AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoN_ecoli_bsub_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 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 yjcQ 140 putative enzyme #11 yjcR 300 putative membrane protein #12 yckK 114 similar to glutamine ABC transporter (glutamine-binding protein) #13 yclA 89 similar to transcriptional regulator (LysR family) #14 yfjN 300 similar to hypothetical proteins #15 yfjM 195 yfjM #16 yfjL 29 alternate gene name: yztA #17 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #18 acoR 115 transcriptional regulator #19 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #20 ynbA 220 similar to GTP-binding protein protease modulator #21 ynbB 187 similar to hypothetical proteins #22 glnR 110 transcriptional regulator #23 glnA 60 glutamine synthetase #24 yqiY 80 similar to amino acid ABC transporter (permease) #25 yqiX 268 similar to amino acid ABC transporter (binding protein) #26 yqiW 162 similar to hypothetical proteins from B. subtilis #27 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #28 glnQ 155 glutamine ABC transporter (ATP-binding protein) #29 glnH 21 glutamine ABC transporter (glutamine-binding protein) #30 glnM 60 glutamine ABC transporter (integral membrane protein) #31 ytmM 29 similar to amino acid ABC transporter (permease) #32 ytmL 21 similar to amino acid ABC transporter (permease) #33 ytmI 152 similar to hypothetical proteins from B. subtilis #34 yufT 300 similar to NADH dehydrogenase #35 yxeN 22 similar to amino acid ABC transporter (permease) #36 yxeM 24 similar to amino acid ABC transporter (binding protein) #37 yxeK 185 similar to monooxygenase #38 yxeI 154 similar to penicillin amidase #39 yxeH 39 similar to hypothetical proteins #40 yxeF 87 yxeF #41 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 AAACTCTGACGAAAAACAGGCTGTCGTCAG 9 64 0 GAAAAACAGG 0.890291 -134 GTAGAGAGCAAAAAGGGCGGTATAAATAAT 11 233 0 AAAAGGGCGG 0.915051 -68 TAAAAGGTATGATAAGGAGGCGCTTTCTT 13 71 1 GATAAGGAGG 0.743759 -19 TAAATTAGAGAAAAGACAGGCTGAGTAAAA 15 120 0 AAAAGACAGG 0.688361 -76 GCATGCAAAAAAAAGACCGGATATCACCCG 17 54 0 AAAAGACCGG 0.628597 -178 TAAAGGAAAAAGCAGGCGCATGGATA 18 7 1 AAAAAGCAGG 0.940294 -109 TTCAACAATAAAAAAGCAGGCGCCTTATAT 18 34 0 AAAAAGCAGG 0.940294 -82 AAATACGAGCAAAAAACAGACCTCTCAAAA 20 21 0 AAAAAACAGA 0.557095 -200 CGATTGCTTTGAAAAGGCGGAAATACGAGC 20 41 0 GAAAAGGCGG 0.975354 -180 ACTAAGTTAAGAAAAGGAGGAAATTGAG 22 93 1 GAAAAGGAGG 0.981006 -18 AAAAAAGCGGCTCAACTTTT 24 1 1 AAAAAAGCGG 0.915525 -80 TTTCCTGTAAGAAAAGGAGACAAAGGCT 24 63 1 GAAAAGGAGA 0.916535 -18 ACTGCTTACAGAAAAAGGGGATTATATAAC 26 39 0 GAAAAAGGGG 0.819106 -124 ACAGATGATGAAAAAGGAGAGGTCTTCA 26 145 1 AAAAAGGAGA 0.888955 -18 GTAAAAAGAGAGGGAGCAGTG 32 4 1 AAAAGAGAGG 0.840788 -18 TTTTAATGATGAAAAACAGGAGGGAGCACA 33 11 0 GAAAAACAGG 0.890291 -142 TAAGTCTAACAAAAAAGAGGTTATTTGTAT 34 45 0 AAAAAAGAGG 0.933968 -256 TTGAGAACGAGAAAAGGAGGTCTTATCTTT 34 202 1 GAAAAGGAGG 0.981006 -99 AAAGCAAATAAAAAAGGCGATAAAATAGCA 34 247 0 AAAAAGGCGA 0.859826 -54 GAAACGGCGGTGACTCACCA 35 1 1 GAAACGGCGG 0.885359 -22 AAATAGAAAAGGCGGGAAAATCAA 36 6 1 GAAAAGGCGG 0.975354 -19 AATCTGAATTGAAAAGGGGACTGATCAA 38 137 1 GAAAAGGGGA 0.719324 -18 CATTCGCCCAAAAAAGGAGGAAAGA 40 73 1 AAAAAGGAGG 0.974128 -15 ATTTTATAAAAAAACGGAGAGGATATGCAA 41 181 0 AAAACGGAGA 0.609716 -60 ********** Masking position 4 Map Score: 34.7321 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 453 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 ATCTGGTGCGCTAAAATTGTGCACTCAACACAG 2 115 0 CAAAAGTGCA 0.958845 -186 TTTTAGCGCACCAGATTGGTGCCCCAGAATGGT 2 132 1 CAGATGTGCC 0.978788 -169 GATTGGTGCCCCAGAATGGTGCATCTTCAGGGT 2 145 1 CAGAAGTGCA 0.956119 -156 CACATATATGAAAAAATCGTGCCAGTTTTGCAA 2 232 0 AAAAAGTGCC 0.750211 -69 ACTGTTAATACAATTTGCGTGCCAATTTTTTAT 3 54 1 CATTTGTGCC 0.807409 -98 CAGCTACAAGCAATAATTGTGCCAGTGTTGATT 5 33 1 CATAAGTGCC 0.957157 -179 CTATAATGCACTAAAATGGTGCAACCTGTTCAG 7 252 1 CAAAAGTGCA 0.958845 -34 CATTGAAGCACTATATTGGTGCAACATTCACAT 8 116 1 CATATGTGCA 0.913418 -185 AAAGATAAAGCGAAATCTGTGCCAACTTTTAAA 8 203 0 CAAATGTGCC 0.980135 -98 GCGACACGGCCAAAATAATTGCAGATTTCGTTA 8 242 1 CAAATTTGCA 0.730168 -59 ATTACCAACGCAAAATAATTGCCCTGTTA 14 7 0 CAAATTTGCC 0.851423 -294 ATTATAAATGCAAGAAGTGTGCCAGTCTTTTGA 17 178 0 CAGAAGTGCC 0.978788 -54 ACGAAGAGGCCAAAAAAAGTGCACGGCGAAGCA 26 71 1 CAAAAGTGCA 0.958845 -92 TATATAAATGCAAGTTCTGTGCCAAATCAAGAA 41 62 1 CAGTTGTGCC 0.896466 -179 * **** ***** Masking position 3 Map Score: 16.0134 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 107 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 GAGGATTAGGGTGAGGGGCGCAAACCCGCT 1 61 1 GTGAGGGGCG 0.96944 -78 CGCCTGTTTGGGGATGGGCGTGTCGATGAG 4 41 1 GGGATGGGCG 0.98963 -84 ACTCGCCCACGGTAGCGGCGGCCAGGCG 6 21 1 GGTAGCGGCG 0.901854 -18 TGGCAGGCCTGGGATCGGTGGCAAGCACAT 7 47 1 GGGATCGGTG 0.929869 -239 GAAGAGTTAAGCGAGCGGCGACCAGGTCGC 10 67 1 GCGAGCGGCG 0.949 -74 GGCAATCCCGGTGATCGGCGCTTATTATCC 11 109 1 GTGATCGGCG 0.959413 -192 AACTCGCCTCGTGATGAGCGTCAAAATAAG 11 167 0 GTGATGAGCG 0.914529 -134 CGGCGTGTAAGGGAGGAGCGATCAAGGAA 18 97 1 GGGAGGAGCG 0.983042 -19 CAACCATCCCGGGATGAGCAGGCGATGCTC 30 11 1 GGGATGAGCA 0.905083 -50 TTATCAAATTGGGATGAGCATCGCCTGCTC 30 26 0 GGGATGAGCA 0.905083 -35 TAAAAAGAGAGGGAGCAGTG 32 12 1 GGGAGCAGTG 0.889553 -10 GTGACCATGAGGGAACGGCATTGAT 37 6 0 GGGAACGGCA 0.813902 -180 ********** Masking position 4 Map Score: 14.0438 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 609 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 TGAAAAAATCGTGCCAGTTTTGCAACTCCTT 2 226 0 GTGCCAGTTT 0.986903 -75 TACAATTTGCGTGCCAATTTTTTATCTTTTT 3 62 1 GTGCCAATTT 0.965138 -90 GCTGAGGCTTTGCCCGTTTTGCAGGCGTTA 4 10 1 TTGCCCGTTT 0.833316 -115 AGCAATAATTGTGCCAGTGTTGATTATCCCT 5 41 1 GTGCCAGTTT 0.986903 -171 AGCATTTTTTGTGCCAACTTTTAATTTATTG 5 155 0 GTGCCAACTT 0.962812 -57 TTTAACAGAGATGCCAGCTTTAAGCATTTTT 5 177 0 ATGCCAGCTT 0.873552 -35 AGCGAAATCTGTGCCAACTTTTAAATTGCCC 8 197 0 GTGCCAACTT 0.962812 -104 TGAATAAATAGTGCCCGTAATATCAGGGAAT 9 94 1 GTGCCCGTAT 0.786077 -104 TTCTGCGCCATTGCCAGCCTTATTTTGACGC 11 149 1 TTGCCAGCTT 0.924139 -152 TGCAAGAAGTGTGCCAGTCTTTTGAGCCCGT 17 172 0 GTGCCAGTTT 0.986903 -60 ATAAATAGGTGTGCAAATTTTTTCATACAAA 27 121 1 GTGCAAATTT 0.685666 -32 ******** ** Masking position 2 Map Score: 12.55 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 177 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 CTTTTTACGGATAAAAAGCGCGAAGCATCA 7 222 0 ATAAAAAGCG 0.890274 -64 TTCACGGAGCATAAAAAGGGTTATCCAAAG 8 55 1 ATAAAAAGGG 0.926618 -246 GCCGTAAAAAAGATAAAGCGAAATCTGTGC 8 214 0 AGATAAAGCG 0.888115 -87 TCATTCCCTGATATTACGGGCACTATTTAT 9 97 0 ATATTACGGG 0.538996 -101 ACCAGCTGGGATAATAAGCGCCGATCACCG 11 117 0 ATAATAAGCG 0.636911 -184 AAGGCTAACAAAATAAAGGGATTTTTACAC 15 31 1 AAATAAAGGG 0.886215 -165 TGGAGATATCATATAAAGGGGGAGAGGAAA 15 176 1 ATATAAAGGG 0.94906 -20 AGGCGCATGGATATAAGGCGCCTGCTTTTT 18 24 1 ATATAAGGCG 0.869249 -92 TGTAGGGGAAAAATAAAGCGCTTTCAACAA 18 56 0 AAATAAAGCG 0.833455 -60 TTTCTTTTTCATACAACGGGCTGATTTTTG 19 56 0 ATACAACGGG 0.751446 -245 ATATGAATAAATATTAAGGGATTATTCAAT 25 72 1 ATATTAAGGG 0.801113 -197 TACTGCTTACAGAAAAAGGGGATTATATAA 26 40 0 AGAAAAAGGG 0.89331 -123 GGAAATGAAAAGATAAAGGGGTTTTCTGAA 27 12 0 AGATAAAGGG 0.925115 -141 AAATTTTTTCATACAAAGGGGTATCGGG 27 135 1 ATACAAAGGG 0.9124 -18 AAAAGCAAATAAAAAAGGCGATAAAATAGC 34 248 0 AAAAAAGGCG 0.653215 -53 AAATAGAAAAGGCGGGAAAATCAA 36 5 1 AGAAAAGGCG 0.74923 -20 TTGAAACAGAAAACAAGGGGGAATTCAAAT 41 11 0 AAACAAGGGG 0.707436 -230 ACTTGCATTTATATAAAGGGAAAGCAGGAT 41 47 0 ATATAAAGGG 0.94906 -194 ********** Masking position 6 Map Score: 17.3015 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 109 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 GCCCATCCCCAAACAGGCGTAACGCCTGCAAAAC 4 26 0 AAAAGCAACG 0.933109 -99 AGTTGGCACAAAAAATGCTTAAAGCTGGCATCTC 5 167 1 AAAAGCAAAG 0.975758 -45 GGCCTGCCAGAGACAGGCGAAAAGTTTCCACGGC 7 22 0 AGAAGCAAAG 0.933109 -264 CCTATTCAATAAAAAGGCTCAACGAAAAAGTTGA 24 22 0 AAAAGCAACG 0.933109 -59 ATCACTGGAAAGATAAGCCTAAAGATAATTTTTA 25 147 1 AGAAGCAAAG 0.933109 -122 ATAAATATTCAAATACACCAAAAGTAATGAATAC 25 231 1 AAAAACAAAG 0.928482 -38 CTGACTGACTAAAGAAACATAAAGAATAATTCCT 28 47 0 AAAAACAAAG 0.928482 -109 CTTCTTGGCAAAATACGCAAAAAGA 34 286 1 AAAAGCAAAG 0.975758 -15 TTCAGCCTAAAAACATGATAAAAGGAGTATCGCC 37 162 1 AAAAGAAAAG 0.848312 -24 CATTACATCAAATAAAACGAAAAGATCCAGCCTT 38 30 0 AATAACAAAG 0.600594 -125 CATTCGCCCAAAAAAGGAGGAAAGA 40 73 1 AAAAGAAAAG 0.848312 -15 TCTATTTTATAAAAAAACGGAGAGGATATGCAAA 41 180 0 AAAAACAGAG 0.690278 -61 *** * ** **** Masking position 5 Map Score: 10.0444 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 GTAAAACGCACTGGCAGTTCCCTCTCCCCTAT 1 24 1 CTGGCATCCC 0.922416 -115 GGTGCATCTTCAGGGTATTGCCCTATAAATCG 2 162 1 CAGGGTTGCC 0.804093 -139 GAATGTCACGCAGGGGATCGTCCCGTGGATAG 2 264 1 CAGGGGTGTC 0.906363 -37 GCCCGTTTTGCAGGCGTTACGCCTGTTTGGGG 4 22 1 CAGGCGTCGC 0.791905 -103 CAGGCATTCCTCAGGTGATTGT 4 113 0 CAGGCATCTC 0.947106 -12 TTGCTTGTAGCTGGCAATAGTTAATGGGAGGC 5 14 0 CTGGCATGTT 0.576298 -198 TGACGAAAAACAGGCTGTCGTCAGTTTTGACG 9 56 0 CAGGCTTGTC 0.93992 -142 CCCGTAATATCAGGGAATGACCCCACATAAAA 9 107 1 CAGGGATACC 0.613529 -91 CAAAATAAGGCTGGCAATGGCGCAGAAAAACC 11 144 0 CTGGCATGCG 0.68621 -157 AAATATCAATCTGGCATTTGTCGGAATTATTT 11 208 1 CTGGCATGTC 0.960061 -93 GCTGTTCTGGCTGGCATTTTTCTAATCTATTT 11 268 1 CTGGCATTTC 0.677436 -33 TTCTGGTTAACTGGCGCTGACCTTCGTCTTTC 14 114 0 CTGGCGTACC 0.803679 -187 CGACACATGATAGGCGTTTGTCACAATCGGCA 19 240 1 TAGGCGTGTC 0.679025 -61 CCGGGATGAGCAGGCGATGCTCATCCCAATTT 30 19 1 CAGGCGTCTC 0.948046 -42 ATGTCGTTTTCAGGCTATAGTCCCA 39 4 0 CAGGCTTGTC 0.93992 -36 GGCACAGTGGCACGCATTCGCCCAAAAAAGGA 40 59 1 CACGCATGCC 0.769473 -29 ****** * *** Masking position 8 Map Score: 7.82305 Number of sites scoring better than the average of aligned sites = 1758 Number in coding regions = 1671 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 8 AATTTACTTAATCAGCTGGAGATAGCAGATGG 2 4 0 ATTGAAACAA 0.961311 -297 CGATTGTGTGATGATGTGGATACAAAAAATTTACTTAAT 2 31 0 ATTGAAAAAA 0.889064 -270 AATAATGTCGATGATGTCGAAATGACACGTCGACACGGC 5 78 1 ATTGAAGCAG 0.767263 -134 TTTCTGGTTGATTTTATTGAAATAAAAAATTAGCTTACA 12 73 0 ATTGAAAAAA 0.889064 -42 ATAGATATTTTTCATATGGATATATCAGGAGTATGATTG 13 13 0 TTTGAAACAG 0.809192 -77 TTTTCTTACAATAAATTAGAGAAAAGACAGGCTGAGTAA 15 122 0 ATTGAAAGAA 0.86918 -74 ATAATGGTATATTTAGTGGAGATATCATATAAAGGGGGA 15 160 1 ATTGAAACAA 0.961311 -36 AGACAAATGAATCAGTTTGAGACAAAACGAGACACACGT 17 93 1 ATTGAAAAAG 0.879363 -139 ATTCACGGACATGGGGTGGACAAACCATGAGATTTTGTT 19 131 0 ATTGAAACAG 0.957626 -170 GAAAAAAGCAATTGTTTCGACACATGATAGGCGTTTGTC 19 223 1 ATTGAAAGAA 0.86918 -78 CCGCTTGAATATCATATAGAGAGAACAGAGAGGTGAAG 19 273 1 ATTGAAACAA 0.961311 -28 AGAAAGGAACATCCATTTGAACGAACAAGAAACGATTCA 20 128 1 ATTGACACAG 0.767263 -93 GAATCCTTACATCGTATTGACACATAATATAACATCACC 22 45 1 ATTGAAAAAA 0.889064 -66 TTGCTGAAATTTTCGCTCGAAATATCAGAATGTTTTTGC 41 129 0 TTTGAAACAA 0.823403 -112 ** * ** * * ** * Masking position 10 Map Score: 9.78828 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 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 9 CAACAGCAACATGCCAGGATGAGTTAGCGA 3 119 1 ATGCCAGGAT 0.572435 -33 GCAAGCACATCACGCCGGATGCGACGCAAA 7 67 1 CACGCCGGAT 0.82454 -219 CATCACCGTGTAGGCCGGATAAGACGCATT 7 95 0 TAGGCCGGAT 0.861063 -191 CTCAAAAAAACAGCCTGGATAATTCCCGTC 11 50 1 CAGCCTGGAT 0.899808 -251 TGACTAAAATAAACCTGGATTTTCGGTAAA 15 67 1 AAACCTGGAT 0.829355 -129 CGTACAAAAAAGACCCGGATTTACCGAAAA 15 86 0 AGACCCGGAT 0.721196 -110 ATCATTGTCAAAGGCCGGGTGATATCCGGT 17 39 1 AAGGCCGGGT 0.927456 -193 ATGCAAAAAAAAGACCGGATATCACCCGGC 17 52 0 AAGACCGGAT 0.831038 -180 CTTCTTGGACATAGCCGGATATGTCATACT 21 113 0 ATAGCCGGAT 0.78141 -75 AGACGAACAACCCGGATGCTCAAAGCA 25 8 1 CAACCCGGAT 0.917112 -261 ATGCTCAAAGCAGCCCGGGTTTTTTTGTGC 25 26 1 CAGCCCGGGT 0.889894 -243 CAGCCTTTAGAAGGCTGGATTTTTTA 38 7 0 AAGGCTGGAT 0.934238 -148 CAGCCTTCTAAAGGCTGGATCTTTTCGTTT 38 20 1 AAGGCTGGAT 0.934238 -135 ATATAAAGGGAAAGCAGGATAACATGTTGA 41 37 0 AAAGCAGGAT 0.751593 -204 ********** Masking position 10 Map Score: 8.01514 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 475 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 10 GCCAGTTTTGCAACTCCTTGATTTTTCGAGATG 2 212 0 CAATCTTATT 0.742894 -89 AGCATTTCCTTTTTTCTATCCACGG 2 286 0 CATTCTTTTT 0.946677 -15 AATGACATTTCATCGGCATGTTTTCGTCAAAAA 4 78 1 CATGCATTTT 0.838516 -47 ATTTCGACATCATCGACATTATTCACCGCAGGG 5 68 0 CATGCATATT 0.790439 -144 CCCATCTCTGCATGGGCTTTTTTCTCCGTCAAT 7 185 1 CATGCTTTTT 0.935918 -101 TGTGTCGAAACAATTGCTTTTTTCGGGAACAAT 19 214 0 CAATCTTTTT 0.799106 -87 TCATACTGTTCATTTTCTTCATTAAAATAGAAG 21 87 0 CATTCTTATT 0.928037 -101 TTCCTTCCTACATATACTTCTTTAATTCACCGA 21 155 0 CATTCTTTTT 0.946676 -33 TTTATCTTTTCATTTCCTTTATTGTCCAGCGGA 27 25 1 CATTCTTATT 0.928038 -128 AGTCAGAAGTCATGGACATTTTTTCACTTTTAA 28 75 1 CATGCATTTT 0.838516 -81 AAAGTTTGATCATTTACTTTTTGGTCAAATTTT 28 116 1 CATTCTTTTG 0.860183 -40 CCTGCATCTCCTTCATGTCGTTTTCAG 39 23 0 CATTCTTATG 0.817165 -17 *** * *** *** Masking position 2 Map Score: 7.04686 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 68 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 11 TTTCGACACTCATCGACACGCCCATCCCCAA 4 48 0 CTCGACACGC 0.9435 -77 TAACTATTGCCAGCTACAAGCAATAATTGTG 5 23 1 CGCTACAAGC 0.808872 -189 CGAAATGACACGTCGACACGGCGACGAAATT 5 95 1 CTCGACACGG 0.930628 -117 CCCACGGTAGCGGCGGCCAGGCG 6 26 1 CGCGGCCAGG 0.956376 -13 GGCCTGGGATCGGTGGCAAGCACATCACGCC 7 52 1 CGTGGCAAGC 0.916216 -234 ATCTTTTTTACGGCGACACGGCCAAAATAAT 8 230 1 CGCGACACGG 0.984927 -71 GTTAAGCGAGCGGCGACCAGGTCGCGTGCCG 10 72 1 CGCGACCAGG 0.944537 -69 GTTGCACGGTCTGCGGCACGCGACCTGGTCG 10 85 0 CGCGGCACGC 0.990911 -56 GTCATTGGCACAGTGGCACGCATTCGCCCAA 40 53 1 CGTGGCACGC 0.955238 -35 * ********* Masking position 7 Map Score: 6.85769 Number of sites scoring better than the average of aligned sites = 829 Number in coding regions = 798 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 ATTAACAGTTCAGCAGGACAATCCTGAACGC 3 32 0 CAGCGGACAA 0.734651 -120 TTAATACAATTTGCGTGCCAATTTTTTATCT 3 58 1 TTGCTGCCAA 0.583668 -94 AATTCATCTTTAGCTTAAAAATCTCTTTAAT 5 122 1 TAGCTAAAAA 0.666464 -90 GGGCTACAGATAGCTGACAAACTTCACGTTG 7 157 0 TAGCGACAAA 0.722053 -129 TCATGCGCACCATCGTGCAAAAGGGCTGCAC 8 153 0 CATCTGCAAA 0.433993 -148 AGAACGCCAGCAGCCTGACCACCGGTAATGG 10 31 0 CAGCTGACCA 0.646589 -110 CACCAGCAGGCAGCCTACCCAGAGTTGCACG 10 108 0 CAGCTACCCA 0.734318 -33 GCGAGTTATTCAGCGGGCAAATATCAATCTG 11 190 1 CAGCGGCAAA 0.911342 -111 AATAAAAAATTAGCTTACAAATCTAAAGGAT 12 61 0 TAGCTACAAA 0.814473 -54 TGAGTAAAAGCTGCGTACAAAAAAGACCCGG 15 98 0 CTGCTACAAA 0.815913 -98 TCTCGTTTTACAGCATGCAAAAAAAAGACCG 17 65 0 CAGCTGCAAA 0.945567 -167 TTCCCTTCACTTGCCGGCACATGTGCTTCAA 21 17 0 TTGCGGCACA 0.354093 -171 AAAAATAGTATTGCATAAAAATGAGAAACTG 25 180 1 TTGCTAAAAA 0.425769 -89 TCTTCGTTTACTGCTTACAGAAAAAGGGGAT 26 47 0 CTGCTACAGA 0.634124 -116 CTTTATTGTCCAGCGGAAAAAATATTTTGTC 27 41 1 CAGCGAAAAA 0.76287 -112 CGAAGCGTGGCAGCTTGCAGAAAAGTGCGAT 34 117 1 CAGCTGCAGA 0.871677 -184 TCGCATTATTCAGCCTAAAAACATGATAAAA 37 154 1 CAGCTAAAAA 0.844639 -32 TTGGTTTTATCAGCATAACGAAAGTCAAATC 38 82 0 CAGCTAACGA 0.557132 -73 TGGGACTATAGCCTGAAAACGACATGAAG 39 9 1 TAGCTGAAAA 0.743985 -31 **** ****** Masking position 11 Map Score: 7.86915 Number of sites scoring better than the average of aligned sites = 1552 Number in coding regions = 1391 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 13 TCTCCCCATAGGGGAGAGGGAACTGCCAGT 1 33 0 GGGGAGAGGG 0.985788 -106 TCTCCCCTATGGGGAGAGGATTAGGGTGAG 1 46 1 GGGGAGAGGA 0.990392 -93 TCATATAAAGGGGGAGAGGAAA 15 184 1 GGGGAGAGGA 0.990392 -12 TGTCTCCAAAGTGAAGATGAGAAGACTGAT 17 139 1 GTGAAGATGA 0.721606 -93 AATGAATACGGGGGAAATGGATC 25 256 1 GGGGAAATGG 0.752486 -13 TCGGATGAGGGGGGAGAAGA 31 20 1 GGGGAGAAGA 0.951814 -10 TATATATTTTGTGAAGAGGAGTGACAAAA 33 134 1 GTGAAGAGGA 0.884673 -19 ********** Masking position 5 Map Score: 4.17376 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 68 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 AGCGCACCAGATTGGTGCCCCAGAATGGTGC 2 136 1 ATTGGTGCCC 0.913496 -165 GGTGCCCCAGAATGGTGCATCTTCAGGGTAT 2 149 1 AATGGTGCAC 0.984621 -152 TTGCCCTATAAATCGTGCATCACGTTTTTGC 2 179 1 AATCGTGCAC 0.92487 -122 AATGCACTAAAATGGTGCAACCTGTTCAGGA 7 256 1 AATGGTGCAC 0.984622 -30 GAAGCACTATATTGGTGCAACATTCACATCG 8 120 1 ATTGGTGCAC 0.971686 -181 ACATTCACATCGTGGTGCAGCCCTTTTGCAC 8 139 1 CGTGGTGCAC 0.898744 -162 TTGCATTTATAATGGTGAACCCTAAATAGAA 17 198 1 AATGGTGAAC 0.892541 -34 ********* * Masking position 6 Map Score: 3.27129 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 82 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 GTTACATAAAGATTGTTTTTTCATCAGGTT 2 69 1 GATTGTTTTT 0.813878 -232 ACTGACGACAGCCTGTTTTTCGTCAGAGTT 9 63 1 GCCTGTTTTT 0.833235 -135 GAATTATCCAGGCTGTTTTTTTGAGTTGCA 11 45 0 GGCTGTTTTT 0.867773 -256 GCCATTGCCAGCCTTATTTTGACGCTCATC 11 155 1 GCCTTATTTT 0.715497 -146 ACAAATGCCAGATTGATATTTGCCCGCTGA 11 199 0 GATTGATATT 0.437331 -102 CCACTTTTCTGGTTGATTTTATTGAAATAA 12 87 0 GGTTGATTTT 0.888145 -28 CGAAAATCCAGGTTTATTTTAGTCAAGAAT 15 62 0 GGTTTATTTT 0.673029 -134 AAGATGAGAAGACTGATTTTACGGGCTCAA 17 152 1 GACTGATTTT 0.931625 -80 TGTTGAAAGCGCTTTATTTTTCCCCTACAA 18 57 1 GCTTTATTTT 0.610458 -59 TCATACAACGGGCTGATTTTTGTACGAAAC 19 48 0 GGCTGATTTT 0.927232 -253 TTTTTGAGAGGTCTGTTTTTTGCTCGTATT 20 20 1 GTCTGTTTTT 0.557047 -201 GCTTGATCAGGATTGATTTTAAATATACAA 34 21 1 GATTGATTTT 0.89463 -280 TTTTTTGTTAGACTTATTTTGAGGTCAAAA 34 59 1 GACTTATTTT 0.779354 -242 AATGAGTTAAGATTAATTTTTTCTATTCAA 37 52 0 GATTAATTTT 0.400832 -134 CGAAATATCAGAATGTTTTTGCACCTTGTC 41 121 0 GAATGTTTTT 0.439348 -120 ********** Masking position 4 Map Score: 5.80347 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 405 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285