AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifnr_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 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 pflA 191 pyruvate formate lyase activating enzyme 1 #3 pflB 54 formate acetyltransferase 1 #4 focA 300 probable formate transporter (formate channel 1) #5 ndh 300 respiratory NADH dehydrogenase #6 narK 300 nitrite extrusion protein #7 narG 300 nitrate reductase 1, alpha subunit #8 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #9 ansB 175 periplasmic L-asparaginase II #10 yggN 182 orf, hypothetical protein #11 yggH 160 orf, hypothetical protein #12 yhfC 270 putative transport #13 nirB 261 nitrite reductase (NAD(P)H) subunit #14 nirC 300 nitrite reductase activity #15 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #16 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #17 nrfE 79 formate-dependent nitrite reductase; possible assembly function #18 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #19 HI0179 130 pyruvate formate-lyase activating enzyme (act) #20 HI0180 27 formate acetyltransferase (pfl) #21 HI0181 300 formate transporter #22 HI0745 225 L-asparaginase II (ansB) #23 HI0746 155 anaerobic C4-dicarboxylate membrane transporter protein (dcuB) #24 HI0747 203 NADH dehydrogenase (ndh) #25 HI0936 108 cytochrome C-type biogenesis #26 HI0937 200 extragenic suppressor (suhB) #27 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #28 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #29 HI1074 264 conserved hypothetical protein #30 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) Motif number 1 TCACGACAGTAACCGCACCTACACTGTCAT 15 229 0 AACCGCACCT 0.982269 -72 GTTTATTTTTGACCGCACTTTGGCGGGAAC 19 17 1 GACCGCACTT 0.986025 -114 GCTCAAGTATAACCGCACTTGGGTTATCTT 22 45 1 AACCGCACTT 0.996198 -181 GGTTATTTATAACCGCACTTTGTTTATTAC 23 19 0 AACCGCACTT 0.996198 -137 GGTTATAAATAACCGCACTTTTGACCACAA 23 35 1 AACCGCACTT 0.996198 -121 TCAAAAAAATAACCGCACTTTGATATATAA 24 84 1 AACCGCACTT 0.996198 -120 TCATAAAAATAACCGCACTTATATATCAAA 24 102 0 AACCGCACTT 0.996198 -102 TCCAATTTTCCACCGCACTTTAACCATAAA 26 18 1 CACCGCACTT 0.992357 -183 ATGAAAAATGCACCGCACTTTTTAGTGCAA 27 11 1 CACCGCACTT 0.992357 -33 CCATTTTTTTAACCGCACTTT 29 254 1 AACCGCACTT 0.996198 -11 ********** Masking position 7 Map Score: 34.6664 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 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 Motif number 2 AGATAAATTGTTCTCGATCAAATTGGCTGAA 1 8 1 TTGTTATCAA 0.569004 -293 AGATGAGAAATTGATATAGATCATATCTCGCCTG 4 227 0 TTGATATCAT 0.604244 -74 CATACCAAAATTGATGTTAATCAAGTTTTGTTGC 5 151 0 TTGATATCAA 0.632309 -150 TTATCTATCATTGATATTTATCATTACCCATAGT 6 190 0 TTGATATCAT 0.882145 -111 ATCTTATCGTTTGATTTACATCAAATTGCCTTTA 6 228 1 TTGATATCAA 0.499837 -73 CCCATCACTCTTGATCGTTATCAATTCCCACGCT 7 196 1 TTGAGATCAA 0.608479 -105 CCTTCGCAAATTGACCTACCTCAATAGCGGTAGA 8 99 0 TTGATCTCAA 0.603831 -133 GATGTTCTTTTTGATTTCGCGCAAAAAGATTCAG 8 154 1 TTGATCGCAA 0.705933 -78 TATGGGAAATTTGACGTTAAACAATTTACAACGT 9 105 0 TTGATAACAA 0.858181 -71 AAAGGTGAATTTGATTTACATCAATAAGCGGGGT 13 190 1 TTGATATCAA 0.499837 -72 AGGGTAATTTTTGAAGGTCAGCAACAAAAGTTGA 15 44 1 TTGAGAGCAA 0.867636 -257 ACTGTGAATGTTGTCTTTAATCAATTGTAAGTGC 15 160 0 TTGTTATCAA 0.900816 -141 TCAACAAACTTTGATATTTTGCAAGGTTTGTTTA 21 139 0 TTGATTGCAA 0.706832 -162 ATGCTAAAGTTTGAGCTTGATCAAGCTTATCTTT 28 94 0 TTGATATCAA 0.774797 -68 TTTTATTTAATTGACTTAGATCAAATTGAC 30 7 0 TTGATATCAA 0.624759 -294 **** * ***** Masking position 13 Map Score: 18.6937 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 24 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 CTGAAAGGCGGTAATTTAGCTATAAATTGATCACCGTC 1 37 1 GAATTTAATT 0.756888 -264 ATACGTGGGATCAATTTGAGTTTTTATTAACATGTTTG 1 136 1 TAATTTTATT 0.847585 -165 ACTCATTTGTTAATTTTTAAAATTTATTTTTATTTGGA 4 131 1 TATTTTTATT 0.858211 -170 GGGTATCTTAGGAATTTACTTTATTTTTCATCCCCATC 7 164 1 GAATTTTTTT 0.883186 -137 AAATTAAGCTGAATTTTATAGCATTTTTTTAACTGGCC 8 40 1 GATTTTTTTT 0.891647 -192 AAAAGATTCAGAATTTTACTGTTAGTTTCCTCGCGCAG 8 177 1 GATTTTATTT 0.786699 -55 TTGCTAAATTGCATTTTAAGAGGTGATTTTGATCACGG 12 142 0 GATTTTTATT 0.883186 -129 CGATTTTAGGTGATTTTGTGATCTGTTTAAATGTTTTA 12 190 0 TATTTTTTTT 0.868211 -81 ATAAACCCGCTCATTTTGTCTATTTTTTGCACAAACAT 13 82 1 TATTTTTTTT 0.868211 -180 ACTTTTTGTTTTATTTTTTGTTTTTATTTTTTAAAGGA 14 14 1 TATTTTTATT 0.858211 -287 TAGATATAGCTAAATTTTACCAAAGATTTAGTCTATAA 19 85 0 TAATTTAATT 0.713665 -46 AGTAAAGTACTTAATTTGAAACTTGTTTTATTCGCGTA 21 47 0 TAATTTTTTT 0.858211 -254 TATTAATATGGGAATTTTGTCTTTAATTAAACAAACCT 21 112 1 GAATTTTATT 0.874157 -189 TTTGTTGAAATAATTTTTGCTTTTCTTTGCAATGAAAG 21 165 1 TATTTTTTTT 0.868211 -136 TTAAAAGTATTAAATTTTCATCAACTTTTTCAATGTCA 21 256 1 TAATTTATTT 0.73066 -45 ATGCAAGTACGGAATTTAAGCATAATTTTTTTGAAAGA 22 71 0 GAATTTATTT 0.772137 -155 CTCGATCACATAATTTTTTTTGTTGATTGTATAACCTT 22 110 0 TATTTTTATT 0.858211 -116 CAAAGTGCGGTTATTTTTTTGAGTTATTTTAAGTTGAT 24 68 0 TATTTTTATT 0.858211 -136 ATAAGTGCGGTTATTTTTATGAAAGTTTTCCGCCCTGT 24 110 1 TATTTTATTT 0.747005 -94 ATAATGGCACGGAATTTTTCTGTTCTTTAAAAGCTGGT 26 167 1 GAATTTTTTT 0.883186 -34 TAAAACCGCCTTAATTTTGAGTATTATTATCA 28 5 0 TAATTTTATT 0.847585 -157 TAAAAAAATGGAAATTTTGGTAAATATTCTAGCATAGA 29 227 0 GAATTTAATT 0.756879 -38 GATCTATATAGCATTTTTTACTATTTTTTATCCTTATG 30 83 1 GATTTTTTTT 0.891647 -218 * ***** * *** Masking position 7 Map Score: 22.6867 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 171 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 4 TAAGGATTTTGCGGCGTAATATATACGTGG 1 114 1 GCGGCGTAAT 0.91494 -187 GCACACAAAAACGGCGTAAAGAAAGGTTGC 1 173 0 ACGGCGTAAA 0.97135 -128 TTATGCAAATACGGAGTAAATATTTGATTA 4 169 0 ACGGAGTAAA 0.839314 -132 TACCTCAATAGCGGTAGAAAAACGCACCAC 8 87 0 GCGGTAGAAA 0.890505 -145 CTATTTTAAGACGGCATAATACTTTTTTAT 9 15 1 ACGGCATAAT 0.712335 -161 GAAGAATTAAACGGCATAAAAAAGTATTAT 9 30 0 ACGGCATAAA 0.934504 -146 CATGCCGGATGCGGCGTAAACACCTTATCC 10 95 0 GCGGCGTAAA 0.984121 -88 CAGCGACGGCAGGGTGTAAACCGGAACTTT 11 51 1 AGGGTGTAAA 0.718337 -110 TAAGGCCGTGGCTGCGGAAAGTTCCGGTTT 11 68 0 GCTGCGGAAA 0.791848 -93 GATTTTGATCACGGAATAAAAAGTGATCGT 12 126 0 ACGGAATAAA 0.687316 -145 CGCCTCGCAAGGGGCGGAAAACACAATGGA 16 19 1 GGGGCGGAAA 0.94622 -20 CGAAAAATTAGCGGCAGAAAAAGGCATCCA 18 12 1 GCGGCAGAAA 0.965863 -289 ACAACGAAACAGGGCGGAAAACTTTCATAA 24 126 0 AGGGCGGAAA 0.905881 -78 TGGTTAAAGTGCGGTGGAAAATTGGAGCGT 26 14 0 GCGGTGGAAA 0.950801 -187 ATAAATTAAGGCGGTATAAAACCGCCTTAA 28 29 0 GCGGTATAAA 0.882312 -133 ********** Masking position 8 Map Score: 16.6503 Number of sites scoring better than the average of aligned sites = 1452 Number in coding regions = 1201 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 5 AATGCACCATTCATGTTATTCTCAATAGCGAAGAACAT 5 188 1 TTATTCTCAG 0.709143 -113 TATTTTTCATCCCCATCACTCTTGATCGTTATCAATTC 7 185 1 CTACTCTTAG 0.698642 -116 CTATAAAATTCAGCTTAATTTTTAACGGCAAGAGAGAC 8 23 0 CTATTTTTAG 0.965833 -209 TGCTTTCCTCTTTTTTCAGGGGTATTACTGC 8 211 0 TTTTTTTTAG 0.717755 -21 CAAATGCTGGCCTGATTTTTCTTGAGGGAAGACT 10 159 1 CTTTTCTTAG 0.866868 -24 TCCCGCTATGCCATTTTATTTTTGAACGCAGGCCAATC 12 243 1 CTATTTTTAG 0.965833 -28 TTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAA 14 22 1 TTATTTTTAG 0.869677 -279 AAATAAACGGCAGGGTAATTTTTGAAGGTCAGCAACAA 15 33 1 CTATTTTTAG 0.965833 -268 TAGTCAGTATCTTCCTCTTTTTCAACAGCATGCATAAC 15 100 0 CTTTTTTCAG 0.866868 -201 AAACATGTTTATTTTTGACCGCACTTTGGCG 19 4 1 CTATTTTTAG 0.965833 -127 TGATTTAAATCAGGCTCATTTTTTATAGACTAAATCTT 19 63 1 CTATTTTTAG 0.965833 -68 AAAACGCTCCAATTTTCCACCGCACTTTAACC 26 5 1 CCATTTTCAG 0.698637 -196 CTCAAATTTACCTTTTTTTTCTTTATTGATGGTGCATT 29 76 0 CTTTTCTTAG 0.866868 -189 TAGAAATTCGTAAAATTATTTTCCATTGTTGTTGAGAA 29 193 0 TTATTTTCAG 0.801336 -72 GACTTATCTACATAATTATTTTTAAAGGTTAAAAAAAC 30 170 0 CTATTTTTAG 0.965833 -131 * * ****** * * Masking position 15 Map Score: 10.6096 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 67 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TTACTTTATTCGCCTGATGCTCCCTTTTAA 4 66 1 CGCCTGATGC 0.934309 -235 ATGCCTGATGCGCTTCTTATC 5 2 1 TGCCTGATGC 0.978824 -299 GCGTTCGGTAGGCCTGATAAGAAGCGCATC 5 17 0 GGCCTGATAA 0.807878 -284 AACGCACCACTGCCTGACAGGCCAGTTAAA 8 67 0 TGCCTGACAG 0.796681 -165 AATGCAAAACTGCCTGATGCGCTACGCTTA 10 32 1 TGCCTGATGC 0.978824 -151 CATCTTTCCAGGCCTGATAAGCGTAGCGCA 10 49 0 GGCCTGATAA 0.807878 -134 GCGTTTTCCATGCCGGATGCGGCGTAAACA 10 103 0 TGCCGGATGC 0.980422 -80 CAAAGTTAGTTGCCGGATGCAAGCATGATA 11 96 0 TGCCGGATGC 0.980422 -65 TTGCTCATGCCGGACGGCACTATCGTC 13 8 1 TGCCGGACGG 0.937677 -254 GAGAGGAAAAGGCCGGACGACGATAGTGCC 13 26 0 GGCCGGACGA 0.919975 -236 ********** Masking position 7 Map Score: 9.65957 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 591 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 7 CTCGCGCTAAAAAAGGCCCCACTTTCGTGGAGCC 2 53 0 AAAACCCATT 0.966136 -139 AATAATAAACAATAAACTCTGTTTTTTGATCTCA 5 92 1 AATACCTGTT 0.693811 -209 TAGCGGTAGAAAAACGCACCACTGCCTGACAGGC 8 75 0 AAAACCCATG 0.869718 -157 GAAAAACAATAAAAACCGCCATTGCAACAATGGC 15 257 1 AAAACCCATG 0.869428 -44 GAGGAGAGTAAAATAGCACCAATTATAGAAGTAT 21 205 1 AAATCCCATT 0.910959 -96 GTGCGGTTATAAATAACCGCACTTTTGACCACAA 23 31 1 AAATCGCATT 0.735 -125 TTGTTGCTATATTACACGCCGTTTCAACAAATAA 23 98 1 ATTACCCGTT 0.405361 -58 CTAGGTTAATAAAAAACACTGTGTTTTATTTGTT 23 123 0 AAAACCTGGT 0.384745 -33 AACGGTGCTGAAATAGCACCGTTTTTGTTGTTCT 24 31 1 AAATCCCGTT 0.892703 -173 TAACTCAAAAAAATAACCGCACTTTGATATATAA 24 80 1 AAATCGCATT 0.735 -124 ACTTTCATAAAAATAACCGCACTTATATATCAAA 24 102 0 AAATCGCATT 0.735 -102 AAAACGCTCCAATTTTCCACCGCA 26 1 1 AAAACCCATT 0.966198 -200 GAAAACCTATAAAAACCACTGTTTTATGATTTTC 26 107 1 AAAACCTGTT 0.84007 -94 AAATATAACAAATAAGCCCTATTTTTGTATTTAT 30 38 1 AATACCTATT 0.76642 -263 TTAGTAGTAGAATAGCCGCCAATTTGGATTATCT 30 122 1 AATACCCATT 0.898801 -179 TTAAAGGTTAAAAAAACACCAGTTATTATAGAGA 30 153 0 AAAACCCATT 0.96622 -148 CGATGCCTTAAATAATCCCTAATTACTCAACTCC 30 227 0 AATACCTATT 0.767118 -74 **** * *** ** Masking position 1 Map Score: 10.0224 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 340 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 8 AAAAATCCACTTAAGAAGGTAGGTGTTAC 3 36 1 TTAAGAAGGT 0.757299 -19 TCTCTCTTTATTAAGTCGGCGACGAGATAC 4 275 0 TTAAGTCGGC 0.880191 -26 GTTAATAAATTTAAGGGGGTCACG 5 287 1 TTAAGGGGGT 0.900854 -14 AGACTGTAAATTAAGACGTTTTATACCTGT 7 104 0 TTAAGACGTT 0.860608 -197 TCCTCTATTTTAAGACGGCATAATACTTT 9 10 1 TTAAGACGGC 0.932007 -166 ATCACCAGCGTTAAGGCGATACCAAAGGTC 14 247 0 TTAAGGCGAT 0.873081 -54 TATTCCTTCCTGAAGTCGGTTTTCTGGCGT 17 37 1 TGAAGTCGGT 0.782835 -43 CGTGGCTATATTAAAGCGGTCGCCGTGGTT 18 73 1 TTAAAGCGGT 0.846834 -228 TTCGAGATCTTTAAGACGTTTTGTAACCAC 18 97 0 TTAAGACGTT 0.860608 -204 ATACTCAAAATTAAGGCGGTTTTATACCGC 28 19 1 TTAAGGCGGT 0.985949 -143 TTTAAATAAATTAAGGCGGTATAAAACCGC 28 34 0 TTAAGGCGGT 0.985949 -128 ********** Masking position 4 Map Score: 7.76942 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 172 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 AGATAAATTGTTCTCGATCAAATTGGCTG 1 7 1 ATTGTTTATC 0.815526 -294 TAGATGAGAAATTGATATAGATCATATCTCGCC 4 229 0 ATTGATTATC 0.951763 -72 TCATACCAAAATTGATGTTAATCAAGTTTTGTT 5 153 0 ATTGATTATC 0.951763 -148 TTTATCTATCATTGATATTTATCATTACCCATA 6 192 0 ATTGATTATC 0.951763 -109 TATCTTATCGTTTGATTTACATCAAATTGCCTT 6 227 1 TTTGATTATC 0.951763 -74 CAGCGTGGGAATTGATAACGATCAAGAGTGATG 7 198 0 ATTGATAATC 0.695621 -103 AAACGCGTACTTTGTTATCAATCTGGGGCCAGC 10 127 1 TTTGTTTATC 0.815526 -56 TAAAGGTGAATTTGATTTACATCAATAAGCGGG 13 189 1 TTTGATTATC 0.951763 -73 AAAACAAATTTATGATCTCGATCACATAATTTT 22 131 0 TATGATTATC 0.695621 -95 AATGCTAAAGTTTGAGCTTGATCAAGCTTATCT 28 96 0 TTTGAGTATC 0.787945 -66 ATTTTATTTAATTGACTTAGATCAAATTGAC 30 9 0 ATTGACTATC 0.787945 -292 AGATCACATTTTTGATATAAATACAAAAATAGG 30 55 0 TTTGATTATA 0.586048 -246 ****** * *** Masking position 11 Map Score: 7.50766 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 33 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 10 GGCCCGTAACTCGCATGGTTTTTATGCAAATACG 4 186 0 TCCATTTTTA 0.667011 -115 CCCGGTAAAGTCGCCTATCTTTTCAGCAACAAAA 5 126 1 TCCCCTTTTC 0.882148 -175 CCGTGAAAAATCTCATAATTTTTATGAAGTCACT 6 150 1 TCCATTTTTA 0.667011 -151 TCTTAGGAATTTACTTTATTTTTCATCCCCATCA 7 169 1 TTCTTTTTTC 0.624881 -132 TGCTTTCCTCTTTTTTCAGGGGTATTA 8 215 0 TTCCTTTTTC 0.958706 -17 CAGCAAATGCTGGCCTGATTTTTCTTGAGGGAAG 10 156 1 TGCCTTTTTC 0.877205 -27 GGCCATCCCTTTACCTAATTTTACGTATCTGAAA 12 79 1 TTCCTTTTAC 0.665161 -192 GGTCTTGGGATCATCCTGATTTTCACGCTCGGTA 14 173 1 TCTCATTTTC 0.594953 -128 TTAGTCAGTATCTTCCTCTTTTTCAACAGCATGC 15 105 0 TCTCTTTTTC 0.941333 -196 CAATGGCGGTTTTTATTGTTTTTCACGACAGTAA 15 247 0 TTTATTTTTC 0.614496 -54 ATTATGCCTCCCCAACTTTTTCAATATTTACC 18 279 0 TCCCTTTTTC 0.982196 -22 TATTAAATTTTCATCAACTTTTTCAATGTCAATA 21 263 1 TCTCTTTTTC 0.941333 -38 AATGTCGTCGTTTTTTTCGTTGATGCGC 25 91 0 TCTCTTTTTC 0.941333 -18 GCGATCTGTATCGCAAAGTTTTTCTGAAAACCTA 26 82 1 TCCATTTTTC 0.928691 -119 TTCCTCAAATTTACCTTTTTTTTCTTTATTGATG 29 83 0 TTCCTTTTTC 0.958706 -182 TTTACCAAAATTTCCATTTTTTTAACCGCACTTT 29 241 1 TTCCTTTTTA 0.781222 -24 ** ** ****** Masking position 10 Map Score: 9.79096 Number of sites scoring better than the average of aligned sites = 767 Number in coding regions = 681 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 11 CCCCACTTTCGTGGAGCCTTTATTGTACGCT 2 40 0 GTGGAGCTTT 0.886123 -152 CTCCACGAAAGTGGGGCCTTTTTTAGCGCGA 2 55 1 GTGGGGCTTT 0.86738 -137 AATAACATGAATGGTGCATTGGTCATACCAA 5 177 0 ATGGTGCTTG 0.788699 -124 CTGTCAGGCAGTGGTGCGTTTTTCTACCGCT 8 77 1 GTGGTGCTTT 0.965509 -155 CATTGCAACAATGGCGCAATTCGGATGAAGC 15 276 1 ATGGCGCATT 0.786789 -25 ACTTCTATAATTGGTGCTATTTTACTCTCCT 21 206 0 TTGGTGCATT 0.907794 -95 AACAACAAAAACGGTGCTATTTCAGCACCGT 24 32 0 ACGGTGCATT 0.87165 -172 AGCACCTTGATAGGTGCTATTGTGCTTATAA 25 14 0 TAGGTGCATT 0.732389 -95 AGCACCTATCAAGGTGCTATTTTTAATTTTA 25 27 1 AAGGTGCATT 0.814485 -82 CGGTGGAAAATTGGAGCGTTTT 26 2 0 TTGGAGCTTT 0.79025 -199 ACTAAAAAGTGCGGTGCATTTTTCAT 27 6 0 GCGGTGCTTT 0.923292 -38 TTCTTTATTGATGGTGCATTTCGCGCTAGCC 29 65 0 ATGGTGCTTT 0.95603 -200 ******* *** Masking position 10 Map Score: 5.89884 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 242 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 TTCAACTCATTTGTTAATTTTTAAAATTTA 4 127 1 TTGTTAATTT 0.769478 -174 ACAGAGTTTATTGTTTATTATTTGAGCGAA 5 84 0 TTGTTTATTA 0.872104 -217 CTGTAACCTGTTGTTAATTAAGAGCTATGT 5 234 1 TTGTTAATTA 0.949024 -67 TATTAACCAATTGTTAATTAATGGTTATTA 5 264 0 TTGTTAATTA 0.949024 -37 TATGTGGTGGCTGTTAATTATCCTAAAGGG 7 136 1 CTGTTAATTA 0.831856 -165 TTCCTTTGTTAATTAATAAATAAAT 20 13 0 TTGTTAATTA 0.949024 -15 TAACCGCACTTTGTTTATTACCATTGATC 23 10 0 TTGTTTATTA 0.872104 -146 AGGCATCGCCTTGTTAATCATTGTTGGAAC 30 253 1 TTGTTAATCA 0.831835 -48 ********** Masking position 7 Map Score: 5.40147 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 10 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 TTGTTGAAGCAAATTTGCATTTTTCGACGGTGATCA 1 64 0 AAATTTTTTG 0.883632 -237 TTATAAGGTTAAATATCGGTAATTTGTATTTAATAA 4 15 1 AAATATTTTG 0.797502 -286 AAACATGTTTATTTTTGACCGCACTT 19 1 1 AAACATTTTT 0.729369 -130 ACTTAATTTGAAACTTGTTTTATTCGCGTAATACCG 21 41 0 AAACTTTTTG 0.959254 -260 TTATTTCAACAAACTTTGATATTTTGCAAGGTTTGT 21 142 0 AAACTTTTTG 0.959253 -159 ACGACTACAAATACTTCTATAATTGGTGCTATTTTA 21 213 0 ATACTTTTTG 0.731677 -88 TACGGAATTTAAGCATAATTTTTTTGAAAGATAACC 22 66 0 AAGCATTTTG 0.677018 -160 TTTATTAATGAAACATACTTGATTAGCGACTTTATC 25 54 1 AAACATTTTG 0.924302 -55 GCGAGTAGAAAAACTTTTTTCTTTTGGTATCTTACG 28 131 1 AAACTTTTTG 0.959254 -31 TTTATTCCTCAAATTTACCTTTTTTTTCTTTATTGA 29 85 0 AAATTTTTTT 0.62632 -180 ATATTTACCAAAATTTCCATTTTTTTAACCGCACTT 29 238 1 AAATTTTTTT 0.626344 -27 AAGTCAATTTAAACTTAGCTGATTGGAGTTGAGTAA 30 203 1 AAACTTTTTG 0.959254 -98 ****** * ** * Masking position 1 Map Score: 3.96232 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 32 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 GTTTTGGCAGTCACCTTAAAGTATAGATAGCTGAC 2 97 0 TCCCTAGATA 0.604426 -95 GGCTGAAGTATACCCATACCCGGAAAGAGTTACTC 6 59 1 TACCAACGAA 0.749933 -242 GTAAAGCGACTAACCACACGGCAAATAAGGAGTAA 6 88 0 TACCAAGAAA 0.931047 -213 TATTTATCATTACCCATAGTGAGTACAGTGACTTC 6 175 0 TACCAAGGTA 0.952132 -126 ATTAATATGTTACCCATGGGGAATACTCCTTAATA 7 33 1 TACCAGGATA 0.859808 -268 GGCTGTTAATTATCCTAAAGGGGTATCTTAGGAAT 7 144 1 TACCTAGGTA 0.868204 -157 GTCGCGCCCATCACCAAAGGGCGTACGGATGGATC 14 215 0 TCCCAAGGTA 0.921339 -86 GTGTAACAAATAACCACACTGTGAATGTTGTCTTT 15 176 0 TACCAAGGAA 0.962504 -125 CGCTTTAATATAGCCACGACGAGAAGTAATTTTTA 18 56 0 TACCAGGGAA 0.90789 -245 ATACACCCACTACCCAAATCGCATATAACATTCTA 29 18 0 TACCAAGATA 0.940794 -247 CATTTCGCGCTAGCCAAATTGCAAACAATACACCC 29 45 0 TACCAAGAAA 0.931031 -220 ** *** * * *** Masking position 15 Map Score: 3.90142 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 89 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 TGCGCACCAACACGGCCTCAGATGGGCCACAT 2 154 1 CCGGCCTCGA 0.760634 -38 GAATTTTTTCCGCATCCTCCGCTAAAACAGTT 4 98 0 CCATCCTCGC 0.825246 -203 TAGGATAATTAACAGCCACCACATAACAGACT 7 129 0 ACAGCCACAC 0.661102 -172 CCACAAAATAATCCGCCTTCGCAAATTGACCT 8 116 0 ACCGCCTTGC 0.864488 -116 AAGATTGCAGCACAGCGACGGCAGGGTGTAAA 11 39 1 CCAGCGACGC 0.972306 -122 CGGAACTTTCCGCAGCCACGGCCTTATCATGC 11 72 1 CCAGCCACGC 0.987521 -89 GTGCAATGCGCGCAGCGTTAGCCGCACACTTA 14 79 0 CCAGCGTTGC 0.910985 -222 TTTGGGTCAGCTCCGCCATGGCGGGCGCGTAT 14 138 1 CCCGCCATGC 0.970675 -163 AAACAATAAAAACCGCCATTGCAACAATGGCG 15 260 1 ACCGCCATGC 0.903286 -41 GTTTTGTAACCACGGCGACCGCTTTAATATAG 18 78 0 CCGGCGACGC 0.959392 -223 * ******* ** Masking position 6 Map Score: 2.65736 Number of sites scoring better than the average of aligned sites = 1311 Number in coding regions = 1256 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392