AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -irpoN_aquae_opreg_100.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 0.856212 -121 ACTTGAACTTTCCTTTATTGCACCTGA 2 284 0 CTTTCCTTTA 0.842692 -17 CGTATCAGGACTTACATTTACTTCGTACAT 4 68 0 CTTACATTTA 0.436556 -346 TTTTGAATAATTTATCTTTATAAGGAGCTC 8 36 0 TTTATCTTTA 0.472012 -265 AAGGGAATTTCTTTTCTTTTCTTTTTGAAT 8 58 0 CTTTTCTTTT 0.833735 -243 TAAGCTTCAACTTAGCTTTGAAAGGGAATT 8 79 0 CTTAGCTTTG 0.88757 -222 TACTGCGTTTTTTTGCTTTCATCTACATCT 8 131 0 TTTTGCTTTC 0.766932 -170 CAGTAAACCTTTTAGATTTGATTCAGAAGA 8 259 1 TTTAGATTTG 0.560598 -42 AATTTTGATTTTACATTTGCCT 8 289 0 TTTTGATTTT 0.817184 -12 TTGGGGTTCCTTTTCCTTTACCTTCACCCT 9 15 1 TTTTCCTTTA 0.801615 -202 GCTTTTTTTACTTTGCTTTTACTCTCCTGC 9 156 0 CTTTGCTTTT 0.965107 -61 TAGGGTTAATCTTAGCTTTTTTTACTTTGC 9 170 0 CTTAGCTTTT 0.949165 -47 TCGAGGGAAATTTTCCTTTTGACTCCGAGG 10 111 0 TTTTCCTTTT 0.92026 -166 AAATTTTTATCTTTGATTTTCAGTCTAT 11 9 0 CTTTGATTTT 0.855618 -292 TTAAAACACTTTTTGATTTTTGTTATAAAT 12 34 0 TTTTGATTTT 0.817184 -80 GCTTTCCTTTTTCCCTTCTTT 16 2 1 CTTTCCTTTT 0.938651 -39 TTTTCCCTTCTTTTTCTTTTAAAATTTTTA 16 19 1 TTTTTCTTTT 0.7909 -22 TCCTGCGCTCTTTTGCTTTTACAAAGCCTA 19 102 1 TTTTGCTTTT 0.954261 -108 AACGAAGCGCCTTACCTTTTCACTGTTTAA 19 154 0 CTTACCTTTT 0.911728 -56 TTATTTTTAATTTAGCTTTTCAAGAACTTT 19 190 0 TTTAGCTTTT 0.933704 -20 ********** Masking position 7 Map Score: 23.5331 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 721 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 AATTCCAACAATAAAAAGGAGGTAAAAA 1 5 0 ATAGGAGGTA 0.976328 -192 CATGTTTACAATTGAACAAAGGTACTAAATCAGC 1 74 0 ATAAAAGGTA 0.879578 -123 TCAGAATACGCTTTTACAAAGGTATGGAAATTTT 1 129 0 CTAAAAGGTA 0.930323 -68 TGCATAATAACTTACAAGGAGGAAGGAAG 1 178 1 CTAGGAGGAA 0.956644 -19 ATATCCCCATCTAGTAAAGAGGGACAAGTTCGGA 2 22 0 CTAAGAGGGA 0.844881 -279 CAATTCTAAGAAAAGACGGAGGTATATGGGAAG 3 36 1 AAAGGAGGTA 0.94518 -23 TTAAATTTAAAACTTATGGAGGTAGGAATGCTTT 4 17 1 AAAGGAGGTA 0.94518 -397 AATCCGAACCCTTCAAAAGAGGAAATAGTAAGTG 4 374 1 CTAAGAGGAA 0.902775 -40 AAGGATGGAAATTTTATAAAGGTATACTCAAGTT 6 122 0 ATAAAAGGTA 0.879578 -179 CATAAAAATTCCTTAAGGAAGGTAAATAACCACG 7 207 0 CCAGAAGGTA 0.85663 -94 AAGAAATGGAAAAAGAGGAAGGTATGT 10 260 1 AAAGAAGGTA 0.878872 -17 TTATTCCCTAACAAGGAGGTCATAA 13 8 1 CTAGGAGGTC 0.952919 -18 AAACTTTAAAGGAGGTAATATAG 15 4 1 CTAGGAGGTA 0.98691 -20 AAAGAAAAAGAAGGGAAAAAGGAAAGC 16 4 0 AAAAAAGGAA 0.471911 -37 TTATGAGAGCCTTTGAAGGAGGTCTGGT 18 53 1 CTAGGAGGTC 0.952919 -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 0.904207 -53 CCTATCGGTCTTCCGAACTTGTCCCTCTTT 2 8 1 GTTCGAACTT 0.966957 -293 ACCTGATAAAGCTTACTGGACTTTACGTTCAAT 2 257 0 GCTCGGACTT 0.839629 -44 AGAGGAGAGGCGTATCAGGACTTACATTTACTT 4 75 0 CGACGGACTT 0.85873 -339 ATTCCCTTACCGCATCCGAACTTCGTCCCGGTA 4 133 0 CGACGAACTT 0.950594 -281 TCCGCACTGGGGAACCTGAAGTTCAATCCATGC 4 293 0 GGACGAAGTT 0.899298 -121 AGAACTTCAGGTTAGCGGAAATTAACATTCATT 6 86 0 GTACGAAATT 0.936597 -215 GTATACTCAAGTTTGCAGAACTTCAGGTTAGCG 6 102 0 GTTCGAACTT 0.966958 -199 ACAGATTTTCGGAACCCGAAATTATAAGTACCT 7 74 0 GGACGAAATT 0.951978 -227 GTATGCTCAAGTTTGCAGAACTTGGGGTTAGCG 11 46 1 GTTCGAACTT 0.966958 -255 AGAACTTGGGGTTAGCGGAAATTAACATTCGTT 11 62 1 GTACGAAATT 0.936597 -239 CGGTACATTAGGAACAGGAACTTAAACAAGCGC 11 207 0 GGAAGAACTT 0.801909 -94 TTTTACAAAGCCTATCCGAACTTTGTGAAAAAG 19 118 1 CCACGAACTT 0.890337 -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 ATTGGTGTCGTTTCCGCTGTGGAACAGGCTACA 2 57 0 TTCCCTGGGA 0.986478 -244 CTGATACGCCTCTCCTCTGGGTAATAAGGGAGA 4 90 1 TTCCCTGGTA 0.884466 -324 AATAGACGGAAATCCTGTGAGGAGCTGTCAGTA 4 187 1 ATCCGTGGGA 0.964411 -227 AACTTCAGGTTCCCCAGTGCGGATACTGCCAGC 4 303 1 TCCCGTGGGA 0.659973 -111 TCCGAAAATCTGTACCCTGCGGAGTTCGAAGAA 7 94 1 TTACCTGGGA 0.985643 -207 CTCACAAAACTGTACAGTATGGATAGGCCGTTG 8 170 0 TTACGTAGGA 0.928861 -131 ATCTAAAAGGTTTACTGTGGGAATTATCCTGTG 8 243 0 TTACGTGGAA 0.935664 -58 GGGTTCCTAATGTACCGTGTGGAGTTGAAACTT 11 158 1 TTACGTGGGA 0.992276 -143 CTGTTCCTAATGTACCGTGTGGAGTTGAAACAT 11 223 1 TTACGTGGGA 0.992276 -78 * *** *** *** Masking position 8 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 TGAGTTGAGCTAAAATGTTTATTTAAATTCC 1 33 0 TAAAATTTTA 0.935959 -164 ACAATTTTGTTAACATGTTTACAATTGAACA 1 90 0 TAACATTTTA 0.817747 -107 AAATTCCTTATAATATTTATTTGCTCAAT 3 9 1 TATAATTTTA 0.935915 -50 GTTTTATGATTATAATGTTTAAATAAGGCCC 6 276 0 TATAATTTTA 0.935915 -25 GAATCAAATCTAAAAGGTTTACTGTGGGAAT 8 252 0 TAAAAGTTTA 0.80145 -49 ATCTAAGTTTTATAATATTTCCCGC 9 202 1 TATAATTTTC 0.754699 -15 ACCGAAGGAATATAATTATTAAAGTAGACAT 10 17 1 TATAATATTA 0.674417 -260 CATACATTTGTAAAATTTTTATCTTTGATTT 11 20 0 TAAAATTTTA 0.677648 -281 TCTCTAGAGGTAAAATCTTTAAGT 12 4 0 TAAAATTTTA 0.935959 -110 CTTTTTCTTTTAAAATTTTTAAA 16 28 1 TAAAATTTTA 0.677648 -13 ****** **** Masking position 5 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 AATAATAACCATCGAGGGAATTCCCGAAGA 4 247 1 ATCGAGGGAA 0.728306 -167 AATTTCGGGTTCCGAAAATCTGTACCCTGC 7 84 1 TCCGAAAATC 0.491581 -217 CCCTGCGGAGTTCGAAGAAAAAGACACTCT 7 108 1 TTCGAAGAAA 0.863713 -193 CTGTTATGTGTCCGAAGGTCAGGGTGAAGG 9 35 0 TCCGAAGGTC 0.913973 -182 CCATTCACCGAAGGAATATAATTATT 10 7 1 ACCGAAGGAA 0.920944 -270 TCCTTTTGACTCCGAGGGTATCCACAAGGG 10 98 0 TCCGAGGGTA 0.945468 -179 CTGGCATGAGTTCGAGGGAAATTTTCCTTT 10 122 0 TTCGAGGGAA 0.915274 -155 TCTTGAGCTTTTCGAAGAAATAATAGAAGA 10 234 1 TTCGAAGAAA 0.863713 -43 CGCTCTCCTCCGAAAGTAGAGTGTAATT 12 96 0 TCCGAAAGTA 0.872724 -18 ACAAAAAGAGTCCGAAAGAAAGACACGAGC 14 17 0 TCCGAAAGAA 0.920822 -42 GGCGCTTCGTTCCGAAGAAAGTTCTTGAAA 19 173 1 TCCGAAGAAA 0.945204 -37 ********** Masking position 5 Map Score: 9.17184 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 401 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 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 0.875385 -99 ATTACCCAGAGGAGAGGCGTATCAGGACTT 4 85 0 GGAGAGGCGT 0.978135 -329 GGGTAATAAGGGAGAGGTTGAGACTTACCG 4 108 1 GGAGAGGTTG 0.950398 -306 ACTCAGAAGTGCATAGGCTTCCACTATTTG 4 341 0 GCATAGGCTT 0.882391 -73 GAATAAGGGTGGATAGGTCTTAGTGAGTGA 6 216 0 GGATAGGTCT 0.946483 -85 ATCCCGAAACGGAGAGGCTTTCGTGTCAGG 7 155 1 GGAGAGGCTT 0.985181 -146 TGTACAGTATGGATAGGCCGTTGTATAACA 8 163 0 GGATAGGCCG 0.951635 -138 GTTTCGTGAAGGTTAGGTGTCTAATAAGTT 11 92 1 GGTTAGGTGT 0.736007 -209 CACAAAGTTCGGATAGGCTTTGTAAAAGCA 19 115 0 GGATAGGCTT 0.981002 -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 0.984788 -199 CATTAGAAACCCTGCGTGCCTGTGTCTAAAA 6 11 1 CCTGCGGCCT 0.995174 -290 ATAAGGCCCTGCTGAGGGCTTTCGGGCTCCT 6 254 0 GCTGAGGCTT 0.931562 -47 CCGTTTTCTTCCAGAGTGTCTTTTTCTTCGA 7 119 0 CCAGAGGTCT 0.792868 -182 GCTCAAGACTCTTGAGGGCTTCCTCTTCATC 10 211 0 CTTGAGGCTT 0.901806 -66 CATTAGGAACCCTGCGCGCCTATGTCTGAAA 11 139 0 CCTGCGGCCT 0.995174 -162 AACATAAGTGCCTGCGTGTTTTGAAACTTCG 11 251 1 CCTGCGGTTT 0.979643 -50 CTTTTTCATTCCTGCGCTCTTTTGCTTTTAC 19 93 1 CCTGCGTCTT 0.959175 -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 AAAACGGTGCAGGAACCGCATATTCCCTTA 4 157 0 AGGAACCGCA 0.976106 -257 TACCCAGTCAAGGAAGCGGAATGAAAAGAA 4 218 1 AGGAAGCGGA 0.950275 -196 ATCCGCACTGGGGAACCTGAAGTTCAATCC 4 297 0 GGGAACCTGA 0.871929 -117 TCAATTGCCAAGGAGCCCGAAAGCCCTCAG 6 244 1 AGGAGCCCGA 0.95893 -57 TTTACAGGAACGGGATAGAAATAGA 7 6 1 AGGAACGGGA 0.956893 -295 TACAGATTTTCGGAACCCGAAATTATAAGT 7 78 0 CGGAACCCGA 0.964349 -223 GTAAAGGAAAAGGAACCCCAAGAGT 9 6 0 AGGAACCCCA 0.968849 -211 ACGGTACATTAGGAACAGGAACTTAAACAA 11 211 0 AGGAACAGGA 0.937411 -90 ********** Masking position 4 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 GCTTAATTTCCTTGAGTTGAGCTAAAATGTTT 1 44 0 CTTGGTGAGC 0.954961 -153 TCTTGCAACGCTTCCGGCGAGCTTTTCCCAGG 2 99 1 CTTCGGGAGC 0.971123 -202 ATGGATTGAACTTCAGGTTCCCCAGTGCGGAT 4 295 1 CTTCGGTCCC 0.928458 -119 GTTTGCAGAACTTCAGGTTAGCGGAAATTAAC 6 93 0 CTTCGGTAGC 0.985674 -208 GTTCTGCAAACTTGAGTATACCTTTATAAAAT 6 114 1 CTTGGTTACC 0.972237 -187 CGCCTTTTCCGTTCAGTTTAGCCTGACACGAA 7 174 0 GTTCGTTAGC 0.835749 -127 TAGACATGTGCTTGGCTATACCTTCTAAAGTT 10 41 1 CTTGCTTACC 0.835749 -236 CGGAACAGCCCTTGTGGATACCCTCGGAGTCA 10 90 1 CTTGGGTACC 0.985674 -187 GTTTGCAGAACTTGGGGTTAGCGGAAATTAAC 11 56 1 CTTGGGTAGC 0.988402 -245 **** ** **** Masking position 3 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 12 CCAACAATAAAAAGGAGGTAAAAA 1 3 0 AAAGGATAAA 0.622593 -194 ACAATTGAACAAAGGTACTAAATCAGCTTAAT 1 69 0 AAAGGTTAAA 0.888219 -128 ACGCTTTTACAAAGGTATGGAAATTTTTCGTG 1 124 0 AAAGGTGGAA 0.872333 -73 CACCCTGTTAAAAGGGCATGGATTGAACTTCA 4 278 1 AAAGGGTGGA 0.962148 -136 CAATAGGGTTAAAGGGATTGAAAATCAAGGAT 6 150 0 AAAGGGTGAA 0.971923 -151 CTCTGGAAGAAAACGGCATGGATCCCGAAACG 7 134 1 AAACGGTGGA 0.71276 -167 GGGCAGAAGTAGAGGGAGTGGATCTAGGCCTT 9 114 0 AGAGGGTGGA 0.800365 -103 TATACCTTCTAAAGTTGTGGAAGTTTACGAGG 10 57 1 AAAGTTGGAA 0.576332 -220 CAAAAATCAAAAAGTGTTTTAAATTAACTTGA 12 42 1 AAAGTGTTAA 0.575745 -72 GCGAAGTTGCAAAGGTTATAAACGAAACCTGT 17 14 1 AAAGGTTAAA 0.888219 -37 CAGGAATGAAAAAGGGGCTTGACGGAATTATC 19 75 0 AAAGGGTTGA 0.83348 -135 ACTTTGTGAAAAAGGTTTTAAACAGTGAAAAG 19 137 1 AAAGGTTAAA 0.888219 -73 CGTTCCGAAGAAAGTTCTTGAAAAGCTAAATT 19 180 1 AAAGTTTGAA 0.811528 -30 ****** **** Masking position 3 Map Score: 5.63439 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 657 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 AAGTTGCTGATAAAACGTTATTTTTTAGACAC 6 32 0 TAACGTTATT 0.977701 -269 AGTTGAAGCTTAAAGCGTTATTTGATTTTATA 8 97 1 TAACGTTATT 0.979416 -204 GTATAACAAATACTGCGTTTTTTTGCTTTCAT 8 139 0 TACCGTTTTT 0.864733 -162 GTTAGGTGTCTAATAAGTTATTGATAAAGCGT 11 103 1 TAAAGTTATT 0.861015 -198 AAGTTATTGATAAAGCGTTATTTTTCAGACAT 11 117 1 TAACGTTATT 0.979416 -184 TAAACCGTTATTGATTCCGTAA 18 1 1 TAACGTTATT 0.979416 -70 TTTCACTGTTTAAAACCTTTTTCACAAAGTTC 19 135 0 TAACCTTTTT 0.798861 -75 *** ******* Masking position 2 Map Score: 3.82731 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 14 ACAATAAAAAGGAGGTAAAAA 1 1 0 GGAGGTAAAA 0.733937 -196 TAACTTACAAGGAGGAAGGAAG 1 185 1 GGAGGAGGAA 0.984927 -12 CTAAAAATTGGAAGGATTGAAGTAGATATAC 2 164 0 GAAGGATGAA 0.896163 -137 TAAAACTTATGGAGGTAGGAATGCTTTTAAA 4 24 1 GGAGGTGGAA 0.978085 -390 TTCATTTCGTGAAGGTTAGAAGTTTAATAAG 6 61 0 GAAGGTAGAA 0.916659 -240 GATTGAAAATCAAGGATGGAAATTTTATAAA 6 136 0 CAAGGAGGAA 0.872282 -165 TTTTACCCGAGCAGGAGAGTAAAAGCAAAGT 9 146 1 GCAGGAAGTA 0.709804 -71 TGGAAGTTTACGAGGACGGAACAGCCCTTGT 10 74 1 CGAGGAGGAA 0.945865 -203 TCCCTAACAAGGAGGTCATAA 13 15 1 GGAGGTATAA 0.733937 -11 GCAAAAGAGCGCAGGAATGAAAAAGGGGCTT 19 87 0 GCAGGATGAA 0.903069 -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 TTTTACAAAGGTATGGAAATTTTTCGTGTT 1 122 0 GTATGGAAAT 0.645349 -75 TTCGGATGCGGTAAGGGAATATGCGGTTCC 4 146 1 GTAAGGGAAT 0.643982 -268 TCAAGGAAGCGGAATGAAAAGAAATAATAA 4 225 1 GGAATGAAAA 0.909712 -189 TGAAAATCAAGGATGGAAATTTTATAAAGG 6 134 0 GGATGGAAAT 0.88834 -167 AGGGTTAAAGGGATTGAAAATCAAGGATGG 6 148 0 GGATTGAAAA 0.823461 -153 ATGATGTGATGAAATGAAATCATGATGCAA 6 179 0 GAAATGAAAT 0.831729 -122 TACAGGAACGGGATAGAAATAGACAGCGCC 7 13 1 GGATAGAAAT 0.579002 -288 AGGCTAAACTGAACGGAAAAGGCGACGTGG 7 182 1 GAACGGAAAA 0.792847 -119 AATTCCTTAAGGAAGGTAAATAACCACGTC 7 205 0 GGAAGGTAAA 0.74599 -96 TATTCAAAAAGAAAAGAAAAGAAATTCCCT 8 57 1 GAAAAGAAAA 0.76034 -244 ACTTAGCTTTGAAAGGGAATTTCTTTTCTT 8 70 0 GAAAGGGAAT 0.851281 -231 AATAATAGAAGAAATGGAAAAAGAGGAAGG 10 252 1 GAAATGGAAA 0.770435 -25 AAAAGAAAAAGAAGGGAAAAAGGAAAGC 16 9 0 GAAGGGAAAA 0.792847 -32 TCCGAATATTGAAAGGATAACTCCGCAAAT 19 25 0 GAAAGGATAA 0.626873 -185 AAAGAGCGCAGGAATGAAAAAGGGGCTTGA 19 85 0 GGAATGAAAA 0.909712 -125 ********** Masking position 3 Map Score: 6.12678 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 756 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639