AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_bsub_reg_300.orf -o00220_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yitV 120 similar to hypothetical proteins #2 yitW 63 similar to hypothetical proteins #3 yitX 54 yitX #4 yitY 57 similar to L-gulonolactone oxydase #5 yitZ 44 similar to multidrug resistance protein #6 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #7 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #8 proB 300 gamma-glutamyl kinase #9 yodT 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #10 argG 169 argininosuccinate synthase #11 moaB 84 molybdopterin precursor biosynthesis protein B #12 ackA 300 acetate kinase #13 ureA 300 urease (gamma subunit) #14 ywhF 201 similar to spermidine synthase #15 rocF 73 arginase #16 rocE 222 amino acid permease #17 rocD 240 ornithine aminotransferase Motif number 1 GTTATACTGTAGAAAAAAGGAGTGAGGGAAC 2 43 1 AAAAAAAGGG 0.974932 -21 AACAAAAAAGGACAGCCTGACATGT 3 2 1 AAAAAAAGGG 0.974932 -53 CCTTTCAGCTGTAAAAAAGGACAGCCTCACATGT 3 30 0 GAAAAAAGGG 0.952811 -25 TGGTCATAAAAACAGCAGGGAGAGCACTA 4 6 1 AAAAAACAGG 0.974932 -52 TCAGCCGCATAAAAAAACAGGCTGACCGCG 6 7 0 AAAAAACAGG 0.974932 -200 TTCCGCTCAAAAAAAATCAGCACGACTCCAGCAC 6 66 0 AAAAATCAGG 0.899957 -141 GCATAATATAAAAAAATCATTGAGCGTTGAAGAG 8 31 1 AAAAATCATG 0.69608 -270 ATAAGAAAGGATGAAAACAGCATGTATGGATACT 9 47 1 AGAAAACAGG 0.938873 -254 GACAGAAAACATAAAAGAGGTGGGCCA 11 68 1 AAAAAGAGGG 0.933972 -17 GATATTCACCGGGAAAAAAGTACGAAAAACGAAG 12 245 1 GGAAAAAAGG 0.906781 -56 AGAAATTTCCAGAAAAAAAGACATTTGTTATCTT 13 52 1 AAAAAAAAGT 0.65357 -249 GCTTTATATGACAAAAGAAGGAGGACTACAG 13 280 1 AAAAAGAAGG 0.94522 -21 TAGTAGAAACATAAAAAAAGGGGGAACCCGTT 14 9 0 AAAAAAAAGG 0.979356 -193 TACTATTATGAGAAAAAAAGATCGTTTTTAAACA 14 38 1 AAAAAAAAGG 0.979356 -164 GAGGATGGCGGGGAAAAAGTAAAGATGCGTCCTG 14 80 0 GGAAAAAGTG 0.669998 -122 TTTTCACCTAAGGAAAAAGTATAGAGGATGGCGG 14 103 0 AGAAAAAGTG 0.796356 -99 AGCAATATTAAGAAAATAATTGAGGGAGGTTCAT 17 14 0 AAAAATAATG 0.736415 -227 TCTATTTTATAAAAAAACGGAGAGGATATGCAAA 17 48 1 AAAAAACGGG 0.969588 -193 GAGAGGATATGCAAAAGAATTTTGCACTTGCTGA 17 67 1 GAAAAGAATG 0.6952 -174 AGGACAAGGTGCAAAAACATTCTGATATTTCGAG 17 109 0 GAAAAACATG 0.837155 -132 ATGTTGAAACAGAAAACAAGGGGGAATTCAAAT 17 218 1 AAAAACAAGG 0.865532 -23 * ******** * Masking position 6 Map Score: 27.4888 Number of sites scoring better than the average of aligned sites = 1454 Number in coding regions = 1123 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 330 Fraction of orfs with sites within 600 bp upstream = 0.0530035 Motif number 2 ACAGTATAACGTAAATTCAGCTCTTGTTAATA 2 21 0 GTAATCAGCT 0.918083 -43 TTCCGCTCAAAAAAAATCAGCACGACTCCAGC 6 68 0 AAAATCAGCA 0.951152 -139 CTCTGTCACAGAAAGGTCTGCTTACTAATCCT 8 63 0 GAAATCTGCT 0.951837 -238 AGGCTCTTTTGAAATTTCAGCATCTAGCAAAT 9 173 0 GAAATCAGCA 0.98879 -128 TAAATACTATGAAACTTCACCTGAAATTTAGG 10 16 1 GAAATCACCT 0.949892 -154 TTTTATAAAAAAAACTTCACCTAAATTTCAGG 10 35 0 AAAATCACCT 0.807127 -135 TGTTTAAATGGAAAAGTCAGATATTTTTCGGA 12 204 1 GAAATCAGAT 0.951152 -97 GTCGATCACGGAAAGATCAGATTAACGCGTTT 13 104 0 GAAATCAGAT 0.951152 -197 ATTTACAACAGAAAAATCAGCACTCCCTATTT 16 49 1 GAAATCAGCA 0.98879 -174 GATCTAAGCTGGAACATCTGCATGGTGCTATC 16 172 0 GGAATCTGCA 0.788214 -51 ATTTCGAGCGAAAATTTCAGCAAGTGCAAAAT 17 85 0 AAAATCAGCA 0.951152 -156 ATTTTCGCTCGAAATATCAGAATGTTTTTGCA 17 102 1 GAAATCAGAA 0.951152 -139 **** ****** Masking position 4 Map Score: 16.5747 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 316 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 ATCTAAGGTTAAAGGAGCTTTTC 1 2 0 AAAGGCTTTT 0.846511 -119 TTAATTATAAAAATGAATTTTTATGCCTTTAT 7 23 0 AAAGATTTTT 0.868336 -48 TGCAAAGAAAAAAGACACTTGTC 8 2 0 AAAAACTTGT 0.686788 -299 CACCTTGATTGAACGCGCTTGTGCACGCTCCG 8 198 0 GAAGGCTTGT 0.963535 -103 AATCAGGATGAAATGGGTTTTTTTATTGTAGA 8 259 1 AAAGGTTTTT 0.924653 -42 CAATTAACACAAATGTATTTGTCCCGCAGCCA 9 100 0 AAAGATTTGT 0.889519 -201 TCCTAATAAGGAAGGCTCTTTTGAAATTTCAG 9 185 0 GAAGTCTTTT 0.835295 -116 TCCTTATTAGGAAGGCTCTTTTTATGTGAAAA 9 205 1 GAAGTCTTTT 0.835295 -96 CTTTTTATGTGAAAAAGTTTTTGCGGGGAACG 9 222 1 GAAAGTTTTT 0.570978 -79 ACAATATGGTAAAAGGGGTTTTGAGGTGGGAG 9 278 1 AAAGGGTTTT 0.852439 -23 TGAAAAAACGAAACGTACTTGTTAAAGTGTAT 10 71 1 AAAGACTTGT 0.938915 -99 TATACATACAAAATGTATTTTTATTAAATATA 10 100 1 AAAGATTTTT 0.856639 -70 ACATTCAAGAGAATGTGCTTTCATGCGAT 11 8 0 GAAGGCTTTC 0.807384 -77 ACATTCTCTTGAATGTGCTTTTTTGTTGATGC 11 24 1 GAAGGCTTTT 0.912774 -61 AAAGTACGAAAAACGAAGTTGTTGATACAGAG 12 261 1 AAAGAGTTGT 0.798256 -40 TTCCAGAAAAAAAGACATTTGTTATCTTAGTC 13 58 1 AAAAATTTGT 0.519279 -243 CGATGTTTAAAAACGATCTTTTTTTCTCATAA 14 43 0 AAAGTCTTTT 0.796091 -159 CGAAATATCAGAATGTTTTTGCACCTTGTCCT 17 111 1 GAAGTTTTGC 0.520243 -130 *** * ****** Masking position 9 Map Score: 16.7748 Number of sites scoring better than the average of aligned sites = 1057 Number in coding regions = 846 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 ATTTATAAATTTTCTGTTCAATGGGAATTCCG 6 95 0 TTTTGTTAAT 0.77149 -112 ATATTTAATATTTTTATTCATTTATAAATTTT 6 114 0 TTTTATTATT 0.927862 -93 ATTGAATTAATTTTTATTCATGTTATAATGTT 6 149 1 TTTTATTATG 0.939872 -58 GACAAATACATTTGTGTTAATTGTTGTCTTGT 9 109 1 TTTTGTTATT 0.855483 -192 TGTCTTGTTCATTTTATTAATTATTGTTGGAG 9 133 1 ATTTATTATT 0.577773 -168 GGTGAAGTTTTTTTTATAAAAGGCTTGAAAAA 10 46 1 TTTTATAAAG 0.774802 -124 ACAAAATGTATTTTTATTAAATATAATTTATT 10 107 1 TTTTATTAAT 0.879816 -63 TGAATGTGCTTTTTTGTTGATGCATGATAGTG 11 33 1 TTTTGTTATG 0.877964 -52 TGCTTTTATTTATGCTTTTGAAGA 12 3 1 CTTTATTATG 0.711266 -298 CACTATAGGTTTTGTATTGATGAACGCTTACA 12 96 0 TTTTATTATG 0.939872 -205 ATTCACTTCGTTTGTATAAATTTACAACAGAA 16 30 1 TTTTATAATT 0.842974 -193 AGAAGTGAATTTTATATTAAATAGATAGAGAC 16 121 1 TTTTATTAAT 0.879816 -102 CCTCTCCGTTTTTTTATAAAATAGAAGCAATA 17 41 0 TTTTATAAAT 0.745192 -200 CTGCTTTCCCTTTATATAAATGCAAGTTCTGT 17 180 0 TTTTATAATG 0.866954 -61 *** **** *** Masking position 10 Map Score: 12.1535 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 245 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 CCTCACATGTCAGGCTGTCCTTTTTTGTT 3 10 0 CAGGCTGTCC 0.852705 -45 CCTGACATGTGAGGCTGTCCTTTTTTACAG 3 26 1 GAGGCTGTCC 0.928816 -29 CATAAAAAAACAGGCTGACCGCG 6 4 0 CAGGCTGACC 0.877033 -203 CAAAGACCAAGAGGGTGAACTTGTT 6 192 1 GAGGGTGAAC 0.906512 -15 TATTCATCAAGAGGTGGGCTGTTAG 7 56 1 GAGGTGGGCT 0.9133 -15 GCGTTCAATCAAGGTGGTACCACGGAAACC 8 214 1 AAGGTGGTAC 0.850778 -87 AAGGGGTTTTGAGGTGGGAGC 9 290 1 GAGGTGGGAG 0.823226 -11 AAACATAAAAGAGGTGGGCCA 11 74 1 GAGGTGGGCC 0.970291 -11 GCGGAACAGTCAGGCGGGACATCACCTCCC 13 229 0 CAGGCGGGAC 0.957764 -72 AACATAAAAAAAGGGGGAACCCGTT 14 6 0 AAGGGGGAAC 0.873177 -196 TCTCCCTTTCGAGGCTGTATTCATTTATTG 14 176 0 GAGGCTGTAT 0.805072 -26 CTTAAATGTTGAGGTGGAATCACAG 15 59 1 GAGGTGGAAT 0.889253 -15 AACAGAAAACAAGGGGGAATTCAAAT 17 225 1 AAGGGGGAAT 0.689508 -16 ********** Masking position 2 Map Score: 9.40401 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 455 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 CAGCCTGTTTTTTTATGCGGCTGAAATGCG 6 17 1 TTTTATGCGG 0.972838 -190 GCACAAAAACGTTGATGCGGTGCCGCATTT 6 40 0 GTTGATGCGG 0.936316 -167 TGCTGATTTTTTTTGAGCGGAATTCCCATT 6 78 1 TTTTGAGCGG 0.865727 -129 ATCATTGAGCGTTGAAGAGGATTAGTAAGC 8 46 1 GTTGAAGAGG 0.616235 -255 GCGGCAAAATGTTTCAGCGGTTCATTTTGC 8 96 0 GTTTCAGCGG 0.897044 -205 GTTCGGCAGGTTTCATGCGGCAAAATGTTT 8 112 0 TTTCATGCGG 0.881926 -189 ATATACGACATTTTATGCGGGCCAAGTCCC 9 13 0 TTTTATGCGG 0.972838 -288 GGTTACGGATTTGGCTGCGGGACAAATACA 9 89 1 TTGGCTGCGG 0.886759 -212 ATGTGAAAAAGTTTTTGCGGGGAACGTCAT 9 228 1 GTTTTTGCGG 0.78726 -73 TTTTACCATATTGTATGAGTGTCCAAATGG 9 262 0 TTGTATGAGT 0.570321 -39 AAACCGCAAATTGTAAGCGTTCATCAATAC 12 85 1 TTGTAAGCGT 0.900552 -216 CGACTTCTTATTGTAAGCGTTATCAATACG 12 145 1 TTGTAAGCGT 0.900552 -156 TATTCATTTATTGTAAGCGTCTTATCAGCT 14 159 0 TTGTAAGCGT 0.900552 -43 ********** Masking position 2 Map Score: 9.36767 Number of sites scoring better than the average of aligned sites = 1030 Number in coding regions = 936 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 CTGTTTTTTTATGCGGCTGAAATGCGGCAC 6 21 1 ATGCGGCTGA 0.928708 -186 TGCGGCTGAAATGCGGCACCGCATCAACGT 6 32 1 ATGCGGCACC 0.9751 -175 GGCAGGTTTCATGCGGCAAAATGTTTCAGC 8 108 0 ATGCGGCAAA 0.926362 -193 ACGACATTTTATGCGGGCCAAGTCCCAA 9 9 0 ATGCGGGCCA 0.961204 -292 ACGGATTTGGCTGCGGGACAAATACATTTG 9 93 1 CTGCGGGACA 0.919808 -208 TAGCAAATAAAAGCGGCTCCAACAATAATT 9 151 0 AAGCGGCTCC 0.883796 -150 TTCTTCGAGAATGGGGGTCATACGGTAAGA 13 198 0 ATGGGGGTCA 0.897691 -103 CGGAACAGTCAGGCGGGACATCACCTCCCT 13 228 0 AGGCGGGACA 0.9278 -73 TATAAAGCAGATGCGGCTACTACGAATTTG 13 258 0 ATGCGGCTAC 0.916909 -43 ATAATGTCCTATGCGGGTTATAACAAAGAT 15 29 0 ATGCGGGTTA 0.897847 -45 ********** Masking position 5 Map Score: 7.56768 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 204 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 GCAAAAACTTTTTCACATAAAAAGAGCCTT 9 216 0 TTTCACATAA 0.908893 -85 TACTATGAAACTTCACCTGAAATTTAGGTG 10 20 1 CTTCACCTGA 0.929048 -150 ATAAAAAAAACTTCACCTAAATTTCAGGTG 10 33 0 CTTCACCTAA 0.97704 -137 ATATCAACATCTTCTCCGAAAAATATCTGA 12 220 0 CTTCTCCGAA 0.909551 -81 ACGATCTTTTTTTCTCATAATAGTAGAAAC 14 33 0 TTTCTCATAA 0.884546 -169 GAAATCTCATTTTCACCTAAGGAAAAAGTA 14 116 0 TTTCACCTAA 0.953712 -86 AAATTCACTTCTTCTCATAAAGATACATTA 16 103 0 CTTCTCATAA 0.94056 -120 ********** Masking position 10 Map Score: 4.47961 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 96 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 AGAGCACTATGAAAAAGAAATTGCTTGCAT 4 31 1 GAAAAAGAAA 0.931056 -27 TGGGGAAAAACAAATTAAAATGGC 5 5 1 GAAAAACAAA 0.946632 -40 AAAAGGCTTGAAAAAACGAAACGTACTTGT 10 63 1 AAAAAACGAA 0.66419 -107 TGACAGACAGAAAACATAAAAGAGGTGGGC 11 63 1 AAAACATAAA 0.603092 -22 ATCCAGCTTTGAAACACAAAATACAGAGGG 12 53 1 GAAACACAAA 0.958048 -248 AAAAAAGTACGAAAAACGAAGTTGTTGATA 12 258 1 GAAAAACGAA 0.909456 -43 CATAATAGTAGAAACATAAAAAAAGGGGGA 14 18 0 GAAACATAAA 0.885275 -184 GGATGGCGGGGAAAAAGTAAAGATGCGTCC 14 82 0 GAAAAAGTAA 0.737093 -120 ATAACATGTTGAAACAGAAAACAAGGGGGA 17 213 1 GAAACAGAAA 0.945612 -28 ********** Masking position 6 Map Score: 5.06881 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 540 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 10 AAACAGCAGGGAGAGCACTATGAAAAAGAAATTG 4 20 1 GAGAGCATGA 0.990914 -38 TTCTGTGACAGAGAGCAAAATGAACCGCTGAAAC 8 82 1 GAGAGCATGA 0.990914 -219 CGTTACAGGAGAGCGGAGCGTGCACAAGCGCGTT 8 185 1 GAGCGGATGA 0.949521 -116 AAGAAAGGATGAAAACAGCATGTATGGATACTCT 9 49 1 GAAAACATGA 0.878047 -252 ATATTTTTCGGAGAAGATGTTGATATTCACCGGG 12 224 1 GAGAAGATGT 0.727167 -77 TATCTTAGTCGAGCGCAGTCTGGAAAACGCGTTA 13 80 1 GAGCGCATGA 0.984065 -221 AGCAAACTGGGATAGCACCATGCAGATGTTCCAG 16 162 1 GATAGCATGA 0.961455 -61 TACAATTTTCGAGGACAAGGTGCAAAAACATTCT 17 120 0 GAGGACATGA 0.944689 -121 GGGAAAGCAGGATAACATGTTGAAACAGAAAACA 17 202 1 GATAACATGA 0.926985 -39 ******* ** * Masking position 7 Map Score: 6.04404 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 86 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 GAAACCTGCCGAACCTGCCTTGGAGTCCTA 8 128 1 GAACCTGCCT 0.981525 -173 AATTTCAAAAGAGCCTTCCTTATTAGGAAG 9 189 1 GAGCCTTCCT 0.989875 -112 CACATAAAAAGAGCCTTCCTAATAAGGAAG 9 203 0 GAGCCTTCCT 0.989875 -98 TGTATGAACCTCCCTCAATTATTTT 17 6 1 GAACCTCCCT 0.981525 -235 ********** Masking position 6 Map Score: 2.83739 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 20 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 12 ATCGTGATAAGAAAGGATGAAAACAGCATGTAT 9 41 1 GAAGGTGAAA 0.916495 -260 ATCGACAGGGGAACGGTTGTTGACCATGGCAAG 13 130 1 GAAGGTGTGA 0.992502 -171 GTTGACCATGGCAAGGCTGATGAAGAAACGGCA 13 148 1 GCAGGTGTGA 0.979757 -153 CATTCTCGAAGAAAGGGAGGTGATGTCCCGCCT 13 215 1 GAAGGAGTGA 0.9861 -86 ATACAGCCTCGAAAGGGAGATGACAA 14 186 1 GAAGGAGTGA 0.9861 -16 ACAAGTTGCTGAAGGGGTGCAGAAT 16 208 1 GAAGGTGAGA 0.9861 -15 *** ** ** *** Masking position 3 Map Score: 4.52647 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 49 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 ATTTATAAATGAATAAAAATATTAAATATA 6 117 1 GAATAAAAAT 0.767941 -90 ATTATAACATGAATAAAAATTAATTCAATC 6 148 0 GAATAAAAAT 0.767941 -59 AGCATCTAGCAAATAAAAGCGGCTCCAACA 9 157 0 AAATAAAAGC 0.935351 -144 ATGAATAAATACTATGAAACTT 10 3 1 GAATAAATAC 0.721657 -167 TTTTTATACAAAATAGAAACACGGTTGAGA 10 137 1 AAATAGAAAC 0.837802 -33 TCAAAAGCATAAATAAAAGCA 12 2 0 AAATAAAAGC 0.935351 -299 TTTCAACCGAGAATAAAAGCTGATAAGACG 14 142 1 GAATAAAAGC 0.958244 -60 TTTTTTTATAAAATAGAAGCAATATTAAGA 17 35 0 AAATAGAAGC 0.891221 -206 ********** Masking position 5 Map Score: 3.74708 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 180 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 14 TGGGGAAAAACAAATTAAAATGGCT 5 3 1 GGGAAACAAT 0.604227 -42 TTTTTTTTGAGCGGAATTCCCATTGAACAGAAA 6 84 1 GCGGATCCAT 0.97444 -123 GGAGTCCTAGGGGGAAAACCTAGGCGCATAACC 8 149 1 GGGGAACCAG 0.780195 -152 AGGTGGTACCACGGAAACCCATTTCGTCCTTAT 8 225 1 ACGGAACCTT 0.750259 -76 TGTCCAAATGGCGGCATGACGTTCCCCGCAAAA 9 240 0 GCGGATACTT 0.835937 -61 GTGTTTCAAAGCTGGATTCAATTCGTCAAGTCC 12 37 0 GCTGATCATT 0.839689 -264 GCCTTTCAAAGCGGCATGCCGTTTCTTCATCAG 13 164 0 GCGGATCCTT 0.984771 -137 CATAAAAAAAGGGGGAACCCGTT 14 1 0 GGGGAACCTT 0.969667 -201 CCCTTTCGAGGCTGTATTCATTTATTGTAAGCG 14 170 0 GCTGATCATT 0.83969 -32 GCACCATGGCGGGATATTCACTTCGTTTGTATA 16 15 1 GGGAATCATT 0.81453 -208 AGAAAACAAGGGGGAATTCAAAT 17 228 1 GGGGATCAAT 0.943844 -13 **** ** ** ** Masking position 6 Map Score: 3.43118 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 595 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 15 TCACATGTCAGGCTGTCCTTTTTTGTT 3 8 0 GGCTGTCCTT 0.98545 -47 TGACATGTGAGGCTGTCCTTTTTTACAGCT 3 28 1 GGCTGTCCTT 0.98545 -27 AAATTAAAATGGCTGACATTATCACAAAGC 5 22 1 GGCTGACATT 0.948971 -23 TAAAAAAACAGGCTGACCGCG 6 2 0 GGCTGACCGC 0.951678 -205 AGGATTAGTAAGCAGACCTTTCTGTGACAG 8 63 1 AGCAGACCTT 0.849678 -238 ********** Masking position 5 Map Score: 0.686392 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 131 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432