AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_ecoli_reg_300.orf -o00710_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 aspC 184 aspartate aminotransferase #2 ompF 300 outer membrane protein 1a (Ia;b;F) #3 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #4 yebK 300 orf, hypothetical protein #5 pykA 127 pyruvate kinase II, glucose stimulated #6 talA 288 transaldolase A #7 rpiA 55 ribosephosphate isomerase, constitutive #8 yqfE 141 orf, hypothetical protein #9 fba 214 fructose-bisphosphate aldolase, class II #10 pgk 49 phosphoglycerate kinase #11 epd 284 D-erythrose 4-phosphate dehydrogenase #12 yggD 21 putative transcriptional regulator #13 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #14 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #15 tktA 151 transketolase 1 isozyme #16 mdh 300 malate dehydrogenase #17 yheS 127 putative ATP-binding component of a transport system #18 prkB 53 probable phosphoribulokinase #19 dam 106 DNA adenine methylase #20 damX 91 putative membrane protein; interferes with cell division #21 aroB 56 3-dehydroquinate synthase #22 aroK 199 shikimate kinase I #23 yrfD 68 orf, hypothetical protein #24 pckA 300 phosphoenolpyruvate carboxykinase #25 tpiA 107 triosephosphate isomerase #26 yiiQ 100 orf, hypothetical protein #27 ppc 249 phosphoenolpyruvate carboxylase #28 argE 153 acetylornithine deacetylase #29 rpiB 300 ribose 5-phosphate isomerase B #30 fbp 175 fructose-bisphosphatase Motif number 1 GATTCGCTTTCCGGCAGTGCGCCCAGAAAGC 3 239 1 CCGGCGTGCG 0.953692 -62 TCTGTAGACTCCGGCAGGGTAATAATGTGCG 6 79 0 CCGGCGGGTA 0.905821 -210 TATACCGAAGCCGTCGGCGGGTAACATTTGT 8 76 1 CCGTCGCGGG 0.982743 -66 ATCCAGCAAATCGTCCGGGGAAACCTTACCT 11 218 0 TCGTCGGGGA 0.917145 -67 CTTGATATGTCCGTTTGCGGACAAGCAATAG 14 43 1 CCGTTGCGGA 0.851136 -258 TTTTAGGGTACCGTCCGGCGGTAAAAATAAA 14 262 0 CCGTCGGCGG 0.900132 -39 GATTAAGGTCGCGGCAGCGGAGCAACATATC 16 250 1 GCGGCGCGGA 0.926927 -51 AAAAACCATACCGGGAGGGGG 17 1 0 CCGGGGGGGG 0.941687 -127 CCTGCAACCGTCGGCGGACGAGATAATA 18 8 1 CCGTCGCGGA 0.986448 -46 TACACCTTCTCCGGCTGTGGAGAAAGCTCCG 19 72 0 CCGGCGTGGA 0.97633 -35 TTATATACACTCGTCTGCGGGTACAGTAATT 21 19 1 TCGTCGCGGG 0.932958 -38 GACCTGCTGCCCTGCGGGGCGGCCATCTTCC 25 57 1 CCTGCGGGCG 0.776671 -51 TCATCTTCCCCGTCCGTGCAAAACTTCACA 29 281 0 CCGTCGTGCA 0.915348 -20 ***** ***** Masking position 2 Map Score: 14.501 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 804 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 TCACGTCTTGCAAAAACAGCCTGCGTTTTCA 1 84 1 CAAAACAGCC 0.809428 -101 AAAAGGAAAACAAAAACAGCGTTTCAAAAAA 3 23 0 CAAAACAGCG 0.975574 -278 GGGAAAAGCGCGCAAAGTGCGGCAAAACTGA 4 100 1 CCAAAGTGCG 0.898882 -201 GCATTATATACAAAAAAAGCGAT 7 3 0 CAAAAAAGCG 0.873487 -53 ATTGCGTGCTCTAAAAGCGCGCTGAAACAAG 9 37 0 CAAAAGCGCG 0.898054 -178 GACGCAAGCAGCGTCTGCAAAAC 10 3 1 CCAAGCAGCG 0.981204 -47 CCTTACCTGTCGCAAACTGCGACTGATTGGT 11 195 0 CCAAACTGCG 0.965793 -90 AACAATTTACCGCAAGCCGCGCGTCATGTAC 15 49 0 CCAAGCCGCG 0.977331 -103 TCCGGCGTAGCCCAAAACGCGCTGTCGTCAA 15 89 1 CCAAAACGCG 0.901136 -63 CAATGGTAGCCCAAAACAGCGACTATACACA 17 31 0 CAAAACAGCG 0.975574 -97 CATCATGGAACGCAGGCAGCGAAGAGCACCA 22 106 0 CCAGGCAGCG 0.902964 -94 GCGGTGACGTCAAATGCTGCGAAATCGCTTC 27 117 0 CAATGCTGCG 0.686508 -133 * ********* Masking position 4 Map Score: 11.5191 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 378 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 GCTTTCTGGGCGCACTGCCGGAAAGCGAATCCGG 3 236 0 CGCTGCCGAA 0.918601 -65 ACTGCTTTTACGAGCTTGCGAAAACTGTAAACGC 4 46 1 CGCTTGCGAA 0.892411 -255 ATTAACACGGCACACAGGCGTAATATCTGACAAA 4 218 1 CACAGGCGAT 0.907072 -83 GAAATAACGCCGCGATGGCGATAAATTAATCTCA 5 50 0 CGATGGCGAA 0.978695 -78 ATTCGAGTTGCAGGAAGGCGACAAGAGAGTGAAT 9 85 1 CAAAGGCGAA 0.90271 -130 AGCTTTATTCCAGGCTGGCGTAATAATAACCCTA 11 30 0 CACTGGCGAT 0.944794 -255 TAGCCCAAAACGCGCTGTCGTCAAGTCGTTAAGG 15 96 1 CGCTGTCGAA 0.883912 -56 CTTCATCATCCGATCTGGAGTCAAA 15 137 1 CGCTGGAGAA 0.875574 -15 ACAGCCGTAAAAGCGGTAATGTTTTTACG 22 6 1 CGAAAGCGAA 0.76825 -194 GATGATTTATCATTCAGGCGGCATTTTGCTGTCT 22 136 1 CACAGGCGAT 0.907072 -64 CGCTCTGGCGATAAATCACCGGGT 22 186 0 CGCTGGCGAA 0.991424 -14 TCCTTCACGTCGCATTGGCGCGAATATGCTCGGG 27 185 0 CGTTGGCGAA 0.918916 -65 CATCTGACAGCGCAATAGCGTTAAAGACACTCAC 29 164 0 CGATAGCGAA 0.853204 -137 TAAAACAGATCAGGAAGGCGTAATTCATCGATTT 29 206 1 CAAAGGCGAT 0.795032 -95 ** ****** ** Masking position 13 Map Score: 14.2957 Number of sites scoring better than the average of aligned sites = 1180 Number in coding regions = 1135 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 GACCAAAGTCCTGTTTTTTCGGCATTTAACA 1 24 0 CTGTTTTTCG 0.877373 -161 ATTCCTCTGCACGCTTTTTCGATGTCACCTA 3 172 1 ACGCTTTTCG 0.975051 -129 GTGCACTGTACTGCTTTTACGAGCTTGCGAA 4 37 1 CTGCTTTTCG 0.978922 -264 CGCACTTTGCGCGCTTTTCCCGTAATCGCAC 4 90 0 GCGCTTTTCC 0.8477 -211 ACTTTTTTATCTGCTTTTGTCATTAACACGG 4 197 1 CTGCTTTTTC 0.735924 -104 CCTGTCTGCTATGCTTTTTTGATGCGTTTAG 6 202 1 ATGCTTTTTG 0.817738 -87 CTCCTGGTAAATGCTTTTTCCTGCACTATGA 8 23 1 ATGCTTTTCC 0.918984 -119 AAAAACATTACCGCTTTTACGGCTGT 22 6 0 CCGCTTTTCG 0.984208 -194 AAAAGCGGTAATGTTTTTACGCTGAACGTGT 22 19 1 ATGTTTTTCG 0.817738 -181 TTTGACGTCACCGCTTTTACGTGGCTTTATA 27 134 1 CCGCTTTTCG 0.984208 -116 AGTGTCTTTAACGCTATTGCGCTGTCAGATG 29 167 1 ACGCTATTCG 0.832377 -134 ******** ** Masking position 5 Map Score: 9.6933 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 326 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 CATTCAAACTAACGTTTCGCTACCGTGAAA 2 158 0 AACGTTTCGC 0.963834 -143 AACAGGCACTCACGTTGGGCTGAGACACAA 3 136 1 CACGTTGGGC 0.897178 -165 AGTTTTGCCGCACTTTGCGCGCTTTTCCCG 4 99 0 CACTTTGCGC 0.841507 -202 CCCTGCCCACAACGTGGCGCACATTATTAC 6 62 1 AACGTGGCGC 0.952965 -227 GATCGTTTCGCCTGTGGTATG 7 45 0 ATCGTTTCGC 0.913905 -11 CCTTTTATTCCACGTTTCGCTTATCCTAGC 11 130 1 CACGTTTCGC 0.943476 -155 CACCTGTTGGAATGTTGCGCTAATGCATAA 16 106 1 AATGTTGCGC 0.963834 -195 GCAATGGTTTATCGTTGCGGGAGTTGCCTG 19 26 1 ATCGTTGCGG 0.910811 -81 AAAATACACTAACGTTGAGCGTAATAAAAC 28 79 0 AACGTTGAGC 0.903842 -75 AAATAATCTCAATGTTGCGCTCAGGTGAAT 30 105 0 AATGTTGCGC 0.963834 -71 ATTTGTTAAGATTGTTGCGGTCGCTTTACT 30 131 1 ATTGTTGCGG 0.716682 -45 ********** Masking position 5 Map Score: 9.48401 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 725 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 CTTTATGTGTCTGCAGGCATCTTTCCATTCAAA 2 180 0 CGCAGCATCT 0.675905 -121 CGGATTTCATGTTCAAGCAACACCTGGTTGTTT 5 87 1 GTCAGCAACC 0.963656 -41 AAAATCACAGGGCAGGGAAACCTGCCCTTGTT 9 10 1 GGCAGGAAAC 0.897311 -205 CGCGCTTTTAGAGCACGCAATTTTTCATACTCT 9 47 1 GGCAGCAATT 0.693925 -168 CTCTTGTCGCCTTCCTGCAACTCGAATTATTTA 9 79 0 CTCCGCAACC 0.907765 -136 CGCAGACGCAGCACATGCAACTTGAAGTATGAC 9 159 1 GACAGCAACT 0.855812 -56 TGGCAAATTTGCTCAGGGAAAACCTTGCAGGAG 11 258 1 GTCAGGAAAC 0.863475 -27 GAAAGCAATTGAGCAGGGAAACCGGTGTTTTGA 14 211 0 GGCAGGAAAC 0.897311 -90 CGCGCGTCATGTACATGGAACATCCTTTTGCCG 15 30 0 GACAGGAACT 0.799913 -122 GCCTGCGTCACGGCATGCAAATTCTGCTTAAAA 16 14 1 CGCAGCAAAT 0.889719 -287 GCATCCAGCGCTTCAGGCAACTCCCGCAACGAT 19 36 0 CTCAGCAACC 0.95881 -71 GATAAATCATCATCATGGAACGCAGGCAGCGAA 22 114 0 CTCAGGAACC 0.940043 -86 AAAAGACAACCATCAAGGAACTTAC 26 3 0 CTCAGGAACT 0.917399 -98 AGACACTCACCATCCAGCAACATCTATCATCTA 29 141 0 CTCCGCAACT 0.874557 -160 CAGGTGAATCGCGCCAGCAAATTACGGATTATC 30 81 0 GGCCGCAAAT 0.795313 -95 * *** ***** * Masking position 9 Map Score: 9.28475 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 489 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 AAACTGTAAACGCTTATCCACCCGTGCGAT 4 67 1 CGCTTATCCA 0.947984 -234 TTCCACGTTTCGCTTATCCTAGCTGAAGCG 11 137 1 CGCTTATCCT 0.914866 -148 TCGACTGAAACGCTTCAGCTAGGATAAGCG 11 147 0 CGCTTCAGCT 0.934604 -138 ATCCTTTTGCCGCTTCAGAAATCTCTGGAT 15 12 0 CGCTTCAGAA 0.789683 -140 AATTAACAGTCGCTTATGCATTAGCGCAAC 16 119 0 CGCTTATGCA 0.938252 -182 GCAAGTTTAGCGTTTATGCATTTAATTGCC 16 172 0 CGTTTATGCA 0.750584 -129 AAGGTCAGGCCGCTTATCAAGCGGTCTATT 20 19 1 CGCTTATCAA 0.737411 -73 GGTAAAGTATCGATTCACCACGCTAACTTT 24 14 0 CGATTCACCA 0.851279 -287 GCTGCGAAATCGCTTCAGCAAACGAATAAA 27 103 0 CGCTTCAGCA 0.960243 -147 GAATGTTTTACGTTTAACCTGGCAACCAGA 28 33 0 CGTTTAACCT 0.715485 -121 TTTGCTGGCGCGATTCACCTGAGCGCAACA 30 93 1 CGATTCACCT 0.771423 -83 ********** Masking position 5 Map Score: 6.3101 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 581 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 AGTTCCTTAAATTTTACTTTTGGTTACATAT 2 89 1 ATTTACTTTT 0.932971 -212 TTGCCCACACACTTTATTTGTGAACGTTACG 6 27 0 ATTTATTTGT 0.728208 -262 CTCATCTAACACTTTACTTTTCAAGGAGTAT 6 263 1 ATTTACTTTT 0.932971 -26 CCGCACGAGTATTTTATTTTTACCGCCGGAC 14 250 1 ATTTATTTTT 0.927784 -51 AATTATCCTTATTTTATTTTTAGGGTACCGT 14 279 0 ATTTATTTTT 0.927784 -22 GATAACAATTAATTTACTTTTAAGCAGAATT 16 33 0 ATTTACTTTT 0.932971 -268 CCCCAAAAAGACTTTACTATTCAGGCAATAC 24 258 1 ATTTACTATT 0.661994 -43 GCTCAACGTTAGTGTATTTTTATTCATAAAT 28 89 1 ATGTATTTTT 0.728208 -65 AACTTTATAAATTTTATTTTTTTGTGAAGTC 29 21 0 ATTTATTTTT 0.927784 -280 AAATTTATAAAGTTTATTTTATTGTGAACAA 29 38 1 ATTTATTTTA 0.643842 -263 * ********* Masking position 6 Map Score: 5.98106 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 41 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 GGTGTCTTTATGTGTCTGCAGGCATCTTTCCAT 2 185 0 TGTGCTGGGC 0.935375 -116 TGTCAGATATTACGCCTGTGTGCCGTGTTAATG 4 217 0 TACGCTGTGC 0.978639 -84 CCAGCAATACCATGCCTGTCTGCTATGCTTTTT 6 188 1 CATGCTGTGC 0.806366 -101 GACACAATTTTGTGTCAGGTTGCATATACCGAA 8 52 1 TGTGCAGTGC 0.93634 -90 TTGCATGTGCTGCGTCTGCGTTCGCTCACCCCA 9 146 0 TGCGCTGTTC 0.902934 -69 GGGTTATTATTACGCCAGCCTGGAATAAAGCTT 11 32 1 TACGCAGTGG 0.892542 -253 TGTCGCAAACTGCGACTGATTGGTTAATTGTCG 11 186 0 TGCGCTGTGG 0.976482 -99 ATTACCTTGATATGTCCGTTTGCGGACAAGCAA 14 38 1 TATGCCGTGC 0.843165 -263 TTGCGCCCGGTGCGGCAGCTCGCCCATACATTA 17 59 1 TGCGCAGCGC 0.802061 -69 GGTATATCAATGCGTCTGGCTTGCCTTTATACT 23 39 0 TGCGCTGTTG 0.840054 -30 TACCTTTTGTTATGACTGGCTCCGATTAAAACG 26 72 0 TATGCTGTCC 0.752225 -29 TTCACCTTCTTATGTCTGGTTGCCAGGTTAAAC 28 19 1 TATGCTGTGC 0.966157 -135 ACATTCACCTTACGGCTGGTGGGTTTTATTACG 28 57 1 TACGCTGGGG 0.890996 -97 AGATGATAGATGTTGCTGGATGGTGAGTGTCTT 29 142 1 TGTTCTGTGG 0.611642 -159 **** *** *** Masking position 6 Map Score: 8.40371 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 836 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 10 AATGCTTTTTCCTGCACTATGACACAATTT 8 32 1 CCTGCACTAT 0.868774 -110 AGCGCAAATCCCTGATCTTTTAAGCTGCGC 8 121 0 CCTGATCTTT 0.912422 -21 GGCAGGTTTCCCTGCCCTGTGATTTT 9 7 0 CCTGCCCTGT 0.975883 -208 GGCAGGGAAACCTGCCCTTGTTTCAGCGCG 9 21 1 CCTGCCCTTG 0.827718 -194 TCCGGGGAAACCTTACCTGTCGCAAACTGC 11 206 0 CCTTACCTGT 0.766231 -79 CTACAACACGCCTTATCTATTGCTTGTCCG 14 60 0 CCTTATCTAT 0.55211 -241 CACCGGTTTCCCTGCTCAATTGCTTTCATT 14 217 1 CCTGCTCAAT 0.659126 -84 TGATAAGCGGCCTGACCTTTCTTGTTG 20 8 0 CCTGACCTTT 0.930621 -84 GACGTAAATTCCTGCTATTTATTCGTTTGC 27 86 1 CCTGCTATTT 0.753261 -164 ATTACGCCTTCCTGATCTGTTTTACAGAGT 29 200 0 CCTGATCTGT 0.942767 -101 AAAACTTTCCCTGCAATGTTTATGGAGTA 30 157 0 CCTGCAATGT 0.678099 -19 ********** Masking position 3 Map Score: 3.18555 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 479 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 11 TAATTTCAGCGTATAATGCGCGCCAATTGACTCT 3 58 1 GTATAAGCGC 0.921503 -243 GGCAAAACTGATAAAAAAATCATCGTTTTCCATT 4 120 1 ATAAAAACAC 0.661436 -181 TGAACGTTACGTGAAAGGAACAACCAA 6 4 0 GTGAAAGCAC 0.890692 -285 TGTATCCGTGGTTAAAAGCGCAGCTTAAAAGATC 8 104 1 GTTAAAGCAC 0.932847 -38 AGTATGACGAGTATAAGGCCCGACGATACAGGAC 9 184 1 GTATAAGCGC 0.921503 -31 GTTTCAGTCGATTAAATGTTCGACAATTAACCAA 11 166 1 ATTAAAGCGC 0.792936 -119 TAAGATTAGCGTAAAAAAGACAGCAAAATGCCGC 22 153 0 GTAAAAACAC 0.918708 -47 TTATGGAAATGTTAAAAAATCGCCCCAAGTAACA 27 20 0 GTTAAAACGC 0.904341 -230 CAGGTTAAACGTAAAACATTCACCTTACGGCTGG 28 42 1 GTAAAAACAC 0.918692 -112 CGACATATGCGTAAAATGAGCGGCAGATTAAAAA 30 24 0 GTAAAAGCGC 0.976868 -152 ****** * ** * Masking position 6 Map Score: 2.63719 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 118 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 CCGTCATATTTCCATAGAGACGTGATGATATTTAC 2 45 0 TCAGGCGTGA 0.98006 -256 CAAACTCTCATCAATAGTTCCGTAAATTTTTATTG 2 217 1 TCAGTCGTAA 0.809743 -84 GGTGCCTCGCTCTAAGGATAGGTGACATCGAAAAA 3 186 0 TCAGTGGTGA 0.868132 -115 TTAATTTATCGCCATCGCGGCGTTATTTCATTCGG 5 55 1 GCAGGCGTTA 0.935334 -73 CACTTTATTTGTGAACGTTACGTGAAAGGAACAAC 6 14 0 GTAGTCGTGA 0.921634 -275 GAAGCTTTATTCCAGGCTGGCGTAATAATAACCCT 11 31 0 TCACGCGTAA 0.550903 -254 GTCGCAAACTGCGACTGATTGGTTAATTGTCGAAC 11 183 0 GCAGTGGTTA 0.659521 -102 TTTAATGAAAGCAATTGAGCAGGGAAACCGGTGTT 14 215 0 GCAGGAGGGA 0.807632 -86 ATGCATAAACGCTAAACTTGCGTGACTACACATTC 16 181 1 GCACTCGTGA 0.920974 -120 CCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAA 19 23 1 TTAGTCGGGA 0.617149 -84 TGCGATAATAGCAACCGTTTCGTGACAGGAATCAC 24 157 1 GCAGTCGTGA 0.984818 -144 ATACATATTGGCTAAGGAGCAGTGAA 24 285 1 GCAGGAGTGA 0.935334 -16 GTTACGCTTATTTAAAGCGTCGTGAATTTAATGAC 27 54 1 TTAGGCGTGA 0.899114 -196 GCATATTCGCGCCAATGCGACGTGAAGGATACAGG 27 190 1 GCAGGCGTGA 0.990485 -60 ** * * * ***** Masking position 4 Map Score: 8.66285 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 538 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 13 TGCAAAAACAGCCTGCGTTTTCATCAGTAA 1 92 1 GCCTGCGTTT 0.832028 -93 GAGTCAATTGGCGCGCATTATACGCTGAAA 3 61 0 GCGCGCATTA 0.744529 -240 GCTTATCCACCCGTGCGATTACGGGAAAAG 4 78 1 CCGTGCGATT 0.74545 -223 GCCGCACTTTGCGCGCTTTTCCCGTAATCG 4 93 0 GCGCGCTTTT 0.80048 -208 TCGTCATTACCCGTGAGTCTCTTTACATC 4 282 1 CCGTGAGTCT 0.576354 -19 AGTGTTAGATGAGTGCGTTAATTCACACTT 6 246 0 GAGTGCGTTA 0.787043 -43 GCCCTTGTTTCAGCGCGCTTTTAGAGCACG 9 34 1 CAGCGCGCTT 0.677297 -181 TTACCGCAAGCCGCGCGTCATGTACATGGA 15 44 0 CCGCGCGTCA 0.968181 -108 GACTTGACGACAGCGCGTTTTGGGCTACGC 15 93 0 CAGCGCGTTT 0.918256 -59 CATGCCTGCGTCACGGCATGCAA 16 4 1 GCCTGCGTCA 0.747479 -297 CTAAATACCTGCGCGCGTCAAATAGATGAA 22 50 0 GCGCGCGTCA 0.968181 -150 CTTTATACTACCGCGCGTTTGTTTATAAAC 23 18 0 CCGCGCGTTT 0.980737 -51 ********** Masking position 5 Map Score: 3.42066 Number of sites scoring better than the average of aligned sites = 1655 Number in coding regions = 1593 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 14 ********** No masking Map Score: 1.04048e-11 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 TTATACCTTCCAGAGCAATCTCACGTCTTG 1 64 1 CAGAGCAATC 0.835644 -121 AAAAAACCATGAGGGTAATAAATA 2 287 1 GAGGGTAATA 0.746491 -14 TAGACTCCGGCAGGGTAATAATGTGCGCCA 6 76 0 CAGGGTAATA 0.957878 -213 ATTTGCCAGACAGAGTAATCCAGCAAATCG 11 236 0 CAGAGTAATC 0.877164 -49 CTCTCCTCTACAGGATAATATT 13 16 1 CAGGATAATA 0.797208 -12 ACGGACATATCAAGGTAATAAAAAAGGTCG 14 27 0 CAAGGTAATA 0.797208 -274 TCAAGGTTATCTCCCGCAATG 19 2 1 CAAGGTTATC 0.63539 -105 GTGAAGGATACAGGGCTATCAAACGATAAG 27 211 1 CAGGGCTATC 0.877713 -39 TTACATCTGACAGCGCAATAGCGTTAAAGA 29 171 0 CAGCGCAATA 0.728245 -130 AAACGCATTTCAGGATAATCCGTAATTTGC 30 68 1 CAGGATAATC 0.86243 -108 ********** Masking position 8 Map Score: 1.46097 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 610 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795