AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -iarcA_synecho_opreg_100.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 1651827 181 hypothetical protein #2 phdD 86 dihydrolipoamide dehydrogenase #3 icd 300 isocitrate dehydrogenase (NADP+) #4 merA 300 mercuric reductase #5 cydA 276 cytochrome oxidase d subunit I #6 frdA 175 succinate dehydrogenase flavoprotein subunit #7 sdhB 293 succinate dehydrogenase iron- sulphur protein subunit #8 sodB 300 superoxide dismutase #9 glcD 153 glycolate oxidase subunit GlcD #10 gltA 193 citrate synthase #11 sdhB 166 succinate dehydrogenase iron-sulfur protein Motif number 1 TTCCCCCCTGGCGATCGGGTCT 1 1 1 TTCCCCTGGC 0.990716 -181 ACTGTTTTTCCTTCTCCCTGGTAGTCTAAACC 1 95 0 CTTCCCTGGT 0.923576 -87 TACGAAATTTTTATCCCATTGCGGAACTGAAA 3 206 0 TTCCCATTGC 0.909031 -95 GGATTATGATCTGCTCCGTGCCGTTTTTTCAA 3 267 1 CTTCCGTGCC 0.854958 -34 TTTACGGCAGTTCCCCCCTTCTCAAGGGGGGC 4 130 1 TTCCCCTTCT 0.882271 -171 TCCTCAATTATTCACCTATGGCGTGAGTCAGC 5 117 1 TTCCTATGGC 0.654171 -160 TGTGCCCACCCTATCCCCTGCTCAAAACTAAC 5 196 0 CTCCCCTGCT 0.975226 -81 ATGACTACTTTTCACCCAGTCCTAGAGCATA 7 10 0 TTCCCAGTCC 0.836325 -284 AAATCATTCGCTGCCCCCTGGGCATTAACCCA 7 54 1 CTCCCCTGGG 0.947114 -240 CCCCTGGGCATTAACCCATGGAAAGTATGGAA 7 68 1 TTCCCATGGA 0.899398 -226 CCCATATTGCTTTTCCCAGGGTATTTCCT 7 275 1 TTCCCAGGGT 0.90123 -19 TGACAGTTTTTTAATCCCTTGTTAATCTCTCG 8 101 0 TTTCCCTTGT 0.697029 -200 CGCTCTTTTTCTTGCCCATGGCCACCGGCAAT 8 168 1 CTCCCATGGC 0.981305 -133 GGCATAGGTACTTTTCCCTTCCCCACC 9 137 1 CTTCCCTTCC 0.871257 -17 GAAATTTACCTTCACCCCTGGATTGAGCCCAG 10 57 0 TTCCCCTGGA 0.959277 -137 TGGGGACAGGCTGGCCCGGGCCGGCGCAATTT 10 120 1 CTCCCGGGCC 0.938267 -74 ATTTTTATTCCTGGTCCCGGCAAAATTCCATA 11 79 0 CTTCCCGGCA 0.793898 -88 ATAAAAATTATTGCCCCCGGCCCTTCCGTAAT 11 103 1 TTCCCCGGCC 0.982003 -64 ** ******** Masking position 2 Map Score: 22.7127 Number of sites scoring better than the average of aligned sites = 3340 Number in coding regions = 3000 Number in noncoding regions = 340 Number of orfs with sites within 600 bp upstream = 360 Fraction of orfs with sites within 600 bp upstream = 0.057822 Motif number 2 ATTCTAACACCCCATCAAAGTTTGGCATTTTCACTGTTTTTCCT 1 115 0 CCCAATTTTC 0.989413 -67 TTGCCTTCATCCCACTCAAACCCATCAATTTTTGGATTCATGCC 3 32 1 CCCAAATTTG 0.935162 -269 TAGAAATTCTCCTTACTAGTGGAGTGATTTTCAGTTCCGCAATG 3 178 1 CCTAATTTTG 0.508569 -123 CACTAAAGCTCCGGCTTAAAAAGGAGAATTTTACGGCAGTTCCC 4 101 1 CCGAAATTTC 0.972217 -200 CCCCCTAGCCCCCCTTGAGAAGGGGGGAACTGCCGTAAAATTCT 4 125 0 CCCAGAACTC 0.848132 -176 TAACAGAAATCCCAGGTAAAGTCTCTGTATTGTCAGCTACATTC 5 156 0 CCCAGTATTC 0.957202 -121 GTTGTGCCCACCCTATCCCCTGCTCAAAACTAACAGAAATCCCA 5 186 0 CCCCAAACTC 0.780993 -91 AGGCGATCGCCCCTAAAATCCAATCTAAATTAGCCGTATTTTCC 7 96 0 CCCAAAATTC 0.982816 -198 GTCGAGAACCCCCTAGAATTGTGCCTATTTTCCCAAGTCTTTGA 7 182 0 CCCAATTTTC 0.989413 -112 TTCAAGCCCACCCGCTTAATAGGCTCGTTTTGACCTACTTTGAT 8 15 0 CCCAGTTTTC 0.973364 -286 CGGTGGAGAACCGCACAAAAGACAAAATATTGCCGGTGGCCATG 8 184 0 CCGAATATTC 0.95539 -117 ATTTGTTCGGCCCAAACCCTCGTCAAATTTTCCCAAAT 9 5 0 CCCCATTTTC 0.958906 -149 CTGCTGTCCACCGCAAAATCCACTAGAATTTGGCATAGGTACTT 9 106 1 CCGAAATTTC 0.972215 -48 ATTAGGGAATCTGAAGGAATTCTGGAAATTTACCTTCACCCCTG 10 69 0 CTGAAATTTC 0.649076 -125 TAAATTTTATCCCCATTAGTCCCAGCAAATTAGCC 11 2 0 CCCAAAATTC 0.982817 -165 CCTACAATTCCCCATTGATCTATGGAATTTTGCCGGGACCAGGA 11 59 1 CCCAATTTTC 0.989413 -108 *** * ***** * Masking position 21 Map Score: 19.1347 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 598 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 TTCCCCCCTGGCGATCGGGTCTT 1 4 1 CCCCCTGGCG 0.888283 -178 AGCGTTTGGAGCCCCAGGCC 1 172 1 GCCCCAGGCC 0.934522 -10 TGGAAAGTTGACCCCCGTCCTGGCGATCGC 2 24 0 ACCCCCGTCC 0.928595 -63 CTGTTTAATCCCCCCTAGCCCCCCTTGAGA 4 149 0 CCCCCTAGCC 0.992623 -152 CCAAACTCTCCGCCCCATCCTGGCTGAGAC 5 50 0 CGCCCCATCC 0.916865 -227 GAGTTGTGCCCACCCTATCCCCTGCTCAAA 5 202 0 CACCCTATCC 0.909216 -75 GGGAAGGCAGGCCCCTAGGGATTGTCATTG 6 134 1 GCCCCTAGGG 0.789548 -42 GACTACTTTTCACCCAGTCCTAGAGCATA 7 10 0 CACCCAGTCC 0.888435 -284 TCATTCGCTGCCCCCTGGGCATTAACCCAT 7 57 1 CCCCCTGGGC 0.774253 -237 TCTTTTTCTTGCCCATGGCCACCGGCAATA 8 171 1 GCCCATGGCC 0.598988 -130 GCCAGCCTGTCCCCATATCCATATTAGGGA 10 105 0 CCCCATATCC 0.891539 -89 GGGACAGGCTGGCCCGGGCCGGCGCAATTT 10 122 1 GGCCCGGGCC 0.498726 -72 AAAAATTATTGCCCCCGGCCCTTCCGTAAT 11 105 1 GCCCCCGGCC 0.940013 -62 ********** Masking position 4 Map Score: 18.3682 Number of sites scoring better than the average of aligned sites = 2362 Number in coding regions = 2100 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 4 TCGAAGACAATGGGCGATCGCCAGGAC 2 8 1 CAATGGGCGA 0.937697 -79 AATGTATGTACAATTGGCAATACTTTATTG 3 88 1 CAATTGGCAA 0.762257 -213 ATTTTTATCCCATTGCGGAACTGAAAATCA 3 202 0 CATTGCGGAA 0.932434 -99 GCTCTAAGCTCATTGAGGAATTTGTCATAA 4 202 1 CATTGAGGAA 0.927452 -99 ATAGGTGAATAATTGAGGAAGTTCTATCTT 5 106 0 AATTGAGGAA 0.639798 -171 AATGATTCAGCATTAGGGAAGGCAGGCCCC 6 119 1 CATTAGGGAA 0.958355 -57 TCTTTGACACCATTGAGCAACATCACTAAG 7 159 0 CATTGAGCAA 0.878341 -135 GGTGGGCTTGAAATGGGCGATAGCAATGTT 8 47 1 AAATGGGCGA 0.676494 -254 TTGCCGGTGGCCATGGGCAAGAAAAAGAGC 8 169 0 CCATGGGCAA 0.826714 -132 ATTCTCTACTCAATAGGGGATTCCATGGCT 8 271 0 CAATAGGGGA 0.91372 -30 GTCAGTAGTACAATAGGGAAACTAGCTAGC 9 75 0 CAATAGGGAA 0.958355 -79 CCCATATCCATATTAGGGAATCTGAAGGAA 10 94 0 TATTAGGGAA 0.761757 -100 TTCCATAGATCAATGGGGAATTGTAGGAGG 11 56 0 CAATGGGGAA 0.983025 -111 TCGACCTTCCTATTACGGAAGGGCCGGGGG 11 116 0 TATTACGGAA 0.432445 -51 ********** Masking position 10 Map Score: 12.8504 Number of sites scoring better than the average of aligned sites = 1583 Number in coding regions = 1368 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 5 TCAAGACTTTAGTTTAGGGGTTAAGGGCAA 2 58 0 AGTTTAGGGG 0.952769 -29 TAGTGAGGAGATTTAGGGGGATAAATACCT 4 76 0 ATTTAGGGGG 0.913657 -225 AAAAAGGAGAATTTTACGGCAGTTCCCCCC 4 118 1 ATTTTACGGC 0.792576 -183 TTTAGATTGGATTTTAGGGGCGATCGCCTT 7 111 1 ATTTTAGGGG 0.98855 -183 CGCCTTGGGAATTTTAGTGGCAGGCTTAGT 7 135 1 ATTTTAGTGG 0.944448 -159 AATAGGCACAATTCTAGGGGGTTCTCGACA 7 197 1 ATTCTAGGGG 0.986152 -97 CTACTTAACAATTCAACGGGAAACATTGCT 8 68 0 ATTCAACGGG 0.919215 -233 CCTATGCCAAATTCTAGTGGATTTTGCGGT 9 115 0 ATTCTAGTGG 0.933436 -39 TGGGGATAAAATTTAAGGGGGACATCCTCC 11 31 1 ATTTAAGGGG 0.978397 -136 ********** Masking position 3 Map Score: 10.8046 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 184 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 TATTGCTCCCCAAGCTTGGCCGAGCCGGCAGTTTCCA 1 36 0 CAGGCGAGCG 0.975677 -146 GGTGAAGCAAAAATAACGGTTTAGACTACCAGGGAGA 1 78 1 AATGTTAGCT 0.76965 -104 CCAAACGCTCAAATGTGGCCCGATTCTAACACCCCAT 1 144 0 AATGCGATCT 0.943246 -38 TCGTAACAGCCAATGCAATCAGAGCCTCCAGAAAGGA 3 233 1 CATACGAGCT 0.862228 -68 ACGCTTTCTTAGATAACGATGGATACGTGAATGTAAA 4 22 0 AATGTGATCG 0.807917 -279 CAACAACTTAAGATTCAGATTAATACTCCAAAATTTA 4 234 1 AATGTAATCT 0.650728 -67 ACTCTCCGCCCCATCCTGGCTGAGACGCGATACAACC 5 39 0 CATGCGAGCG 0.979904 -238 GATGGGGCGGAGAGTTTGGTAGAGGCTTAACTATAAG 5 61 1 AAGGTGAGCT 0.965537 -216 TGATGTTGCTCAATGGTGTCAAAGACTTGGGAAAATA 7 164 1 CATGCAAGCT 0.955763 -130 CTGGGAAAAGCAATATGGGCGGAGGCTACCTCACAGT 7 257 0 CATGCGAGCT 0.988665 -37 TGGGCAAGAAAAAGAGCGACAAAGCCTTGGTAATCAT 8 149 0 AAGGCAAGCT 0.938814 -152 CCCTTCCGTAATAGGAAGGTCGAGCCTTTTTTGCCCT 11 123 1 AAGGTGAGCT 0.965562 -44 * ** * * *** ** Masking position 13 Map Score: 7.76649 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 197 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 AAGACCCGATCGCCAGGGGGGAA 1 4 0 CGCCAGGGGG 0.905409 -178 TTTTCAGTTCCGCAATGGGATAAAAATTTC 3 205 1 CGCAATGGGA 0.891672 -96 TTCCCCCCTTCTCAAGGGGGGCTAGGGGGG 4 140 1 CTCAAGGGGG 0.974383 -161 ATGCTCTAAGCTCATTGAGGAATTTGTCAT 4 200 1 CTCATTGAGG 0.627927 -101 AAAATGATTCAGCATTAGGGAAGGCAGGCC 6 117 1 AGCATTAGGG 0.83354 -59 AGTGATGTTGCTCAATGGTGTCAAAGACTT 7 162 1 CTCAATGGTG 0.859526 -132 AAAAAAAGCCAGCAACGGGGTCTTAATCTA 7 226 1 AGCAACGGGG 0.964093 -68 CCCTGGGAAAAGCAATATGGGCGGAGGCTA 7 266 0 AGCAATATGG 0.638101 -28 AAATTCTCTACTCAATAGGGGATTCCATGG 8 273 0 CTCAATAGGG 0.966165 -28 AATTCCATAGATCAATGGGGAATTGTAGGA 11 58 0 ATCAATGGGG 0.976146 -109 GTATGAGGAAATCAACAGGGCAAAAAAGGC 11 146 0 ATCAACAGGG 0.880253 -21 ********** Masking position 3 Map Score: 7.60711 Number of sites scoring better than the average of aligned sites = 1157 Number in coding regions = 1015 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 8 AGTGAAAATGCCAAACTTTGATGGGGTGTT 1 124 1 CCAAACTTTG 0.910006 -58 GCCTGGGGCTCCAAACGCTCAAATGTGGCC 1 161 0 CCAAACGCTC 0.97546 -21 ACAGCCAAAACCCAACTTTCCAAATATGCT 4 175 1 CCCAACTTTC 0.972542 -126 TAAGCCTCTACCAAACTCTCCGCCCCATCC 5 60 0 CCAAACTCTC 0.990885 -217 ATAGGGTGGGCACAACTCTCTTCTTTTTTT 5 214 1 CACAACTCTC 0.904658 -63 GCCGTATTTTCCATACTTTCCATGGGTTAA 7 78 0 CCATACTTTC 0.91616 -216 TTTGTTCGGCCCAAACCCTCGTCAAATTTT 9 18 0 CCAAACCCTC 0.97546 -136 ********** Masking position 5 Map Score: 5.72639 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 115 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CAATTTTTGGATTCATGCCCCCAGTTTAAC 3 57 1 ATTCATGCCC 0.94395 -244 GTTACGAAATTTTTATCCCATTGCGGAACT 3 210 0 TTTTATCCCA 0.709487 -91 AAGACTAGGTATTTATCCCCCTAAATCTCC 4 70 1 ATTTATCCCC 0.92367 -231 AAATTCTCCTTTTTAAGCCGGAGCTTTAGT 4 102 0 TTTTAAGCCG 0.694324 -199 GTTTTGGCTGTTTAATCCCCCCTAGCCCCC 4 156 0 TTTAATCCCC 0.939069 -145 TTGATCAATTTTTTTTGCCCCACCTGTGTA 6 81 0 TTTTTTGCCC 0.968553 -95 CTTTCCATGGGTTAATGCCCAGGGGGCAGC 7 63 0 GTTAATGCCC 0.862684 -231 CTATCGCCCATTTCAAGCCCACCCGCTTAA 8 40 0 TTTCAAGCCC 0.938301 -261 CCTGACAGTTTTTTAATCCCTTGTTAATCT 8 105 0 TTTTAATCCC 0.676788 -196 TGTCGCTCTTTTTCTTGCCCATGGCCACCG 8 165 1 TTTCTTGCCC 0.956388 -136 CCCCCTTAAATTTTATCCCCATTAGTCCCA 11 22 0 TTTTATCCCC 0.971458 -145 AGGAATAAAAATTATTGCCCCCGGCCCTTC 11 99 1 ATTATTGCCC 0.832167 -68 AGGTCGAGCCTTTTTTGCCCTGTTGATTTC 11 139 1 TTTTTTGCCC 0.968553 -28 ********** Masking position 3 Map Score: 13.7818 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 786 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 10 TCGCCAGGACGGGGGTCAACTTTCCAGAGG 2 28 1 GGGGGTCAAC 0.814252 -59 TTTGTTAAACTGGGGGCATGAATCCAAAAA 3 60 0 TGGGGGCATG 0.913615 -241 CCCCTTGAGAAGGGGGGAACTGCCGTAAAA 4 129 0 AGGGGGGAAC 0.672446 -172 CCCTTCTCAAGGGGGGCTAGGGGGGATTAA 4 145 1 GGGGGGCTAG 0.969472 -156 AAGACAAAAAGTGGGGGTTGTATCGCGTCT 5 24 1 GTGGGGGTTG 0.448013 -253 TCTATCTTTTGGTGGACTTATAGTTAAGCC 5 84 0 GGTGGACTTA 0.545848 -193 CAGGGGATAGGGTGGGCACAACTCTCTTCT 5 208 1 GGTGGGCACA 0.727309 -69 ATATACACAGGTGGGGCAAAAAAAATTGAT 6 78 1 GTGGGGCAAA 0.629583 -98 GTTAATGCCCAGGGGGCAGCGAATGATTTG 7 53 0 AGGGGGCAGC 0.821472 -241 CTATTAAGCGGGTGGGCTTGAAATGGGCGA 8 37 1 GGTGGGCTTG 0.938242 -264 AAATATTGCCGGTGGCCATGGGCAAGAAAA 8 174 0 GGTGGCCATG 0.804271 -127 TCGGTAATCCGGTGGAGAACCGCACAAAAG 8 207 0 GGTGGAGAAC 0.757784 -94 TGGATTTTGCGGTGGACAGCAGCGTCAGTA 9 98 0 GGTGGACAGC 0.87508 -56 GGTGGGGAAGGGAAAAGTAC 9 144 0 GGTGGGGAAG 0.928373 -10 TTCGATCAATTGTGGGCTAGAT 10 3 0 TGTGGGCTAG 0.745486 -191 AATATGGATATGGGGACAGGCTGGCCCGGG 10 110 1 TGGGGACAGG 0.735881 -84 TAAAATTTAAGGGGGACATCCTCCTACAAT 11 37 1 GGGGGACATC 0.938798 -130 ********** Masking position 5 Map Score: 12.3026 Number of sites scoring better than the average of aligned sites = 3587 Number in coding regions = 3183 Number in noncoding regions = 404 Number of orfs with sites within 600 bp upstream = 335 Fraction of orfs with sites within 600 bp upstream = 0.0538066 Motif number 11 GTTAAGGGCAACCTCTGGAAAGTTGACCCC 2 39 0 ACCTCTGGAA 0.949563 -48 TTTCTTAGATAACGATGGATACGTGAATGT 4 25 0 AACGATGGAT 0.840464 -276 AACTATTTTCAACTATGGATTAGCTAGGTG 6 42 0 AACTATGGAT 0.896661 -134 CTGGGCATTAACCCATGGAAAGTATGGAAA 7 71 1 ACCCATGGAA 0.963272 -223 GTAAAGTGAGAGCCATGGAATCCCCTATTG 8 261 1 AGCCATGGAA 0.928605 -40 ATTTACCTTCACCCCTGGATTGAGCCCAGT 10 56 0 ACCCCTGGAT 0.943672 -138 TTCCCCATTGATCTATGGAATTTTGCCGGG 11 66 1 ATCTATGGAA 0.867508 -101 ********** Masking position 9 Map Score: 2.43971 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 164 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 TGTACATACATTTGTTAAACTGGGGGCATG 3 70 0 TTTGTTAAAC 0.673484 -231 GGTTCTTCTATTTGGTTATCTTCATGCTTG 3 136 0 TTTGGTTATC 0.75914 -165 TGAATCTTAAGTTGTTGATTTATGACAAAT 4 221 0 GTTGTTGATT 0.632576 -80 CACTTTTTGTCTTGTTGATGCCAATA 5 7 0 CTTGTTGATG 0.678232 -270 ATTCAGTTAATTCGTTGATCAATTAATCAC 6 15 1 TTCGTTGATC 0.870968 -161 CTGAATCATTTTTGGTGATTGATCAATTTT 6 99 0 TTTGGTGATT 0.739809 -77 TTTTTAATCCCTTGTTAATCTCTCGGAGCT 8 96 0 CTTGTTAATC 0.930507 -205 AGCCTGACAGTTTTTTAATCCCTTGTTAAT 8 107 0 TTTTTTAATC 0.561227 -194 GCGACAAAGCCTTGGTAATCATCGCCGCCA 8 141 0 CTTGGTAATC 0.926048 -160 CGGTTAAAAGGTCGGTAATCCGGTGGAGAA 8 218 0 GTCGGTAATC 0.767411 -83 GGCGCAATTTTTTGTTAATCCAAATCTCTA 10 142 1 TTTGTTAATC 0.941973 -52 ********** Masking position 8 Map Score: 1.14246 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 451 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 13 CTTGGCCGAGCCGGCAGTTTCCACAAAGAC 1 29 0 CCGGCAGTTT 0.976286 -153 CCATCAAAGTTTGGCATTTTCACTGTTTTT 1 118 0 TTGGCATTTT 0.804657 -64 TGTTTCTGGCATTTTTGTTCGTTGC 3 6 1 CTGGCATTTT 0.959723 -295 TGGATTCATGCCCCCAGTTTAACAAATGTA 3 64 1 CCCCCAGTTT 0.807248 -237 AAGTTGGGTTTTGGCTGTTTAATCCCCCCT 4 163 0 TTGGCTGTTT 0.77507 -138 CGATACAACCCCCACTTTTTGTCTTGTTGA 5 19 0 CCCACTTTTT 0.753578 -258 GACCCCGTTGCTGGCTTTTTTTGTCGAGAA 7 218 0 CTGGCTTTTT 0.925923 -76 CGGAGGCTACCTCACAGTTTAGATTAAGAC 7 245 0 CTCACAGTTT 0.895627 -49 CCAACCAAGCCTGACAGTTTTTTAATCCCT 8 114 0 CTGACAGTTT 0.950838 -187 CACCGGATTACCGACCTTTTAACCGAGGAA 8 223 1 CCGACCTTTT 0.801709 -78 ********** Masking position 8 Map Score: 5.15972 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 612 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 14 TTCGTTGCCTTCATCCCACTCAAACCCATC 3 28 1 TCATCCCACT 0.923904 -273 TTATTGATTTTCTCTCCACTCATGCAAGCA 3 112 1 TCTCTCCACT 0.975784 -189 TTATAGAAATTCTCCTTACTAGTGGAGTGA 3 175 1 TCTCCTTACT 0.885339 -126 GAACTGAAAATCACTCCACTAGTAAGGAGA 3 185 0 TCACTCCACT 0.96566 -116 TCCCCCTAAATCTCCTCACTAAAGCTCCGG 4 85 1 TCTCCTCACT 0.975784 -216 ********** Masking position 8 Map Score: 0.29544 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 74 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 ********** No masking Map Score: -3.24475e-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