AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_aquae_reg_300.orf -o00260_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.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 Purged sequences: glyS 22 glycyl-tRNA synthetase beta subunit putative 27 putative protein Input sequences: #1 serS 29 seryl-tRNA synthetase #2 thrC2 26 threonine synthase #3 aq_428 274 hypothetical protein #4 oppB 300 transporter (OppBC family) #5 aq_609 300 hypothetical protein #6 lpdA 85 dihydrolipoamide dehydrogenase #7 aq_943 300 putative protein #8 gcsH3 72 glycine cleavage system protein H #9 glyQ 290 glycyl-tRNA synthetase alpha subunit #10 aq_1104 45 putative protein #11 gcsH4 269 glycine cleavage system protein H #12 lysC 35 aspartokinase #13 thrB 300 homoserine kinase #14 gcvT 144 aminomethyltransferase (glycine cleavage system T protein) #15 thrS 36 threonyl-tRNA synthetase #16 thrA 168 homoserine dehydrogenase #17 asd 300 aspartate-semialdehyde dehydrogenase #18 serA 27 D-3-phosphoglycerate dehydrogenase Motif number 1 CAATCCCTTATTGTAAGGGCATAACCCTGCACG 5 16 0 TTTAGGGCAA 0.987584 -285 TGGGAAATTTTTTTAAATGCACAGAAAGAAATG 5 52 0 TTTAATGCAA 0.924298 -249 CAATCCCTTATTGTAAGGGCATAACATTGATTG 5 83 0 TTTAGGGCAA 0.987584 -218 TGGGAAATTTTTTTAAATGCACAGAAAGAAATG 5 119 0 TTTAATGCAA 0.924298 -182 CAATCCCTTATTGTAAGGGCATAACATTGATTG 5 150 0 TTTAGGGCAA 0.987584 -151 CGATCCCTTACTGTTAGGGCGTAACGTATGCCT 5 215 0 CTTAGGGCGA 0.977411 -86 TCGCTTCCTCCTTTTAAGGCAAATTATTAGTAT 6 11 1 CTTAAGGCAA 0.982204 -75 GGTAAAAATTTTATAAAGGCATACTCAATTTTG 7 28 1 TTTAAGGCAA 0.982561 -273 CAATCCCTCATTATTAGGGCGTAACCCTGCACG 7 150 0 TTTAGGGCGA 0.977862 -151 ACGCTTTTTGTTATCATTGCAGAGAGCCACATT 7 193 0 TTTATTGCAA 0.658083 -108 TACTTTTCCATTCTCAGGGAGAAGCTCGGTAAA 11 38 1 TTTAGGGAGA 0.871052 -232 ATAAGACTTACTATAAAGACAAAAACAAAATAA 13 156 1 CTTAAGACAA 0.894616 -145 GAAGTAAGGGCTGTAAGGGAAGAGCCGGA 14 126 1 CTTAGGGAAA 0.922981 -19 GGTTAAAGGACTATTAAGAAATACTTATGAATG 16 36 1 CTTAAGAAAA 0.566288 -133 TAAGAAATACTTATGAATGCATAAAATGTCTTA 16 50 1 TTTAATGCAA 0.924299 -119 ACAAAAACGTCTATAAAGACGTAATTTTACTGA 17 164 1 CTTAAGACGA 0.825003 -137 ** * ****** * Masking position 6 Map Score: 23.4451 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 94 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 GTACCCTTCCAGGGAGGGGTGGTACGTTTGT 3 145 1 AGGGAGGGTG 0.934738 -130 TTAAAGTTCAAGGAAGAGGTCCTTATAAGCT 3 200 1 AGGAAGAGTC 0.891818 -75 GAGTATCCTGAAGAGGAGTTTGGCGTCCAGA 4 65 0 AAGAGGAGTT 0.852584 -236 ATGCCCTTACAATAAGGGATTGCGACATTTC 5 27 1 AATAAGGGTT 0.951878 -274 ATGCCCTTACAATAAGGGATTGCGACATTTC 5 94 1 AATAAGGGTT 0.951878 -207 ATGCCCTTACAATAAGGGATTGCGACTTTGC 5 161 1 AATAAGGGTT 0.951878 -140 ACGCCCTAACAGTAAGGGATCGTGATAAAAT 5 226 1 AGTAAGGGTC 0.930889 -75 ACCCCTTTTCAGGAGGAGCTTC 6 74 1 AGGAGGAGTT 0.90305 -12 ACGCCCTAATAATGAGGGATTGCGACTATAA 7 161 1 AATGAGGGTT 0.941956 -140 GCCCTAAGTAAATAAGAGGTTTTTCTTTCTC 7 232 1 AATAAGAGTT 0.903294 -69 ATTAATTATAAGTGAGTGTTTATTTATTAAG 7 273 0 AGTGAGTGTT 0.893958 -28 TATAATGATAAGTAAGTGTTGATTTACTTTG 8 27 1 AGTAAGTGTG 0.812891 -46 AGCTAATGGTAAGGAGTGTTCCTTCCACGGT 9 167 1 AAGGAGTGTC 0.741494 -124 AAAGCAATAGAGGAGGGGGTTTAACTTTATA 9 250 1 AGGAGGGGTT 0.95175 -41 GGTAAAGAAAAGGAAGAGTTTGAGTTTGAAG 11 65 1 AGGAAGAGTT 0.951214 -205 AAAACAAAATAATGAGTGCTTCACCAAACGA 13 177 1 AATGAGTGTT 0.83958 -124 GGACATAGTAAAGGGGAGTTTGCATAAAGTA 14 21 0 AAGGGGAGTT 0.825934 -124 TAATAGAAGAAGTAAGGGCTGTAAGGGAAGA 14 118 1 AGTAAGGGTG 0.930889 -27 ******** ** Masking position 10 Map Score: 23.2697 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 353 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 AATGTCGCAATCCCTTATTGTAAGGGCATAAC 5 24 0 TCCCTTTTTA 0.985811 -277 AATGTCGCAATCCCTTATTGTAAGGGCATAAC 5 91 0 TCCCTTTTTA 0.985811 -210 AAAGTCGCAATCCCTTATTGTAAGGGCATAAC 5 158 0 TCCCTTTTTA 0.985811 -143 TTTATCACGATCCCTTACTGTTAGGGCGTAAC 5 223 0 TCCCTTCTTT 0.893966 -78 TCGCTTCCTCCTTTTAAGGCAAATTA 6 5 1 TTCCTCTTTA 0.784021 -81 ATAGTCGCAATCCCTCATTATTAGGGCGTAAC 7 158 0 TCCCTCTTTT 0.950641 -143 TTTAACTTTATACCTTTTTATAATCTTTAAGT 9 269 1 TACCTTTTTA 0.932582 -22 GGCTTTTACCTCTTTGTAGAGTTAAGTA 10 7 1 TACCTCTTTA 0.901693 -39 CTCAAACTCTTCCTTTTCTTTACCGAGCTTCT 11 57 0 TCCTTTCTTA 0.78524 -213 TTTTTCCAATTCCTTCTTTATATCGTGCAACA 13 71 1 TCCTTCTTTA 0.893077 -230 ATTTATAAAATACCTTATTTGATTCTATAATG 13 276 0 TACCTTTTGA 0.685709 -25 AAGAGAATTATCCTTTATTTTTAAAAGGGGGA 16 147 0 TCCTTTTTTT 0.840406 -22 GTTTTTGTAGTCCCTTTTTAAAATCTGAGCGA 17 140 0 TCCCTTTTAA 0.880867 -161 TTTAGGTTTTTCCCTTCTTTTTTAAGTTCAAG 17 211 0 TCCCTTTTTT 0.966717 -90 ****** ** ** Masking position 5 Map Score: 18.1547 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 273 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TTTTGATTCAGGACGGAGTCCTGAGGTACCCTTC 3 120 1 GGCGAGCTGA 0.944487 -155 CCATGGAGTACGTCAGAAACCTGATTCTGGACGC 4 40 1 CGCAAACTGA 0.903274 -261 CTTATTGTAAGGGCATAACCCTGCACGCTTGT 5 9 0 GGCAAACTGC 0.968187 -292 CTTATTGTAAGGGCATAACATTGATTGGGAAATT 5 76 0 GGCAAATTGA 0.982099 -225 CTTATTGTAAGGGCATAACATTGATTGGGAAATT 5 143 0 GGCAAATTGA 0.982099 -158 GTTTCATTAAGGTCAGAAGTCTAATAAGTTATTT 7 92 1 GGCAAACTAA 0.982099 -209 CTCATTATTAGGGCGTAACCCTGCACGCCTGTGT 7 143 0 GGCGAACTGC 0.9134 -158 CTTTGATAAAGGTCATAATATTAATATCAA 8 53 1 GGCAAATTAA 0.971654 -20 GCAGGTACTGGGTCACAAAGCTAATGGTAAGGAG 9 149 1 GGCAAACTAA 0.982099 -142 AAAAGATACAGGACAAAGGGTTAAAGGACTATTA 16 18 1 GGCAAGTTAA 0.950405 -151 TTTAAAAGGGGGACAAGGACTTAAGACTTAAACT 16 126 0 GGCAGGTTAA 0.766885 -43 CCGGAAAAAATGTTAAACTCGAATAT 17 3 1 GGAAAATTAA 0.710943 -298 ** ** ** **** Masking position 12 Map Score: 11.642 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 82 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 CTTATTGTAAGGGCATAACCCTGCACGCTTG 5 12 0 GGGCATAACC 0.986586 -289 CTTATTGTAAGGGCATAACATTGATTGGGAA 5 79 0 GGGCATAACT 0.991287 -222 CTTATTGTAAGGGCATAACATTGATTGGGAA 5 146 0 GGGCATAACT 0.991287 -155 CTTACTGTTAGGGCGTAACGTATGCCTTATC 5 211 0 GGGCGTAACT 0.991924 -90 CTCATTATTAGGGCGTAACCCTGCACGCCTG 7 146 0 GGGCGTAACC 0.987524 -155 ATAGAGGAGGGGGTTTAACTTTATACCTTTT 9 256 1 GGGTTTAACT 0.911316 -35 TTTTCTCCTGGGGCTTAAAATCCTGCTCAAT 17 60 0 GGGCTTAAAT 0.911503 -241 ********* * Masking position 7 Map Score: 9.89425 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ACCCATGGTAAAATTCTACCAAGGGGTGGATA 3 15 0 AATTCTCCAA 0.737934 -260 GAGCTGCTGTAAAATCTTCCCTTGCCTCCTCA 4 119 0 AAATCTCCCT 0.865997 -182 TGCATTTAAAAAAATTTCCCAATCAATGTTAT 5 64 1 AAATTTCCAA 0.911702 -237 TGCATTTAAAAAAATTTCCCAATCAATGTTAT 5 131 1 AAATTTCCAA 0.911702 -170 GGATCGTGATAAAATTTCCCCAAATTTACTTG 5 242 1 AAATTTCCCA 0.969708 -59 GCCTTTATAAAATTTTTACCCTTGATTTTCAA 7 16 0 AATTTTCCCT 0.946402 -285 ATTCTTCCTGAAGTTTTTTCCAGAGGGCATCC 9 75 0 AATTTTTCCA 0.685268 -216 CACCTCCAAGAAGTTTTAACCACCGCTAACTG 11 243 0 AATTTTACCA 0.793361 -27 CGGAAAGTAATATTTTACCTTAAAATTTAT 12 16 0 AAATTTACCT 0.739727 -20 GTTTTTGATTAAGTTTTTCCAATTCCTTCTTT 13 58 1 AATTTTCCAA 0.899121 -243 TATATCGTGCAACATTTGCCTTACATCAATAA 13 89 1 AAATTTCCTT 0.667261 -212 CACAGGTTTTAGGTTTTTCCCTTCTTTTTTAA 17 218 0 AGTTTTCCCT 0.735797 -83 TAATTTTATTAAGATTTACCCACTTTAACGAT 17 274 0 AAATTTCCCA 0.969708 -27 ** **** **** Masking position 1 Map Score: 10.018 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 210 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 CCGCCTCTTCTATTAGTTTAATGATATCTTTGTAGCT 3 227 0 TTATTAGAAT 0.969652 -48 TTGCCTTTAATTTTAGCATTTTGATATACTAATAATT 6 32 0 TTAATTGAAT 0.898803 -54 TTATTAGACTTCTGACCTTAATGAAACGAATGTTAAT 7 82 0 TTATTAGAAC 0.869508 -219 AGTGTTTATTTATTAAGTTTATGAAATGAGAAAGAAA 7 253 0 TTATTAGAAT 0.969652 -48 AACACTTACTTATCATTATAAGGATATAAGAATTTC 8 10 0 TTAATAGAAT 0.969652 -63 TTGATATTAATATTATGACCTTTATCAAAGT 8 52 0 TTAATAGACT 0.869508 -21 CGGCTTTAAGTATGAAGTTCTGGACATAGGTACTCCG 9 108 1 TTATTTGAAT 0.898803 -183 CTGCCGCAATTATAAAAATCAAGATATATTGCTATAA 13 228 1 TTAATAGAAT 0.969652 -73 TTTTATCATTTTTGAAAATTAAGACATTTTATGCATT 16 65 0 TTAATAGAAT 0.969652 -104 TTCCCTTCTTTTTTAAGTTCAAGAAATCCTGCTTTCT 17 197 0 TTATTAGAAT 0.969652 -104 * * * ** * ** ** Masking position 9 Map Score: 9.35387 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 13 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ATTCTACCAAGGGGTGGATAAAGT 3 3 0 GGGGGATAAA 0.98936 -272 ATGCCGAAGCGAGAGGATTAAAGTTCAAGGAA 3 183 1 GGAGATTAAA 0.79551 -92 ACTAATAGAAGAGGCGGATAAAATAGTGGTCT 3 247 1 GGGGGATAAA 0.98936 -28 AATCAAGTACGTGAAGGAAAAACACAAAGAGG 4 227 1 GGAGGAAAAA 0.848108 -74 TGGGTGCGAAGGATAAACACGTTATTC 9 6 1 GGAGGATAAA 0.975419 -285 AGCAATAGAGGAGGGGGTTTAACTTTATACCT 9 252 1 GGGGGTTTAA 0.928997 -39 GTACGTGGATGAGGACTATAAAATCTCCGACG 11 187 1 GGGCTATAAA 0.709097 -83 CCTCCAGTTAGCGGTGGTTAAAACTTCTTGGA 11 239 1 GGGGGTTAAA 0.98936 -31 AGAAATTATTGATGTGGTTAAAAAGTACAATC 17 90 1 GTGGGTTAAA 0.890398 -211 AGAAATAGAAGTGATCGTTAAAGTGGGTAAAT 17 261 1 GGACGTTAAA 0.913859 -40 * ** ******* Masking position 11 Map Score: 9.38879 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 134 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 CTTTGGCTCGTGAGGAAACTGGGAGACTTT 3 56 1 TGAGGAAACT 0.95476 -219 AAACTCCTCTTCAGGATACTCTCCGACCCT 4 75 1 TCAGGATACT 0.950403 -226 GGTTCCCATGTTAGGATACTGGGACGACTA 4 191 1 TTAGGATACT 0.924166 -110 ATAACATTGATTGGGAAATTTTTTTAAATG 5 66 0 TTGGGAAATT 0.923788 -235 ATAACATTGATTGGGAAATTTTTTTAAATG 5 133 0 TTGGGAAATT 0.923788 -168 CAAGTAAATTTGGGGAAATTTTATCACGAT 5 244 0 TGGGGAAATT 0.929002 -57 GTATCTGAGCTCAGGAAACTACTACTGAGT 11 101 1 TCAGGAAACT 0.968495 -169 ATTTTCTATCTCGGGATACTTACTCAGTAG 11 122 0 TCGGGATACT 0.968148 -148 ********** Masking position 6 Map Score: 6.78564 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 102 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 AGGTAATCCGAGGAAAAGTCTCCCAGTTTCCT 3 68 0 AGGAAATCTC 0.874677 -207 TAGAAGGAAACTCGCAAAAGTCCCT 4 4 1 AAGGAATCGC 0.911757 -297 AATGCACAGAAAGAAATGTCGCAATCCCTTAT 5 38 0 AAGAATTCGC 0.980944 -263 TGTGCATTTAAAAAAATTTCCCAATCAATGTT 5 62 1 AAAAATTCCC 0.758874 -239 AATGCACAGAAAGAAATGTCGCAATCCCTTAT 5 105 0 AAGAATTCGC 0.980944 -196 TGTGCATTTAAAAAAATTTCCCAATCAATGTT 5 129 1 AAAAATTCCC 0.758874 -172 AAGTATTATAAAGCAAAGTCGCAATCCCTTAT 5 172 0 AAGCAATCGC 0.911758 -129 TGAAATGAGAAAGAAAAACCTCTTATTTACTT 7 237 0 AAGAAACCTC 0.874763 -64 TATAAAAATCAAGATATATTGCTATAATTTAC 13 238 1 AAGAATTTGC 0.867931 -63 AGCTAAGCCTAAAATAAATCTCT 15 24 1 AAAAAATCTC 0.814886 -13 TTAAAAATAAAGGATAATTCTCTT 16 155 1 AGGAAATCTC 0.874677 -14 CGTCCTCTATAAGAGAACTCGCTCAGATTTTA 17 122 1 AAGAAATCGC 0.983653 -179 TTTTAAGTTCAAGAAATCCTGCTTTCTTCAGT 17 192 0 AAGAATCTGC 0.674981 -109 **** ** **** Masking position 6 Map Score: 8.95665 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 126 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 GTACGTTTGTAAAGAGGATGCCGAAGCGAG 3 166 1 AAAGAGGATG 0.78113 -109 ATTAAAGTTCAAGGAAGAGGTCCTTATAAG 3 199 1 AAGGAAGAGG 0.896851 -76 CATTAAACTAATAGAAGAGGCGGATAAAAT 3 241 1 ATAGAAGAGG 0.957886 -34 TTGGTACTTCATAGAAGAAAAGGACAGGAT 4 152 1 ATAGAAGAAA 0.72207 -149 GGAAAAACACAAAGAGGAGATAGACAGGTA 4 242 1 AAAGAGGAGA 0.928017 -59 TTTGCCTTAAAAGGAGGAAGCGA 6 4 0 AAGGAGGAAG 0.773155 -82 TGCCCTAAGTAAATAAGAGGTTTTTCTTTC 7 231 1 AAATAAGAGG 0.645815 -70 ACGCAAAGCAATAGAGGAGGGGGTTTAACT 9 246 1 ATAGAGGAGG 0.965088 -45 TTAACTCTACAAAGAGGTAAAAGCC 10 6 0 AAAGAGGTAA 0.459256 -40 GAAGCTCGGTAAAGAAAAGGAAGAGTTTGA 11 58 1 AAAGAAAAGG 0.645815 -212 CACCTCAATAATAGAAGAAGTAAGGGCTGT 14 110 1 ATAGAAGAAG 0.880042 -35 GAGTTCTCTTATAGAGGACGGATTGTACTT 17 112 0 ATAGAGGACG 0.800658 -189 TGAACTTAAAAAAGAAGGGAAAAACCTAAA 17 213 1 AAAGAAGGGA 0.645523 -88 ATATGAAGAAATAGAAGTGATCGTTAAAGT 17 255 1 ATAGAAGTGA 0.621951 -46 ********** Masking position 5 Map Score: 7.52504 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 1066 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 CCACTACATCGTCCTCGCCGAGGTAATCCG 3 90 0 GTCCTCGCCG 0.82775 -185 GAGTCCTGAGGTACCCTTCCAGGGAGGGGT 3 135 1 GTACCCTTCC 0.944701 -140 AGCTTATAAGGACCTCTTCCTTGAACTTTA 3 201 0 GACCTCTTCC 0.785852 -74 CGGGTATCCTGTCCTTTTCTTCTATGAAGT 4 157 0 GTCCTTTTCT 0.740768 -144 TGATTACCTTGTAGTCGTCCCAGTATCCTA 4 202 0 GTAGTCGTCC 0.820722 -99 TTTCCTTAAAGTACCTGTCTATCTCCTCTT 4 253 0 GTACCTGTCT 0.621198 -48 ACTTAAAGCCGTATTCTTCCTGAAGTTTTT 9 89 0 GTATTCTTCC 0.824618 -202 TTGTGACCCAGTACCTGCCCTCCGGAGTAC 9 137 0 GTACCTGCCC 0.843104 -154 TGGAGATAAGGTACTTTTCCATTCTCAGGG 11 27 1 GTACTTTTCC 0.947923 -243 CCTCATCCACGTACTCTTCGTTAACGGCAA 11 171 0 GTACTCTTCG 0.889677 -99 AGATTTTATAGTCCTCATCCACGTACTCTT 11 183 0 GTCCTCATCC 0.860718 -87 CAGAGCTGTTGTATTTTCCCCTTTGTTTTT 13 21 0 GTATTTTCCC 0.560775 -280 TAAGTCTTAAGTCCTTGTCCCCCTTTTAAA 16 130 1 GTCCTTGTCC 0.955528 -39 ********** Masking position 9 Map Score: 6.84217 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 689 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 CCGACCCTAACTTTGACCTGAGTGAGGAGG 4 97 1 CTTTGACCTG 0.932253 -204 TCCGGAGTACCTATGTCCAGAACTTCATAC 9 117 0 CTATGTCCAG 0.978388 -174 CTCCCCTTTACTATGTCCATAAACACCTGA 14 34 1 CTATGTCCAT 0.896647 -111 ACTGGAGTGGCATTGTCCAGCCTGCGAAGT 14 79 0 CATTGTCCAG 0.951732 -66 TCCTTTAACCCTTTGTCCTGTATCTTTTAT 16 16 0 CTTTGTCCTG 0.978389 -153 ********** Masking position 4 Map Score: 0.765517 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 49 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 AGAGGTCCTTATAAGCTACAAAGATATCAT 3 214 1 ATAAGCTACA 0.714318 -61 TAGTATATCAAAATGCTAAAATTAAAGGCA 6 38 1 AAATGCTAAA 0.926007 -48 AGAAAGGCTAAAAAACAAAGGG 13 3 1 AAAGGCTAAA 0.88011 -298 AGTAAACAACAAAAGCTAAATAAATAAGAC 13 133 1 AAAAGCTAAA 0.965082 -168 CAGCTACAGAAAAAGCTAGATCGTTTGGTG 13 198 0 AAAAGCTAGA 0.88011 -103 ATTGAAAAAGATAAGCTAAGCCTAA 15 6 1 AAAAGATAAG 0.689558 -31 CAAGTATAAAAGATACAGGACAAAGGG 16 8 1 AAAAGATACA 0.893594 -161 TAATTTTCAAAAATGATAAAATGGTAAATT 16 81 1 AAATGATAAA 0.842291 -88 CCGGAAAAAATGTTAAACTCGAATATG 17 8 1 AAATGTTAAA 0.6188 -293 CCACTGAATTAAAAGATACATATTCGAGTT 17 26 0 AAAAGATACA 0.893594 -275 AAAGAAGGGAAAAACCTAAAACCTGTGGTG 17 223 1 AAAACCTAAA 0.763463 -78 ********** Masking position 3 Map Score: 4.56079 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 204 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 ********** No masking Map Score: -5.85955e-12 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