AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00410_ecoli_reg_300.orf -o00410_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/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 speE 105 spermidine synthase = putrescine aminopropyltransferase #2 yacC 42 orf, hypothetical protein #3 panD 273 aspartate 1-decarboxylase #4 panB 113 3-methyl-2-oxobutanoate hydroxymethyltransferase #5 yadC 49 putative fimbrial-like protein #6 yadK 26 putative fimbrial protein #7 htrE 34 probable outer membrane porin protein involved in fimbrial assembly #8 ecpD 97 probable pilin chaperone similar to PapD #9 yadN 300 putative fimbrial-like protein #10 pepD 260 aminoacyl-histidine dipeptidase (peptidase D) #11 ycjL 121 probable amidotransferase subunit #12 ycjC 26 orf, hypothetical protein #13 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #14 goaG 37 4-aminobutyrate aminotransferase #15 tynA 247 copper amine oxidase (tyramine oxidase) #16 maoC_ydbO 284 maoC: putative aldehyde dehydrogenase, ydbO: orf, hypothetical protein #17 gadB 300 glutamate decarboxylase isozyme #18 b2654 300 orf, hypothetical protein #19 b2657 171 putative enzyme #20 b2658 138 orf, hypothetical protein #21 b2659 230 orf, hypothetical protein #22 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #23 gadA 210 glutamate decarboxylase isozyme #24 yhjA 300 putative cytochrome C peroxidase (EC 1.11.1) #25 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase Motif number 1 AGCCACACGGAAGACAGGGAAG 3 2 0 AAGACAGGAA 0.481531 -272 GAATTTCCTCAAAGCAGGCATCGCCTGCTTC 3 224 1 AAAGCAGGAT 0.929602 -50 GGAATAATATAAAATAGAAATTATTATTCCC 8 46 0 AAAATAGAAT 0.422702 -52 AGAGTTAATTAAAACAGGGAATAATATAAAA 8 63 0 AAAACAGGAA 0.809138 -35 AAGCCGTAGATAAACAGGCTGGGACACTTCA 10 12 0 TAAACAGGTG 0.645344 -249 GTTCGAGGGGAAAATAGGTTGCGCGAGATTA 10 50 1 AAAATAGGTG 0.855756 -211 TTGTCAACACAAGACAGGCTTGCGAGATATG 10 177 0 AAGACAGGTT 0.87494 -84 GATCACCCGCAAAACAGTATTGCAGGTCACA 10 224 0 AAAACAGTTT 0.643351 -37 TTAATTCACGAAAACTGGAATCGTAAAGGTG 16 16 0 AAAACTGGAT 0.611012 -269 ATGATTTATAAAAATAGGGTGCGAAATCCGT 16 127 0 AAAATAGGTG 0.855757 -158 TCGCATTAAAAAAGTAGGATTTATCGATAAA 17 256 0 AAAGTAGGTT 0.834471 -45 GATAATTAATAAAACAGATTTAAGCATTATC 18 161 1 AAAACAGATT 0.81854 -140 ATATATAGATAAAGCAGGAATATGGAGCGCA 20 64 1 AAAGCAGGAT 0.929604 -75 CCTTTGAAAACAGGATGTAGCG 22 7 1 AAAACAGGTG 0.96007 -16 GATAATATTAAAAACAGACTTTATTATCGTA 23 53 0 AAAACAGATT 0.820576 -158 AGGCAATAAAAAAGTAGGATTTATCCGCAAT 23 166 0 AAAGTAGGTT 0.834471 -45 GATTGCGGCGAGAGCAGGATTGAATGTTCTG 24 88 0 AGAGCAGGTT 0.696204 -213 GCCATCATAAAAAACAGGGAGATACGCTTTT 24 203 0 AAAACAGGAG 0.939543 -98 ******** ** Masking position 7 Map Score: 11.156 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 599 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 2 TTTACTCCAATGTTTCTTTATTGTTATGGT 5 29 0 TGTTTCTTTA 0.651279 -21 ATGTGATTCGTGTTTTTAATTAATTCACGA 16 36 0 TGTTTTTAAT 0.717526 -249 TTCACATTTCTGTTGCTAATAGTTAAATCG 16 248 0 TGTTGCTAAT 0.780104 -37 TGTTTTATGCTGTTATTTTTATGCGCATTC 17 99 0 TGTTATTTTT 0.842979 -202 AAAATCCTAATGTTATTTATCGTGAGATAT 17 192 0 TGTTATTTAT 0.887905 -109 ATTAGGATTTTGTTATTTAAACACGAGTCC 17 211 1 TGTTATTTAA 0.751152 -90 TTATGATATCTGTTACTTTTCACTCCATAA 18 30 1 TGTTACTTTT 0.853455 -271 AGCCATTTACTGTTTTTTATCGACCAGATA 21 84 1 TGTTTTTTAT 0.869549 -147 CCCCCTAACCTGTTGCTTTAGTTATTCATT 21 135 1 TGTTGCTTTA 0.706267 -96 CTACGTTAAATGTTACTAATTTGTTGCTTT 21 190 1 TGTTACTAAT 0.766054 -41 GTTACTAATTTGTTGCTTTTGATCACAATA 21 201 1 TGTTGCTTTT 0.863193 -30 TAATAAAGTCTGTTTTTAATATTATCATGT 23 58 1 TGTTTTTAAT 0.717526 -153 CTTAGGATTTTGTTATTTAAATTAAGCCTG 23 121 1 TGTTATTTAA 0.751152 -90 ACCGATTTGGTGTTGTTTTTCATTTTCAGA 24 62 1 TGTTGTTTTT 0.853294 -239 CGTATCTCCCTGTTTTTTATGATGGCTTTG 24 208 1 TGTTTTTTAT 0.869549 -93 ********** Masking position 4 Map Score: 9.71777 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 174 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 CTCGAACACTTTTTAAGCCGTAGATAAACAGGCTGGGA 10 19 0 TTTACTAAAA 0.835505 -242 ATGACTCCTGTTTCACGTCTATCAGATATATGCAGTTT 13 246 0 TTTACATAAA 0.957757 -29 TGATTATTATTTTGAACGCATTTATAAAATTA 17 5 0 TTTACTTAAA 0.957757 -296 CTTAAAATGATTGGATCGCATTAAAAAAGTAGGATTTA 17 264 0 TTGACTTAAA 0.795592 -37 TTTAAACTCCTTAAAATGATTGGATCGC 17 283 0 TTTACTTAAG 0.795592 -18 ATCTGTTACTTTTCACTCCATAAAAATAAACTTCGTAT 18 37 1 TTTACTAAAA 0.835523 -264 TTGCAATTACTTTCACAACAATTAAACATTTTTATGTT 18 231 1 TTTACATAAA 0.957752 -70 AAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTA 19 12 1 TTTACTTATA 0.72422 -160 ATTTGTTGCTTTTGATCACAATAAGAAAACAAT 21 208 1 TTTACATAAA 0.95775 -23 TTTGGGCGATTTTTATTACGATAATAAAGTCTGTTTTT 23 37 1 TTTACATAAA 0.954692 -174 CTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTA 23 174 0 TTTACATAAA 0.957757 -37 CATGTAATTGATTGATTCCTATCAAAAAGCGTATCTCC 24 179 1 ATTACATAAA 0.72422 -122 *** * * ** * * * Masking position 5 Map Score: 7.39666 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 31 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 GCTATTATGTTGCGCCCTTTTTTTACGGGTGT 1 63 1 TGCGCTTTTT 0.985592 -43 CACGCAGTATTGCCCGATTTTTGTTTAGTGTC 3 191 0 TGCCCTTTTT 0.985592 -83 TGTTATGGTTTGCGCTGTTTTTGTTTG 5 6 0 TGCGCTTTTT 0.985592 -44 CCGGGCCGTATGCCCGTTTATTTCTGGCGACA 13 190 0 TGCCCTTATT 0.961601 -85 GGCGAATAGTTGCCCTTTTATTTCACTAAGTT 15 30 1 TGCCCTTATT 0.961601 -218 TAGTTTCGTATGAGCGATTTTTGACAGTTGCC 18 114 1 TGAGCTTTTT 0.898712 -187 ACATATTATCTGCCCCGTTTTATCGGGGCAGA 21 23 0 TGCCCTTTTA 0.924578 -208 CAGCAATGTTTGGGCGATTTTTATTACGATAA 23 29 1 TGGGCTTTTT 0.929332 -182 ***** ***** Masking position 8 Map Score: 7.19762 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 58 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 GCAACATAATAGCTAACATTGACCGCGGAT 1 46 0 AGCTAACATT 0.908471 -60 GCTCATTAATATCTAACATTTGTTTCTCCT 9 213 1 ATCTAACATT 0.910122 -88 TGCAAACTCAATTTAACATTTGACAAACAT 11 16 0 ATTTAACATT 0.937688 -106 CAGATCGCATAGTTAACATTTCGTTAAAAG 16 196 1 AGTTAACATT 0.936508 -89 TTTCACAACAATTAAACATTTTTATGTTTC 18 241 1 ATTAAACATT 0.729494 -60 ATCGGGGCAGATATAACATTAAA 21 4 0 ATATAACATT 0.787799 -227 GGTTAGGGGGAGTTAACATTAGAGAACAGA 21 115 0 AGTTAACATT 0.936508 -116 TAATATAAACATTTAACATGATAATATTAA 23 73 0 ATTTAACATG 0.799878 -138 ********** Masking position 5 Map Score: 4.63258 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 16 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 TCCCTGATAGAGTTAATTAAAACAGGGAATA 8 71 0 ATTAATTAAA 0.929813 -27 CTTAATTCAAAATTAAGTAAAAATAAGTTCA 9 96 0 ATTAAGTAAA 0.928495 -205 CTTAATTTTGAATTAAGTAAATTTAATTTGT 9 110 1 ATTAAGTAAA 0.928495 -191 GACTAATGGAATTTTATTAAAGGATTTTT 9 282 1 ATTTATTAAA 0.829053 -19 AGTTTTCGTGAATTAATTAAAAACACGAATC 16 31 1 ATTAATTAAA 0.929813 -254 GTTACACAATAGTTAAGTAAAATCACAAATT 16 78 1 ATTAAGTAAA 0.928495 -207 CCACATCGATAATTAATAAAACAGATTTAAG 18 154 1 ATTAATAAAA 0.829045 -147 ATATCAATGGAATTTATAAAAATACCGATTT 24 39 1 ATTTATAAAA 0.639695 -262 * ********* Masking position 6 Map Score: 3.36859 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 18 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CAGAAGGTGACAGTGCTGCTACGTTA 4 7 0 CAGTGCTGCT 0.951422 -107 CACCTTCTGGCAGTGCTGCTACGGATAAAT 4 28 1 CAGTGCTGCT 0.951422 -86 TAACAAATATCATTGCTCATTAATATCTAA 9 199 1 CATTGCTCAT 0.916184 -102 TTGCCGGGCGCATTGCGCTTACCCGGCTTA 13 24 0 CATTGCGCTT 0.829102 -251 CCCTTTGCATCAGTACTGATAATGTGAACC 15 167 1 CAGTACTGAT 0.764718 -81 AGATGTTTCACATTTCTGTTGCTAATAGTT 16 254 0 CATTTCTGTT 0.739958 -31 ATCGCCCAAACATTGCTGTTCGGGCGATCA 23 17 0 CATTGCTGTT 0.962238 -194 GCCTTGCTTCCATTGCGGATAAATCCTACT 23 155 1 CATTGCGGAT 0.966784 -56 CATGATATGCCATTCCTGATCTGGGTAATA 24 118 1 CATTCCTGAT 0.871229 -183 GACCAGATCACCTTGCGGATTCAGGAGACT 25 167 1 CCTTGCGGAT 0.858556 -23 ********** Masking position 4 Map Score: 3.99558 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 398 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 TATTCTTAAGCAGGCGAAACAAAATCAAACG 2 22 1 CAGGCGAAAA 0.73613 -21 CAATTCGTTACAGGCGATACATGGCACGCTT 3 115 1 CAGGCGATAA 0.918753 -159 TCGTTAACGACAGGGTAGAAAGGTAGAAGTT 3 253 1 CAGGGTAGAA 0.785605 -21 CTCTCCCTGACGCGGGATAAAGTGGTATTCT 10 142 1 CGCGGGATAA 0.869417 -119 TACTGTTTTGCGGGTGATCGACAAGGAGACT 10 236 1 CGGGTGATCA 0.878429 -25 GTAAGTGATTCGGGGGAGCGAACGCAGCCAA 13 121 1 CGGGGGAGCA 0.986248 -154 CATCTATTTTCAGGGCATCCACTGTATGAAA 15 94 1 CAGGGCATCA 0.924535 -154 CCCGTTTTATCGGGGCAGATATAACATTAAA 21 11 0 CGGGGCAGAA 0.971522 -220 CCCGATAAAACGGGGCAGATAATATGTTTAG 21 28 1 CGGGGCAGAA 0.971522 -203 CATTGCTGTTCGGGCGATCAAATTAA 23 6 0 CGGGCGATCA 0.966339 -205 ********* * Masking position 7 Map Score: 3.97289 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 197 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 ATGTATCGCCTGTAACGAATTGATATTTCTCT 3 105 0 TGTAAGAATG 0.807097 -169 GTCCGCGTCTTTTTACGCACTGCCTCTCCCTG 10 119 1 TTTTAGCATG 0.784221 -142 CCACTACAGTTTAAGGAAATGCAAAT 12 10 1 TTTAAGAATG 0.952522 -17 TGCGGAAAACATTAATGCACTGATAAATAATG 16 155 0 ATTAAGCATG 0.921232 -130 CAAAGGATCTTTTAACGAAATGTTAACTATGC 16 202 0 TTTAAGAATG 0.952522 -83 TTACTGGATCTTTAATGAATGGAATCAAAACC 19 19 0 TTTAAGAAGG 0.943014 -153 ACGCTTTTCTTTTAATGCATGGAGGTTTTCCC 19 141 0 TTTAAGCAGG 0.955167 -31 AACGTAGGGTATTAAGGCAAAGTGAGACAGGA 21 165 0 ATTAAGCAAG 0.70829 -66 ATTAGTAACATTTAACGTAGGGTATTAAGGCA 21 178 0 TTTAAGTAGG 0.803247 -53 CAAACAAAAGATTAAAGAAATGCCGATCTGAT 25 93 0 ATTAAGAATG 0.900836 -97 ***** *** ** Masking position 5 Map Score: 3.76125 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 55 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 GCCACACGGAAGACAGGGAAG 3 2 0 AGACAGGGAA 0.815798 -272 TGTGGCTTTGCGTGAAGGCAGTATCCAGTC 3 26 1 CGTGAAGGCA 0.771486 -248 GGCAGTATCCAGTCAAGGCGCGCTATCGTC 3 42 1 AGTCAAGGCG 0.89302 -232 GCTTCGTTAACGACAGGGTAGAAAGGTAGA 3 250 1 CGACAGGGTA 0.794759 -24 CTTTATCCCGCGTCAGGGAGAGGCAGTGCG 10 134 0 CGTCAGGGAG 0.981766 -127 TGCGGGTGATCGACAAGGAGACTTAAC 10 244 1 CGACAAGGAG 0.940105 -17 ATTCAAGTTGCATCAAGGCGGCAAGTGAGC 13 69 1 CATCAAGGCG 0.836443 -206 AGTTTGTGAACGTCAGGGCGCAGAGATCCC 13 221 0 CGTCAGGGCG 0.985723 -54 CCATCATAAAAAACAGGGAGATACGCTTTT 24 203 0 AAACAGGGAG 0.642093 -98 AACTCACCACCGTGAGGGAAGAATA 24 286 1 CGTGAGGGAA 0.860038 -15 ********** Masking position 5 Map Score: 4.99116 Number of sites scoring better than the average of aligned sites = 957 Number in coding regions = 892 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 TTATTCCCTGTATATTCATTCAATCAATTTA 8 23 0 TATATTATTC 0.826556 -75 ATTTCTATTTTATATTATTCCCTGTTTTAAT 8 56 1 TATATTTTCC 0.875979 -42 TATAGGAAGTTATATTATTTCCGCAAAGAGA 9 21 0 TATATTTTTC 0.958252 -280 CTTTATGTTCAATATTTTTTCAATCTAGCAG 11 60 0 AATATTTTTC 0.908975 -62 TTACGCGAATAATATTTTTTCATTGAAAAAC 17 162 0 AATATTTTTC 0.908975 -139 CGTATAGCAATATATTCTTTCATAGATCTTA 18 70 1 TATATTTTTC 0.958254 -231 ATTAGTGCGTTATATTTTTTGACAGGTTAA 24 10 0 TATATTTTTG 0.815258 -291 ****** **** Masking position 4 Map Score: 1.54152 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 27 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 CCTTTGTTAACACCCGTAAAAAAAGGGCGCA 1 73 0 CACCCGTAAA 0.963699 -33 GTATTCACCAGTTAAATTGATTGAAT 8 6 1 CACCAGTAAA 0.906829 -92 CCTTGTCGATCACCCGCAAAACAGTATTGCA 10 231 0 CACCCGCAAA 0.962992 -30 AAATGTTTGTCAAATGTTAAATTGAGTTTGC 11 14 1 CAAATGTAAA 0.632634 -108 AAAGCTGGCACACCTGCCAAACAACCTGGCA 15 123 1 CACCTGCAAA 0.974792 -125 ATCTGTATAGCAACTGCGGAAAACATTAATG 16 170 0 CAACTGCGAA 0.80059 -115 TCTGGAGAGGCAACTGTCAAAAATCGCTCAT 18 123 0 CAACTGTAAA 0.939103 -178 TTAACCTGTCAAAAAATATAACG 24 3 1 AACCTGTAAA 0.815006 -298 ******* *** Masking position 2 Map Score: 0.866214 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 235 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 ATCCTGATAAATTGATGTTGTGCTGTCTGGCAT 4 86 0 AGATGTGTGC 0.885811 -28 GTCATTCTTCAAACATGTAGTCTGACTAATGGA 9 259 1 ACATGTGTCT 0.90338 -42 ATGCAACTTGAATGATTTTGTGTATAGATTGCC 13 49 0 AGATTTGTGT 0.93802 -226 AGGCGGCTTGAAGGATGAAGTGTATATAAAGAA 13 157 1 AGATGAGTGT 0.910879 -118 TTGTCACATTATGCATGATGTGTACATCTATTT 15 70 1 ACATGAGTGT 0.856158 -178 ATTAACCTCGTCAGATGTTGTGTTCTTGTTAGC 15 224 0 TGATGTGTGT 0.83956 -24 TTTATTAATTATCGATGTGGTCTGGAGAGGCAA 18 141 0 AGATGTGTCT 0.94133 -160 ATTCATCCTTAGAGATGTTATCTTTACTTGCTT 19 108 0 AGATGTATCT 0.611325 -64 TTTGCAGTGAAGCCATTTACTGTTTTTTATCGA 21 74 1 ACATTTCTGT 0.702233 -157 TGCTTTAGTTATTCATTTCCTGTCTCACTTTGC 21 148 1 ACATTTCTGT 0.702234 -83 TTATAAAAATACCGATTTGGTGTTGTTTTTCAT 24 52 1 AGATTTGTGT 0.938019 -249 * ***** **** Masking position 5 Map Score: 0.95211 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 182 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 14 TTTATTGTTTACCGAGCAGCGTTCAGAGAA 3 81 1 ACCGAGCAGC 0.980981 -193 TAACGTAGCAGCACTGTCACCT 4 3 1 ACGTAGCAGC 0.944906 -111 AATGATTTATCCGTAGCAGCACTGCCAGAA 4 32 0 CCGTAGCAGC 0.964245 -82 GTGAGCGAATCCCGATGAGCTTACTCAGGT 13 93 1 CCCGATGAGC 0.891959 -182 AGGTTGCTCTACCTATCAGCAGCTCTACAA 20 19 1 ACCTATCAGC 0.935743 -120 AATTTGATCGCCCGAACAGCAATGTTTGGG 23 13 1 CCCGAACAGC 0.953309 -198 ********** Masking position 5 Map Score: 0.799615 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 189 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 ACTGTCACCTTCTGGCAGTGCTGCTACGGA 4 23 1 TCTGGCAGTG 0.729724 -91 TGTCTGGCATTTTATCAGTCACATTGGTGG 4 66 0 TTTATCAGTC 0.716037 -48 ACAACATCAATTTATCAGGATACGTT 4 98 1 TTTATCAGGA 0.737234 -16 TTTAATTAACTCTATCAGGGATGGTTT 8 81 1 TCTATCAGGG 0.910436 -17 ATTTTTTCAATCTAGCAGTGGGTTTTCATT 11 48 0 TCTAGCAGTG 0.910436 -74 GTGTACATCTATTTTCAGGGCATCCACTGT 15 89 1 ATTTTCAGGG 0.645821 -159 TCAGGTTCACATTATCAGTACTGATGCAAA 15 170 0 ATTATCAGTA 0.42673 -78 TAAATCATTATTTATCAGTGCATTAATGTT 16 150 1 TTTATCAGTG 0.945517 -135 CTTCGAAGTCTTTTGCAGTGAGATGTATAT 19 81 0 TTTTGCAGTG 0.880225 -91 TCTGCCCCGTTTTATCGGGGCAGATATAAC 21 17 0 TTTATCGGGG 0.753477 -214 CTAACGGTCATTTTGCAGTGAAGCCATTTA 21 63 1 TTTTGCAGTG 0.880225 -168 ********** Masking position 3 Map Score: 0.983526 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 331 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918