137 CTTGCAGCAGCGGCTGGATTCGCTG 6 243 1 CGGCGATTGC 0.927227 -15 ATAAAAAACCCGGCGCTAAATGCTTACCGGGTT 7 37 0 CGGCTAAAGC 0.955018 -235 AACACGAATACGGCAATATTTGCTTTTCACAAA 18 229 0 CGGCTATTGC 0.981993 -71 **** **** ** Masking position 1 Map Score: 1.90558 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 539 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 ********** No masking Map Score: -3.91976e-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: -3.91976e-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