AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoN_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 pspF 151 psp operon transcriptional activator #4 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #5 hycA_hypA 211 hycA: transcriptional repression of hyc and hyp operons, hypA: pleiotrophic effects on 3 hydrogenase isozymes #6 hypE 38 plays structural role in maturation of all 3 hydrogenases #7 glnL 285 histidine protein kinase sensor for GlnG regulator (nitrogen regulator II, NRII) #8 glnA 300 glutamine synthetase #9 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #10 yckK 114 similar to glutamine ABC transporter (glutamine-binding protein) #11 acoR 115 transcriptional regulator #12 glnR 110 transcriptional regulator #13 glnA 60 glutamine synthetase #14 yqiY 80 similar to amino acid ABC transporter (permease) #15 yqiX 268 similar to amino acid ABC transporter (binding protein) #16 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #17 glnQ 155 glutamine ABC transporter (ATP-binding protein) #18 glnH 21 glutamine ABC transporter (glutamine-binding protein) #19 glnM 60 glutamine ABC transporter (integral membrane protein) #20 ytmM 29 similar to amino acid ABC transporter (permease) #21 ytmL 21 similar to amino acid ABC transporter (permease) #22 ytmI 152 similar to hypothetical proteins from B. subtilis #23 yufT 300 similar to NADH dehydrogenase #24 yxeN 22 similar to amino acid ABC transporter (permease) #25 yxeM 24 similar to amino acid ABC transporter (binding protein) #26 yxeK 185 similar to monooxygenase #27 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 CTGACGACAGCCTGTTTTTCGTCAGAGTTT 9 64 1 CCTGTTTTTC 0.943252 -134 TATCCATGCGCCTGCTTTTTCCTTTA 11 7 0 CCTGCTTTTT 0.972281 -109 ATATAAGGCGCCTGCTTTTTTATTGTTGAA 11 34 1 CCTGCTTTTT 0.972281 -82 CTCAATTTCCTCCTTTTCTTAACTTAGT 12 93 0 CCTCCTTTTC 0.989604 -18 AAAAGTTGAGCCGCTTTTTT 14 1 0 CCGCTTTTTT 0.917272 -80 AGCCTTTGTCTCCTTTTCTTACAGGAAA 14 63 0 TCTCCTTTTC 0.940627 -18 TCAAAGCAGCCCGGGTTTTTTTGTGCATAA 15 30 1 CCGGGTTTTT 0.77087 -239 TGTGCTCCCTCCTGTTTTTCATCATTAAAA 22 11 1 CCTGTTTTTC 0.943252 -142 ATACAAATAACCTCTTTTTTGTTAGACTTA 23 45 1 CCTCTTTTTT 0.931034 -256 AAAGATAAGACCTCCTTTTCTCGTTCTCAA 23 202 0 CCTCCTTTTC 0.989604 -99 TGCTATTTTATCGCCTTTTTTATTTGCTTT 23 247 1 TCGCCTTTTT 0.876819 -54 TGGTGAGTCACCGCCGTTTC 24 1 0 CCGCCGTTTC 0.954524 -22 TTGATTTTCCCGCCTTTTCTATTT 25 6 0 CCGCCTTTTC 0.987371 -19 AACATGTTATCCTGCTTTCCCTTTATATAA 27 39 1 CCTGCTTTCC 0.896903 -202 TTGCATATCCTCTCCGTTTTTTTATAAAAT 27 181 1 TCTCCGTTTT 0.699395 -60 ********** Masking position 7 Map Score: 22.2898 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 401 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 CTGTGTTGAGTGCACAATTTTAGCGCACCAGATT 2 115 1 TGCACATTGC 0.93999 -186 ACCATTCTGGGGCACCAATCTGGTGCGCTAAAAT 2 131 0 GGCACAATGT 0.979069 -170 TTGCAAAACTGGCACGATTTTTTCATATATGTGA 2 232 1 GGCACATTTC 0.873332 -69 ATAAAAAATTGGCACGCAAATTGTATTAACAGTT 3 53 0 GGCACCATGT 0.898052 -99 AATCAACACTGGCACAATTATTGCTTGTAGCTGG 5 32 0 GGCACATTGC 0.981968 -180 ATTAAAAGTTGGCACAAAAAATGCTTAAAGCTGG 5 161 1 GGCACAAAGC 0.974221 -51 AAAGCTATAATGCACTAAAATGGTGCAACCTGTT 7 248 1 TGCACAATGT 0.930775 -38 CAAAGGTCATTGCACCAACATGGTGCTTAATGTT 8 80 1 TGCACAATGT 0.930775 -221 ATGTGAATGTTGCACCAATATAGTGCTTCAATGG 8 115 0 TGCACAATGT 0.930775 -186 TTTAAAAGTTGGCACAGATTTCGCTTTATCTTTT 8 203 1 GGCACGATGC 0.976074 -98 TGATATTACGGGCACTATTTATTCAAAACTCTGA 9 85 0 GGCACATATC 0.68882 -113 CATAAAATGTGGCATAAAAGATGCATACTGTAGT 9 132 1 GGCATAAAGC 0.713397 -66 TTCTTGATTTGGCACAGAACTTGCATTTATATAA 27 61 0 GGCACGATGC 0.976074 -180 ***** ** * ** Masking position 4 Map Score: 16.3579 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 306 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 GCCCATCCCCAAACAGGCGTAACGCCTGCAAAAC 4 26 0 AAAAGCAACG 0.974176 -99 AGTTGGCACAAAAAATGCTTAAAGCTGGCATCTC 5 167 1 AAAAGCAAAG 0.98873 -45 GGCCTGCCAGAGACAGGCGAAAAGTTTCCACGGC 7 22 0 AGAAGCAAAG 0.974176 -264 CCTATTCAATAAAAAGGCTCAACGAAAAAGTTGA 14 22 0 AAAAGCAACG 0.974176 -59 ATCACTGGAAAGATAAGCCTAAAGATAATTTTTA 15 147 1 AGAAGCAAAG 0.974175 -122 ATAAATATTCAAATACACCAAAAGTAATGAATAC 15 231 1 AAAAACAAAG 0.961172 -38 CTGACTGACTAAAGAAACATAAAGAATAATTCCT 17 47 0 AAAAACAAAG 0.961172 -109 CTTCTTGGCAAAATACGCAAAAAGA 23 286 1 AAAAGCAAAG 0.98873 -15 TTCAGCCTAAAAACATGATAAAAGGAGTATCGCC 26 162 1 AAAAGAAAAG 0.884593 -24 TCTATTTTATAAAAAAACGGAGAGGATATGCAAA 27 180 0 AAAAACAGAG 0.837728 -61 *** * ** **** Masking position 5 Map Score: 12.058 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 48 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 4 GAGGATTAGGGTGAGGGGCGCAAACCCGCT 1 61 1 GTGAGGGGCG 0.944633 -78 CGCCTGTTTGGGGATGGGCGTGTCGATGAG 4 41 1 GGGATGGGCG 0.99345 -84 ACTCGCCCACGGTAGCGGCGGCCAGGCG 6 21 1 GGTAGCGGCG 0.920311 -18 TGGCAGGCCTGGGATCGGTGGCAAGCACAT 7 47 1 GGGATCGGTG 0.966633 -239 CGGCGTGTAAGGGAGGAGCGATCAAGGAA 11 97 1 GGGAGGAGCG 0.988143 -19 TGCTCATCCCGGGATGGTTG 19 1 0 GGGATGGTTG 0.788992 -60 CAACCATCCCGGGATGAGCAGGCGATGCTC 19 11 1 GGGATGAGCA 0.948091 -50 TTATCAAATTGGGATGAGCATCGCCTGCTC 19 26 0 GGGATGAGCA 0.948091 -35 TAAAAAGAGAGGGAGCAGTG 21 12 1 GGGAGCAGTG 0.940887 -10 GTGACCATGAGGGAACGGCATTGAT 26 6 0 GGGAACGGCA 0.877256 -180 ********** Masking position 4 Map Score: 10.8081 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 425 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 AATGTTGTCCTCTTGATTTCTGCGTTCAGG 3 3 1 TTTCTCTTGC 0.876952 -149 GAAAATGACATTTCATCGGCATGTTTTCGTCAAAAATG 4 75 1 TTTCGCATGC 0.829952 -50 TAAAGATGAATTTCGTCGCCGTGTCGACGTGTCATTTC 5 96 0 TTTCCCGTGC 0.993825 -116 GTGTTTTAGTTGCCGTGGAAACTTTTCGCCTG 7 5 1 TTTTCCGTGC 0.972623 -281 TCGCATCCGGCGTGATGTGCTTGCCACCGATCCCAGGC 7 53 0 CTTGGCTTGC 0.637809 -233 CGGCCTACCACATCATCACCGTGTAGGCCGGATAAGAC 7 100 0 CTTCCCGTGC 0.986678 -186 CTGCATGGGCTTTTTTCTCCGTCAATTCTCTGATGCTT 7 192 1 TTTCCCGTCC 0.96657 -94 GATAACCCTTTTTATGCTCCGTGAAAGCGATCACAAAG 8 42 0 TTGCCCGTGC 0.986678 -259 AATCTGCAATTATTTTGGCCGTGTCGCCGTAAAAAAGA 8 231 0 TTTGCCGTGC 0.974588 -70 CTGGATTGGTCATGGTCGTCGTGGTAACGAAATCTGCA 8 261 0 CTTCTCGTGC 0.91942 -40 AATGTCTGCCGCGTGATGGCTGTCACGCGG 9 3 1 TTGCGCGTGC 0.962558 -195 TCTTTAGGCTTATCTTTCCAGTGATCTCTTCTGATATT 15 134 0 TTTTCAGTGC 0.683808 -135 TATTTGCTTTTATCATTCCCTTCTTGGCAAAATACGCA 23 267 1 TTTTCCTTCC 0.647225 -34 TATCAGAATGTTTTTGCACCTTGTCCTCGAAAATTGTA 27 108 0 TTGCCCTTGC 0.955134 -133 * * ** ***** * Masking position 12 Map Score: 10.6131 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 292 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 GTGCCAATTTTTTATCTTTTTGATTTATAA 3 72 1 TTTATCTTTT 0.923681 -80 CAGATTTCGCTTTATCTTTTTTACGGCGAC 8 217 1 TTTATCTTTT 0.923681 -84 TTGAAAGCGCTTTATTTTTCCCCTACAATA 11 59 1 TTTATTTTTC 0.857059 -57 TATATACATTTTTACCTTTTAAGAGGAGGA 13 31 1 TTTACCTTTT 0.883454 -30 TGTACAGCGATTTAATTTTTATCTAGTAAT 15 107 1 TTTAATTTTT 0.767529 -162 AGAAAACCCCTTTATCTTTTCATTTCCTTT 16 15 1 TTTATCTTTT 0.923681 -138 TCACCTCACCTATATCTTTTGAGGTTTACA 17 17 1 TATATCTTTT 0.562929 -139 TTTTTTCACTTTTAATTTTCAGAAAAGTTT 17 93 1 TTTAATTTTC 0.625009 -63 AGTTTGATCATTTACTTTTTGGTCAAATTT 17 118 1 TTTACTTTTT 0.881502 -38 GAAGTGAAGGTTTACTTTTTTTGATTAGTC 22 46 1 TTTACTTTTT 0.881502 -107 TTACTAAGCTTTTATTGTTTATACTATAAA 22 92 0 TTTATTGTTT 0.65197 -61 TGAGTTAAGATTAATTTTTTCTATTCAAGC 26 50 0 TTAATTTTTT 0.558293 -136 AATATAGGAGTTTATTTTTCGCATTATTCA 26 136 1 TTTATTTTTC 0.857059 -50 ********** Masking position 4 Map Score: 9.63257 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 133 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 7 TGTGTTGAGTGCACAATTTTAGCGCACCAGAT 2 116 1 GCACAATTAG 0.849943 -185 CAATTTTAGCGCACCAGATTGGTGCCCCAGAA 2 129 1 GCACCAGTGG 0.966871 -172 CCCTGAAGATGCACCATTCTGGGGCACCAATC 2 145 0 GCACCATTGG 0.976378 -156 ATCAACACTGGCACAATTATTGCTTGTAGCTG 5 33 0 GCACAATTTG 0.762722 -179 TGAACAGGTTGCACCATTTTAGTGCATTATAG 7 252 0 GCACCATTAG 0.960976 -34 GAAACATTAAGCACCATGTTGGTGCAATGACC 8 84 0 GCACCATTGG 0.927517 -217 TTCCATTGAAGCACTATATTGGTGCAACATTC 8 113 1 GCACTATTGG 0.955934 -188 CAAAAGGGCTGCACCACGATGTGAATGTTGCA 8 135 0 GCACCACTGT 0.74554 -166 GTTATCATGCGCACCATCGTGCAAAAGGGCTG 8 156 0 GCACCATTGC 0.635599 -145 CTTATTCCCCACTTTTCTGGTTGATTTTAT 10 95 0 CCACTTTTGG 0.575581 -20 AAATTATATCGCACTTTTCTGCAAGCTGCCAC 23 123 0 GCACTTTTGC 0.753631 -178 ******* *** Masking position 3 Map Score: 9.32005 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 313 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 AGCTGATTAAGTAAATTTTTTGTATCCACA 2 26 1 GTAAATTTTT 0.660133 -275 CAATTTGCGTGCCAATTTTTTATCTTTTTG 3 64 1 GCCAATTTTT 0.934846 -88 CATTTTTTGTGCCAACTTTTAATTTATTGT 5 154 0 GCCAACTTTT 0.958273 -58 TAGTTGCCGTGGAAACTTTTCGCCTGTCTC 7 17 1 GGAAACTTTT 0.894519 -269 CGAAATCTGTGCCAACTTTTAAATTGCCCC 8 196 0 GCCAACTTTT 0.958273 -105 AAATCTAAAGGATAACTTTTTTTTAGTATG 10 44 0 GATAACTTTT 0.741994 -71 AGATTTGTAAGCTAATTTTTTATTTCAATA 10 68 1 GCTAATTTTT 0.901231 -47 TTATTGAATAGGAAACTTTTTTCCTGTAAG 14 44 1 GGAAACTTTT 0.894519 -37 TAAGCCTAAAGATAATTTTTAAAAATAGTA 15 160 1 GATAATTTTT 0.642345 -109 ATAGGGTTGTGCAAATTATTGCAACGGAAT 16 93 1 GCAAATTATT 0.668296 -60 AAATAGGTGTGCAAATTTTTTCATACAAAG 16 123 1 GCAAATTTTT 0.945604 -30 AAGTAAATGATCAAACTTTTCTGAAAATTA 17 105 0 TCAAACTTTT 0.666414 -51 ********** Masking position 5 Map Score: 8.58573 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 108 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 TCACATATATGAAAAAATCGTGCCAGTTTT 2 236 0 GAAAAAATCG 0.803953 -65 TCAGAGTTTTGAATAAATAGTGCCCGTAAT 9 85 1 GAATAAATAG 0.9261 -113 AAGGATATATGAATAAATATTAAGGGATTA 15 66 1 GAATAAATAT 0.920427 -203 ACAAATTAACGAATAAATATTCAAATACAC 15 219 1 GAATAAATAT 0.920427 -50 TTGTCCAGCGGAAAAAATATTTTGTCAAGA 16 46 1 GAAAAAATAT 0.93443 -107 TATTGCAACGGAATAAATAGGTGTGCAAAT 16 109 1 GAATAAATAG 0.9261 -44 CCCTTTGTATGAAAAAATTTGCACACCTAT 16 125 0 GAAAAAATTT 0.718614 -28 AATTAAAAGTGAAAAAATGTCCATGACTTC 17 80 0 GAAAAAATGT 0.791018 -76 CCCCTCATCCGAAGAAATATA 20 2 0 GAAGAAATAT 0.838989 -28 TAAAAAAGGCGATAAAATAGCAAGATGTAA 23 239 0 GATAAAATAG 0.684788 -62 ********** Masking position 5 Map Score: 5.66149 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 75 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 ACCTGTTCAGGAGACTGCTTT 7 275 1 GAGATGCTTT 0.912015 -11 GAGTCCCTTTGTGATCGCTTTCACGGAGCAT 8 36 1 GTGACGCTTT 0.837904 -265 ATGACCTTTGGATAACCCTTTTTATGCTCCG 8 59 0 GATACCCTTT 0.962078 -242 TGGTGCGCATGATAACGCCTTTTAGGGGCAA 8 172 1 GATACGCCTT 0.941574 -129 AGTTGGCACAGATTTCGCTTTATCTTTTTTA 8 209 1 GATTCGCTTT 0.912423 -92 TTTTATTGTTGAAAGCGCTTTATTTTTCCCC 11 51 1 GAAACGCTTT 0.942212 -65 CTTCAGAAAACCCCTTTATCTTTTCA 16 6 1 GAAACCCCTT 0.825953 -147 CCCGATACCCCTTTGTATGAAAAA 16 139 0 GATACCCTTT 0.962078 -14 TCAAAGATCAGAGTATGCTTTATAGTATAAA 22 74 1 GAGTTGCTTT 0.742361 -79 GGCGATACTCCTTTTATCATGTTT 26 172 0 GATATCCTTT 0.877426 -14 **** ****** Masking position 10 Map Score: 5.78218 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 158 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 TACTTAATCAGCTGGAGATAGCAGATGG 2 6 0 GCTGGGATGA 0.781039 -295 TGTTTTTTCATCAGGTTTTACGCTAAATAATCA 2 82 1 TCAGGTTTCC 0.73097 -219 TGGTGCATCTTCAGGGTATTGCCCTATAAATCG 2 161 1 TCAGGTATGC 0.907187 -140 TGAATGTCACGCAGGGGATCGTCCCGTGGATAG 2 263 1 GCAGGGATGC 0.989031 -38 TGCCCGTTTTGCAGGCGTTACGCCTGTTTGGGG 4 21 1 GCAGGGTTCC 0.961634 -104 GTTACGCCTGTTTGGGGATGGGCGTGTCGATGA 4 37 1 TTTGGGATGC 0.691052 -88 CAGGCATTCCTCAGGTGATTGTCATTTTTGACG 4 102 0 TCAGGGATGC 0.982621 -23 GTAGGCCGGAGCAGGTGAGTCGCTCTCCAACGT 7 130 1 GCAGGGAGCC 0.974856 -156 CCCGGGATGAGCAGGCGATGCTCATCCCAATTT 19 18 1 GCAGGGATCC 0.989031 -43 TCTGGTGAGTCACCGCCGTTTC 24 10 0 TCTGGGAGCC 0.916726 -13 ***** *** * * Masking position 5 Map Score: 6.363 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 797 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 12 TGCATGGGCTTTTTTCTCCGTCAATTCTCT 7 193 1 TTTTTCTCCG 0.68659 -93 CCAACTTTTAAATTGCCCCTAAAAGGCGTT 8 185 0 AATTGCCCCT 0.907683 -116 AAGCGCTTTATTTTTCCCCTACAATAGATG 11 63 1 TTTTTCCCCT 0.859871 -53 ATTTTTTAAAAATTTCTCCTGGATTTGATG 12 11 1 AATTTCTCCT 0.913552 -100 CTCAATTTCCTCCTTTTCTTAACT 12 97 0 ATTTCCTCCT 0.95619 -14 TTGGTAAAATTCCTCCTCTTAAAAGGT 13 44 0 AATTCCTCCT 0.95619 -17 GATCCATTTCCCCCGTATTCATTAC 15 254 0 ATTTCCCCCG 0.951465 -15 ATTTGAATTCCCCCTTGTTTTCTGT 27 6 1 AATTCCCCCT 0.971925 -235 ********** Masking position 4 Map Score: 3.48301 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 57 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 13 TGTGATGATGTGGATACAAAAAATTTACTTAAT 2 31 0 TGATAAAAAA 0.927799 -270 GATCGTCCCGTGGATAGAAAAAAGGAAATGCT 2 279 1 TGATAAAAAA 0.927799 -22 CAATCAGATCTTTATAAATCAAAAAGATAAAAA 3 80 0 TTATAACAAA 0.80948 -72 GTTGATTTTATTGAAATAAAAAATTAGCTTACA 10 73 0 TTAAAAAAAA 0.728178 -42 AAGGTAAAAATGTATATAGCAAAACAGTTGCTA 13 16 0 TGATAACAAA 0.88594 -45 TCTTCTGATATTACTAGATAAAAATTAAATCGC 15 113 0 TTCTAAAAAA 0.748251 -156 TGAGAAACTGTTTAAAATACAAATTAACGAATA 15 201 1 TTAAATCAAA 0.380893 -68 GACTTCTGACTGACTAAAGAAACATAAAGAATA 17 53 0 TGCTAAAAAC 0.59326 -103 TTTCTGAAAATTAAAAGTGAAAAAATGTCCATG 17 85 0 TTAAATAAAA 0.505162 -71 CTCTGATCTTTGACTAATCAAAAAAAGTAAACC 22 54 0 TGCTATAAAA 0.674317 -99 AGAGGTTATTTGTATATTTAAAATCAATCCTGA 23 27 0 TGATATAAAA 0.83041 -274 TCTTTTCGCTTGAATAGAAAAAATTAATCTTAA 26 43 1 TGATAAAAAA 0.927799 -143 TCGTTTAATATGAATAAATCAAAATGTACCTTT 26 98 0 TGATAACAAA 0.88594 -88 GGATAACATGTTGAAACAGAAAACAAGGGGGAA 27 18 0 TTAAAAAAAA 0.728178 -223 TTGCTTCTATTTTATAAAAAAACGGAGAGGATA 27 186 0 TTATAAAAAC 0.65364 -55 ** *** * **** Masking position 6 Map Score: 6.02653 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 87 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 14 ATCACCGTGTAGGCCGGATAAGACGCATTTG 7 93 0 AGGCCGGAAA 0.946466 -193 ATGATGTGGTAGGCCGGAGCAGGTGAGTCGC 7 122 1 AGGCCGGACA 0.965568 -164 TGCCCCTAAAAGGCGTTATCATGCGCACCAT 8 171 0 AGGCGTTACA 0.779155 -130 CGTGTAAGGGAGGAGCGATCAAGGAA 11 100 1 AGGAGCGACA 0.930113 -16 CAATTTGATAAGGAGTGAATAGGCAG 19 45 1 AGGAGTGATA 0.813004 -16 TCTTCGGATGAGGGGGGAGAAGA 20 17 1 AGGGGGGAAA 0.942809 -13 GATGAAAAACAGGAGGGAGCACA 22 3 0 AGGAGGGACA 0.983064 -150 TTTTGTGAAGAGGAGTGACAAAA 22 140 1 AGGAGTGAAA 0.934659 -13 AAATAGAAAAGGCGGGAAAATCAA 25 10 1 AGGCGGGAAA 0.983064 -15 ******** ** Masking position 8 Map Score: 5.65004 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 152 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 CAAGGAGTTGCAAAACTGGCACGATTTTTT 2 225 1 CAAAACTGGC 0.982126 -76 GTAACGCCTGCAAAACGGGCAAAGCCTCAG 4 12 0 CAAAACGGGC 0.952587 -113 CGATGAGTGTCGAAAATGACATTTCATCGG 4 64 1 CGAAAATGAC 0.81194 -61 ATGTTTTCGTCAAAAATGACAATCACCTGA 4 95 1 CAAAAATGAC 0.921922 -30 CAGGGATAATCAACACTGGCACAATTATTG 5 43 0 CAACACTGGC 0.952587 -169 TTCGTCACGTCAAAACTGACGACAGCCTGT 9 49 1 CAAAACTGAC 0.972179 -149 ********** Masking position 5 Map Score: 2.61455 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 137 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555