AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icytR_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 tsx 298 nucleoside channel; receptor of phage T6 and colicin K #2 yajI 90 orf, hypothetical protein #3 yohJ 238 orf, hypothetical protein #4 cdd 129 cytidine/deoxycytidine deaminase #5 udp 298 uridine phosphorylase #6 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #7 priA 202 primosomal protein N'(= factor Y)(putative helicase) #8 deoC 257 2-deoxyribose-5-phosphate aldolase #9 deoA 126 thymidine phosphorylase #10 deoB 51 phosphopentomutase #11 deoD 56 purine-nucleoside phosphorylase #12 yhjM 103 similar to transcriptional regulator (LacI family) #13 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #14 yjlC 300 yjlC #15 yjlD 39 similar to NADH dehydrogenase #16 yjmA 197 similar to glucuronate isomerase #17 yjmB 67 similar to Na+:galactoside symporter #18 yjmC 104 similar to malate dehydrogenase #19 yjmE 24 similar to D-mannonate hydrolase #20 yjmG 47 similar to hexuronate transporter #21 yjmH 87 similar to transcriptional regulator (LacI family) #22 deoD 300 purine nucleoside phosphorylase #23 drm 160 phosphodeoxyribomutase #24 ripX 300 integrase/recombinase #25 cdd 118 cytidine/deoxycytidine deaminase #26 yqfF 78 yqfF #27 yqfC 56 yqfC #28 yqfB 24 yqfB #29 yqfA 21 yqfA #30 yqeZ 130 yqeZ #31 rpsU 163 ribosomal protein S21 #32 ccpA 274 transcriptional regulator (Lacl family) #33 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #34 ytxJ 23 alternate gene name: csb40; similar to general stress protein #35 ytxH 27 alternate gene name: csb40; similar to general stress protein #36 ytxG 161 alternate gene name: csb40; similar to general stress protein #37 murC 249 UDP-N-acetyl muramate-alanine ligase #38 ytpS 159 ytpS #39 ytpP 234 similar to thioredoxin H1 #40 pdp 29 pyrimidine-nucleoside phosphorylase #41 nupC 115 pyrimidine-nucleoside transport protein #42 dra 105 deoxyribose-phosphate aldolase #43 deoR 90 transcriptional regulator #44 yxxB 72 yxxB #45 yxeR 69 similar to ethanolamine transporter #46 yxeN 22 similar to amino acid ABC transporter (permease) #47 yxeM 24 similar to amino acid ABC transporter (binding protein) #48 yxeK 185 similar to monooxygenase #49 yxeI 154 similar to penicillin amidase #50 yxeH 39 similar to hypothetical proteins #51 yxeF 87 yxeF Motif number 1 GTACTGACTTTCGCCCTTGTTGCAAACTTT 1 96 0 TCGCCCTTGT 0.622098 -203 AACGCAATTTGCGCCTTTTTCACTCCCGCA 1 253 1 GCGCCTTTTT 0.988487 -46 CAAAAGCGTTGCGCCTTTGTTGTATCGTCA 2 58 0 GCGCCTTTGT 0.975435 -33 TAACATAGCGCCTCATTTTTTTGCGGGTGA 3 15 0 CCTCATTTTT 0.618053 -224 GCGATGCGTCGCGCATTTTTGATGTATGTT 4 16 1 GCGCATTTTT 0.92955 -114 GTATGATTTCGCGCCTTCGTACGAAATGAT 7 95 0 GCGCCTTCGT 0.775571 -108 CGAAGGTGATGCGCCATTGTAAGAAGTTTC 8 29 1 GCGCCATTGT 0.729281 -229 AGAGTATGAGGCGGCTTTTGCCGGATGCGT 9 89 0 GCGGCTTTTG 0.784726 -38 AGCGTTGACTCCGCCTTTGTTATGTCACAA 11 24 1 CCGCCTTTGT 0.955842 -33 CCTTTTTAAGTCGGATTTTTACAAGAAGTA 13 92 0 TCGGATTTTT 0.474033 -32 TTGAATCATCCTCCTTTTTAAGTCGGATT 13 105 0 CCTCCTTTTT 0.91327 -19 TAAGCAGTTTGCTGATTTTTTTGGAAAGGG 14 262 0 GCTGATTTTT 0.568653 -39 GCAGGTGGCTGCGGCTTTTTTGTTTAGAGC 23 13 1 GCGGCTTTTT 0.974445 -148 CTTGAAAGCCTCCTTTTTTTCTATACGT 23 143 0 CCTCCTTTTT 0.91327 -18 GTCGAACCATCCGCCTTTTTCATCCTGATC 24 241 0 CCGCCTTTTT 0.979081 -60 ACATAATCGCGCGCTTTTTTTCACGCCCAT 25 49 0 GCGCTTTTTT 0.876112 -70 AGGCCGCACGGCGGCCTTTTGGATTGTTCA 32 12 0 GCGGCCTTTT 0.91133 -263 AGGCCGCCGTGCGGCCTTTTTTTATGCTTT 32 25 1 GCGGCCTTTT 0.91133 -250 ATATCATCTGGCGCTTTTTTTTGTAAAAAA 33 25 1 GCGCTTTTTT 0.876112 -211 CAAGGGCTTAGCGGCTTTTCACATGATTCG 38 36 0 GCGGCTTTTC 0.870273 -124 GGTTTTCTCCTTTTTCAAACGTATG 45 55 0 TCTCCTTTTT 0.748182 -15 TTGATTTTCCCGCCTTTTCTATTT 47 6 0 CCGCCTTTTC 0.891708 -19 TCTTTCCTCCTTTTTTGGGCGAATG 51 73 0 CCTCCTTTTT 0.91327 -15 ********** Masking position 7 Map Score: 25.6752 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 908 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 2 GCAGTCCTGCAGAATGAAGGGTGATTTATGT 5 140 1 AAATGAAGGG 0.742695 -159 AACAACTTTTTTAAGGAAGGGAAAAT 12 88 1 TAAGGAAGGG 0.870825 -16 CCTTTTTATTATAAGGAAATGGAGGTACACT 13 50 0 AAAGGAAATG 0.643267 -74 AAAGCGTGAGACAGGGAGAGGCACTACCCTT 14 236 1 AAGGGAGAGG 0.909562 -65 CAAAAAACTGAAAAGGAAGGAGGCACTTGC 18 85 1 AAAGGAAGGA 0.939537 -20 AGCCGGTATGATAAGGAAGGGAATTAG 21 71 1 AAAGGAAGGG 0.983109 -17 CCTAACCGCAGGAAGGAGGGGTGGGACATGG 22 106 0 GAAGGAGGGG 0.974945 -195 AACTGGAACCATAGGGAAAGGATCGATTAGG 24 44 1 AAGGGAAAGG 0.918453 -257 CACTTATTATAAAAGGAAGGAGGGATACACC 30 106 1 AAAGGAAGGA 0.939537 -25 TCTATATAATGAAAGAAAGGGGTTG 31 5 0 GAAGAAAGGG 0.683654 -159 TGGTGTATTCGGAGGGAGGGAAAGAGA 31 147 1 GAGGGAGGGA 0.902696 -17 TGTATCCAGTAAAAGGAGTGGTTTTAGG 32 257 1 AAAGGAGTGG 0.773923 -18 AAATGAATGTGCAGGGAAAGGATGAAAAAA 33 216 1 GAGGGAAAGG 0.893984 -20 GCAGGGAAGGAAGAGCTTGAG 34 1 1 GAGGGAAGGA 0.912197 -23 ATGGATATACATAAGGAGGGATTTTTATT 39 9 0 AAAGGAGGGA 0.932778 -226 ATCTTAACAAAAAAGGAAGTGTGCGAAGG 42 87 1 AAAGGAAGTG 0.892717 -19 GGACTGATCCACAGGGAGGTGCAGA 43 76 1 AAGGGAGGTG 0.869028 -15 * ********* Masking position 7 Map Score: 15.5972 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 147 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 TTGTGCGTCCCGCAACATCTTTCCCCGTCATTT 1 29 1 CGCACATTTC 0.726381 -270 ACAACAAAGGCGCAACGCTTTTGAGATAAAGGA 2 65 1 CGCACGCTTG 0.99094 -26 TGCCTGAGTTCGCTGCGCATTGCGTAATGCCGG 3 121 1 CGCTCGCTTC 0.935302 -118 ATCAAAAATGCGCGACGCATCGCAAATT 4 6 0 CGCGCGCTCC 0.938018 -124 TTATGTGATTTGCATCACTTTTGGTGGGTAAAT 5 165 1 TGCACACTTG 0.908708 -134 GGTAAATTTATGCAACGCATTTGCGTCATGGTG 5 191 1 TGCACGCTTG 0.964403 -108 GGTTTAAGGCCGCGTCGCTCTTCCAGCCCTAAC 7 22 1 CGCGCGCCTC 0.938018 -181 CTTACAATGGCGCATCACCTTCGGCATAAAAGG 8 19 0 CGCACACTTG 0.975718 -239 ACATCTACTCCGCAACACACTTCGATACACATC 8 178 0 CGCACACCTC 0.928218 -80 GCCTGATAAGCGCAGCGCATCAGGCGTAAAGCA 9 17 0 CGCACGCTCG 0.976732 -110 CAGTTTCTGTTGCACCGCTTTCG 20 1 0 TGCACGCTTG 0.964403 -47 **** *** ** * Masking position 6 Map Score: 8.21359 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 574 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TCCCGCAACATCTTTCCCCGTCATTTTGTTA 1 36 1 TCTTTCCCGT 0.910382 -263 CGGTAAAGTGTCTTTTTGCTTCTTCTGACTA 5 254 1 TCTTTTTGTT 0.425205 -45 CTTCTTTTCCTTTTATGCCGAAG 8 3 1 TCTTTTCCTT 0.873281 -255 AAGTATCGTTTCTATCCCTTTTTATTATAAG 13 66 0 TCTATCCCTT 0.67884 -58 CAAAAGCATTCCTTTCCGAGTGCTTTCTGGC 16 35 1 CCTTTCCGGT 0.881322 -163 TTCTTTCCCGTGTGCTTCTTCA 22 2 1 TCTTTCCCTG 0.779834 -299 TAAACCGTTTTCATTCCCGTTGACAATGTAT 23 77 0 TCATTCCCTT 0.67884 -84 TAAAACCTTTCTGATTTGGCATATGG 24 6 1 CCTTTCTGTT 0.73168 -295 CCTAATCGATCCTTTCCCTATGGTTCCAGTT 24 44 0 CCTTTCCCAT 0.699299 -257 CTTTTTTTATGCTTTCTCGTTTATTTAGTTA 32 40 1 GCTTTCTCTT 0.732555 -235 TTTTTTCATCCTTTCCCTGCACATTCATTT 33 216 0 CCTTTCCCGC 0.683185 -20 CCTTTAATAAGCTTTCCCATCAGATAAATAA 36 36 0 GCTTTCCCTC 0.827185 -126 TCAGGTTATTTCTTTCCGATTAAACCCAGAT 37 107 0 TCTTTCCGTT 0.957353 -143 TGTAAGATTGGCTTTCCCATTATCATTATCA 39 104 0 GCTTTCCCTT 0.953508 -131 GGTCACCGATCCTTTTCGATTAAGT 40 5 0 CCTTTTCGTT 0.834379 -25 AAGGCAGACTGCTTTCCGTTTTCTGAGGAAA 41 56 1 GCTTTCCGTT 0.942804 -60 CACGCAAGGGTCTTTTCGCTTGAATAGAAAA 48 33 1 TCTTTTCGTT 0.847069 -153 AAAGGCTGGATCTTTTCGTTTTATTTGATGT 49 29 1 TCTTTTCGTT 0.847069 -126 ******** ** Masking position 5 Map Score: 10.7809 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 236 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 ATCGTCAGTTCAGGGTAAAATAGATTTCCG 2 35 0 CAGGGTAAAA 0.702053 -56 GCAAACGCATCAGGATCAAAGTGAACATCA 8 60 0 CAGGATCAAA 0.81395 -198 ATGTCACAAAAAGGATAAAACA 11 45 1 AAGGATAAAA 0.59492 -12 CTGAATATGGCAAGATGAAAAACTGGGTAG 14 146 1 CAAGATGAAA 0.74695 -155 CAACGAATGTCATGATGAAACAAACTTCAG 22 233 0 CATGATGAAA 0.881773 -68 AACCGGTAAACAGGATGAAAACTTTCAATG 24 108 0 CAGGATGAAA 0.971253 -193 GGTGAATCAAGAGTATGAAAACTATCATCG 24 169 1 GAGTATGAAA 0.564617 -132 TGAAATGGATCAGGATGAAAAAGGCGGATG 24 234 1 CAGGATGAAA 0.971253 -67 CGTTTTTATAGATGATGAAAACGTATACTT 32 79 0 GATGATGAAA 0.812957 -196 TGTGCAGGGAAAGGATGAAAAAA 33 223 1 AAGGATGAAA 0.869331 -13 TCGTGTACATGAGGGTGAAATTTACAGATG 39 37 0 GAGGGTGAAA 0.861502 -198 AAATCAGGTGGATGAAAGCCGGCGCCA 43 8 1 GTGGATGAAA 0.676924 -83 AGCCTAAAAACATGATAAAAGGAGTATCGC 48 165 1 CATGATAAAA 0.622134 -21 ********** Masking position 8 Map Score: 7.72141 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 452 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 GATTTCTTAATGTGATCGGTAGCACGTTTTACGA 3 174 1 TGTACGTACA 0.862001 -65 AGATAGCGCGTGAAAACGGTTACAGAATTTTCAT 6 63 0 TGAACGTTCA 0.505624 -93 TCCTAGTTTCTGAAATCGGTAACATGTCAACAAC 12 60 1 TGAACGTACA 0.515397 -44 TTTATGTTTATGACAGCGTTAACATTTCATTTTC 16 76 1 TGAACGTACA 0.6146 -122 TATTTCAAAATGTTAACGTTAACATTTTGATTTG 16 154 0 TGTACGTACA 0.499505 -44 ATCATATACCTGAAAAAGATATCATTGCAGCTGA 22 30 0 TGAAAGTACA 0.661093 -271 AAATATAAAGTGATAGCGGTACCATTATAGGTAA 25 80 1 TGAACGTACA 0.566064 -39 AAACAGTAATTGTAAGCGAATACAAATAAAGGAG 41 84 1 TGTACGATCA 0.531628 -32 *** * ** ** ** Masking position 5 Map Score: 5.58677 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ATAAAATCATTGGAGGTACTGTTC 12 5 0 TGGAGGTACT 0.950512 -99 TATAAGGAAATGGAGGTACACTTTAAAACG 13 42 0 TGGAGGTACA 0.858561 -82 CTGAAAAGGAAGGAGGCACTTGC 18 92 1 AGGAGGCACT 0.96795 -13 ATAGAAAAAAAGGAGGCTTTCAAG 23 147 1 AGGAGGCTTT 0.706188 -14 ATGTTTCAAGAGGAGGTTCTT 26 68 1 AGGAGGTTCT 0.967365 -11 ATGATTTGAAAGGAGGTTCTAACACT 27 7 0 AGGAGGTTCT 0.967365 -50 ATGAGATGAAAGGGGGTTCTTTTTGT 27 41 1 AGGGGGTTCT 0.874066 -16 ACGTATGAAGAGAAGGCACTTATTATAAAA 30 90 1 AGAAGGCACT 0.7475 -41 AGACGTTTGTTGGAGGTACAATT 37 237 1 TGGAGGTACA 0.858561 -13 ********** Masking position 5 Map Score: 5.07932 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 33 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 GGCCGCGTCGCTCTTCCAGCCCTAACGCCAGA 7 29 1 CTTTCCGCCC 0.774069 -174 AGCATCATCCTGACTTGAAATTCGG 7 188 0 ATATCCGACT 0.778302 -15 ATGCGCTGCGCTTATCAGGCCTACGAGACGTA 9 30 1 CTATCAGCCT 0.791685 -97 GCGTCTACGCCTTATCCGGCCTACGGGTAGAT 9 61 0 CTATCCGCCT 0.96473 -66 TGTATCATCAAACATACCGCCTCTCCCACTAT 21 20 0 AAATACGCCT 0.73687 -68 AATCTAAATTATCATCCAGCCCGTCCATTTTA 22 263 0 ATATCCGCCC 0.96473 -38 CTCCTCTTGAAACATCAAGCCCATAAGCAATC 26 51 0 AAATCAGCCC 0.734088 -28 AATAAAAATCCCTCCTTATGTATATC 39 5 1 AAATCCTCCT 0.718321 -230 TTGATTTTCCCGCCTTTTCTATTT 47 10 0 ATTTCCGCCT 0.916405 -15 TATTTTTCGCATTATTCAGCCTAAAAACATGA 48 148 1 ATATTCGCCT 0.794034 -38 TAAAAAATCCAGCCTTCTAAAGGCT 49 4 1 AAATCCGCCT 0.972634 -151 ATAAAACGAAAAGATCCAGCCTTTAGAAGGCT 49 21 0 AAATCCGCCT 0.972634 -134 ** **** **** Masking position 5 Map Score: 6.58448 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 324 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 9 CCGTACCTTATAAAAATGTTGCGCAATGTT 5 57 1 TAAAAATGTT 0.935445 -242 GAGTATCACGAAAAAATGTTAAACCCTTCG 5 226 1 AAAAAATGTT 0.721979 -73 CGCTATCTGCTAAAAATGTTGCCGATGTGA 6 89 1 TAAAAATGTT 0.935445 -67 TTCCCTTCCTTAAAAAAGTTGTTGACATGT 12 81 0 TAAAAAAGTT 0.721981 -23 TAAAAACAAATCAAAATGTTAACGTTAACA 16 148 1 TCAAAATGTT 0.934227 -50 TCATTCTATTTCAAAATGTTAACGTTAACA 16 164 0 TCAAAATGTT 0.934227 -34 CGCCCATTTCTAAAAATGTAAAATAAATGT 25 26 0 TAAAAATGTA 0.841389 -93 TATGAATAAATCAAAATGTACCTTTGTCTT 48 93 0 TCAAAATGTA 0.838704 -93 ********** Masking position 5 Map Score: 3.36656 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 27 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 TTTCTATCCCTTTTTATTATAAGGAAATGG 13 59 0 TTTTTATTAT 0.574797 -65 GAATTGGAGTTTTTTGTGTTTGCTATTTTC 14 60 1 TTTTTGTGTT 0.60683 -241 CTTATTCAATTGTTTATTTTTAGATAAAAA 14 111 1 TGTTTATTTT 0.719509 -190 GCAATGTCTTTTTTTATGTTTATGACAGCG 16 64 1 TTTTTATGTT 0.924072 -134 TTTTGATTTGTTTTTATTTTACCTTTATAT 16 134 0 TTTTTATTTT 0.822034 -64 CCGCTATCACTTTATATTTTACATAATCGC 25 69 0 TTTATATTTT 0.427142 -50 TATCGGGTCATTTTTATGATTGCTTATGGG 26 34 1 TTTTTATGAT 0.780789 -45 AGGTTTCATTTTTTTATGTATAAAAAAAGA 30 46 0 TTTTTATGTA 0.662689 -85 GTGCGGCCTTTTTTTATGCTTTCTCGTTTA 32 33 1 TTTTTATGCT 0.793601 -242 CTACATAAAGTGTTTATGCTATAGATAAGG 32 222 1 TGTTTATGCT 0.681052 -53 GCACATTCATTTTTTATTTTGTAGTTATCA 33 198 0 TTTTTATTTT 0.822034 -38 ATCTCACTGCTTTTTATTTATCTGATGGGA 36 23 1 TTTTTATTTA 0.427142 -139 CCAGTACACATGTTTATGATTGAAGAAAAC 36 103 1 TGTTTATGAT 0.664209 -59 TTTATATGTTTTGTTATGTTTAGTATCAGG 37 133 0 TTGTTATGTT 0.60683 -117 AGCGGCGTATTTTATATGTTTTGTTATGTT 37 143 0 TTTATATGTT 0.662689 -107 TCCCTCCAGTTGTTTATGTTCTTACATGTT 39 209 0 TGTTTATGTT 0.871114 -26 ********** Masking position 5 Map Score: 4.92249 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 148 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 11 TAAAACGTTGATTTTATTTACGAAAGGGGTT 13 18 0 ATTTTTTTAC 0.582474 -106 CTTTCTGGCAATGTCTTTTTTTATGTTTATG 16 57 1 ATGTCTTTTT 0.880035 -141 CAGCGTTAACATTTCATTTTCAAAAAAGAGA 16 89 1 ATTTCTTTTC 0.856204 -109 CTACAAACACATTTTATTTACAAATTATTTT 18 33 0 ATTTTTTTAC 0.582474 -72 AGCTGCAATGATATCTTTTTCAGGTATATGA 22 32 1 ATATCTTTTC 0.644099 -269 TCCGGTTACGATGTTTTTTACCCATGTCCCA 22 85 1 ATGTTTTTAC 0.791541 -216 ATCCTCGAACATTTCTTTTTTCGATATATTC 22 188 1 ATTTCTTTTT 0.729377 -113 TCTTAGAAAGATGTCCTTTTCTTTGCCAT 30 9 0 ATGTCTTTTC 0.941882 -122 TCTAAGAGAGATGTCTTTTTTTATACATAAA 30 33 1 ATGTCTTTTT 0.880035 -98 GTCCGAATTTATGTCGTTTATGATTTGTAAG 32 177 0 ATGTCTTTAT 0.841991 -98 ATGTTCTTACATGTTTTTTATCGATACTCGT 39 193 0 ATGTTTTTAT 0.632182 -42 CATCTCCTTCATGTCGTTTTCAGGCTATAGT 50 15 0 ATGTCTTTTC 0.941882 -25 ***** ***** Masking position 1 Map Score: 4.62222 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 110 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 GGCGTTGCCTCATAATCATGTAATGGGA 4 112 0 TTCTATATCA 0.933303 -18 TGCAACGCATTTGCGTCATGGTGATGAGTATCAC 5 201 1 TTCTATGTGA 0.935668 -98 TTTAACATTTTTTCGTGATACTCATCACCATGAC 5 215 0 TTCTATATCA 0.933303 -84 TTGTAAGAAGTTTCGTGATGTTCACTTTGATCCT 8 45 1 TTCTATGTCA 0.947411 -213 GTAAGTAGATTTCCTTAATTGTGATGTGTATCGA 8 156 1 TTCTATTTGA 0.735941 -102 TGTACCTCCATTTCCTTATAATAAAAAGGGATAG 13 52 1 TTCTATATAA 0.684018 -72 TTTCGATATATTCCTTTATAATCAATGCTGAAGT 22 206 1 TTCTATATCA 0.933303 -95 AACCCCTTTCTTTCATTATATAGACAGGCAGTCG 31 12 1 TTCTATAAGA 0.613839 -152 ATCAATGCCGTTCCCTCATGGTCACGCAAGGGTC 48 11 1 TTCTATGTCA 0.947411 -175 TCGATTTGACTTTCGTTATGCTGATAAAACCAAT 49 80 1 TTCTATGTGA 0.935668 -75 ** * * *** *** Masking position 8 Map Score: 4.34844 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 66 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 TTGGCGACAAGCCAGGAGAATGAA 8 244 1 GCCAGAGTGA 0.801009 -14 ACCTCCCGAGGAAAAGAGTATGAGGCGGCTTTT 9 100 0 GAAAGAGTGA 0.967882 -27 TTTTATTTACGAAAGGGGTTAGACACG 13 5 0 GAAAGGGAGA 0.872978 -119 TCCTTATAATAAAAAGGGATAGAAACGATACTT 13 64 1 AAAAGGGAGA 0.756743 -60 ATCCGACTTAAAAAGGAGGATGATTCAA 13 106 1 AAAAGAGTGA 0.931696 -18 TTCATTTTCAAAAAAGAGATTGATCCCAAAGGA 16 101 1 AAAAGAGTGA 0.931696 -97 AAATACATTGTCAACGGGAATGAAAACGGTTTA 23 75 1 TCAAGGGTGA 0.768453 -86 TACATTTTTAGAAATGGGCGTGAAAAAAAGCGC 25 36 1 GAAAGGGTGA 0.973422 -83 GTCGCAAATTGAAATGAGCGTCATATACTGGGG 37 197 1 GAAAGAGTCA 0.731095 -53 TAACATCGTGTACATGAGGGTGAAATTTACAGA 39 39 0 TACAGAGTGA 0.632681 -196 GATGTTAAACGAAACGAGCTTGATAATGCAAAT 39 65 1 GAAAGAGTGA 0.967882 -170 GAAACGGCGGTGACTCACCAGA 46 1 1 GAAAGGCTGA 0.767671 -22 ATCTGAATTGAAAAGGGGACTGATCAA 49 138 1 AAAAGGGTGA 0.94311 -17 GAATTCACCCACAAGGAGACTGATCAC 51 5 0 ACAAGAGTGA 0.862585 -83 **** *** *** Masking position 4 Map Score: 10.8318 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 112 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 14 AAATAGCAAACACAAAAAACTCCAATTCGA 14 58 0 CACAAAAAAC 0.535828 -243 CACTACCCTTTCCAAAAAAATCAGCAAACT 14 257 1 TCCAAAAAAA 0.505395 -44 AAAAGACATTGCCAGAAAGCACTCGGAAAG 16 46 0 GCCAGAAAGC 0.731083 -152 TTGGAGAGTGCCCAAAAAACTGAAAAGGAA 18 73 1 CCCAAAAAAC 0.941481 -32 CGGATCACCGGCCAAAAAAAGAACAATCAT 22 59 0 GCCAAAAAAA 0.789284 -242 TAGGCACTTCCTCAGAAAAACGGATAATCG 22 154 0 CTCAGAAAAA 0.513059 -147 ATGGGAAGATTCCTGAAAACAGCTGTCGAT 24 77 1 TCCTGAAAAC 0.598054 -224 CCATAAATCCGCCAAAAAAAACGAATCATG 38 15 1 GCCAAAAAAA 0.789284 -145 TGCTGGTCGGCCCAGAAAAGATTAAGCTAT 38 88 0 CCCAGAAAAG 0.87348 -72 TAAAAACCGTCCCAGAAAACTATAAGGGAG 38 127 1 CCCAGAAAAC 0.962712 -33 TTACTGTTTCCTCAGAAAACGGAAAGCAGT 41 63 0 CTCAGAAAAC 0.765626 -53 GCATTATTCAGCCTAAAAACATGATAAAAG 48 156 1 GCCTAAAAAC 0.772662 -30 TGGGACTATAGCCTGAAAACGACATGAAGG 50 11 1 GCCTGAAAAC 0.845064 -29 CACGCATTCGCCCAAAAAAGGAGGAAAGA 51 69 1 CCCAAAAAAG 0.811393 -19 ********** Masking position 6 Map Score: 5.66836 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 523 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 15 TGAACATCACGAAACTTCTTACAATGGCGC 8 39 0 GAAACTTCTT 0.91452 -219 GGATAGAAACGATACTTCTTGTAAAAATCC 13 80 1 GATACTTCTT 0.726369 -44 TTGAATAAGTCAAAATCCTTTACTCTCTCT 14 90 0 CAAAATCCTT 0.761318 -211 AAAAAATCAGCAAACTGCTTATAGTAAAGG 14 271 1 CAAACTGCTT 0.908166 -30 ATCACTATCCGAAAATTCTTAAGACACAGA 17 40 1 GAAAATTCTT 0.775296 -28 TGGCTGAAAATTCTTACATTTATTT 25 6 1 GAAAATTCTT 0.775296 -113 AGTGTTAGAACCTCCTTTCAAATCATA 27 8 1 GAACCTCCTT 0.744454 -49 CGTTATGTAAGAAAATCCTTTAATAAGCTT 36 53 0 GAAAATCCTT 0.845522 -109 TGGATCATACCAAACTGCTTGAGGCAAAAC 39 158 0 CAAACTGCTT 0.908166 -77 TGACGGAAGGCAGACTGCTTTCCGTTTTCT 41 50 1 CAGACTGCTT 0.67345 -66 CAGTCCTGATAAAACTGCTTTTGATTTGCT 43 52 0 AAAACTGCTT 0.654574 -39 GGCGATACTCCTTTTATCATGTT 48 173 0 GATACTCCTT 0.808082 -13 ********** Masking position 2 Map Score: 3.49188 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 64 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172