AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -intrC_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 glnP 138 glutamine high-affinity transport system; membrane component #2 glnH 300 periplasmic glutamine-binding protein; permease #3 glnL 285 histidine protein kinase sensor for GlnG regulator (nitrogen regulator II, NRII) #4 glnA 300 glutamine synthetase #5 yckK 114 similar to glutamine ABC transporter (glutamine-binding protein) #6 acoR 115 transcriptional regulator #7 glnR 110 transcriptional regulator #8 glnA 60 glutamine synthetase #9 yqiY 80 similar to amino acid ABC transporter (permease) #10 yqiX 268 similar to amino acid ABC transporter (binding protein) #11 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #12 glnQ 155 glutamine ABC transporter (ATP-binding protein) #13 glnH 21 glutamine ABC transporter (glutamine-binding protein) #14 glnM 60 glutamine ABC transporter (integral membrane protein) #15 ytmM 29 similar to amino acid ABC transporter (permease) #16 ytmL 21 similar to amino acid ABC transporter (permease) #17 ytmI 152 similar to hypothetical proteins from B. subtilis #18 yxeN 22 similar to amino acid ABC transporter (permease) #19 yxeM 24 similar to amino acid ABC transporter (binding protein) #20 yxeK 185 similar to monooxygenase #21 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 AGCATTTCCTTTTTTCTATCCACGGGA 2 284 0 CCTTTTTTCT 0.630403 -17 TGATGCTTCGCGCTTTTTATCCGTAAAAAG 3 222 1 CGCTTTTTAT 0.930274 -64 CTTTGGATAACCCTTTTTATGCTCCGTGAA 4 55 0 CCCTTTTTAT 0.946388 -246 CGCATGATAACGCCTTTTAGGGGCAATTTA 4 177 1 CGCCTTTTAG 0.741319 -124 GCACAGATTTCGCTTTATCTTTTTTACGGC 4 214 1 CGCTTTATCT 0.92626 -87 CTTATTCCCCACTTTTCTGGTTGATTTT 5 97 0 CCACTTTTCT 0.754758 -18 AAAAAGCAGGCGCCTTATATCCATGCGCCT 6 24 0 CGCCTTATAT 0.925366 -92 TTGTTGAAAGCGCTTTATTTTTCCCCTACA 6 56 1 CGCTTTATTT 0.684685 -60 CTCAATTTCCTCCTTTTCTTAACTTAGTT 7 92 0 CTCCTTTTCT 0.93516 -19 AGCCTTTGTCTCCTTTTCTTACAGGAAAA 9 62 0 CTCCTTTTCT 0.93516 -19 TTCAGAAAACCCCTTTATCTTTTCATTTCC 11 12 1 CCCTTTATCT 0.943245 -141 CCCGATACCCCTTTGTATGAAAAAATTT 11 135 0 CCCTTTGTAT 0.859509 -18 ACAAGCTCCCCCATTTCTGTT 13 4 0 CCCCATTTCT 0.823836 -18 TTGATTTTCCCGCCTTTTCTATTT 19 5 0 CGCCTTTTCT 0.977781 -20 GGCGATACTCCTTTTATCATGTTTTTA 20 169 0 CTCCTTTTAT 0.887512 -17 ATTTGAATTCCCCCTTGTTTTCTGTTTCAA 21 11 1 CCCCTTGTTT 0.777201 -230 ATCCTGCTTTCCCTTTATATAAATGCAAGT 21 47 1 CCCTTTATAT 0.900909 -194 ********** Masking position 6 Map Score: 20.1804 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 267 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 2 CTGTGTTGAGTGCACAATTTTAGCGCACCAGATTGG 2 115 1 TGCACATTGC 0.987465 -186 ACCCTGAAGATGCACCATTCTGGGGCACCAATCTGG 2 142 0 TGCACATTGC 0.987464 -159 CGATTTATAGGGCAATACCCTGAAGATGCACCATTC 2 158 0 GGCAAACTGA 0.927734 -143 TTCGAGATGCGGCAAAAACGTGATGCACGATTTATA 2 185 0 GGCAAACTGC 0.973153 -116 ATCAAGGAGTTGCAAAACTGGCACGATTTTTTCATA 2 223 1 TGCAAATGGA 0.899017 -78 TGGGATCGGTGGCAAGCACATCACGCCGGATGCGAC 3 56 1 GGCAACCTGC 0.840968 -230 CTGAACAGGTTGCACCATTTTAGTGCATTATAGCTT 3 249 0 TGCACATTGC 0.987465 -37 AAAGGGACTCTGCAATACTTGTTTGCGGAGGATGT 4 10 0 TGCAAATGGC 0.961743 -291 CAAAGGTCATTGCACCAACATGGTGCTTAATGTTTC 4 80 1 TGCACACTGC 0.986235 -221 ATGTGAATGTTGCACCAATATAGTGCTTCAATGGAA 4 113 0 TGCACATTGC 0.987465 -188 CTCATTTTTATGCAATACTATTTTTAAAAATTATCT 10 169 0 TGCAAATTTA 0.668892 -100 TTTATTCCGTTGCAATAATTTGCACAACCCTATGTT 11 90 0 TGCAAATTCA 0.749617 -63 GAGGACAAGGTGCAAAAACATTCTGATATTTCGAGC 21 118 1 TGCAAACTGA 0.965394 -123 TTTCAGCAAGTGCAAAATTCTTTTGCATATCCTCTC 21 159 1 TGCAAATTGC 0.988585 -82 ***** * * * ** Masking position 4 Map Score: 20.8238 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 277 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 TCTCCCCATAGGGGAGAGGGAACTGCCAGT 1 33 0 GGGGAGAGGG 0.953869 -106 TCTCCCCTATGGGGAGAGGATTAGGGTGAG 1 46 1 GGGGAGAGGA 0.976168 -93 GGAGAGGATTAGGGTGAGGGGCGCAAACCC 1 58 1 AGGGTGAGGG 0.683489 -81 TTAATCAGCTGGAGATAGCAGATGG 2 6 0 GGAGATAGCA 0.768796 -295 TAAAGGAAAAAGCAGGCGCATGGA 6 5 1 GGAAAAAGCA 0.707179 -111 CGGCGTGTAAGGGAGGAGCGATCAAGGAA 6 97 1 GGGAGGAGCG 0.948852 -19 ATATAGGTGAGGTGAAAGCAG 12 2 0 GGTGAAAGCA 0.718602 -154 CAACCATCCCGGGATGAGCAGGCGATGCTC 14 11 1 GGGATGAGCA 0.946787 -50 TTATCAAATTGGGATGAGCATCGCCTGCTC 14 26 0 GGGATGAGCA 0.946787 -35 CTTCGGATGAGGGGGGAGAAGA 15 18 1 GGGGGGAGAA 0.917826 -12 GTAAAAAGAGAGGGAGCAGTG 16 9 1 AGAGGGAGCA 0.891414 -13 ATGAAAAACAGGAGGGAGCACA 17 3 0 GGAGGGAGCA 0.976323 -150 ATTTATATAAAGGGAAAGCAGGATAACATG 21 41 0 AGGGAAAGCA 0.838345 -200 ********** Masking position 7 Map Score: 11.9108 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 436 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 ACATTCACATATATGAAAAAATCGTGCCAGTT 2 238 0 ATGAAAAAAT 0.942423 -63 TTTGGTTTTCATAAGACAAAATCTT 5 4 0 ATGACAAAAT 0.674879 -111 TAAGTTAAGAAAAGGAGGAAATTGAG 7 95 1 AAGAGGAAAT 0.729286 -16 CCTCCTCTTAAAAGGTAAAAATGTATATAGCA 8 28 0 AAGTAAAAAT 0.626079 -33 TTCCAAGGATATATGAATAAATATTAAGGGAT 10 62 1 ATGAATAAAT 0.894619 -207 ATCTAGTAATATCAGAAGAGATCACTGGAAAG 10 127 1 ATGAAGAGAT 0.795614 -142 AAATACAAATTAACGAATAAATATTCAAATAC 10 215 1 TAGAATAAAT 0.480556 -54 ACAATAAAGGAAATGAAAAGATAAAGGGGTTT 11 18 0 AAGAAAAGAT 0.829506 -135 TTTATTGTCCAGCGGAAAAAATATTTTGTCAA 11 42 1 AGGAAAAAAT 0.812996 -111 ATATTTTGTCAAGAGAAGAAAACGTGGTAACA 11 62 1 AAGAAGAAAA 0.630475 -91 AAATTATTGCAACGGAATAAATAGGTGTGCAA 11 105 1 AAGAATAAAT 0.915341 -48 ATACCCCTTTGTATGAAAAAATTTGCACACCT 11 127 0 GTGAAAAAAT 0.674879 -26 TGAAAATTAAAAGTGAAAAAATGTCCATGACT 12 82 0 AAGAAAAAAT 0.954226 -74 CTCCCCCCTCATCCGAAGAAATATA 15 4 0 ATGAAGAAAT 0.943436 -26 TTTTCGCTTGAATAGAAAAAATTAATCTTAAC 20 45 1 AAGAAAAAAT 0.954226 -141 TAGTCGTTTAATATGAATAAATCAAAATGTAC 20 102 0 ATGAATAAAT 0.894619 -84 TTTTTTATAAAATAGAAGCAATATTAAGAAAA 21 198 1 AAGAAGCAAT 0.716615 -43 ** ******** Masking position 11 Map Score: 11.3902 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 216 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 CAATTTTAGCGCACCAGATTGGTGCCCCAGAA 2 129 1 GCACCAATGG 0.994237 -172 CCAGATTGGTGCCCCAGAATGGTGCATCTTCA 2 142 1 GCCCCAATGG 0.982375 -159 AAGCTATAATGCACTAAAATGGTGCAACCTGT 3 249 1 GCACTAATGG 0.979849 -37 GAAACATTAAGCACCATGTTGGTGCAATGACC 4 84 0 GCACCAGTGG 0.970588 -217 TTCCATTGAAGCACTATATTGGTGCAACATTC 4 113 1 GCACTAATGG 0.97254 -188 CAAAAGGGCTGCACCACGATGTGAATGTTGCA 4 135 0 GCACCAGTGT 0.957784 -166 GTTATCATGCGCACCATCGTGCAAAAGGGCTG 4 156 0 GCACCACTGC 0.615762 -145 ****** * *** Masking position 6 Map Score: 8.29518 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 84 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ATTAAGTAAATTTTTTGTATCCACATCATCACACAATCGTT 2 31 1 TTTTCAAATA 0.708669 -270 TGTAAGCTAATTTTTTATTTCAATAAAATCAACCAGAAAAG 5 73 1 TTTTAAAATA 0.928039 -42 AGCGCTTTATTTTTCCCCTACAATAGATGAAAACGGCGTGT 6 64 1 TTTTAAATGA 0.868866 -52 CTATATACATTTTTACCTTTTAAGAGGAGGAATTTTACCAA 8 30 1 TTTTAAAAGA 0.981157 -31 AATAGGAAACTTTTTTCCTGTAAGAAAAGGAGACAAAGGCT 9 50 1 TTTTAAAAGA 0.981179 -31 GCGATTTAATTTTTATCTAGTAATATCAGAAGAGATCACTG 10 113 1 TTTTAAAAGA 0.981179 -156 ACTTCAGTAATTTTAATGATGAAAAACAGGAGGGAGCACA 17 10 0 TTTTAAAAGA 0.981157 -143 TACTCTGATCTTTGACTAATCAAAAAAAGTAAACCTTCACT 17 48 0 TTTGAAAAGA 0.90758 -105 ATTTTTCGCATTATTCAGCCTAAAAACATGATAAAAGGAGT 20 149 1 TTATAAAATA 0.621392 -37 CTTGCTGAAATTTTCGCTCGAAATATCAGAATGTTTTTGCA 21 128 0 TTTTAAAAGA 0.981179 -113 ATCCTCTCCGTTTTTTTATAAAATAGAAGCAATATTAAGAA 21 187 1 TTTTAAAAGA 0.981155 -54 **** ** * ** * Masking position 13 Map Score: 11.2496 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 19 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TGTAAATAATCAAATTCAGGGTAATTAATGGCC 1 95 0 CAATCAGGTA 0.950399 -44 CAGAATGGTGCATCTTCAGGGTATTGCCCTATA 2 156 1 CACTCAGGTA 0.896174 -145 CCAGGCCTGCCAGAGACAGGCGAAAAGTTTCCA 3 26 0 CAAGCAGGGA 0.968385 -260 ATGTGGTAGGCCGGAGCAGGTGAGTCGCTCTCC 3 125 1 CCGACAGGGA 0.977343 -161 AATGGTGCAACCTGTTCAGGAGACTGCTTT 3 266 1 CCGTCAGGGA 0.990016 -20 ACGACCATGACCAATCCAGGAGAGTTAAAGT 4 280 1 CCATCAGGGA 0.987968 -21 TTCTTAACATCAAATCCAGGAGAAATTTTTAAA 7 15 0 CAATCAGGGA 0.988204 -96 ACCATCCCGGGATGAGCAGGCGATGCTCATCCC 14 13 1 GAGACAGGGA 0.879282 -48 ** ** **** ** Masking position 8 Map Score: 4.75708 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 242 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TGTGGATACAAAAAATTTACTTAATCAGCTG 2 25 0 AAAAATTTCT 0.918934 -276 GAGACAGGCGAAAAGTTTCCACGGCAACTAA 3 16 0 AAAAGTTTCA 0.827806 -270 CATACTAAAAAAAAGTTATCCTTTAGATTTG 5 44 1 AAAAGTTACC 0.898339 -71 TATTGAAATAAAAAATTAGCTTACAAATCTA 5 67 0 AAAAATTACT 0.930897 -48 CTTACAGGAAAAAAGTTTCCTATTCAATAAA 9 43 0 AAAAGTTTCT 0.938321 -38 ATTACTAGATAAAAATTAAATCGCTGTACAA 10 106 0 AAAAATTAAT 0.674835 -163 TACTATTTTTAAAAATTATCTTTAGGCTTAT 10 159 0 AAAAATTACT 0.930893 -110 CTTTGTATGAAAAAATTTGCACACCTATTTA 11 122 0 AAAAATTTCA 0.78177 -31 TAATTTTCAGAAAAGTTTGATCATTTACTTT 12 105 1 AAAAGTTTAT 0.700932 -51 ACTAATCAAAAAAAGTAAACCTTCACTTCAG 17 44 0 AAAAGTAACC 0.686771 -109 GAATAATGCGAAAAATAAACTCCTATATTCC 20 134 0 AAAAATAACT 0.769717 -52 ******** ** Masking position 4 Map Score: 5.49605 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 127 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 ATGTGAATGTCACGCAGGGGATCGTCCCGT 2 260 1 CACGCAGGGG 0.963215 -41 CTGTCTCTGGCAGGCCTGGGATCGGTGGCA 3 40 1 CAGGCCTGGG 0.951232 -246 GCAAGCACATCACGCCGGATGCGACGCAAA 3 67 1 CACGCCGGAT 0.978497 -219 CATCACCGTGTAGGCCGGATAAGACGCATT 3 95 0 TAGGCCGGAT 0.931838 -191 GATGATGTGGTAGGCCGGAGCAGGTGAGTC 3 121 1 TAGGCCGGAG 0.955917 -165 AGACGAACAACCCGGATGCTCAAAGCA 10 8 1 CAACCCGGAT 0.802066 -261 ATGCTCAAAGCAGCCCGGGTTTTTTTGTGC 10 26 1 CAGCCCGGGT 0.97105 -243 CCCTCATGGTCACGCAAGGGTCTTTTCGCT 20 23 1 CACGCAAGGG 0.77255 -163 ********** Masking position 2 Map Score: 2.87865 Number of sites scoring better than the average of aligned sites = 891 Number in coding regions = 810 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 ACCCTGAATTTGATTATTTACACCACGGTA 1 106 1 TGATTATTTA 0.871517 -33 CTCAACACAGTGATTATTTAGCGTAAAACC 2 95 0 TGATTATTTA 0.871517 -206 TAAAAAAAAGTTATCCTTTAGATTTGTAAG 5 49 1 TTATCCTTTA 0.917484 -66 TGCGCCTGCTTTTTCCTTTA 6 1 0 TTTTCCTTTA 0.778449 -115 ATTTGAATATTTATTCGTTAATTTGTATTT 10 215 0 TTATTCGTTA 0.759008 -54 TTACAAGGAATTATTCTTTATGTTTCTTTA 12 42 1 TTATTCTTTA 0.930939 -114 TTATTCTTTATGTTTCTTTAGTCAGTCAGA 12 52 1 TGTTTCTTTA 0.845779 -104 CAGAAAAGTTTGATCATTTACTTTTTGGTC 12 112 1 TGATCATTTA 0.848376 -44 TACTAAGCTTTTATTGTTTATACTATAAAG 17 91 0 TTATTGTTTA 0.755541 -62 ********** Masking position 4 Map Score: 2.39401 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 48 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 CTACACCTGTAAAACGCACTGGCAGTTCCCTCT 1 16 1 AAAAGCACGC 0.989294 -123 TTGACGGAGAAAAAAGCCCATGCAGAGATGGGC 3 184 0 AAAAGCCCGC 0.993165 -102 TAAAGGAAAAAGCAGGCGCATGGATATAA 6 7 1 AAAAGCAGGC 0.979715 -109 TTCAACAATAAAAAAGCAGGCGCCTTATATCCA 6 31 0 AAAAGCAGGC 0.979715 -85 TTTATGCACAAAAAAACCCGGGCTGCTTTGAGC 10 28 0 AAAAACCCGC 0.980039 -241 TATTCAAGCGAAAAGACCCTTGCGTGACCATGA 20 26 0 AAAAACCCGC 0.980039 -160 **** **** ** Masking position 4 Map Score: 5.69698 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 90 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 CAGGGTAATTAATGGCCCCGGAGCGGGTTT 1 82 0 AATGGCCCCG 0.90123 -57 CCAACTTTTAAATTGCCCCTAAAAGGCGTT 4 185 0 AATTGCCCCT 0.977811 -116 ATTTTTTAAAAATTTCTCCTGGATTTGATG 7 11 1 AATTTCTCCT 0.886656 -100 CTCAATTTCCTCCTTTTCTTAACT 7 97 0 ATTTCCTCCT 0.946693 -14 TTGGTAAAATTCCTCCTCTTAAAAGGT 8 44 0 AATTCCTCCT 0.97609 -17 GATCCATTTCCCCCGTATTCATTAC 10 254 0 ATTTCCCCCG 0.961062 -15 ATTTGAATTCCCCCTTGTTTTCTGT 21 6 1 AATTCCCCCT 0.988279 -235 ********** Masking position 1 Map Score: 5.18413 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 63 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 AGCATTTCCTTTTTTCTATCCA 2 289 0 CATTTCCTTT 0.959779 -12 ACGAAATCTGCAATTATTTTGGCCGTGTCG 4 243 0 CAATTATTTT 0.806271 -58 CCCCCGTATTCATTACTTTTGGTGTATTTG 10 240 0 CATTACTTTT 0.804013 -29 TTTATCTTTTCATTTCCTTTATTGTCCAGC 11 25 1 CATTTCCTTT 0.959779 -128 AAAGTTTGATCATTTACTTTTTGGTCAAAT 12 116 1 CATTTACTTT 0.920342 -40 CAAGCTCCCCCATTTCTGTT 13 1 0 CATTTCTGTT 0.858762 -21 GAACCTCCCTCAATTATTTTCTTAATATTG 21 216 0 CAATTATTTT 0.806271 -25 ********** Masking position 2 Map Score: 1.99126 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 34 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 AGGCCTGGGATCGGTGGCAAGCACATCACG 3 51 1 TCGGTGGCAA 0.950472 -235 TAAAGCGAAATCTGTGCCAACTTTTAAATT 4 201 0 TCTGTGCCAA 0.987399 -100 GATGTTATATTATGTGTCAATACGATGTAA 7 51 0 TATGTGTCAA 0.906664 -60 CCCCTTGTTTTCTGTTTCAACATGTTATCC 21 21 1 TCTGTTTCAA 0.906664 -220 AAATGCAAGTTCTGTGCCAAATCAAGAATT 21 67 1 TCTGTGCCAA 0.987399 -174 ********** Masking position 5 Map Score: 0.863627 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 29 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 TAAAGATTGTTTTTTCATCAGGTTTTACGC 2 75 1 TTTTTCATCA 0.899678 -226 CTGGCACGATTTTTTCATATATGTGAATGT 2 240 1 TTTTTCATAT 0.940398 -61 TAAGTATTTGGTTTTCATAAGACAAAATCT 5 12 0 GTTTTCATAA 0.854812 -103 CTTACACGCCGTTTTCATCTATTGTAGGGG 6 78 0 GTTTTCATCT 0.924089 -38 CCCTTAATATTTATTCATATATCCTTGGAA 10 62 0 TTATTCATAT 0.814051 -207 ATGTTACCACGTTTTCTTCTCTTGACAAAA 11 65 0 GTTTTCTTCT 0.631389 -88 GTGTGCAAATTTTTTCATACAAAGGGGTAT 11 129 1 TTTTTCATAC 0.82907 -24 CTCCCTCCTGTTTTTCATCATTAAAATTAC 17 15 1 TTTTTCATCA 0.899678 -138 ACATTTTGATTTATTCATATTAAACGACTA 20 104 1 TTATTCATAT 0.814051 -82 TGCAAAATTCTTTTGCATATCCTCTCCGTT 21 169 1 TTTTGCATAT 0.76649 -72 ********** Masking position 4 Map Score: 4.88968 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 229 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269