AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -irpoN_aquae_opreg_300.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glnB 196 nitrogen regulatory PII protein #2 folK 300 folate biosynthesis 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase #3 rpsO 58 ribosomal protein S15 #4 aldH2_ntrC3 413 aldH2: aldehyde dehydrogenase, ntrC3: transcriptional regulator (NtrC family) #5 aq_291 28 hypothetical protein #6 pcnB1 300 poly A polymerase #7 mbhS1 300 hydrogenase small subunit #8 hypE 300 hydrogenase expression/formation protein #9 aq_1111 216 hypothetical protein #10 hypD 276 hydrogenase expression/formation protein HypD #11 aq_1391 300 hypothetical protein #12 icd 113 isocitrate dehydrogenase #13 aq_1515 25 putative protein #14 aq_1516 58 putative protein #15 pycA 23 pyruvate carboxylase c-terminal domain #16 aq_1525 40 putative protein #17 aq_1526 50 hypothetical protein #18 aq_1527 70 hypothetical protein #19 ntrC2 209 transcriptional regulator (NtrC family) Motif number 1 CCTTCCAATTTTTAGCTTTGGTAAGTTCAT 2 180 1 TTTAGCTTTG 0.856446 -121 ACTTGAACTTTCCTTTATTGCACCTGA 2 284 0 CTTTCCTTTA 0.881994 -17 CGTATCAGGACTTACATTTACTTCGTACAT 4 68 0 CTTACATTTA 0.484017 -346 TTTTGAATAATTTATCTTTATAAGGAGCTC 8 36 0 TTTATCTTTA 0.472487 -265 AATTTCTTTTCTTTTCTTTTTGAATAATTT 8 53 0 CTTTTCTTTT 0.86689 -248 TAAGCTTCAACTTAGCTTTGAAAGGGAATT 8 79 0 CTTAGCTTTG 0.897646 -222 TACTGCGTTTTTTTGCTTTCATCTACATCT 8 131 0 TTTTGCTTTC 0.780927 -170 CAGTAAACCTTTTAGATTTGATTCAGAAGA 8 259 1 TTTAGATTTG 0.54531 -42 AATTTTGATTTTACATTTGCCT 8 289 0 TTTTGATTTT 0.830861 -12 TTGGGGTTCCTTTTCCTTTACCTTCACCCT 9 15 1 TTTTCCTTTA 0.835646 -202 AGATGTCTACCTTTCCTATTTTTCCCACGG 9 68 1 CTTTCCTATT 0.598193 -149 GCTTTTTTTACTTTGCTTTTACTCTCCTGC 9 156 0 CTTTGCTTTT 0.972916 -61 TAGGGTTAATCTTAGCTTTTTTTACTTTGC 9 170 0 CTTAGCTTTT 0.957316 -47 TCGAGGGAAATTTTCCTTTTGACTCCGAGG 10 111 0 TTTTCCTTTT 0.940125 -166 AAATTTTTATCTTTGATTTTCAGTCTAT 11 9 0 CTTTGATTTT 0.878362 -292 TTAAAACACTTTTTGATTTTTGTTATAAAT 12 34 0 TTTTGATTTT 0.830861 -80 GCTTTCCTTTTTCCCTTCTTT 16 2 1 CTTTCCTTTT 0.958474 -39 TTTTCCCTTCTTTTTCTTTTAAAATTTTTA 16 19 1 TTTTTCTTTT 0.815848 -22 TCCTGCGCTCTTTTGCTTTTACAAAGCCTA 19 102 1 TTTTGCTTTT 0.960687 -108 AACGAAGCGCCTTACCTTTTCACTGTTTAA 19 154 0 CTTACCTTTT 0.93511 -56 TTATTTTTAATTTAGCTTTTCAAGAACTTT 19 190 0 TTTAGCTTTT 0.938488 -20 ********** Masking position 7 Map Score: 23.3725 Number of sites scoring better than the average of aligned sites = 860 Number in coding regions = 781 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 AATTCCAACAATAAAAAGGAGGTAAAAA 1 5 0 ATAGGAGGTA 0.976185 -192 CATGTTTACAATTGAACAAAGGTACTAAATCAGC 1 74 0 ATAAAAGGTA 0.878922 -123 TCAGAATACGCTTTTACAAAGGTATGGAAATTTT 1 129 0 CTAAAAGGTA 0.929921 -68 TGCATAATAACTTACAAGGAGGAAGGAAG 1 178 1 CTAGGAGGAA 0.956386 -19 ATATCCCCATCTAGTAAAGAGGGACAAGTTCGGA 2 22 0 CTAAGAGGGA 0.844069 -279 CAATTCTAAGAAAAGACGGAGGTATATGGGAAG 3 36 1 AAAGGAGGTA 0.944859 -23 TTAAATTTAAAACTTATGGAGGTAGGAATGCTTT 4 17 1 AAAGGAGGTA 0.944859 -397 AATCCGAACCCTTCAAAAGAGGAAATAGTAAGTG 4 374 1 CTAAGAGGAA 0.902231 -40 AAGGATGGAAATTTTATAAAGGTATACTCAAGTT 6 122 0 ATAAAAGGTA 0.878922 -179 CATAAAAATTCCTTAAGGAAGGTAAATAACCACG 7 207 0 CCAGAAGGTA 0.855869 -94 AAGAAATGGAAAAAGAGGAAGGTATGT 10 260 1 AAAGAAGGTA 0.878212 -17 TTATTCCCTAACAAGGAGGTCATAA 13 8 1 CTAGGAGGTC 0.95264 -18 AAACTTTAAAGGAGGTAATATAG 15 4 1 CTAGGAGGTA 0.98683 -20 AAAGAAAAAGAAGGGAAAAAGGAAAGC 16 4 0 AAAAAAGGAA 0.470371 -37 TTATGAGAGCCTTTGAAGGAGGTCTGGT 18 53 1 CTAGGAGGTC 0.95264 -18 ** * ******* Masking position 6 Map Score: 15.4105 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 216 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 TTGTAAAAGCGTATTCTGAAATTGGCACGGAAA 1 144 1 GTTCGAAATT 0.901667 -53 CCTATCGGTCTTCCGAACTTGTCCCTCTTT 2 8 1 GTTCGAACTT 0.966018 -293 ACCTGATAAAGCTTACTGGACTTTACGTTCAAT 2 257 0 GCTCGGACTT 0.835688 -44 AGAGGAGAGGCGTATCAGGACTTACATTTACTT 4 75 0 CGACGGACTT 0.855178 -339 ATTCCCTTACCGCATCCGAACTTCGTCCCGGTA 4 133 0 CGACGAACTT 0.949215 -281 TCCGCACTGGGGAACCTGAAGTTCAATCCATGC 4 293 0 GGACGAAGTT 0.896643 -121 AGAACTTCAGGTTAGCGGAAATTAACATTCATT 6 86 0 GTACGAAATT 0.934854 -215 GTATACTCAAGTTTGCAGAACTTCAGGTTAGCG 6 102 0 GTTCGAACTT 0.96602 -199 ACAGATTTTCGGAACCCGAAATTATAAGTACCT 7 74 0 GGACGAAATT 0.950636 -227 GTATGCTCAAGTTTGCAGAACTTGGGGTTAGCG 11 46 1 GTTCGAACTT 0.96602 -255 AGAACTTGGGGTTAGCGGAAATTAACATTCGTT 11 62 1 GTACGAAATT 0.934854 -239 CGGTACATTAGGAACAGGAACTTAAACAAGCGC 11 207 0 GGAAGAACTT 0.797265 -94 TTTTACAAAGCCTATCCGAACTTTGTGAAAAAG 19 118 1 CCACGAACTT 0.887475 -92 ** * * ****** Masking position 10 Map Score: 13.2497 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 125 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 TGTAGCCTGTTCCACAGCGGAAACGACACCAAT 2 57 1 TCCCAGGGAA 0.985552 -244 TCTCCCTTATTACCCAGAGGAGAGGCGTATCAG 4 90 0 TACCAGGGAA 0.878186 -324 TACTGACAGCTCCTCACAGGATTTCCGTCTATT 4 187 0 TCCCACGGAT 0.960841 -227 GCTGGCAGTATCCGCACTGGGGAACCTGAAGTT 4 303 0 TCCCACGGGA 0.669493 -111 TTCTTCGAACTCCGCAGGGTACAGATTTTCGGA 7 94 0 TCCCAGGTAA 0.984175 -207 CAACGGCCTATCCATACTGTACAGTTTTGTGAG 8 170 1 TCCTACGTAA 0.922045 -131 CACAGGATAATTCCCACAGTAAACCTTTTAGAT 8 243 1 TTCCACGTAA 0.929703 -58 AAGTTTCAACTCCACACGGTACATTAGGAACCC 11 158 0 TCCCACGTAA 0.991534 -143 ATGTTTCAACTCCACACGGTACATTAGGAACAG 11 223 0 TCCCACGTAA 0.991534 -78 *** *** *** * Masking position 6 Map Score: 10.3937 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 55 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GGAATTTAAATAAACATTTTAGCTCAACTCA 1 33 1 TAAAATTTTA 0.936668 -164 TGTTCAATTGTAAACATGTTAACAAAATTGT 1 90 1 TAAAATGTTA 0.822572 -107 ATTGAGCAAATAAATATTATAAGGAATTT 3 9 0 TAAAATTATA 0.937825 -50 GGGCCTTATTTAAACATTATAATCATAAAAC 6 276 1 TAAAATTATA 0.937825 -25 ATTCCCACAGTAAACCTTTTAGATTTGATTC 8 252 1 TAAACTTTTA 0.805653 -49 GCGGGAAATATTATAAAACTTAGAT 9 202 0 GAAAATTATA 0.760748 -15 ATGTCTACTTTAATAATTATATTCCTTCGGT 10 17 0 TAATATTATA 0.681583 -260 AAATCAAAGATAAAAATTTTACAAATGTATG 11 20 1 TAAAATTTTA 0.674796 -281 ACTTAAAGATTTTACCTCTAGAGA 12 4 1 TAAAATTTTA 0.936668 -110 TTTAAAAATTTTAAAAGAAAAAG 16 28 0 TAAAATTTTA 0.674796 -13 **** ****** Masking position 7 Map Score: 9.18202 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 18 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TCTTCGGGAATTCCCTCGATGGTTATTATT 4 247 0 TTCCCTCGAT 0.734096 -167 TTAACAGGGTGTTCTTCGGGAATTCCCTCG 4 259 0 GTTCTTCGGG 0.765062 -155 GCAGGGTACAGATTTTCGGAACCCGAAATT 7 84 0 GATTTTCGGA 0.641294 -217 AGAGTGTCTTTTTCTTCGAACTCCGCAGGG 7 108 0 TTTCTTCGAA 0.900089 -193 CCTTCACCCTGACCTTCGGACACATAACAG 9 35 1 GACCTTCGGA 0.947067 -182 AATAATTATATTCCTTCGGTGAATGG 10 7 0 TTCCTTCGGT 0.93869 -270 CCCTTGTGGATACCCTCGGAGTCAAAAGGA 10 98 1 TACCCTCGGA 0.947067 -179 AAAGGAAAATTTCCCTCGAACTCATGCCAG 10 122 1 TTCCCTCGAA 0.917532 -155 TCTTCTATTATTTCTTCGAAAAGCTCAAGA 10 234 0 TTTCTTCGAA 0.900089 -43 AATTACACTCTACTTTCGGAGGAGAGCG 12 96 1 TACTTTCGGA 0.876007 -18 GCTCGTGTCTTTCTTTCGGACTCTTTTTGT 14 17 1 TTCTTTCGGA 0.931609 -42 TTTCAAGAACTTTCTTCGGAACGAAGCGCC 19 173 0 TTTCTTCGGA 0.965435 -37 ********** Masking position 6 Map Score: 9.27933 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 452 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 TAAACACGAAAAATTTCCATACCTTTGTAAAAGCGTA 1 120 1 AATAACCTTG 0.786605 -77 AGCCCGGACAAATAGTGGAAGCCTATGCACTTCTGAG 4 333 1 AATAGCCTTG 0.970596 -81 CATTAGAAACCCTGCGTGCCTGTGTCTAAAAAAT 6 8 1 AATGGCCTTG 0.993119 -293 ACGGGATAGAAATAGACAGCGCCTGCGGCGGGCACGG 7 20 1 AAAGGCCTCG 0.96205 -281 CAGAACCTGTAAACGTAGGTGACTACGTACTTGTACA 10 149 1 AATGGACTCG 0.940464 -128 GTACATTAGGAACCCTGCGCGCCTATGTCTGAAAAAT 11 136 0 AATGGCCTTG 0.993119 -165 TGTGGAGTTGAAACATAAGTGCCTGCGTGTTTTGAAA 11 240 1 AATGGCCTCG 0.99298 -61 CCTTAATCTAAATTATGAGAGCCTTTGAAGGAGGTCT 18 41 1 AATGGCCTTG 0.993119 -30 ** * * **** ** Masking position 2 Map Score: 8.10468 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 8 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 GATATTCTAAGGAGAGGTTAGTATGAACTT 2 202 0 GGAGAGGTTA 0.876054 -99 ATTACCCAGAGGAGAGGCGTATCAGGACTT 4 85 0 GGAGAGGCGT 0.978266 -329 GGGTAATAAGGGAGAGGTTGAGACTTACCG 4 108 1 GGAGAGGTTG 0.950687 -306 ACTCAGAAGTGCATAGGCTTCCACTATTTG 4 341 0 GCATAGGCTT 0.883027 -73 GAATAAGGGTGGATAGGTCTTAGTGAGTGA 6 216 0 GGATAGGTCT 0.946793 -85 ATCCCGAAACGGAGAGGCTTTCGTGTCAGG 7 155 1 GGAGAGGCTT 0.98527 -146 TGTACAGTATGGATAGGCCGTTGTATAACA 8 163 0 GGATAGGCCG 0.951917 -138 GTTTCGTGAAGGTTAGGTGTCTAATAAGTT 11 92 1 GGTTAGGTGT 0.737199 -209 CACAAAGTTCGGATAGGCTTTGTAAAAGCA 19 115 0 GGATAGGCTT 0.981116 -95 ********** Masking position 5 Map Score: 7.98753 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 136 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TGCAACGCTTCCGGCGAGCTTTTCCCAGGAT 2 102 1 CCGGCGGCTT 0.984116 -199 CATTAGAAACCCTGCGTGCCTGTGTCTAAAA 6 11 1 CCTGCGGCCT 0.994959 -290 ATAAGGCCCTGCTGAGGGCTTTCGGGCTCCT 6 254 0 GCTGAGGCTT 0.928708 -47 CCGTTTTCTTCCAGAGTGTCTTTTTCTTCGA 7 119 0 CCAGAGGTCT 0.785562 -182 GCTCAAGACTCTTGAGGGCTTCCTCTTCATC 10 211 0 CTTGAGGCTT 0.897848 -66 CATTAGGAACCCTGCGCGCCTATGTCTGAAA 11 139 0 CCTGCGGCCT 0.994959 -162 AACATAAGTGCCTGCGTGTTTTGAAACTTCG 11 251 1 CCTGCGGTTT 0.978748 -50 CTTTTTCATTCCTGCGCTCTTTTGCTTTTAC 19 93 1 CCTGCGTCTT 0.95742 -117 ****** **** Masking position 11 Map Score: 7.06048 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 45 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 TAAGGGAATATGCGGTTCCTGCACCGTTTT 4 157 1 TGCGGTTCCT 0.982929 -257 TTCTTTTCATTCCGCTTCCTTGACTGGGTA 4 218 0 TCCGCTTCCT 0.964204 -196 GGATTGAACTTCAGGTTCCCCAGTGCGGAT 4 297 1 TCAGGTTCCC 0.905626 -117 CTGAGGGCTTTCGGGCTCCTTGGCAATTGA 6 244 0 TCGGGCTCCT 0.97051 -57 TCTATTTCTATCCCGTTCCTGTAAA 7 6 0 TCCCGTTCCT 0.969029 -295 ACTTATAATTTCGGGTTCCGAAAATCTGTA 7 78 1 TCGGGTTCCG 0.974442 -223 ACTCTTGGGGTTCCTTTTCCTTTAC 9 6 1 TGGGGTTCCT 0.977697 -211 TTGTTTAAGTTCCTGTTCCTAATGTACCGT 11 211 1 TCCTGTTCCT 0.954772 -90 ********** Masking position 7 Map Score: 5.90905 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 48 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 11 CCCATAATTCAAGGCGGAATGGGTGTTGGTAT 2 133 0 AAGGGGATGG 0.966862 -168 ACACCCTGTTAAAAGGGCATGGATTGAACTTC 4 277 1 AAAAGGATGG 0.889384 -137 AACCCTTCAAAAGAGGAAATAGTAAGTGTCAT 4 380 1 AAGAGAATAG 0.839097 -34 ACTCTGGAAGAAAACGGCATGGATCCCGAAAC 7 133 1 AAAAGGATGG 0.889384 -168 CTGAACGGAAAAGGCGACGTGGTTATTTACCT 7 190 1 AAGGGAGTGG 0.925098 -111 CTAAAAAAATAACAGGAGGTGGGT 7 287 1 AACAGAGTGG 0.740982 -14 TTTGATTTTATAGAAGATGTAGATGAAAGCAA 8 117 1 TAGAGAGTAG 0.779864 -184 AGGGCAGAAGTAGAGGGAGTGGATCTAGGCCT 9 115 0 TAGAGGGTGG 0.972568 -102 TTATAAAACTTAGATGGTAGGGTTAATCTTAG 9 185 0 TAGAGGAGGG 0.86681 -32 TCCACAACTTTAGAAGGTATAGCCAAGCACAT 10 46 0 TAGAGGATAG 0.893263 -231 GAAGAAATAATAGAAGAAATGGAAAAAGAGGA 10 247 1 TAGAGAATGG 0.944934 -30 AGAGCCTTTGAAGGAGGTCTGGT 18 58 1 AAGGGGCTGG 0.885707 -13 **** ** **** Masking position 2 Map Score: 6.31675 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 320 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 GTGTCTAAAAAATAACGTTTTATCAGCAACTT 6 32 1 AAAACGTTTA 0.975491 -269 TATAAAATCAAATAACGCTTTAAGCTTCAACT 8 97 0 AAAACGTTTA 0.979439 -204 ATGAAAGCAAAAAAACGCAGTATTTGTTATAC 8 139 1 AAAACGAGTA 0.865324 -162 ACGCTTTATCAATAACTTATTAGACACCTAAC 11 103 0 AAAACTATTA 0.730575 -198 ATGTCTGAAAAATAACGCTTTATCAATAACTT 11 117 0 AAAACGTTTA 0.979439 -184 TTACGGAATCAATAACGGTTTA 18 1 0 AAAACGTTTA 0.979439 -70 GAACTTTGTGAAAAAGGTTTTAAACAGTGAAA 19 135 1 AAAAGGTTTA 0.899949 -75 ** **** **** Masking position 5 Map Score: 3.82731 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 11 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AAACATTTTAGCTCAACTCAAGGAAATTAAGC 1 44 1 GCTCACCAAG 0.952617 -153 CCTGGGAAAAGCTCGCCGGAAGCGTTGCAAGA 2 99 0 GCTCCCGAAG 0.969594 -202 ATCCGCACTGGGGAACCTGAAGTTCAATCCAT 4 295 0 GGGACCGAAG 0.924844 -119 GTTAATTTCCGCTAACCTGAAGTTCTGCAAAC 6 93 1 GCTACCGAAG 0.984903 -208 ATTTTATAAAGGTATACTCAAGTTTGCAGAAC 6 114 0 GGTAACCAAG 0.970765 -187 TTCGTGTCAGGCTAAACTGAACGGAAAAGGCG 7 174 1 GCTAACGAAC 0.828318 -127 AACTTTAGAAGGTATAGCCAAGCACATGTCTA 10 41 0 GGTAAGCAAG 0.828318 -236 TGACTCCGAGGGTATCCACAAGGGCTGTTCCG 10 90 0 GGTACCCAAG 0.984903 -187 GTTAATTTCCGCTAACCCCAAGTTCTGCAAAC 11 56 0 GCTACCCAAG 0.987776 -245 **** ** **** Masking position 10 Map Score: 6.831 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 49 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 ACAATAAAAAGGAGGTAAAAA 1 1 0 GGAGGTAAAA 0.732736 -196 TAACTTACAAGGAGGAAGGAAG 1 185 1 GGAGGAGGAA 0.984835 -12 CTAAAAATTGGAAGGATTGAAGTAGATATAC 2 164 0 GAAGGATGAA 0.89559 -137 TAAAACTTATGGAGGTAGGAATGCTTTTAAA 4 24 1 GGAGGTGGAA 0.977953 -390 TTCATTTCGTGAAGGTTAGAAGTTTAATAAG 6 61 0 GAAGGTAGAA 0.916188 -240 GATTGAAAATCAAGGATGGAAATTTTATAAA 6 136 0 CAAGGAGGAA 0.871596 -165 TTTTACCCGAGCAGGAGAGTAAAAGCAAAGT 9 146 1 GCAGGAAGTA 0.708536 -71 TGGAAGTTTACGAGGACGGAACAGCCCTTGT 10 74 1 CGAGGAGGAA 0.94555 -203 TCCCTAACAAGGAGGTCATAA 13 15 1 GGAGGTATAA 0.732736 -11 GCAAAAGAGCGCAGGAATGAAAAAGGGGCTT 19 87 0 GCAGGATGAA 0.90253 -123 ****** **** Masking position 3 Map Score: 3.88564 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 308 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 15 CACGAAAAATTTCCATACCTTTGTAAAAGCGT 1 124 1 TTCCAACCTT 0.971806 -73 ATTATGCAATTTCCGTGCCAATTTCAGAATAC 1 154 0 TTCCGGCCAT 0.905689 -43 CTGAAGTTCAATCCATGCCCTTTTAACAGGGT 4 279 0 ATCCAGCCTT 0.982038 -135 CTGAGTAAAAATCCGAACCCTTCAAAAGAGGA 4 365 1 ATCCGACCTT 0.971252 -49 CCGTTTCGGGATCCATGCCGTTTTCTTCCAGA 7 135 0 ATCCAGCCTT 0.982034 -166 GAGGGAGTGGATCTAGGCCTTTGTCTTATAGC 9 103 0 ATCTAGCCTT 0.85926 -114 CCTCGTAAACTTCCACAACTTTAGAAGGTATA 10 57 0 TTCCAAACTT 0.887437 -220 CCGTTATTGATTCCGTAACATTTAAACCTTAA 18 15 1 TTCCGAACTT 0.885421 -56 ***** *** ** Masking position 2 Map Score: 2.91932 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 83 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