AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iaraC_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 araD 284 L-ribulose-5-phosphate 4-epimerase #2 araB_araC 338 araB: L-ribulokinase, araC: transcriptional regulator for ara operon #3 araJ 125 involved in either transport or processing of arabinose polymers #4 sbcD 189 ATP-dependent dsDNA exonuclease #5 araH_2 23 high-affinity L-arabinose transport system; membrane protein, fragment 2 #6 araG 69 ATP-binding component of high-affinity L-arabinose transport system #7 araF 300 L-arabinose-binding periplasmic protein #8 araE 300 low-affinity L-arabinose transport system proton symport protein #9 ydjK 300 similar to sugar transporter #10 glvA 300 6-phospho-alpha-glucosidase #11 yfiA 64 similar to hypothetical proteins #12 yfiB 105 similar to ABC transporter (ATP-binding protein) #13 yfiD 154 similar to hypothetical proteins #14 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #15 yfiG 174 similar to metabolite transport protein #16 yfhG 88 yfhG #17 yfhI 142 similar to antibiotic resistance protein #18 yncC 300 similar to metabolite transport protein #19 araA 207 L-arabinose isomerase #20 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #21 ysdC 183 similar to endo-1,4-beta-glucanase #22 ytbD 183 similar to antibiotic resistance protein #23 yufN 300 similar to ABC transporter (lipoprotein) #24 yufO 75 similar to ABC transporter (ATP-binding protein) #25 araE 137 permease #26 ywtG 300 similar to metabolite transport protein #27 rbsR 300 transcriptional regulator (LacI family) #28 iolR 300 transcriptional regulator (DeoR family) #29 iolS 53 alternate gene name: yxbF; myo-inositol catabolism #30 yxcE 261 yxcE #31 yxcC 238 similar to metabolite transport protein Motif number 1 CAGGCGTTACATACCGGATGCGGCTAC 1 6 0 AACCGATGCG 0.947929 -279 CCGGTATGTAACGCCTGATGCGACGCTGACGC 1 21 1 AGCCGATGCG 0.996667 -264 CGCAGCGTGTAGGCCAGATAAGACGCGTCAGC 1 45 0 AGCCGATAAG 0.988764 -240 GCGATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 74 1 AGCCGATAAG 0.988764 -211 CAGGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 91 0 AGCCGATGCG 0.996667 -194 CCGGCATTCAACGCCTGATGCGACGCTGGCGC 1 106 1 AGCCGATGCG 0.996667 -179 CGCAGCGCGTAGGCCTGATAAGACGCGCCAGC 1 130 0 AGCCGATAAG 0.988764 -155 GCGATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 159 1 AGCCGATAAG 0.988764 -126 CAGGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 176 0 AGCCGATGCG 0.996667 -109 CCGGCATTCAACGCCTGATGCGACGCTGGCGC 1 191 1 AGCCGATGCG 0.996667 -94 CGCAGCGTGTAGGCCTGATAAGACGCGCCAGC 1 215 0 AGCCGATAAG 0.988764 -70 GCGATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 244 1 AGCCGATAAG 0.988764 -41 TGACTCCTTCGTGCCGGATGCGCTTTGCTTAT 1 261 0 GGCCGATGCG 0.977591 -24 CTCCCTTCTCAGGCCTGAAACGCGTTTTCTTT 16 61 0 AGCCGAAACG 0.948298 -28 * *** ****** Masking position 8 Map Score: 45.4295 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 61 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 CGCGTCTTATCTGGCCTACACGCTGCGATT 1 50 1 CTGGCCTACA 0.979358 -235 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 71 0 CCGGCCTACA 0.99675 -214 CAAAGCGCATCCGGCATTCAACGCCTGATG 1 96 1 CCGGCATTCA 0.962519 -189 CGCGTCTTATCAGGCCTACGCGCTGCGATT 1 135 1 CAGGCCTACG 0.956937 -150 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 156 0 CCGGCCTACA 0.99675 -129 CAAAGCGCATCCGGCATTCAACGCCTGATG 1 181 1 CCGGCATTCA 0.962519 -104 CGCGTCTTATCAGGCCTACACGCTGCGATT 1 220 1 CAGGCCTACA 0.988189 -65 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 241 0 CCGGCCTACA 0.99675 -44 ********** Masking position 7 Map Score: 16.1015 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 37 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGT 2 153 0 TTTTATTTTA 0.95115 -186 TATGCGTCAGATTTATGACAGATTTATGAAAAGCTCGTCGC 4 60 1 ATTTATTTTA 0.807673 -130 ACCTGCGTGAGTTGTTCACGTATTTTTTCACTATGTCTTAC 8 251 1 GTTTATTTTC 0.60468 -50 GTAGTGATGTTATAGTGACATTTTTGTTATATCTGATATTA 9 16 0 TATTATTTTA 0.595721 -285 TCAGAAAATAGTTGTTCATGTTTTTATCCAATAACCTCATA 9 185 0 GTTTATTTTA 0.896844 -116 AGAGGTCTTTTTTTGTTACAGTTTTATAGTACTTTTATTTC 13 26 1 TTTTATTTTA 0.95115 -129 CAATACCCCTTGTTGTAACCGCTTTCTAAAAAGATTATAAG 15 71 0 TGTTATTTTA 0.884876 -104 TCAATGATTTTTTCTTTAAGAATTCGTGTAAATGTGCTGCA 17 48 0 TTTTATTCTA 0.685924 -95 GTTGTTATGTTGTAGTAATGTCTTTGTCACATTATTGTCAT 18 129 0 TGTTATTTTA 0.884904 -172 GTACAAAATATTTATTTATAGGTTTATTTTCCTATCATTAG 19 123 1 TTTTATTTTC 0.774039 -85 AAATAATCTAATTTGTAAGCGCTTTCTAAAATAAAGGAGGT 20 157 1 ATTTATTTTA 0.808046 -40 ATCGGGTATATGTTTTTACAGCTTTCTTTTAGAAAAAGTGA 21 74 0 TGTTATTTTA 0.884922 -110 TGTGATGGGCTGTCCTGAACAATTTCTTAGAATCGATAAAA 23 195 0 TGTTATTTTA 0.884915 -106 TAAATGTAATTTTCGTTAAATTTTAATATAAGTACGTACAA 25 57 1 TTTTATTATA 0.595552 -81 AAATATTAAGTTTTATTAAAATTGTTTCAAAGTCATGCGTT 27 90 0 TTTTATGTTA 0.639331 -211 CTTCATCCATATTTGTGAAGACTTTGTCAAAAAAAGAGTGA 27 142 1 ATTTATTTTA 0.808041 -159 CAGGTTACTTTTTGGTCATTTCTTGGTTATATTCTAATCGC 28 63 1 TTTTATTGTA 0.854109 -238 AAAACCAAAAGTTAATCAATAGTTGCTTAAAAATGATAACA 28 224 0 GTTTATTGTA 0.713302 -77 AACTTTTGGTTTTTATTATATATTTATGTTACGTAAAGATT 28 252 1 TTTTATTTTA 0.95113 -49 TTCAAAATCAGTTATTTAGGAATTTATCGCACAAAAAAACA 30 42 0 GTTTATTTTA 0.896846 -220 TTATGGCTCATTTTGTAAGGTTTTGCTTCAAAATCAGTTAT 30 68 0 TTTTATTGTA 0.85411 -194 GCGGGTAAGGTTTTTTTAATGGTTTCTCTGAGCATAAAGTT 31 38 1 TTTTATTTTA 0.95115 -201 *** * * *** * * Masking position 13 Map Score: 17.1807 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 38 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 CAGAATGCTTTTAATAAGCGGGGTTACCGGTTG 2 108 0 TTAAAGCGGG 0.949113 -231 AAGCATTCTGTAACAAAGCGGGACCAAAGCCAT 2 131 1 TAAAAGCGGA 0.888873 -208 ATTGTAAACGTTATCAAGGAGGTCGTCAT 10 282 1 TTAAAGGGGT 0.897682 -19 TATAATAGAAAGAAAATGGGGGGATCTGAT 11 45 1 AGAATGGGGG 0.79758 -20 TTTCTTTACTTTACTATGGCGGTCTTTTTGACG 12 46 0 TTAATGGGGT 0.640354 -60 GTGATAACATTTATCAAGGAGGATAAA 13 138 1 TTAAAGGGGA 0.950922 -17 TTCTCTCATCATAACAAGGCGGACAAAAATAAA 14 48 0 ATAAAGGGGA 0.920037 -46 CAAGGGGTATTGCTGAAGGAGGGATGCATTGGC 15 100 1 TGCAAGGGGG 0.870952 -75 GTCCTATTGAATAAAAAGCCGGGCTCTGCCCCC 19 30 1 ATAAAGCGGG 0.917189 -178 CTTTTCTTTTAAAAAAAGCCGGGGGCAGAGCCC 19 50 0 AAAAAGCGGG 0.906915 -158 TTTTATTTTATGAGAAAGGGGCAGTTTAC 19 189 1 TGAAAGGGCA 0.670045 -19 GCGCTTTCTAAAATAAAGGAGGTTGAACAAAA 20 175 1 AAAAAGGGGT 0.820884 -22 TTTTGTATAATAAGAATGCAGGACTGATGAAGG 21 149 1 TAAATGCGGA 0.618799 -35 AATGCAGGACTGATGAAGGAGGGTTTGGAAC 21 163 1 TGAAAGGGGG 0.970322 -21 ACAACACATCTTACAAAGGAGGAACATC 22 166 1 TTAAAGGGGA 0.950922 -18 GAGTATTTCCTTCGAAAGGCGGGGAAGAGAAGG 23 97 0 TTCAAGGGGG 0.891351 -204 TTTTATTTTGAAATAAAGGAGCGGTCAATCA 24 55 1 AAAAAGGGCG 0.725644 -21 AACGGTTACATAAACAAGGAGGAGCTGTT 27 282 1 TAAAAGGGGA 0.94458 -19 ACCAGCAAATAAAAGAAGCTGGGTCAGCTTTAT 30 198 0 AAAAAGCGGG 0.906915 -64 *** **** *** Masking position 6 Map Score: 15.12 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 184 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 ATGCGCTTTGCTTATCCGGCCTACAAAATC 1 76 0 CTTATCCGGC 0.952136 -209 ATGCGCTTTGCTTATCCGGCCTACAAAATC 1 161 0 CTTATCCGGC 0.952136 -124 ATGCGCTTTGCTTATCCGGCCTACAAAATC 1 246 0 CTTATCCGGC 0.952136 -39 CTCTGTATTCATTATCCTGCTGAATAG 3 8 0 ATTATCCTGC 0.798934 -118 CTTGCTGGTCGTTATCCTGCAAGCTATCAC 3 57 1 GTTATCCTGC 0.915527 -69 TGCCATTTGCTTTTTTCTGCGCCACGGAAA 4 121 0 TTTTTTCTGC 0.623064 -69 CAGAGGGGAATTTTTCCGGCAAA 6 4 0 TTTTTCCGGC 0.97525 -66 TTTTTCCTGCCAGCAGAGAG 8 291 0 TTTTTCCTGC 0.969014 -10 ACCTTTGTCCTGCACAGAGGTCT 13 4 1 TTTGTCCTGC 0.938598 -151 TTTATCCTCCTTGATAAATG 13 145 0 TTTATCCTCC 0.935502 -10 ATTTTTTATTTTTGTCCGCCTTGTTATGAT 14 44 1 TTTGTCCGCC 0.89933 -50 AATTAGATTATTTATCCTCCCTTCCTGTCA 20 140 0 TTTATCCTCC 0.935502 -57 CGATGTCACGGTTTTCCGCCCGGAACGCCT 23 60 1 GTTTTCCGCC 0.863648 -241 CGCCGAAACATTTTACCTGCTGCGGCGTCC 26 134 0 TTTTACCTGC 0.727951 -167 TTTTAGCCTCTTTTTCCGGCCATTAAACCT 26 219 0 TTTTTCCGGC 0.97525 -82 TCTGTTTCCTCCATAGACCATC 30 250 0 TGTTTCCTCC 0.647813 -12 ********** Masking position 3 Map Score: 18.8353 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 591 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 6 TATCCGGCCTACAAAATCGCAGCGTGTAGGC 1 63 0 AAAAATCGCA 0.957363 -222 AGGCCGGATAAGCAAAGCGCATCCGGCATTC 1 84 1 ACAAAGCGCA 0.975867 -201 TATCCGGCCTACAAAATCGCAGCGCGTAGGC 1 148 0 AAAAATCGCA 0.957363 -137 AGGCCGGATAAGCAAAGCGCATCCGGCATTC 1 169 1 ACAAAGCGCA 0.975867 -116 TATCCGGCCTACAAAATCGCAGCGTGTAGGC 1 233 0 AAAAATCGCA 0.957363 -52 AGGCCGGATAAGCAAAGCGCATCCGGCACGA 1 254 1 ACAAAGCGCA 0.975867 -31 CCTATTTATTACAACAGGGCAAATC 4 5 0 AAACAGGGCA 0.755646 -185 CGCAGAAAAAAGCAAATGGCACATCTGTTTG 4 130 1 ACAAATGGCA 0.889593 -60 GGAGAGCAATATCACATCGCAGAATTACAGT 7 136 0 ACACATCGCA 0.920413 -165 CTATATAAATAAAAAAGAGCAGATTCAAATC 22 111 0 AAAAAGAGCA 0.747093 -73 AAGATTTCTAAAAAAATCCCACAGACAATGT 26 247 1 AAAAATCCCA 0.723923 -54 * ********* Masking position 6 Map Score: 10.8234 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 90 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 AACGTTATCAAGGAGGTCGTCAT 10 288 1 AGGAGGTCGT 0.923125 -13 AGCGTAACAGGAGGCTGATGATCAGCCT 17 9 1 AGGAGGCTGA 0.980988 -134 TGCAAACAAAAAGAGGCTGATCATCAGCCT 17 22 0 AAGAGGCTGA 0.818442 -121 TCTAAAATAAAGGAGGTTGAACAAAA 20 181 1 AGGAGGTTGA 0.935726 -16 TTTTTCTAAAAGAAAGCTGTAAAAACATAT 21 78 1 AGAAAGCTGT 0.657975 -106 CGCAGGGATAAGGAGGTCGAGCCCTTATCC 24 15 1 AGGAGGTCGA 0.923127 -61 GAGAAGTAAGAGAAGGCCGTCCAATCTTGC 28 178 1 AGAAGGCCGT 0.947814 -123 ATTTTATTCTAGGAGGCAGATC 29 42 1 AGGAGGCAGA 0.914617 -12 TCTCCATTGGAGAAGGCTGTTTTCTTC 30 8 0 AGAAGGCTGT 0.956558 -254 TCTCCAATGGAGAAGGCTGTTTTTTTGTGC 30 25 1 AGAAGGCTGT 0.956558 -237 ********** Masking position 4 Map Score: 9.96953 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 48 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 TCTGATGCAATATGGACAATTGGTTTCTTC 2 36 0 TATGGACAAT 0.697393 -303 CCGCTAATCTTATGGATAAAAATGCTATGG 2 247 0 TATGGATAAA 0.927024 -92 AAAAAACGGGTATGGAGAAACAGTAGAGAG 2 303 0 TATGGAGAAA 0.932262 -36 AGGCTAATCTTATGGATTAATCTGCTGTGC 7 38 1 TATGGATTAA 0.91159 -263 ATTGCTCTCCTATGGAGAATTAATTTCTCG 7 157 1 TATGGAGAAT 0.890286 -144 ATAACCATGATATGGATTATGATGATCTAC 8 49 0 TATGGATTAT 0.858744 -252 TGATAATTAATATGGATTATTTCATAACCA 8 72 0 TATGGATTAT 0.858744 -229 ACAGCATAAATATGGATTAAATTGCTGCGA 8 209 0 TATGGATTAA 0.91159 -92 CATTGCAGCTGATGGAGAAAGGGAGTCATC 26 278 1 GATGGAGAAA 0.721588 -23 TCTTCACAAATATGGATGAAGATTTCTTGA 27 133 0 TATGGATGAA 0.895267 -168 TTCGATGGTCTATGGAGGAAACAGA 30 247 1 TATGGAGGAA 0.902545 -15 ********** Masking position 6 Map Score: 7.70507 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 56 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 TTTTAACGAGAAATGAAATCGCTTCCATAGGG 9 126 1 AAAGAAATCC 0.898082 -175 TTTTGACGGCAAACGAAAACCCTCCCGAAAAG 12 22 0 AAAGAAAACC 0.954708 -84 CATTTTACGAAAATGAAATAAAAGTACTATAA 13 49 0 AAAGAAATAA 0.652728 -106 AGGCGGACAAAAATAAAAAATCCCCCTGCCGT 14 33 0 AAAAAAAAAC 0.775431 -61 GATGTCCTGAAATGACAAAACAATGTCTTCA 15 10 1 AAAGACAAAC 0.716716 -165 TCATTGTAATAAAAGAAAACGCGTTTCAGGCC 16 50 1 AAAGAAAACC 0.954708 -39 ACGAATTCTTAAAGAAAAAATCATTGAATTCA 17 62 1 AAAAAAAAAC 0.775431 -81 CCTTTCTCATAAAATAAAACGCTTTCAAATAC 19 176 0 AAATAAAACC 0.624183 -32 TAAGCTATATAAATAAAAAAGAGCAGATTCAA 22 114 0 AAAAAAAAAA 0.472333 -70 TATCTTGAATAAACGAAAAATCGGATTGGCG 23 280 1 AAAGAAAAAC 0.945486 -21 ATTTCAAAATAAAAGAAAAACAAGGGATAAGG 24 37 0 AAAGAAAAAA 0.818055 -39 TTGAAGGTTTAAATGAAAACGCTTTACTCAAC 25 98 1 AAAGAAAACC 0.954708 -40 TAAAAATATCAAAAGAAATCTAATTGTAAATT 27 211 0 AAAGAAATCA 0.695524 -90 AGTTTAGGAAAAACGAAATAACTTTATGCTCA 31 66 0 AAAGAAATAC 0.878795 -173 *** ****** * Masking position 6 Map Score: 9.45256 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 101 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 CAGATAAGACGCGTCAGCGTCGCATCAGGCG 1 32 0 GCGCAGCGTC 0.997215 -253 CTGATAAGACGCGCCAGCGTCGCATCAGGCG 1 117 0 GCGCAGCGTC 0.997194 -168 CTGATAAGACGCGCCAGCGTCGCATCAGGCG 1 202 0 GCGCAGCGTC 0.997194 -83 ACCCTGCCATGCGGCAGGGTCATAAAA 8 7 0 GCGCAGGGTC 0.990187 -294 CATTTTACCTGCTGCGGCGTCCAATATAAGG 26 125 0 GCTCGGCGTC 0.968621 -176 *** ******* Masking position 10 Map Score: 6.89944 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 73 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 GCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCAG 1 60 0 CCTCCGAGCG 0.97882 -225 GCTTATCCGGCCTACAAAATCGCAGCGCGTAGGCCTG 1 145 0 CCTCCGAGCG 0.97882 -140 GCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCTG 1 230 0 CCTCCGAGCG 0.97882 -55 GTTGACTCCTTCGTGCCGGATGCGCTTTGCTTAT 1 261 0 CCTCGGTGCG 0.926614 -24 TTTTATGACCCTGCCGCATGGCAGGGTTTTTTATAC 8 10 1 CCTCGGAGGG 0.994675 -291 CTTAGCATGTCAATCCCTATGGAAGCGATTTCATTTC 9 135 0 CAACGGAGCG 0.88084 -166 TAGGGATTGACATGCTAAGAAGAAGGGAAGGTTATGA 9 153 1 CATCAGAGGG 0.945682 -148 AGAACCTTTTCATAAGAATTGGAAGGGCGTATATTCA 10 68 1 CATAGGAGGG 0.927233 -233 AGACTGCCCTCCTTTTCGGGAGGGTTTTCGTTTG 12 8 1 CCTCGGAGGG 0.994683 -98 AATCCCCTTGCCGAAATAACGGCAGGGGGATTTTTTA 14 15 1 CCGAGGAGGG 0.802637 -79 GGTGCTCTGCCATTCTTGAAAGAAGGGGAAGAAAGCC 15 148 1 CATCAGAGGG 0.945682 -27 GCTTATTAAGTATTCTTAAAGGCAGGGGAA 18 281 1 TATCGGAGGG 0.868997 -20 CTTTACTCAACATTCGGGAGGGCAGGGAA 25 119 1 CATCGGAGGG 0.990168 -19 *** * ** **** Masking position 12 Map Score: 18.1585 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 119 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 ATCCATATCATGGTTATGAAATAATCCATAT 8 62 1 TGTTATGAAA 0.808977 -239 ATAATTCAACTTAATTTGAAAATTGGAATAT 8 160 1 TTATTTGAAA 0.676755 -141 GCCCTTCCAATTCTTATGAAAAGGTTCTTTT 10 65 0 TTTTATGAAA 0.749992 -236 TCGCCTCCTTTGATTTTAAAAAACAACGAGT 17 117 0 TGTTTTAAAA 0.628335 -26 TGCCCCCGGCTTTTTTTAAAAGAAAAGATTG 19 56 1 TTTTTTAAAA 0.544629 -152 ACGTATCTTTTGTATTTGAAAGCGTTTTATT 19 165 1 TGATTTGAAA 0.747188 -43 CCGGCAAATGTGATTATGAAACATATCGTTA 22 78 0 TGTTATGAAA 0.808977 -106 TGTTTTTCTTTTATTTTGAAATAAAGGAGCG 24 47 1 TTTTTTGAAA 0.917741 -29 TATAAGTTCTTGTTTTTGAAAATTGATAACG 26 78 1 TGTTTTGAAA 0.940286 -223 TCTGTGGGATTTTTTTAGAAATCTTTTAGCC 26 241 0 TTTTTAGAAA 0.502966 -60 TCTAAACGCATGACTTTGAAACAATTTTAAT 27 86 1 TGCTTTGAAA 0.712985 -215 GTTTTCACTCTTTTTTTGACAAAGTCTTCAC 27 156 0 TTTTTTGACA 0.619329 -145 ACAATTAGATTTCTTTTGATATTTTTATTGC 27 216 1 TTTTTTGATA 0.523377 -85 CCTAAATAACTGATTTTGAAGCAAAACCTTA 30 63 1 TGTTTTGAAG 0.68122 -199 TTTGAAACATTTGTTTTGAAAAAACGGAAAC 31 132 0 TTTTTTGAAA 0.917741 -107 ** ******** Masking position 9 Map Score: 6.17014 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 105 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 13 GCGTTACATACCGGATGCGGCTAC 1 4 0 CCGGTGCGGC 0.882931 -281 GTATGTAACGCCTGATGCGACGCTGACGCGT 1 24 1 CCTGTGCGAC 0.933271 -261 CTGATGCGACGCTGACGCGTCTTATCTGGCC 1 35 1 GCTGCGCGTC 0.973041 -250 GATGCGCTTTGCTTATCCGGCCTACAAAATC 1 76 0 GCTTTCCGGC 0.897987 -209 GCATTCAACGCCTGATGCGACGCTGGCGCGT 1 109 1 CCTGTGCGAC 0.933271 -176 CTGATGCGACGCTGGCGCGTCTTATCAGGCC 1 120 1 GCTGCGCGTC 0.97287 -165 GATGCGCTTTGCTTATCCGGCCTACAAAATC 1 161 0 GCTTTCCGGC 0.897987 -124 GCATTCAACGCCTGATGCGACGCTGGCGCGT 1 194 1 CCTGTGCGAC 0.933271 -91 CTGATGCGACGCTGGCGCGTCTTATCAGGCC 1 205 1 GCTGCGCGTC 0.97287 -80 GATGCGCTTTGCTTATCCGGCCTACAAAATC 1 246 0 GCTTTCCGGC 0.897987 -39 TTTTATGACCCTGCCGCATGGCAGGGTTTT 8 10 1 CCTGCGCATG 0.321109 -291 CACATAACGACATGTCGCAGCAATTTAATCC 8 195 1 CATGCGCAGC 0.474466 -106 TATTTATATAGCTTACTCGGCAGAATTTCAA 22 131 1 GCTTCTCGGC 0.661554 -53 GCCCGGAACGCCTTCCGCATCCTTCTCTTCC 23 77 1 CCTTCGCATC 0.632601 -224 TTGGTTCAAAGCTGATCCGGCCAGTCATGTG 23 232 0 GCTGTCCGGC 0.969938 -69 AAACATTTTACCTGCTGCGGCGTCCAATATA 26 128 0 CCTGTGCGGC 0.983811 -173 ATGAAATAAAGCTGACCCAGCTTCTTTTATT 30 193 1 GCTGCCCAGC 0.875851 -69 **** ****** Masking position 8 Map Score: 21.1841 Number of sites scoring better than the average of aligned sites = 2335 Number in coding regions = 1892 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 14 CAATTGGTTTCTTCTCTGAATGGTGGGAGTA 2 19 0 CTTCTCTGAT 0.923862 -320 AGATAATTCGCCCCTCTGTATTCATTATCCT 3 20 0 CCCCTCTGAT 0.987792 -106 CGGAAAAATTCCCCTCTGCATGATGCAGAGG 6 16 1 CCCCTCTGAT 0.987792 -54 TCGTTCACACCCCCTCTGCATCATGCAGAGG 6 28 0 CCCCTCTGAT 0.987792 -42 CTTAGATTTTCGCCTCTGGATTTGTAACCGT 18 207 0 CGCCTCTGAT 0.967931 -94 CAGTTCTATTCTTCCCTGAATAAGCGTGGTG 23 131 0 CTTCCCTGAT 0.816069 -170 ******** ** Masking position 7 Map Score: 3.47882 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 7 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 15 TCACTCCATCCAAAAAAACGGGTATGGAGAA 2 314 0 CAAAAAAAGG 0.908198 -25 AAAACTGTAACAAAAAAAGACCTCTGTGCAG 13 20 0 CAAAAAAAAC 0.860743 -135 AAATGTGCTGCAAACAAAAAGAGGCTGATCA 17 29 0 CAAACAAAAG 0.908198 -114 TTTGTACAGACAAAAAAATAGAATCCACCTC 20 34 0 CAAAAAAAAG 0.969835 -163 TCCTTTATTTCAAAATAAAAGAAAAACAAGG 24 44 0 CAAAATAAAG 0.869705 -32 AAGACTTTGTCAAAAAAAGAGTGAAAACCTT 27 159 1 CAAAAAAAAG 0.969835 -142 ATTTATCGCACAAAAAAACAGCCTTCTCCAT 30 31 0 CAAAAAAAAG 0.969835 -231 ******** ** Masking position 7 Map Score: 2.86992 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 13 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911