AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_mthe_reg_300.orf -o00400_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -x5 -e 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 = 1 Purged sequences: MTH44 27 ribosomal protein Sa (E.coli S2) MTH47 21 conserved protein Input sequences: #1 MTH1 170 conserved protein #2 MTH5 22 ribosomal protein L8 (E.coli L2) #3 MTH9 46 ribosomal protein L35 (E.coli L29) #4 MTH21 109 ribosomal protein L19 #5 MTH31 30 ribosomal protein L14 #6 MTH34 236 ribosomal protein S18 (E.coli S13) #7 MTH40 58 DNA-dependent RNA polymerase, subunit N #8 MTH42 171 DNA-dependent RNA polymerase, subunit K #9 MTH43 51 enolase #10 MTH48 73 conserved protein #11 MTH52 189 aspartate aminotransferase related protein #12 MTH242 231 shikimate 5-dehydrogenase #13 MTH565 52 unknown #14 MTH742 34 phenylalanyl-tRNA synthetase #15 MTH744 124 porphobilinogen synthase #16 MTH746_MTH747 96 MTH746: endonuclease III related protein (probably non-iron-sulfur homolog), MTH747: conserved protein #17 MTH766 29 5-enolpyruvylshikimate 3-phosphate synthase #18 MTH767 83 valyl-tRNA synthetase #19 MTH770 32 phenylalanyl-tRNA synthetase #20 MTH1220 101 chorismate mutase #21 MTH1221 26 conserved protein #22 MTH1224 120 inosine-5'-monophosphate dehydrogenase related protein III #23 MTH1228 117 conserved protein #24 MTH1229 92 conserved protein #25 MTH1230 40 unknown #26 MTH1476 127 tryptophan synthase, beta subunit homolog #27 MTH1501 189 phenylalanyl-tRNA synthetase alpha subunit #28 MTH1587 31 histidinol-phosphate aminotransferase #29 MTH1591 30 phosphonopyruvate decarboxylase #30 MTH1592 21 conserved protein #31 MTH1593 205 ribosomal protein S3a #32 MTH1594 72 conserved protein #33 MTH1598 300 conserved protein #34 MTH1601 246 aspartate aminotransferase #35 MTH1655 78 anthranilate synthase component I #36 MTH1660 37 tryptophan synthase, subunit alpha #37 MTH1692 113 conserved protein #38 MTH1694 207 aspartate aminotransferase related protein #39 MTH1768 26 conserved protein #40 MTH1769 37 translation initiation factor eIF-2, beta subunit #41 MTH1770 30 DNA replication initiator (Cdc21/Cdc54) #42 MTH1827 165 quinolinate synthetase #43 MTH1828 30 unknown #44 MTH1831 92 conserved protein #45 MTH1894 34 aspartate aminotransferase homolog #46 MTH1895 170 conserved protein Motif number 1 CCGAATATCCTCCTGGTTATTT 2 6 0 TCCTCCTGGT 0.931881 -17 TCAAGAAACCTCCTTGTATTCAGCATT 4 93 0 ACCTCCTTGT 0.752399 -17 GTTATATGATACATCCTGTGCCGGGATAGC 6 53 1 ACATCCTGTG 0.644028 -184 GGAGCTTTGCTCCTCCTGGGTTCAAATCCC 6 117 1 TCCTCCTGGG 0.968866 -120 TCATTAACCTCCAGTAAGAGTGAATT 6 221 0 ACCTCCAGTA 0.927081 -16 AATTTTTATTAACTCCAGTGGACTACATGA 11 125 1 AACTCCAGTG 0.883126 -65 GATTTATCCTCCAGAAGTTAATTCAA 11 174 0 TCCTCCAGAA 0.796619 -16 AATAATTCTCCTCCAGTTTACTCAAATA 14 17 0 TCCTCCAGTT 0.953772 -18 TCTTATTACATCCTCAAGGGTAAAAAACAT 15 77 0 TCCTCAAGGG 0.658451 -48 ACCTGCAGATACCTCCAGATGGA 17 4 0 ACCTCCAGAT 0.921688 -26 ACCTCCTTTTTTTTAAGACG 21 1 1 ACCTCCTTTT 0.756223 -26 TCCGGAGTGAAACTCCTGGGTGC 24 4 0 AACTCCTGGG 0.8333 -89 CCTCCTCCATAGATGACAGTAT 24 81 0 TCCTCCATAG 0.762484 -12 ACAGAACCCCCAGTGATCATTATCG 27 175 0 ACCCCCAGTG 0.865602 -15 AGCACTGGCCTCCTCCAGGGGGAGGAGGTT 32 20 1 TCCTCCAGGG 0.978575 -53 GAGGAGGTTGACCTCCATTTCGGGAGGGCC 32 41 1 ACCTCCATTT 0.821269 -32 GTTCTCATGGCCCTCCTGTGGGGCGTTATC 33 13 0 CCCTCCTGTG 0.881279 -288 AAAACCTCCAGATTAAAGTGGAT 34 234 0 ACCTCCAGAT 0.921688 -13 TTCGCATGGATACTCCTGTGCTGATGTGAT 38 185 1 TACTCCTGTG 0.789455 -23 AACTGATACCTCCAGTAAAAGTGTGTA 40 21 0 ACCTCCAGTA 0.927081 -17 ********** Masking position 5 Map Score: 23.5129 Number of sites scoring better than the average of aligned sites = 1403 Number in coding regions = 1312 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 TGAATTCGCGGGACGGGGGTTTGCGAATTCTTC 6 194 0 GGCGGGGTTG 0.862235 -43 CTTCTTCAATGGCTGGGAGGATGGACCAAGCTA 8 23 0 GGTGGAGGTG 0.968727 -149 TCAAAGGAATTTATAGGGTGATGGAAAATTTTT 10 37 1 TTTGGGTGTG 0.807919 -37 AATCTCTTCGGGTTTAGATGCTGCACCGGTCAG 12 114 0 GGTAGATGTG 0.830856 -118 CGAGAGGCTGTGCCCAGGGGATGGCCCATGATT 12 203 0 TGCAGGGGTG 0.902082 -29 TATGGGCGAGAGGCTGTGCCCAGGGG 12 216 0 GGCAGAGGTG 0.931403 -16 TATTAGAGATTTCTTGGGGGGTGTAAT 19 5 0 TTTGGGGGTG 0.893789 -28 CGAGTATTGAGTCGAAGGGGATGAGTTCCTCAC 20 77 0 GTGAGGGGTG 0.934519 -25 TAAAAACTGGGTTCTGGATGATGGGTCCTTCTC 22 29 0 GTCGGATGTG 0.895449 -92 GGTGTCGGGGGGATGCTGCTGGTGT 23 3 1 TGCGGGGGTG 0.966709 -115 GGCAGTCAATAGTTAAGGTGATGAACCATAACC 27 28 1 AGTAGGTGTG 0.641102 -162 AATAAAGTCAAGCTCAGGTGATGAACCATCACC 27 64 1 AGTAGGTGTG 0.641102 -126 CGTCCGTAGAGGACCGGGTGATGGTTCATCACC 27 80 0 GGCGGGTGTG 0.985289 -110 TGACATGGTGGTTTGGGGTGCTGTGTGGTCATG 31 35 0 GTTGGGTGTG 0.951003 -171 CCTCCTCCAGGGGGAGGAGGTTGACCTCCATTT 32 28 1 GGGGGAGGTG 0.972887 -45 GCACCTTGCCGTTGTGGTGGATGTGAGGTCATG 33 59 0 GTGGGTGGTG 0.899556 -242 CGGTTTTCGTGGTGTGGTGGTTGACATAAAGGT 37 33 1 GGGGGTGGTG 0.957206 -81 TTTCGTGGTTGTAGTGGTTGATGTAAAGGTGTT 37 88 1 GTGGGTTGTG 0.817396 -26 ** * ***** ** Masking position 12 Map Score: 21.0166 Number of sites scoring better than the average of aligned sites = 836 Number in coding regions = 795 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 GGCCCATGATTCCGGTTACATGTGTTTTTCCAGT 12 180 0 TCGGACATGG 0.835621 -52 CCATAGCCTATCTGGGCCCTGAGGGGACATTCAC 20 20 1 TCGGCCTGAG 0.993016 -82 GCTGCTGGTGTCTGGATACTGGTGTGTCTGAGGA 23 25 1 TCGGACTGGG 0.990376 -93 CCTTAAAAGATCCGGGTCCTGGCCATATCCTCAG 23 52 0 TCGGCCTGGC 0.991659 -66 ATCGAATAAATCAGGCGACTGATCCTGATTGAAG 27 145 0 TCGGACTGAC 0.984645 -45 CTCGGTTAACTCAGGTCACTGGAGAG 28 3 0 TCGGACTGGG 0.990376 -29 TGGAGACGTCTCGGGCACCTTGCCGTTGTGGTGG 33 72 0 TCGGCCTTGC 0.94292 -229 GGGACCTGAATCAGGCTCCTGAGCTCCAGCTCCC 34 61 0 TCGGCCTGAC 0.990351 -186 GGAGCCTGATTCAGGTCCCTGAAGCCGCGATCCA 34 76 1 TCGGCCTGAG 0.993016 -171 ATATGTACTTTGTGGATACAGAGGTGATATGCAT 35 47 1 TGGGACAGAG 0.770583 -32 TTCCGGTCACAGAACCAAGAAAAAC 42 2 1 TCGGACAGAC 0.957981 -164 ATCAACCTTCTCGGGTTCTTGATGATGACATTGT 46 147 0 TCGGCTTGAG 0.910733 -24 ** ** ***** * Masking position 1 Map Score: 19.7161 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 217 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 ATGCCTCCAAGAAAAACATTAAAATAG 8 155 0 CCAGAAAAAC 0.957563 -17 AATTATAAACCCCAGAAAACAGAAAAA 11 7 0 CCCGAAAACA 0.934819 -183 AACAGGGTATCCCTGAGAAAGAATTTTTTGT 11 46 1 CCCGAGAAAG 0.847063 -144 ATTGTAAGTACCATGAGAAAAAAAATCAGAT 12 77 1 CCAGAGAAAA 0.925446 -155 ATGGGCCATCCCCTGGGCACAGCCTCTCGCC 12 207 1 CCCGGGCACA 0.63682 -25 CACAGGAGGGCCATGAGAACCATTGAGATGA 33 23 1 CCAGAGAACC 0.983072 -278 CCAGCTCCCACCAGGAGAAAACCCAAAGAAT 34 39 0 CCAGAGAAAA 0.925446 -208 AAACCAGCAACCATGAACACATCAGCAA 36 8 0 CCAGAACACA 0.862605 -30 ACTCCCAGCAAACCAGCAACCATG 36 24 0 CCCGCAAACC 0.916535 -14 AACCACCACACCACGAAAACCGGCACACCTA 37 24 0 CCAGAAAACC 0.979502 -90 ACCACTACAACCACGAAAACCGGCAGGGTGA 37 75 0 CCAGAAAACC 0.979502 -39 ACAGGAGTATCCATGCGAAAGAGAAGAAGGC 38 173 0 CCAGCGAAAG 0.743253 -35 GGTCACAGAACCAAGAAAAACCTTTATAAAA 42 15 1 CCAGAAAAAC 0.957563 -151 CCAAAGGTCTCCATGGAAACCTTTATAAAAG 42 77 1 CCAGGAAACC 0.943055 -89 *** ******* Masking position 9 Map Score: 15.7592 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 243 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AATATTGTAAGTACCATGAGAAAAAAAATC 12 74 1 GTACCATGAG 0.812372 -158 CCCAGGGGATGGCCCATGATTCCGGTTACA 12 194 0 GGCCCATGAT 0.935938 -38 GTTCATGAAGGGCCCCGGAATTTATTTTCT 15 32 1 GGCCCCGGAA 0.917854 -93 TAGCCTATCTGGGCCCTGAGGGGACATTCA 20 23 1 GGGCCCTGAG 0.990353 -79 AATGGTGGCCCATGATAAGAGAAGGA 22 7 1 GGCCCATGAT 0.935938 -114 GATATGGCCAGGACCCGGATCTTTTAAGGT 23 57 1 GGACCCGGAT 0.74356 -61 CTCTCCAGTGACCTGAGTTAACCGAGA 28 8 1 GTGACCTGAG 0.679199 -24 CCCCACAGGAGGGCCATGAGAACCATTGAG 33 20 1 GGGCCATGAG 0.982212 -281 ACCTGAATCAGGCTCCTGAGCTCCAGCTCC 34 62 0 GGCTCCTGAG 0.856041 -185 GCCTGATTCAGGTCCCTGAAGCCGCGATCC 34 79 1 GGTCCCTGAA 0.922784 -168 GCCAGTCATGGGGCCCTGAAGAGGTGATTA 34 115 0 GGGCCCTGAA 0.977683 -132 AGCAGTTTAAGTGCCATGAACCTAAATATA 46 96 1 GTGCCATGAA 0.871354 -75 TATTCCCGGAGTTCCATGAGATTATATTTA 46 118 0 GTTCCATGAG 0.812372 -53 ********** Masking position 9 Map Score: 14.5215 Number of sites scoring better than the average of aligned sites = 937 Number in coding regions = 897 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 GGAGGACTGGAAGGGGCATATTTTCC 4 5 1 GCGGAAGGGG 0.880457 -105 AAAGTTTTTTCGCTGGACTGGAAAATATGCCC 4 24 0 CCGGACTGGA 0.947994 -86 TATGATACATCCTGTGCCGGGATAGCCTAGCC 6 57 1 CTTGCCGGGA 0.689139 -180 CCAGGTAAGGCGCAAGACTGGAAATCTTGTGG 6 87 1 CCAGACTGGA 0.818687 -150 TTTAACCGACGCCGGGACTGGGATTTGAACCC 6 134 0 GCGGACTGGG 0.905641 -103 AGAGTGAATTCGCGGGACGGGGGTTTGCGAAT 6 199 0 CCGGACGGGG 0.985117 -38 GAAACTTCTTCAATGGCTGGGAGGATGGACCA 8 28 0 CAGGCTGGGA 0.622409 -144 CCGGCTTCTTCACAGGCTGGGGATTCAGCACA 11 91 1 CCGGCTGGGG 0.891951 -99 TTCTTTGCCTGTAATGCCGGGGTGATAAACTG 12 145 1 GATGCCGGGG 0.679274 -87 GCCTATCTGGGCCCTGAGGGGACATTCACAGA 20 25 1 GCTGAGGGGA 0.675617 -77 CACTCCGGATCTCCAGCCGGGGCCTCCGTGCA 24 25 1 CCAGCCGGGG 0.827991 -68 ATCACCTCATGGCTGGAACTGGTCCCT 26 111 0 CCTGGCTGGA 0.843534 -17 ACCTGCTGCACACCGGGAGGGAGACC 33 285 1 CCGGGAGGGA 0.894821 -16 TTTGGGTTTTCTCCTGGTGGGAGCTGGAGCTC 34 43 1 CCTGGTGGGA 0.800807 -204 TCTTCAGGGCCCCATGACTGGCTGATTTTCAG 34 123 1 CCTGACTGGC 0.603197 -124 ATTTACTGATGGCTGGCCGGGACTCATGTAAA 34 160 1 GCGGCCGGGA 0.978635 -87 TAAATCTTATGTCCAGAAGGGAGATCTGCAAA 44 46 1 GCAGAAGGGA 0.650672 -47 * * ******** Masking position 6 Map Score: 11.9387 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 507 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 GTCCGGATTTATTTATAAATATTTCCACAATGC 1 136 0 ATTTATAAAT 0.852611 -35 AAATAGATGTCATAATATACAGTTATATGATAC 6 32 1 CATAATATAT 0.689265 -205 CAATCGATAACTTTATATATTTTTATTTTATAA 7 13 1 CTTTATATAT 0.874811 -46 TAAAACACCTCATAATAAACTCTAGACTGAAAA 9 29 0 CATAATAAAT 0.795464 -23 GTAACTTTTAATTAATATATCATCGGGGTATTG 16 22 1 ATTAATATAT 0.714744 -75 ATTCAAACATCTTTATAAAGATTGGGTA 18 66 1 CTTTATAAAT 0.924539 -18 AAATAATTTTATTAATAAAAACTGGGTTCTGGA 22 44 0 ATTAATAAAT 0.814576 -77 CTTTATCCACATTTATATATCATTCTTTGGGTT 34 18 1 ATTTATATAT 0.767431 -229 AAACAAACCTCTTAATAAACTTTGTTTACCAGA 38 76 0 CTTAATAAAT 0.902943 -132 ATAATGTTATCATAATATACTTTCC 41 16 1 CATAATATAT 0.689265 -15 CAAGAAAAACCTTTATAAAACATGGGAATGCCG 42 26 1 CTTTATAAAT 0.924539 -140 CCATGGAAACCTTTATAAAAGATTAAATCCTAT 42 87 1 CTTTATAAAT 0.924539 -79 TAAATGGAAGAATTATAAATCTTATGTCCAGAA 44 31 1 AATTATAAAT 0.707481 -62 GATCAGCTGAATTTATAAATCATGCTAGACAGC 46 20 1 ATTTATAAAT 0.852626 -151 ********* * Masking position 7 Map Score: 10.0223 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 11 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 TTAACCGACGCCGGGACTGGGATTTGAACC 6 135 0 CCGGGACTGG 0.613893 -102 AGATTTGAACTCGGGTCTCCAGCGTTCCGG 8 93 0 TCGGGTCTCC 0.95682 -79 AAAATAAATTCCGGGGCCCTTCATGAACAC 15 30 0 CCGGGGCCCT 0.971904 -95 CTTAAAAGATCCGGGTCCTGGCCATATCCT 23 55 0 CCGGGTCCTG 0.940933 -63 GATAGGCTACCCGGGTCCCCATTCAACAGT 23 94 1 CCGGGTCCCC 0.995315 -24 GAGTTTCACTCCGGATCTCCAGCCGGGGCC 24 19 1 CCGGATCTCC 0.83132 -74 GGATCTCCAGCCGGGGCCTCCGTGCATGAA 24 31 1 CCGGGGCCTC 0.977535 -62 TGAACCATCACCCGGTCCTCTACGGACGTT 27 85 1 CCCGGTCCTC 0.872319 -105 TCAAATGGATCGGGACCCCTC 30 10 1 TCGGGACCCC 0.973 -12 GGAGCCTGATTCAGGTCCCTGAAGCCGCGA 34 76 1 TCAGGTCCCT 0.675762 -171 AATCACCTCTTCAGGGCCCCATGACTGGCT 34 116 1 TCAGGGCCCC 0.897227 -131 TGATGGCTGGCCGGGACTCATGTAAATCTT 34 166 1 CCGGGACTCA 0.800967 -81 ********** Masking position 7 Map Score: 9.86624 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 449 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TAAATCACCTCAGTAACTTTT 5 20 0 TAAATCACCC 0.911033 -11 TAAAACACCTCATAATAAACT 9 41 0 TAAAACACCC 0.896021 -11 CAGTTATCAGTTTATCACCCCGGCATTACAG 12 153 0 TTTATCACCC 0.839845 -79 ATTACACCCCCCAAGAAATCTC 19 2 1 TTACACCCCC 0.803978 -31 TTACACACCTCTCTGGGAGAT 22 110 0 TTACACACCC 0.930214 -11 GAGGTCATGTTTAATCATCTCAATGGTTCTC 33 37 0 TTAATCATCC 0.782879 -264 CTTTTCTTAAATAATCTCCACATGAACATGG 33 153 0 ATAATCTCCC 0.781747 -148 GATCCATCAGTTAATCACCTCTTCAGGGCCC 34 104 1 TTAATCACCC 0.976343 -143 TGAACCTCAATTAAACTCCACTTTAGGGTTT 38 122 0 TTAAACTCCC 0.959551 -86 TGAAGGTTCATTAATCTCCGCTGTCTAGCAT 46 41 0 TTAATCTCCC 0.965742 -130 TTCATGGCACTTAAACTGCTCCATGGGGCAA 46 85 0 TTAAACTGCC 0.754407 -86 ********* * Masking position 6 Map Score: 6.45963 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 39 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 AAGCCGGATCACTGCTGGAAAACAAAAAAT 11 68 0 ACTGCTGGAA 0.927628 -122 AGGTAACTGTTGGATTCATTGTGAT 15 110 0 ACTGTTGGAT 0.96268 -15 TTCAACTGTTGAATGGGGACCCGG 23 104 0 ACTGTTGAAT 0.835511 -14 ACTGGTCCCTACTGATGAAATCATCATTTC 26 91 0 ACTGATGAAA 0.616142 -37 CACCGTAAAAACAGCTGGATTTAACATAAA 31 166 0 ACAGCTGGAT 0.927628 -40 GTCTCCATATACTGTTTGATTTCCTCAGAC 33 99 1 ACTGTTTGAT 0.71662 -202 GAGGTGATTAACTGATGGATCGCGGCTTCA 34 95 0 ACTGATGGAT 0.96268 -152 GGTCGGATTTACTGATGGCTGGCCGGGACT 34 154 1 ACTGATGGCT 0.926518 -93 ACATTATCCTACAGCTGGCTAAAAACAGTC 38 21 0 ACAGCTGGCT 0.862359 -187 ********** Masking position 6 Map Score: 4.68441 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 62 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 11 CAATAGGTACTAAAAATTGTATGGTATCCA 1 35 0 TAAAAATTGT 0.738606 -136 CGCAAGACTGGAAATCTTGTGGAGCTTTGC 6 97 1 GAAATCTTGT 0.784332 -140 TTAACGCCCTTAAAAATTTTCCATCACCCT 10 51 0 TAAAAATTTT 0.545819 -23 CCATCAGCGATAAATATTGTTGCCATAGGT 12 38 0 TAAATATTGT 0.875928 -194 TGATGGTAAATAAATATTGTAAGTACCATG 12 62 1 TAAATATTGT 0.875928 -170 GATGTGACTATAAATCTTTTCAT 25 28 1 TAAATCTTTT 0.891041 -13 AAGAACTATTTAAAACTTTACTGTACATAT 26 41 0 TAAAACTTTA 0.447985 -87 AGGGAGTATTTAAATCTTGACATGGTGGTT 31 55 0 TAAATCTTGA 0.826703 -151 GGGACTCATGTAAATCTTTTTAAATGGACA 34 178 1 TAAATCTTTT 0.891041 -69 AGGTACTATTTAAATCTTGTCTGTATAATA 35 11 0 TAAATCTTGT 0.950746 -68 GGAAGAATTATAAATCTTATGTCCAGAAGG 44 36 1 TAAATCTTAT 0.714671 -57 ********** Masking position 4 Map Score: 5.1657 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 22 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 12 ATCAACCGTGGTGTTCATGAAGGGCCCCGG 15 20 1 GTGTTCATGA 0.96887 -105 TTTATGTTCTGTGATCATGAGGATGGCGG 16 78 1 GTGATCATGA 0.983071 -19 AGAACCCCCAGTGATCATTATCGAATAAAT 27 168 0 GTGATCATTA 0.940623 -22 GGGGTGCTGTGTGGTCATGAATATGAACAG 31 24 0 GTGGTCATGA 0.963181 -182 TTGCTGATGTGTTCATGGTTGCTGGTTT 36 9 1 GTGTTCATGG 0.954428 -29 AACCGGCAGGGTGATCATTGCAAACCTTTA 37 59 0 GTGATCATTG 0.914236 -55 CCTACTGAGAGTTATCATGAGTAAAAATTA 42 139 0 GTTATCATGA 0.882799 -27 ********** Masking position 7 Map Score: 5.35289 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 50 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 TGCGCCTTACCTGGCTAGGCTATCCCGGCACAGGA 6 66 0 CGGAGTATCC 0.94737 -171 GTCCCGGCGTCGGTTAAAGCAACCCTGTTGCACCT 6 148 1 CGTAGAACCC 0.975449 -89 CCCGGCATTACAGGCAAAGAATCTCTTCGGGTTTA 12 131 0 CGGAGATCTC 0.774117 -101 TAAGGTGTTTCAGGATAGGCTACCCGGGTCCCCAT 23 81 1 CGGAGTACCC 0.984567 -37 TCCATACTGGCGGTGTATGTAACTCTAAATCATGG 31 103 1 CGTAGAACTC 0.87297 -103 AAAGCACATACCGGATAGAGAACCCCCCTCAATAA 33 213 1 CGGAAAACCC 0.975462 -88 AAAATAGATACAGGTTATGAAATCCACTTTAATCT 34 213 1 CGGAGAATCC 0.975462 -34 GTAATAAAATCAGGCCACATTATCCTACAGCTGGC 38 32 0 CGGAATATCC 0.835498 -176 TTGTTTAATATGGTATAAGAAACCCTAAAGTGGAG 38 103 1 TGTAGAACCC 0.776423 -105 TTCCGGTCACAGAACCAAGAAAAACCT 42 3 1 CGGAAAACCA 0.776443 -163 * ** * * ***** Masking position 7 Map Score: 3.94779 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 171 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 ATTTCCACAATGCAGACTGGGCAAGTAAAA 1 119 0 TGCAGACTGG 0.924684 -52 CATAATAAACTCTAGACTGAAAAATAGTGG 9 22 0 TCTAGACTGA 0.808883 -30 AAAATCAGATTCTATACTGACCGGTGCAGC 12 98 1 TCTATACTGA 0.836877 -134 TGCTGGTGTCTGGATACTGGTGTGTCTGAG 23 27 1 TGGATACTGG 0.741032 -91 CTGGAACTGGTCCCTACTGATGAAATCATC 26 96 0 TCCCTACTGA 0.966509 -32 TATAGAGTATTCCATACTGGCGGTGTATGT 31 93 1 TCCATACTGG 0.966535 -113 AACATGGGAATGCCGACTGAAACTCACCTA 42 44 1 TGCCGACTGA 0.924684 -122 AAGCGTCCCTACTGAGAGTTATCAT 42 151 0 TCCCTACTGA 0.966509 -15 TTTGCAGATCTCCCTTCTGGACATAAGATT 44 48 0 TCCCTTCTGG 0.854266 -45 ********** Masking position 8 Map Score: 3.68964 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 47 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 ACTTCTTCAATGGCTGGGAGGATGGACCAA 8 27 0 TGGCTGGGAG 0.779825 -145 TTTTAATGTTTTTCTTGGAGGCAT 8 158 1 TTTCTTGGAG 0.906671 -14 TTTTTCTGTTTTCTGGGGTTTATAATTCC 11 10 1 TTTCTGGGGT 0.902993 -180 ATATTAGAGATTTCTTGGGGGGTGTAAT 19 9 0 TTTCTTGGGG 0.950216 -24 TTACACACCTCTCTGGGAGATATACTTAC 22 102 0 TCTCTGGGAG 0.902233 -19 GGTGTCGGGGGGATGCTGCTGG 23 3 1 TGTCGGGGGG 0.937169 -115 TCGATAATGATCACTGGGGGTTCTGT 27 174 1 TCACTGGGGG 0.718407 -16 TTGACCTCCATTTCGGGAGGGCCTCCCAGT 32 48 1 TTTCGGGAGG 0.713387 -25 GGTTGCTGGTTTGCTGGGAGT 36 27 1 TTGCTGGGAG 0.891742 -11 GTGTGCCGGTTTTCGTGGTGTGGTGGTTGA 37 27 1 TTTCGTGGTG 0.859899 -87 CCCTGCCGGTTTTCGTGGTTGTAGTGGTTG 37 78 1 TTTCGTGGTT 0.575355 -36 TATAAAGGTTTTTCTTGGTTCTGTGACCGG 42 13 0 TTTCTTGGTT 0.622212 -153 ********** Masking position 1 Map Score: 3.77466 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 324 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159