AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_mthe_reg_100.orf -o00230_mthe_100.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: MTH297 29 DNA-dependent RNA polymerase, subunit A' Input sequences: #1 MTH21 109 ribosomal protein L19 #2 MTH34 236 ribosomal protein S18 (E.coli S13) #3 MTH40 58 DNA-dependent RNA polymerase, subunit N #4 MTH42 171 DNA-dependent RNA polymerase, subunit K #5 MTH141 102 conserved protein #6 MTH147 23 phenylacrylic acid decarboxylase #7 MTH148 47 conserved protein #8 MTH150 75 conserved protein #9 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #10 MTH187 142 conserved protein #11 MTH189 99 unknown #12 MTH255 269 ribosomal protein L7a #13 MTH256 49 ribosomal protein S28 #14 MTH261 24 translation initiation factor eIF-2, gamma subunit #15 MTH262 24 conserved protein #16 MTH296 300 unknown #17 MTH550 118 DNA-dependent DNA polymerase family X #18 MTH615 173 adenylosuccinate synthetase #19 MTH648 65 ribosomal protein L37 #20 MTH649_MTH650 301 MTH649: conserved protein, MTH650: conserved protein #21 MTH709 300 GMP synthetase, subunit A #22 MTH710 102 GMP synthetase, subunit B #23 MTH784 83 ribose-phosphate pyrophosphokinase #24 MTH867 137 conserved protein #25 MTH1048 300 DNA-dependent RNA polymerase, subunit H #26 MTH1049 40 DNA-dependent RNA polymerase, subunit B'' #27 MTH1050 22 DNA-dependent RNA polymerase, subunit B' #28 MTH1051 38 DNA-dependent RNA polymerase, subunit A' #29 MTH1202 236 proteasome, beta subunit #30 MTH1203 69 cleavage and polyadenylation specificity factor #31 MTH1204 46 phosphoribosylformylglycinamidine cyclo-ligase #32 MTH1208 220 DNA-dependent DNA polymerase family B (PolB1) #33 MTH1314 52 transcription elongation factor TFIIS #34 MTH1315 28 mutator MutT protein #35 MTH1318 231 conserved protein #36 MTH1375 22 isoleucyl-tRNA synthetase #37 MTH1376 65 conserved protein #38 MTH1393 141 phosphoribosylaminoimidazole carboxylase #39 MTH1405 82 DNA polymerase delta small subunit #40 MTH1445 64 glycinamide ribonucleotide synthetase #41 MTH1492 51 5'-nucleotidase #42 MTH1493 78 cation transporting P-type ATPase related protein #43 MTH1494 266 conserved protein #44 MTH1537 300 adenylosuccinate lyase #45 MTH1539 246 anaerobic ribonucleoside-triphosphate reductase #46 MTH1864 109 phosphoribosylformylglycinamidine synthase II related protein Motif number 1 CGAATTCACTCTTACTGGAGGTTAATGA 2 219 1 CTACTGGAGG 0.832939 -18 TTTTAATGTTTTTCTTGGAGGCAT 4 158 1 TTCTTGGAGG 0.884388 -14 GTGCATTCAACCTCCCTGAGGTCATTTCCTT 11 61 1 CTCCCTGAGG 0.734245 -39 TAATCCTTGTTTTCCTGGGCGTCTTACTGGA 12 88 1 TTCCTGGGCG 0.818215 -182 CACCTTTAGGCTTCCCTGAGGCTTAAGCCGG 16 93 1 CTCCCTGAGG 0.816081 -208 AATTCGGCTGCATCCTGCTGGAAAAGGGCGT 18 37 1 CTCCTGCTGG 0.9712 -137 TCATATACATCTTCCTGCGGGGAAGGAGTGT 21 114 0 CTCCTGCGGG 0.987474 -187 ATTGATTTATTATCTTGCAGGACATCTATTT 22 70 0 TTCTTGCAGG 0.822913 -33 CAGATTTTTATATCTTGGAGGCCAACCACTT 24 91 1 TTCTTGGAGG 0.884388 -47 TCTAGAGACTTGCCCTGGTGGTGTAGGGGCT 25 104 1 TCCCTGGTGG 0.756827 -197 GTGTAGGGGCTATCATGCGGGCCTGTCGAGC 25 124 1 TTCATGCGGG 0.690896 -177 GGCCAGGGCGTTTCCTGAGGGCCCGTAGCTC 25 177 1 TTCCTGAGGG 0.900351 -124 TTAACAGCCTCCCGGTGGAAAA 27 5 0 CTCCCGGTGG 0.926769 -18 ATAGATGGGGCTTCCTGAGGGGTTGAAGAAC 29 47 0 CTCCTGAGGG 0.94755 -190 GTGTTTAGGATTTCCTGGGGGTGTTGGACTT 32 92 0 TTCCTGGGGG 0.984826 -129 ACCAGACTCCTCCTGCAGGCATCTATTT 34 10 0 CTCCTGCAGG 0.960851 -19 ATAGATGGCACCTCCCGCAGGGACCATTTAC 38 79 0 CTCCCGCAGG 0.945211 -63 CATTCATATACGTCCTGGTGGGGTACATGCT 43 97 0 CTCCTGGTGG 0.9795 -170 * ********* Masking position 11 Map Score: 23.0118 Number of sites scoring better than the average of aligned sites = 963 Number in coding regions = 924 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 GGTTGCTTTAACCGACGCCGGGACTGGGATTTGAACCC 2 134 0 ACCGCGGCGG 0.514914 -103 TGAAGAATTCGCAAACCCCCGTCCCGCGAATTCACTCT 2 193 1 GACCCCGCGG 0.954922 -44 TCCGGTGCTGACCATCCCCGTTCCAGTTGAAAAGTCCG 4 60 0 ACCCCGTCGT 0.772285 -112 TTGAACTCGGGTCTCCAGCGTTCCGGTGCTGACCATCC 4 81 0 GCCACGTCGG 0.914144 -91 AAATCAGGACAGAAACCTCCTGGAACAGATTAACGGGG 7 14 1 AACCCCTACG 0.573206 -34 GGCTGCTGCGGCCCCCCTCCTAACAGATTTGTCACTGT 10 67 0 GCCCCCTCGT 0.971901 -76 CCTTCAGTGTGCATTCAACCTCCCTGAGGTCATTTCCT 11 53 1 GACACCTCGG 0.97636 -47 TCCCTCATTAGGCCTCCACCTTTAGGCTTCCCTGAGGC 16 77 1 GCCCCCTAGT 0.71846 -224 AAACCATAATATAACCCCCCTGGCTCAGGGATCAGATC 16 221 0 AACCCCTCCG 0.947927 -80 TCTGTAAAGTTGATCCACCCTTCCCCTTACAATTAAAT 19 11 0 TACACCTCCT 0.441457 -55 CATTCTGGTTGCACTCGTCCTTGCAGTTGTCGCTTTCT 21 196 0 GACGCCTCGT 0.890919 -105 GGACCTGAAGGTACCCACCCTAACACGGGTCAGAACAC 22 15 1 GACACCTCCG 0.947415 -88 CGGGCCCTCAGGAAACGCCCTGGCCGGGAATTGAACCC 25 164 0 GACGCCTCGG 0.962781 -137 ACCCTCTACCTCCCCGTGTATTAATACT 32 1 1 ACCTCCTCGG 0.842754 -220 ACCATGCATGAGAGCCAGCCGCACACTGGCCTATCTGT 35 33 0 AACACCGCCG 0.741457 -199 ATTAGATGTTAAAAACCACCTTACAGGGCAGTGAAGGA 39 50 1 AACCCCTCGG 0.976598 -33 TCAGCCATAAAACACCCCCCTTACAGGTTTTAACC 41 8 0 ACCCCCTCGT 0.950905 -44 CTGGAGGCACCCTGCCGCCGATAATCATCA 43 3 1 GACACCTCCG 0.947415 -264 CCGGCTAACTATCCTCATCCTCTCGAAGACATGGTCCA 43 143 0 ACCACCTCAG 0.657966 -124 CGAAGAGATAGACCACCACCTCTCAGAGATAATGAGGA 43 207 1 GCCCCCTCGG 0.990954 -60 TAAGGGGCTCTGCATCATCCTCTCTGTTTTTGGCAGAA 45 39 0 TCCACCTCGT 0.727032 -208 * * ** *** * * * Masking position 9 Map Score: 21.6814 Number of sites scoring better than the average of aligned sites = 803 Number in coding regions = 761 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 CGAAAAAACTTTTTAAGGGGATACCTGAAA 1 44 1 TTTTAAGGGG 0.987814 -66 AGCCTTTATGAGGGGTTCAACTGCT 10 128 0 TTATGAGGGG 0.835865 -15 CCCTCCAAGTTTTCAAGGGGTTTTTCACAC 18 78 0 TTTCAAGGGG 0.927458 -96 GCCTCTCATATATTAAGGGGTATCCAATAA 18 132 0 TATTAAGGGG 0.94304 -42 ATTTAATTGTAAGGGGAAGGGTGGAT 19 7 1 TTGTAAGGGG 0.97211 -59 GATTAACTGATTTTAAGGAGGATTAGAAC 19 47 1 TTTTAAGGAG 0.84225 -19 TAATGGATTTAAGGGAATAACAAAAA 28 7 1 ATTTAAGGGA 0.800169 -32 TCATAACAGTATATAAGGGGATTCTACCAA 38 43 0 ATATAAGGGG 0.919867 -99 GGTTAAAACCTGTAAGGGGGGTGTTTTAT 41 10 1 CTGTAAGGGG 0.879065 -42 ATCTCTTCTCTTTTAAGGGACCTTGTCCGG 43 177 0 TTTTAAGGGA 0.918452 -90 TATAGAGGGAAATTAAGGGGCTCTGCATCA 45 60 0 AATTAAGGGG 0.854783 -187 AATAACACCTTTATAAGGGTTTAAATAATT 45 139 0 TTATAAGGGT 0.717838 -108 AGCCGATGATTTTTAAGGGGGGCGCGGCAC 45 173 1 TTTTAAGGGG 0.987814 -74 ********** Masking position 6 Map Score: 11.9704 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 95 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 AAGACTGGAAATCTTGTGGAGCTTTGCTCCTC 2 100 1 ACTGTGGAGC 0.863985 -137 GGGATTTGAACCCAGGAGGAGCAAAGCTCCAC 2 115 0 CCGGAGGAGC 0.959157 -122 GTTGAATGCACACTGAAGGTCCGGCCATGGTA 11 40 0 CCGAAGGTCC 0.777119 -60 CTCTATTACGAACGTGTGGTCCGGTACACCAT 16 25 0 ACTGTGGTCC 0.890352 -276 CTGAGGCTTAAGCCGGAGGACCCACCGTTAAA 16 108 1 ACGGAGGACC 0.973259 -193 AAGGGCGTTCATCCTGAGGTGTGAAAAACCCC 18 60 1 ACTGAGGTGT 0.8654 -114 CCATGAGAGATGCATGTGGTGCACGTAAAGTA 20 117 0 TCTGTGGTGC 0.769165 -185 TAGGGTGGGTACCTTCAGGTCCCAGT 22 5 0 ACTCAGGTCC 0.756526 -98 AGATATAAAAATCTGCTGGAGCCATTGCTGAG 24 74 0 ACGCTGGAGC 0.796904 -64 TAGAGACTTGCCCTGGTGGTGTAGGGGCTATC 25 106 1 CCGGTGGTGT 0.839731 -195 GTGACTTTTTATCTGGAGGACTGAATT 25 284 1 ACGGAGGACT 0.913683 -17 ACCAATATATAACAGGAGGTCCTTATTAAACT 29 94 0 ACGGAGGTCC 0.983462 -143 AATAGATGCCTGCAGGAGGAGTCTGGT 34 12 1 TCGGAGGAGT 0.812863 -17 GTTACAGAGTATCAGAAGGTGTACTG 38 5 0 ACGAAGGTGT 0.719695 -137 AAATGGTCCCTGCGGGAGGTGCCATCTATTAA 38 81 1 TCGGAGGTGC 0.960633 -61 TCTCTCAGTAATCTGGAGGTCCTTCAGTTTCA 44 30 1 ACGGAGGTCC 0.983462 -271 * * ******** Masking position 8 Map Score: 14.1263 Number of sites scoring better than the average of aligned sites = 774 Number in coding regions = 736 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AAAATATGCCCCTTCCAGTCCTCC 1 3 0 CCTCCAGTCT 0.979308 -107 CTTGGTCCATCCTCCCAGCCATTGAAGAAGTT 4 26 1 CCCCCAGCCT 0.982572 -146 GAGGTCATTTCCTTCCATCTTTCAGTAACCCC 11 78 1 CCTCCATCTT 0.883237 -22 GGTTTTTCTACCATCCATCGGTAATTACACCA 12 246 0 CCTCCATCGT 0.944579 -24 TTATATGATCCCATGCAGTCATTCTGCACACT 16 175 0 CCTGCAGTCT 0.926769 -126 GCCCTGGGATCCCCCCATCCATGAGAGATGCA 20 135 0 CCCCCATCCT 0.953946 -167 TTGCACTCGTCCTTGCAGTTGTCGCTTTCTAT 21 194 0 CCTGCAGTTT 0.743234 -107 GGTCAGAACACCGTCCATCCTTAACATTAAAT 22 42 1 CCTCCATCCT 0.97065 -61 ACAATGCTTACCTTACAGTGATCTATGGTTAG 35 187 0 CCTACAGTGT 0.705109 -45 GTATAAGGATCCTTCCAGTCATCTGTGATGAT 43 34 0 CCTCCAGTCT 0.979308 -233 GAAGACACTTCCACCCAGCGGTGCAGGTCTTG 44 154 1 CCCCCAGCGT 0.966727 -147 ** ******* * Masking position 7 Map Score: 11.1207 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 191 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CCGGGACTGGGATTTGAACCCAGGAGGAGCA 2 124 0 GATTGAACCC 0.986209 -113 GGACCGCCGAGATTTGAACTCGGGTCTCCAG 4 101 0 GATTGAACTC 0.942903 -71 GATCCCAGAGCAGTTGAACCCCTCATAAAGG 10 120 1 CATTGAACCC 0.9739 -23 TCACTTCGGGGATCTGATCCCTGAGCCAGGG 16 211 1 GACTGATCCC 0.809723 -90 ATCATTGACTCATTTAAACTCTTCTGCAAGT 20 63 1 CATTAAACTC 0.819806 -239 TGCGCAACCTGATTTAAACTCATTTCATAAA 21 31 0 GATTAAACTC 0.887975 -270 CATCTAAGTTCAGTTAATCCCTCTTATCTCA 24 47 1 CATTAATCCC 0.817764 -91 CCCTGGCCGGGAATTGAACCCGAGTCGCGGG 25 154 0 GATTGAACCC 0.986209 -147 GGCCCGACGGGAATTGAACCCGCGACCACTT 25 236 0 GATTGAACCC 0.986209 -65 TAATAATAATTATTTAAACCCTTATAAAGGT 45 132 1 TATTAAACCC 0.802497 -115 ** ******** Masking position 5 Map Score: 8.86376 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 47 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 GTAAACCCTTCACCCCATCACACTGAACCG 11 13 0 CACCCCATCA 0.910007 -87 AAGTTTTTCCCACCTCATCATTAACCCTCC 18 102 0 CACCTCATCA 0.970469 -72 TGCACTGCAGTACCTCTTCAAATCCATTCC 20 174 0 TACCTCTTCA 0.923421 -128 TCTCCTCTTCTGATTCTGAAA 21 290 0 CTCCTCTTCT 0.904286 -11 CACGGGTGCATTCCTCATCAAT 33 3 0 TTCCTCATCA 0.882582 -50 CCATTCACCTCTTCAAGGTAAAAAC 35 217 0 CACCTCTTCA 0.981385 -15 GTCCCTTCGTCTCCTCTTCAAAGTACCTTA 44 186 0 CTCCTCTTCA 0.981385 -115 TTTCCAAGTCCTCCACTTCAATTGTG 46 7 0 CTCCACTTCA 0.916283 -103 ********** Masking position 8 Map Score: 6.45879 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 149 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CAGCGTTCCGGTGCTGACCATCCCCGTTCCAGT 4 71 0 GGCTACCATC 0.860923 -101 TGCAGTCATTCTGCACACTGTACAATATAAATG 16 161 0 CGCAACTGTC 0.859463 -140 CAGGATGCAGCCGAATTCCATCCAGGTTCTGTG 18 21 0 CGAATCCATC 0.781123 -153 AAGGAACAGACTGCAGACCATTCATAAAATGAA 20 17 0 CGCAACCATC 0.970285 -285 TAACACGGGTCAGAACACCGTCCATCCTTAACA 22 35 1 CGAAACCGTC 0.964885 -68 TTTTAATGACCGGATAACCGTTCTTCAACCCCT 29 28 1 CGATACCGTC 0.975745 -209 GCGTTTATCTCTGGTTACCGTTCTACAAGTAGC 32 157 0 CGGTACCGTC 0.936345 -64 TACCATGCCTCTGATTACCATGCATGAGAGCCA 35 54 0 CGATACCATC 0.973775 -178 CATCTGTCCACTGATTACCATGCCTCTGATTAC 35 69 0 CGATACCATC 0.973775 -163 GGACCTTGTCCGGCTAACTATCCTCATCCTCTC 43 157 0 CGCTACTATC 0.892057 -110 * *** ***** * Masking position 11 Map Score: 7.12844 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 59 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ATGTATCATATAACTGTATATTATGACATCT 2 36 0 TAACTTATAT 0.881531 -201 ATCAATCGATAACTTTATATATTTTTATTT 3 10 1 TAACTTATAT 0.881531 -49 ATTGGCAGCAAAACTTTATATGTGATGAAGC 12 45 1 AAACTTATAT 0.814377 -225 AGTGGGTGAGTACCTTTATATGTTCTCGGTA 12 179 0 TACCTTATAT 0.883483 -91 CCCCGAAGTGAACCATTATATGATCCCATGC 16 191 0 AACCATATAT 0.838164 -110 TGGTTCAGGGAAACAGTAAATTTATTAATCG 17 62 0 AAACATAAAT 0.620023 -57 CGTCCATCCTTAACATTAAATAGATGTCCTG 22 53 1 TAACATAAAT 0.734573 -50 AAAAGTTCTGTACCAATATATAACAGGAGGT 29 106 0 TACCATATAT 0.897793 -131 AGGAAATCCTAAACACTATATCTTAATAGTG 32 107 1 AAACATATAT 0.835594 -114 CAGGTCTTCATAACAGTATATAAGGGGATTC 38 49 0 TAACATATAT 0.896053 -93 CTGTTATGAAGACCTGTAAATGGTCCCTGCG 38 64 1 GACCTTAAAT 0.543359 -78 CTTTAACTTTATATATAGAGAATC 38 128 0 TAACTTATAT 0.881531 -14 CGGACCAATATATGTTTTTTATG 42 66 0 GACCATATAT 0.811096 -13 ***** ***** Masking position 8 Map Score: 7.38485 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 20 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 TCGAATCCAAGAACCTCTATTTTAATGTTTT 4 139 1 GAACCTTATT 0.624425 -33 ATCTAGCACAGCACCTTTTTATACCTTTCTT 5 12 0 GCACCTTTTA 0.848897 -91 AATAGAATTTACACCTATATAAGTATTGGAG 9 78 1 ACACCTTATA 0.929495 -64 AAGTGGGTGAGTACCTTTATATGTTCTCGGT 12 180 0 GTACCTTATA 0.663944 -90 TAAATCACCTTTATTAAATTGAAAT 13 35 0 TCACCTTATT 0.732402 -15 AGATTACACCTATAAACGCTTTTA 14 9 0 ACACCTTAAA 0.872409 -16 AGATACACCTCTAATAAAAATAATA 29 222 0 ACACCTTAAT 0.851939 -15 ATTGCAGTAAACACCTGTTTACTGATATTCC 30 28 1 ACACCTTTTA 0.747078 -42 GGATACAGTGGCACCTGTAAGCGAGACCCAT 42 18 0 GCACCTTAAG 0.800063 -61 CTGATTAATAACACCTTTATAAGGGTTTAAA 45 144 0 ACACCTTATA 0.929495 -103 GGGGGGCGCGGCACCTTTAATATGGGTGGTG 45 189 1 GCACCTTAAT 0.916275 -58 AGTGTATTCTGCACCTGTATTATCTATAATC 46 59 0 GCACCTTATT 0.954752 -51 ****** **** Masking position 3 Map Score: 6.53645 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 39 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CTAGGCTATCCCGGCACAGGATGTATCATA 2 57 0 CCGGCACAGG 0.982914 -180 TTAACCGACGCCGGGACTGGGATTTGAACC 2 135 0 CCGGGACTGG 0.929758 -102 GACTTTTCAACTGGAACGGGGATGGTCAGC 4 62 1 CTGGAACGGG 0.885745 -110 CAGAAACCTCCTGGAACAGATTAACGGGGC 7 23 1 CTGGAACAGA 0.504991 -25 CACTGAAGGTCCGGCCATGGTAAACCCTTC 11 32 0 CCGGCCATGG 0.93206 -68 ATACCCTCATCTGGAAAAGGTTTAACGGTG 16 130 0 CTGGAAAAGG 0.907945 -171 TATAACCCCCCTGGCTCAGGGATCAGATCC 16 220 0 CTGGCTCAGG 0.7598 -81 CTGCATCCTGCTGGAAAAGGGCGTTCATCC 18 44 1 CTGGAAAAGG 0.907945 -130 CAGGGCGGACCCTGGAATGGATTTGAAGAG 20 161 1 CCTGGAATGG 0.633287 -141 ATTCTAGAGACTTGCCCTGGTGGTGTAGGG 25 102 1 CTTGCCCTGG 0.713498 -199 GGTTCAATTCCCGGCCAGGGCGTTTCCTGA 25 165 1 CCGGCCAGGG 0.902265 -136 TTCATTTAACCCTGCAAAGGGCTGTCCCCA 29 144 0 CCTGCAAAGG 0.884172 -93 AATTTCTCCTGAACTGGATGTATATAC 37 8 1 CCTGAACTGG 0.862635 -58 GGATAGTTAGCCGGACAAGGTCCCTTAAAA 43 167 1 CCGGACAAGG 0.939268 -100 GAAACTCACACCGGAACAGGTAGTTGTGAT 44 217 1 CCGGAACAGG 0.975213 -84 ********** Masking position 4 Map Score: 14.6761 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 342 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 ACTTTTTAAGGGGATACCTGAAATTTTTCGGG 1 51 1 GGGTCCTGAA 0.960744 -59 CCAGTCTTGCGCCTTACCTGGCTAGGCTATCC 2 76 0 GCCTCCTGGC 0.70856 -161 GGTAACATTGGAGATCCCAGAGCAGTTGAACC 10 108 1 GAGTCCAGAG 0.725628 -35 GGGGTTACTGAAAGATGGAAGG 11 88 0 GGGTACTGAA 0.790375 -12 TCCACCTTTAGGCTTCCCTGAGGCTTAAGCCG 16 91 1 GGCTCCTGAG 0.978304 -210 CATGGATGGGGGGATCCCAGGGCGGACCCTGG 20 144 1 GGGTCCAGGG 0.929775 -158 ACGGGTAGCAGCCATACCAGAACATAGAAAGC 21 171 1 GCCTCCAGAA 0.774385 -130 GAGATAAGAGGGATTAACTGAACTTAGATGTG 24 45 0 GGATACTGAA 0.463056 -93 ATCTGCTGGAGCCATTGCTGAGATAAGAGGGA 24 64 0 GCCTGCTGAG 0.772858 -74 CCCGGCCAGGGCGTTTCCTGAGGGCCCGTAGC 25 174 1 GCGTCCTGAG 0.974887 -127 ATAATAGATGGGGCTTCCTGAGGGGTTGAAGA 29 49 0 GGGTCCTGAG 0.98521 -188 ATAGTGTTTAGGATTTCCTGGGGGTGTTGGAC 32 94 0 GGATCCTGGG 0.894933 -127 *** * ****** Masking position 5 Map Score: 3.99206 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 631 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 13 GGGACCGTAGGGTAGCTTGG 4 1 1 GGGACCGTAG 0.93972 -171 TCGATTTGATGGGACCGCCGAGATTTGAAC 4 113 0 GGGACCGCCG 0.990548 -59 TGTTAGGAGGGGGGCCGCAGCAGCCCTGGG 10 80 1 GGGGCCGCAG 0.955412 -63 GTTTAACGGTGGGTCCTCCGGCTTAAGCCT 16 111 0 GGGTCCTCCG 0.852734 -190 ATCCATTCCAGGGTCCGCCCTGGGATCCCC 20 153 0 GGGTCCGCCC 0.968782 -149 ACCCTAACACGGGTCAGAACACCGTCCATC 22 31 1 GGGTCAGAAC 0.535984 -72 GCTATCATGCGGGCCTGTCGAGCCCGCGAC 25 132 1 GGGCCTGTCG 0.842649 -169 CGTTTCCTGAGGGCCCGTAGCTCAGTCTGG 25 185 1 GGGCCCGTAG 0.96113 -116 ATTAGATAGCGGGCCCGACGGGAATTGAAC 25 248 0 GGGCCCGACG 0.982018 -53 TATGTCCATGGGGACAGCCCTTTGCAGGGT 29 136 1 GGGACAGCCC 0.908695 -101 CCATGCATGAGAGCCAGCCGCACACTGGCC 35 40 0 GAGCCAGCCG 0.747624 -192 AGGAGACGAAGGGACCGAAACTCACACCGG 44 201 1 GGGACCGAAA 0.604475 -100 ********** Masking position 5 Map Score: 8.00256 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 172 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 TCTTTAGTTTATAAAATAAAAATATATAAAGT 3 22 0 ATAATAAAAA 0.917287 -37 AAAGAAAGGTATAAAAAGGTGCTGTGC 5 6 1 AAGATAAAAA 0.644691 -97 GCTGTGCTAGATAAATTAAAAAAATTATCATA 5 31 1 ATATTAAAAA 0.521875 -72 TTACCGATGGATGGTAGAAAAACCAG 12 254 1 ATGAGAAAAA 0.740469 -16 CCGGTACACCATTTAATAAAAATATT 16 5 0 ATTATAAAAA 0.733429 -296 ATTTAAACTCATTTCATAAAAAGAATTAGTAG 21 19 0 ATTATAAAAA 0.733429 -282 GTTGGCCTCCAAGATATAAAAATCTGCTGGAG 24 85 0 AAGATAAAAA 0.644691 -53 AAATACTAGAAAAATGTAACTCAT 25 3 1 ATAAGAAAAA 0.836159 -298 GAAGCCCCATCTATTATAAAAAAATCGCAAAG 29 64 1 CTAATAAAAA 0.617907 -173 AACCCTTTATATACCATAAAAACACAATGGGA 29 174 1 ATAATAAAAA 0.917287 -63 CCTCTAATAAAAATAATAAAAAACCAGTCCTG 29 208 0 AAAATAAAAA 0.764463 -29 GCAATTAAAAATAGGAGAAAAA 30 1 0 ATAAGAAAAA 0.836159 -69 CAAAATCTTAATACCATAAAAAACATATATTG 42 52 1 ATAATAAAAA 0.917287 -27 TATTAAATGAATAATATAATAATAATTATTTA 45 116 1 ATAATAATAA 0.521869 -131 *** ******* Masking position 8 Map Score: 4.41777 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 37 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 GCCGAGATTTGAACTCGGGTCTCCAGCGTT 4 97 0 GAACTCGGGT 0.969656 -75 TAAGGACCACTAACACGGGTAGCAGCCATA 21 157 1 TAACACGGGT 0.972853 -144 GTACCCACCCTAACACGGGTCAGAACACCG 22 25 1 TAACACGGGT 0.972853 -78 GCCGGGAATTGAACCCGAGTCGCGGGCTCG 25 150 0 GAACCCGAGT 0.900752 -151 TTTTTTAGTGGAACACGGGTGCATTCCTCA 33 16 0 GAACACGGGT 0.987767 -37 ********** Masking position 3 Map Score: 2.15756 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 6 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493