AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarL_ecoli_hinf_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 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #2 narK 300 nitrite extrusion protein #3 narG 300 nitrate reductase 1, alpha subunit #4 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #5 ccmC 41 heme exporter protein C #6 napF 300 ferredoxin-type protein: electron transfer #7 yhfC 270 putative transport #8 nirB 261 nitrite reductase (NAD(P)H) subunit #9 nirC 300 nitrite reductase activity #10 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #11 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #12 nrfE 79 formate-dependent nitrite reductase; possible assembly function #13 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #14 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #15 HI0340 82 conserved hypothetical protein #16 HI0341 84 conserved hypothetical protein #17 HI0342 205 ferredoxin-type protein (napF) #18 HI0343 180 napD protein (napD) #19 HI0345 300 ferredoxin-type protein (napG) #20 HI0833 22 fumarate reductase, 15 kDa hydrophobic protein (frdC) #21 HI0835 181 fumarate reductase, flavoprotein subunit (frdA) #22 HI0936 108 cytochrome C-type biogenesis #23 HI0937 200 extragenic suppressor (suhB) #24 HI1047 253 anaerobic dimethyl sulfoxide reductase, chain A (dmsA) #25 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #26 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #27 HI1074 264 conserved hypothetical protein #28 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) #29 HI1089 248 heme exporter ATP-binding protein A (ccmA) #30 HI1091 57 heme exporter protein C (ccmC) #31 HI1092 41 heme exporter protein D (ccmD) #32 HI1095 138 thiol:disulfide interchange protein (dsbE) Motif number 1 TTATCTATCATTGATATTTATCATTACCCATAG 2 191 0 TTGATTATCA 0.922849 -110 ATCTTATCGTTTGATTTACATCAAATTGCCTTT 2 228 1 TTGATAATCA 0.981029 -73 CCCATCACTCTTGATCGTTATCAATTCCCACGC 3 196 1 TTGATTATCA 0.922849 -105 TCTACCGCTATTGAGGTAGGTCAATTTGCGAAG 4 99 1 TTGAGAGTCA 0.928256 -133 CTGAATCTTTTTGCGCGAAATCAAAAAGAACAT 4 155 0 TTGCGAATCA 0.838427 -77 TTTTTATTCCGTGATCAAAATCACCTCTTAAAA 7 134 1 GTGATAATCA 0.860259 -137 CTTAAGAAAATTTATACAAATCAGCAATATACC 8 142 1 TTTATAATCA 0.719463 -120 AAAGGTGAATTTGATTTACATCAATAAGCGGGG 8 190 1 TTGATAATCA 0.981029 -72 TGAACTTTATTTGTTATAGATCAAAAAATCTAA 17 83 0 TTGTTAATCA 0.927852 -123 TTTGTTTTAGATCATTCATTGTTA 18 167 0 TTGTTAATCA 0.927852 -14 ACCACTTTCTTTGATGCAGGTCAGCTTGCAAAT 19 140 1 TTGATAGTCA 0.949517 -161 CTTAGCTTTTTTGAGGTAGATCACAAAATCCGA 21 39 1 TTGAGAATCA 0.972657 -143 GAAGTTTTACTTGAGCCAAATCAATTAATCATT 24 167 0 TTGAGAATCA 0.972657 -87 ATGCTAAAGTTTGAGCTTGATCAAGCTTATCTT 26 95 0 TTGAGTATCA 0.891637 -67 GTCAATTTGATCTAAGTCAATTAAATAAA 28 7 1 TTGATAGTCA 0.949517 -294 AGCAAAAAAATTGATTTAGATCATTAAATGTTT 29 83 1 TTGATAATCA 0.981029 -166 TTATTAAATTTTGTTTTAAATCAATAAACCTAT 29 137 1 TTGTTAATCA 0.927851 -112 ***** * **** Masking position 11 Map Score: 24.77 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 37 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 ATTTAACACTAAAAGAGCAGGTAAAATTGT 6 14 0 AAAAGAGCAG 0.675595 -287 TAGCAGGATCAAAAGAGTGGCGGGAAGCGT 6 145 0 AAAAGAGTGG 0.858356 -156 GGAAGAGAGGAAAAGGCCGGACGACGATAG 8 30 0 AAAAGGCCGG 0.858443 -232 AAAATAGACAAAATGAGCGGGTTTATAGAA 8 78 0 AAATGAGCGG 0.975247 -184 CACTATTAATAAGTGTGCGGCTAACGCTGC 9 70 1 AAGTGTGCGG 0.894453 -231 GCGAAAAATTAGCGGCAGAAAAAGG 14 6 1 AAATTAGCGG 0.858356 -295 GTTCGTGAAAAAATTGGCGGCGATTATACC 15 54 0 AAATTGGCGG 0.922517 -29 TTCAAATTACAAATGGGTGGCGTAGCACAA 18 70 1 AAATGGGTGG 0.922517 -111 CGACTTCAAAAAATGTGCGGTAAAAGTGGA 19 214 1 AAATGTGCGG 0.985256 -87 TGGGAGAAAATAAAGTGCGGTTGATTTTTA 19 265 0 TAAAGTGCGG 0.915162 -36 CATTTATGGTTAAAGTGCGGTGGAAAATTG 23 20 0 TAAAGTGCGG 0.915162 -181 GTTTGCACTAAAAAGTGCGGTGCATTTTTC 25 13 0 AAAAGTGCGG 0.985256 -31 GAGATAATCCAAATTGGCGGCTATTCTACT 28 127 0 AAATTGGCGG 0.922517 -174 TTCATCGTATAAAAGTGCGGTGGTTTTTCT 30 16 1 AAAAGTGCGG 0.985256 -42 CTCCCCCCATAAATGGGTGGAGCAAAGTTA 32 99 1 AAATGGGTGG 0.922517 -40 AAGTTAATGAAAAAGTGCGGTAAAAA 32 123 1 AAAAGTGCGG 0.985256 -16 ********** Masking position 2 Map Score: 24.0307 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 251 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TCACGACAGTAACCGCACCTACACTGTCAT 10 229 0 AACCGCACCT 0.976468 -72 TTTCCACTTTTACCGCACATTTTTTGAAGT 19 216 0 TACCGCACAT 0.951317 -85 TGTAAAAATCAACCGCACTTTATTTTCTCC 19 263 1 AACCGCACTT 0.992578 -38 TCCAATTTTCCACCGCACTTTAACCATAAA 23 18 1 CACCGCACTT 0.995305 -183 ATGAAAAATGCACCGCACTTTTTAGTGCAA 25 11 1 CACCGCACTT 0.995305 -33 CCATTTTTTTAACCGCACTTT 27 254 1 AACCGCACTT 0.992578 -11 AGAGAAAAACCACCGCACTTTTATACGATG 30 18 0 CACCGCACTT 0.995305 -40 TTTTTACCGCACTTTTTCATTAAC 32 125 0 TACCGCACTT 0.989485 -14 ********** Masking position 7 Map Score: 17.7537 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 11 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 CGGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAA 1 18 1 TTTTGCTTTA 0.773099 -283 TTAAGCTGAATTTTATAGCATTTTTTTAACTGGCCT 4 43 1 TTTTATTTTT 0.734158 -189 TTTTGTGATCTGTTTAAATGTTTTATTGCAATCGGT 7 179 0 TGTTTTTTTT 0.639285 -92 GAGCGGGCGATTTTAGGTGATTTTGTGATCTGTTTA 7 199 0 TTTTATTTTT 0.734158 -72 TAAACTTTTTGTTTTATTTTTTGTTTTTATTT 9 7 1 TTTTGTTTTT 0.770449 -294 GCAATGGCGGTTTTTATTGTTTTTCACGACAGTAAC 10 246 0 TTTTTTTTTA 0.891739 -55 CATATCGCCTTTTTGGATGCCTTTTTCTGCCGCTAA 14 19 0 TTTTGCTTTT 0.677899 -282 AAACTACCTATTTTGGGTTGTTTTCATTCATTCATC 17 126 1 TTTTGTTTTA 0.844567 -80 TTTGTTTTAGATCATTCATTGTTATTGC 18 163 0 TGTTTCATTA 0.45197 -18 CCTTTTCCACTTTTACCGCACATTTTTTGAAGTCGG 19 213 0 TTTTACATTT 0.442526 -88 TGCGGTTGATTTTTACATGGTTTTTACGCAGCCTTT 19 244 0 TTTTATTTTA 0.817214 -57 GGGGATTTATTTTTACTTTCTATTGATTGGAGGATA 21 154 1 TTTTATATTA 0.672069 -28 CAAGGTGCTATTTTTAATTTTATTAATGAAACATAC 22 36 1 TTTTTTATTA 0.79061 -73 GATCAAGTGATTTTTCTACCCATTCATTTATGGTTA 23 38 0 TTTTTCATTA 0.703055 -163 AAAACAGTGGTTTTTATAGGTTTTCAGAAAAACTTT 23 96 0 TTTTTTTTTA 0.891739 -105 TAAAAACCACTGTTTTATGATTTTCAACTAGTTATT 23 116 1 TGTTTTTTTA 0.741547 -85 TGGCACGGAATTTTTCTGTTCTTTAAAAGCTGGTGG 23 171 1 TTTTTCTTTA 0.837795 -30 AATTAACTCGTTTTAGTTATTTTTCAATCTGACTGT 24 214 1 TTTTATTTTA 0.817214 -40 ACCGCCTTAATTTTGAGTATTATTATCA 26 3 0 TTTTGTATTT 0.60607 -159 AATATACCTCTTTTTGAGTATTTTAAAAGATAAGCT 26 69 1 TTTTTTTTTA 0.891739 -93 AAATTTACCTTTTTTTTCTTTATTGATGGTGCATTT 27 75 0 TTTTTTATTA 0.79061 -190 AAAATGGAAATTTTGGTAAATATTCTAGCATAGAAA 27 225 0 TTTTGTATTT 0.60607 -40 AGGGCTTATTTGTTATATTTTATTTAATTGACTTAG 28 22 0 TGTTATATTA 0.416527 -279 TATATAGCATTTTTTACTATTTTTTATCCTTATGTT 28 87 1 TTTTTTTTTA 0.891739 -214 ATAACTGGTGTTTTTTTAACCTTTAAAAATAATTAT 28 161 1 TTTTTCTTTA 0.837795 -140 GATCATTAAATGTTTTTCCTTTTTTAAAAAGTGAAT 29 101 1 TGTTTTTTTA 0.741547 -148 TTCTCTTTAATTTTTAAGGATTTTTT 30 42 1 TTTTTTTTTT 0.83574 -16 GTGCGGTTAGTTTTTAGCGATTTTTTATAAGGAATA 31 12 1 TTTTTTTTTT 0.83574 -30 TTTTTACCGCACTTTTTCATTAACTTT 32 122 0 TTTTACTTTT 0.633929 -17 ***** **** * Masking position 4 Map Score: 22.6922 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 250 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 5 AGTGGTGCGTTTTTCTACCGCTATTGAGGTA 4 86 1 TTTCTACCGC 0.774284 -146 TTTTGCCACGCTTCCCGCCACTCTTTTGATC 6 138 1 CTCCCGCCAC 0.773621 -163 CCTTTTCCTCTCTTCCCCCGCTACGTGCATC 8 44 1 TTTCCCCCGC 0.980766 -218 CCCCGTTCCGCCTCGCAAGGGGCG 11 4 1 CTTCCGCCTC 0.918627 -35 TCCATTGTGTTTTCCGCCCCTTGCGAGGCG 11 19 0 TTTCCGCCCC 0.950589 -20 CTGCGAACGCTATTCCACTGCTCCTTTATAG 13 207 0 TTTCCACTGC 0.774284 -88 TTGGATGCCTTTTTCTGCCGCTAATTTTTCG 14 12 0 TTTCTGCCGC 0.897706 -289 AACGCTCCAATTTTCCACCGCACTTTAACCA 23 13 1 TTTCCACCGC 0.961073 -188 TATATCGTTCCCCCACAGTCAGATTG 24 238 0 CTTCCCCCAC 0.941422 -16 TTTATTCTTGCCTTCCCCTGCTTGCGGGGGA 32 12 1 CTTCCCCTGC 0.918961 -127 CCTTCGGGCACCTTCCCCCGCAAGCAGGGGA 32 25 0 CTTCCCCCGC 0.987896 -114 ACGTAATCCCCCTTCCGCCCTTCGGGCACCT 32 43 0 CTTCCGCCCT 0.688415 -96 * ********* Masking position 3 Map Score: 9.29592 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 581 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 GCGCCTGCGGGCGCTTTTTTTGTCTCC 1 7 1 GCGGGCCTTT 0.875843 -294 ATTTGCGAAGGCGGATTATTTTGTGGCAAAC 4 122 1 GCGGATATTT 0.852932 -110 TATTAATTATGCGGTTTATTTGGTCGCTCTC 6 246 1 GCGGTTATTT 0.973538 -55 TATGCCGCGAGCGGGCGATTTTAGGTGATTT 7 212 0 GCGGGCATTT 0.908322 -59 CAAAAGCCGAGCGGGTTATTTGCCGACAGGC 9 111 0 GCGGGTATTT 0.958406 -190 AAATTACCCTGCCGTTTATTTGCACAATTCT 10 23 0 GCCGTTATTT 0.796433 -278 CAGTGTAGGTGCGGTTACTGTCGTGAAAAAC 10 233 1 GCGGTTCTGT 0.818075 -68 TTTTTTGAAGTCGGTTTCTTTTGAAATTGGG 19 196 0 TCGGTTCTTT 0.652716 -105 AAAATAAAGTGCGGTTGATTTTTACATGGTT 19 258 0 GCGGTTATTT 0.973538 -43 ACTAAAAAGTGCGGTGCATTTTTCAT 25 6 0 GCGGTGATTT 0.940543 -38 GTATAAAAGTGCGGTGGTTTTTCTCTTTAAT 30 22 1 GCGGTGTTTT 0.739234 -36 AGTGCGGTTAGTTTTTAGCGATTT 31 4 1 GCGGTTGTTT 0.907163 -38 ****** **** Masking position 9 Map Score: 9.05703 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 274 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 ACATTCTGGAATGGCAGTATTCTCGGCTAT 2 28 1 ATGGCAGTAT 0.577871 -273 TCTGTAGCTAAAGGCAATTTGATGTAAATC 2 240 0 AAGGCAATTT 0.830568 -61 AACATTAGCAATGTCGATTTATCAGAGGGC 3 255 1 ATGTCGATTT 0.693463 -46 TCAATTTGCGAAGGCGGATTATTTTGTGGC 4 119 1 AAGGCGGATT 0.835085 -113 CTTGTTCTTGAAGGCTATTTAGAATCTCTT 7 50 0 AAGGCTATTT 0.659876 -221 CATTGTTGCAATGGCGGTTTTTATTGTTTT 10 259 0 ATGGCGGTTT 0.939552 -42 TTCCTTCCTGAAGTCGGTTTTCTGGCGTTG 12 39 1 AAGTCGGTTT 0.9336 -41 GGCATCCAAAAAGGCGATATGGTAAAAATT 14 34 1 AAGGCGATAT 0.875511 -267 ACATTTTTTGAAGTCGGTTTCTTTTGAAAT 19 200 0 AAGTCGGTTT 0.9336 -101 ACTCAAAATTAAGGCGGTTTTATACCGCCT 26 21 1 AAGGCGGTTT 0.977628 -141 TAAATAAATTAAGGCGGTATAAAACCGCCT 26 32 0 AAGGCGGTAT 0.939552 -130 TTATGTAGATAAGTCAATTTAAACTTAGCT 28 193 1 AAGTCAATTT 0.612549 -108 ********** Masking position 1 Map Score: 9.58607 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 429 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 GCGCCTGCGGGCGCTTTTTTTG 1 3 1 GCCTGCGGGC 0.945862 -298 TCCTGTGGGAGCCTGTCGGCCCTCTGATAA 3 273 0 GCCTGTCGGC 0.974911 -28 CGGTTTTCTCCTGTGGGAGCCTGTCGGC 3 283 0 TCCTGTGGGA 0.77709 -18 TTTTTAACTGGCCTGTCAGGCAGTGGTGCG 4 65 1 GCCTGTCAGG 0.850084 -167 CGCATTGCACGCCTGTCGGCAAATAACCCG 9 101 1 GCCTGTCGGC 0.974911 -200 TGAAGTACGTGGCTGTGGGATAAAAACAAT 13 262 1 GGCTGTGGGA 0.933856 -33 TGCTTGTAATGGCTGTGGGGCTTGTGTACA 18 117 1 GGCTGTGGGG 0.981045 -64 TTTTCAATCTGACTGTGGGGGAACGATATA 24 234 1 GACTGTGGGG 0.97098 -20 GCCTTCCCCTGCTTGCGGGGGAAGGTGCCC 32 21 1 GCTTGCGGGG 0.861963 -118 GTCGCGAAGTGACTGAGGGGGATACGTAAT 32 67 0 GACTGAGGGG 0.857065 -72 ********** Masking position 4 Map Score: 7.91076 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 272 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 TGAGGTGAGTCGCCGTGGTTTGGTAAAAAC 1 259 1 CGCCGTGGTT 0.960219 -42 GGGTCAGCTCCGCCATGGCGGGCGCGTATG 9 141 1 CGCCATGGCG 0.499692 -160 AAATTTGTCTCGCCGTCGCGTTGCGAGTAG 13 16 0 CGCCGTCGCG 0.931404 -279 AATTACTTCTCGTCGTGGCTATATTAAAGC 14 60 1 CGTCGTGGCT 0.984684 -241 TTAAAGCGGTCGCCGTGGTTACAAAACGTC 14 83 1 CGCCGTGGTT 0.960219 -218 ACGTGGTTTACGTCATGGCGATAAAATTAA 19 31 1 CGTCATGGCG 0.65483 -270 GATTTCATCTCGTCGAGGCGAAATGATTTC 19 61 1 CGTCGAGGCG 0.946121 -240 TAATAAACCACCTCGTGGCTTAGTATTTAC 19 112 1 CCTCGTGGCT 0.918682 -189 ********** Masking position 4 Map Score: 7.65681 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 480 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ACCACGGCGACTCACCTCAGCAGCCAATAC 1 248 0 CTCACCTCAG 0.836968 -53 CCAAAGGTCGCGCCCATCACCAAAGGGCGT 9 226 0 CGCCCATCAC 0.763066 -75 GTGTACGACACGCCCATCAATTTCGAGATC 14 118 0 CGCCCATCAA 0.912791 -183 GCGTGATTGCCTCACCCCAAGATGGTGTTA 14 224 0 CTCACCCCAA 0.881772 -77 GGTTGTGCTACGCCACCCATTTGTAATTTG 18 72 0 CGCCACCCAT 0.861773 -109 ACTTTATTTTCTCCCATCAATAAAAGAGGA 19 279 1 CTCCCATCAA 0.927129 -22 GAGAGCTACTCTCAACTCAATCTTAGCTTT 21 18 1 CTCAACTCAA 0.849947 -164 GATATCCTCCAATCAATAGAAAGTAA 21 166 0 CTCCAATCAA 0.888257 -16 AATTACTCAACTCCAATCAGCTAAGTTTAA 28 211 0 CTCCAATCAG 0.818226 -90 ATGAAATTTTCGCAACTCAAACACATAACT 29 186 0 CGCAACTCAA 0.823315 -63 TTCGCGACAGCTCCCCCCATAAATGGGTGG 32 89 1 CTCCCCCCAT 0.923837 -50 ATTAACTTTGCTCCACCCATTTATGGGGGG 32 101 0 CTCCACCCAT 0.883429 -38 ********** Masking position 9 Map Score: 5.01089 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 245 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 GGAATTTACTTTATTTTTCATCCCCATCACTCT 3 174 1 TTATTTTTAC 0.857725 -127 AAATTCAGCTTAATTTTTAACGGCAAGAGAGAC 4 23 0 TAATTTTTAG 0.797294 -209 CTATGCCATTTTATTTTTGAACGCAGGCCAATC 7 248 1 TTATTTTTAG 0.950636 -23 TTTTTTGTTTTTATTTTTTAAAGGATAATCAAA 9 27 1 TTATTTTTAG 0.950636 -274 AACGGCAGGGTAATTTTTGAAGGTCAGCAACAA 10 38 1 TAATTTTTAG 0.797294 -263 CACAGTGTGGTTATTTGTTACACATAGGGGCGA 10 188 1 TTATTTGTAC 0.655721 -113 CCTATTAAGGTTATATTTGAAGGCATATTCTAT 16 53 0 TTATATTTAG 0.672061 -32 TATTTGAACTTTATTTGTTATAGATCAAAAAAT 17 87 0 TTATTTGTAG 0.858838 -119 CTCGTTTTAGTTATTTTTCAATCTGACTGTGGG 24 220 1 TTATTTTTAC 0.857725 -34 ATTCGTAAAATTATTTTCCATTGTTGTTGAGAA 27 193 0 TTATTTTCAG 0.752315 -72 ATCTACATAATTATTTTTAAAGGTTAAAAAAAC 28 170 0 TTATTTTTAG 0.950636 -131 GTTTTTCTCTTTAATTTTTAAGGATTTTTT 30 38 1 TTAATTTTAG 0.690455 -20 AGTGCGGTTAGTTTTTAGCGATTTTTTATA 31 8 1 TTAGTTTTAG 0.767763 -34 ******** * * Masking position 10 Map Score: 6.61363 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 39 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TGCTTTCCTCTTTTTTCAGGGGTA 4 218 0 TTCCTCTTTT 0.957805 -14 TCTCTTCACTTGCTTTTTTTCTGCTCTGTT 7 26 0 TGCTTTTTTT 0.751033 -245 GTCCGGCCTTTTCCTCTCTTCCCCCGCTAC 8 38 1 TTCCTCTCTT 0.768051 -224 ATTTGCACAATTCTACTTTTGCGTGA 10 7 0 TTCTACTTTT 0.770447 -294 AGTCAGTATCTTCCTCTTTTTCAACAGCAT 10 107 0 TTCCTCTTTT 0.957805 -194 CATCAGATCGTGCTTTTTTTAGTCACTGCC 13 69 0 TGCTTTTTTT 0.751033 -226 ACGCAGCCTTTTCCACTTTTACCGCACATT 19 225 0 TTCCACTTTT 0.928299 -76 CTTCCTCTTTTATTGATGGGA 19 290 0 TTCCTCTTTT 0.957805 -11 GTGGGCATTGTGCCATTTTTCGTTACAAAT 21 107 0 TGCCATTTTT 0.869057 -75 CCTATCAAGGTGCTATTTTTAATTTTATTA 22 31 1 TGCTATTTTT 0.632424 -78 AACAACAATATACCTCTTTTTGAGTATTTT 26 63 1 TACCTCTTTT 0.863202 -99 TCCTCAAATTTACCTTTTTTTTCTTTATTG 27 86 0 TACCTTTTTT 0.797242 -179 TTACCAAAATTTCCATTTTTTTAACCGCAC 27 242 1 TTCCATTTTT 0.889717 -23 TTAAATGTTTTTCCTTTTTTAAAAAGTGAA 29 106 1 TTCCTTTTTT 0.933971 -143 ********** Masking position 7 Map Score: 12.7611 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 157 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 13 CAAAGATGCATACCCCGATCGGGGTAAAACCT 6 176 0 TCCCGATCGG 0.936769 -125 CTTCCATCATTAACGCGCTCTGAAAATTGAGA 6 273 0 TCGCGCTCTG 0.924407 -28 TCACCTAAAATCGCCCGCTCGCGGCATATCCC 7 215 1 TCCCGCTCGC 0.987321 -56 GCTCGCGGCATATCCCGCTATGCCATTTTATT 7 231 1 TCCCGCTATG 0.946216 -40 TTTCCTCTCTTCCCCCGCTACGTGCATCTATT 8 47 1 TCCCGCTACG 0.936656 -215 TGTCGGCAAATAACCCGCTCGGCTTTTGGGTC 9 114 1 TCCCGCTCGG 0.993426 -187 TCATCCTGATTTTCACGCTCGGTAATTTGCTC 9 183 1 TCACGCTCGG 0.95146 -118 TGATGGTGCATTTCGCGCTAGCCAAATTGCAA 27 56 0 TCGCGCTAGC 0.93344 -209 TCGGGCACCTTCCCCCGCAAGCAGGGGAAGGC 32 21 0 TCCCGCAAGC 0.862045 -118 * ********* Masking position 1 Map Score: 5.76079 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 179 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 14 AGTATACCCATACCCGGAAAGAGTTACTCCTTAT 2 65 1 TACCCGGAGT 0.908982 -236 GTAAAATCCCTACCCTTACCGATGTAAAGCGACT 2 112 0 TACCCTGATG 0.837396 -189 TATTTATCATTACCCATAGTGAGTACAGTGACTT 2 176 0 TACCCTGAGT 0.966461 -125 ATTAATATGTTACCCATGGGGAATACTCCTTAAT 3 33 1 TACCCTGAAT 0.913697 -268 ATTCCTAAGATACCCCTTTAGGATAATTAACAGC 3 145 0 TACCCTGGAT 0.944274 -156 TGCGTTTTTCTACCGCTATTGAGGTAGGTCAATT 4 91 1 TACCGTGAGG 0.870154 -141 CTACAGGTTTTACCCCGATCGGGGTATGCATCTT 6 172 1 TACCCGGGGG 0.962361 -129 ATCAGCAATATACCCATTAAGGAGTATATAAAGG 8 161 1 TACCCTGGAG 0.964439 -101 GCATGTAAAATACCACTTTAGAGTTAGTCAGTAT 10 128 0 TACCATGAGT 0.73856 -173 TATACTGTTGTACCTATAAAGGAGCAGTGGAATA 13 194 1 TACCTTGGAG 0.824184 -101 ATTGAAAAACTACCTATTTTGGGTTGTTTTCATT 17 120 1 TACCTTGGGT 0.888555 -86 CACACAATATTACCCTTTTAGGGGATTTATTTTT 21 134 1 TACCCTGGGG 0.986634 -48 ***** * **** Masking position 2 Map Score: 8.39577 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 109 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 15 TGAGCCATTATGAAAACGAAAATCCCTGATG 1 215 1 TAAAACGAAA 0.755359 -86 CGTGGTTTGGTAAAAACGACAGCGATCGGCG 1 272 1 TAAAACGACA 0.885975 -29 CTTTAAAAAATAAAAACAAAAAATAAAACAA 9 19 0 TAAAACAAAA 0.907177 -282 TACAATTGATTAAAGACAACATTCACAGTGT 10 165 1 TAAGACAACA 0.808505 -136 TCTAAATTGAAAACAGCATAGTCAAAAT 17 8 1 TAAAACAGCA 0.808505 -198 TTGCAAGGGATTAAAACAAAACAGCATAGCA 17 39 0 TAAAACAAAA 0.907177 -167 GATGAATGAATGAAAACAACCCAAAATAGGT 17 131 0 TAAAACAACC 0.795044 -75 CCAAAGTTTATTAAAACATCAATCTACTAAA 24 111 1 TAAAACATCA 0.740169 -143 CTTAATTTATTTAAAACAACAATATACCTCT 26 49 1 TAAAACAACA 0.960929 -113 ATTTTTGATATAAATACAAAAATAGGGCTTA 28 50 0 TAATACAAAA 0.530955 -251 TTTTTAAAGGTTAAAAAAACACCAGTTATTA 28 159 0 TAAAAAAACA 0.618308 -142 AACTCCTTTGTATAAACAACATTAGTTCCAA 28 276 0 TTAAACAACA 0.723547 -25 GTTTATTGATTTAAAACAAAATTTAATAAAT 29 135 0 TAAAACAAAA 0.907177 -114 * ********* Masking position 6 Map Score: 5.8466 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 106 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