AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_synecho_reg_100.orf -o294_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY09572 170 Synechocystis #2 RCY03028 235 Synechocystis #3 RCY03061 131 Synechocystis #4 RCY19040 87 Synechocystis #5 RCY00322 209 Synechocystis #6 RCY33348 233 Synechocystis #7 RCY31503 112 Synechocystis #8 RCY45353 165 Synechocystis #9 RCY05245 300 Synechocystis #10 RCY02313 283 Synechocystis #11 RCY34249 175 Synechocystis #12 RCY23408 94 Synechocystis #13 RCY05831 277 Synechocystis #14 RCY50309 68 Synechocystis #15 RCY54010 66 Synechocystis #16 RCY48465 153 Synechocystis #17 RCY04930 300 Synechocystis #18 RCY20723 104 Synechocystis #19 RCY11903 300 Synechocystis #20 RCY08996 83 Synechocystis #21 RCY40124 140 Synechocystis #22 RCY00666 300 Synechocystis #23 RCY52274 113 Synechocystis #24 RCY53600 132 Synechocystis #25 RCY33958 164 Synechocystis #26 RCY50255 220 Synechocystis #27 RCY52021 164 Synechocystis #28 RCY26608 38 Synechocystis #29 RCY00135 42 Synechocystis #30 RCY33655 258 Synechocystis #31 RCY43486 300 Synechocystis Motif number 1 GGGATACTATGCCGACACCCCTATTAAATCA 1 27 1 GCCGACCCCC 0.92478 -144 AATAGACCATTGCCATTACCGTCCAACGAAT 3 17 0 TGCCATACCG 0.607283 -115 CTAGGCCCTGGCCCCGTCGCTGTA 4 4 1 GGCCCTGCCC 0.990928 -84 CTCCAGGGGAGTCCCCTCCCCGATTCTATCT 4 48 1 GTCCCCCCCC 0.908092 -40 ACTAGATGCTTCCCCTGTCCCTTGGCCAGAA 5 32 0 TCCCCTTCCC 0.926062 -178 CAGGCGGCCCTGCGACAGCCCCAAGCTGTCC 5 121 1 TGCGACGCCC 0.929664 -89 TGGGTCAACGGCCGATCGCCAGCAAAACGGG 5 152 0 GCCGATGCCA 0.837602 -58 TTGGGTATTTTTCCATACCCCCCGTGTCCGT 6 158 1 TTCCATCCCC 0.81955 -76 TTCCGCAAATTTCCCCAACCCT 8 2 0 TTCCCCACCC 0.721707 -164 ATATCTTGGTGCTCATCGCCCATATAATTCT 9 71 1 GCTCATGCCC 0.850198 -230 CCAGACCGTGTTCCCTGGCCCATGCAAACCC 9 203 0 TTCCCTGCCC 0.950614 -98 TAACCCAACGGCCGCCAGACCGTGTTCCCTG 9 217 0 GCCGCCGACC 0.750242 -84 TGGGAGGGTTGTTCATTCCCCAAACAATCCG 10 20 0 GTTCATCCCC 0.386997 -264 TTCCGGGTTGGCCCACTACCGATAAGATGGG 10 47 0 GCCCACACCG 0.692599 -237 ATTTTTCTGGGCTCATGGCCCAGGGGGGATC 10 91 1 GCTCATGCCC 0.850197 -193 GGGGTTCGATTCCCCTCACCCGCTTTGGGTA 13 123 1 TCCCCTACCC 0.937042 -155 TGATGTCCGTTGCGACACCCCTCCTCGACCG 13 211 1 TGCGACCCCC 0.84942 -67 GGACTGGGTTTGCCCTGCCCCATCGGTGAGA 16 33 0 TGCCCTCCCC 0.962986 -121 ATCACTTTTTTCCCTTAGCCCAATAATTACC 16 97 1 TCCCTTGCCC 0.84493 -57 CAGTTTAGCAGGCGATCGCCCCGATTACCCA 17 178 0 GGCGATGCCC 0.972655 -123 TGACAAGTTTGTTCCTAGCCCTCCAGTCTAG 18 35 1 GTTCCTGCCC 0.727936 -70 TTCCAGCATAGCCGCCCGACCCTAGAAGTCC 19 114 0 GCCGCCGACC 0.750242 -187 AGTCTTAGGGGGCCCTGGCCAACTGGTAGGA 20 16 1 GGCCCTGCCA 0.9292 -68 CGGATTTAGCGGCGATCGCCCTAAAAATACC 21 19 0 GGCGATGCCC 0.972655 -122 TTAACGTTTTTCCGCTTGACCCTCCATAAAC 22 252 1 TCCGCTGACC 0.714084 -49 ACCCCGCTTTGGCGATCGCCGGGTTGTCAGG 23 24 0 GGCGATGCCG 0.890083 -90 CGGGGACAGTGGCGATCGCCGGGGTAATCCA 23 86 0 GGCGATGCCG 0.890083 -28 GTTTAGCTCCGCCGATCTCCC 24 122 1 GCCGATTCCC 0.879632 -11 AGAAGGCGATCGCCGGTGGCCATTG 26 5 1 GGCGATGCCG 0.890083 -216 TGCACGACTGGGCCCTAACCCAGACCGGTGG 26 46 0 GGCCCTACCC 0.956718 -175 CGATTGTTTTTGCCCTTGCCATAGATTTTT 26 201 1 TGCCCTGCCA 0.879474 -20 GAAGTTATTTGCCCTTGTCCCTGCTCCGATT 27 120 1 GCCCTTTCCC 0.624412 -45 ACCTTTCCCTACCCCCACCCTAACG 29 5 1 TTCCCTCCCC 0.891481 -38 AACGACCATCTCCCCTTACCC 29 32 1 TCCCCTACCC 0.937042 -11 TTGTTGTAGCTCCGATGTCCGACCAGTCCGA 30 115 1 TCCGATTCCG 0.480448 -144 GTATTAAAAATCCCCCTGCCATGCTCTCCAC 30 159 1 TCCCCCGCCA 0.855273 -100 TCCACTGAAATGCCCCTTCCAACCACCGGAA 30 185 1 TGCCCCTCCA 0.452751 -74 AACCCCGGCCTCCCCCTCCCCCAACCAAAAT 30 229 1 TCCCCCCCCC 0.954692 -30 ****** **** Masking position 10 Map Score: 50.0323 Number of sites scoring better than the average of aligned sites = 6784 Number in coding regions = 6199 Number in noncoding regions = 585 Number of orfs with sites within 600 bp upstream = 516 Fraction of orfs with sites within 600 bp upstream = 0.0828783 Motif number 2 GTCCATGGCATCGGTGGAAATGTTTGATTTAA 1 50 0 TCGGTGGATG 0.878289 -121 CATTGCTAACCAGGCGGCCCTGCGACAGCCCC 5 111 1 CAGGCGGCTG 0.935031 -99 TAATACGGACACGGGGGGTATGGAAAAATACC 6 161 0 ACGGGGGATG 0.93578 -73 CCTGGGTGCCCAGGGGGCTTTGGGTTACCCTA 8 68 0 CAGGGGGTTG 0.960953 -98 TGGGTTAAAATCGGGGGAATTACACGTTCGGC 9 241 1 TCGGGGGTTA 0.772557 -60 AATTACACGTTCGGCGGGATTTCGTCCCCAGT 9 258 1 TCGGCGGTTT 0.91832 -43 TTCTGCTTAACCGGGCGGTCTGCTACAATTTT 11 131 1 CCGGGCGCTG 0.835098 -45 TCACTATGGCCGGGGGGAGTTT 12 1 0 CGGGGGGTTT 0.885741 -94 GTTTCTGCCACAGGCGGAAATTCCCTTGGATG 17 248 1 CAGGCGGATT 0.927937 -53 CTTCTAGGGTCGGGCGGCTATGCTGGAAAAGC 19 117 1 CGGGCGGATG 0.948746 -184 AAGGAAGTCTTAGGGGGCCCTGGCCAACTGGT 20 11 1 TAGGGGGCTG 0.83666 -73 TGGAGAAAGACCGGGGGTGTTTAAAAGTCGTT 21 94 1 CCGGGGGTTT 0.981741 -47 GGTATTGGTTTCGGCGGTAACGC 22 2 0 TCGGCGGACG 0.851875 -299 GGGAGATCGGCGGAGCTAAACGCTAAAT 24 115 0 TCGGCGGCTA 0.696501 -18 TGGTTCAATCCTGGGGGAGTTTTTTCTTCTCA 25 82 1 CTGGGGGTTT 0.739725 -83 AGCTTAAGCAACGGCGGTAATG 25 153 1 ACGGCGGATG 0.922881 -12 AAGGCGATCGCCGGTGGCCATTGGGGTAAAAT 26 13 1 CCGGTGGATT 0.92991 -208 CTAACCCAGACCGGTGGAATTTTACCCCAATG 26 31 0 CCGGTGGTTT 0.906961 -190 GCAAGCTTGCCCGGCGGGCATGGTAGGATATA 26 109 0 CCGGCGGATG 0.992271 -112 GATCAAGCCACCGGGGGTCACTCCAGGGGTAC 27 68 1 CCGGGGGACT 0.927926 -97 ATCCGGCGGTAATGTTTCTAAGAT 28 25 0 CCGGCGGATG 0.992272 -14 GCTACAACAACCGGGGGCAAAGCAAAACCCTA 30 93 0 CCGGGGGAAG 0.909777 -166 GAGAGCATGGCAGGGGGATTTTTAATACAGAT 30 155 0 CAGGGGGTTT 0.920129 -104 ******* *** Masking position 7 Map Score: 31.4751 Number of sites scoring better than the average of aligned sites = 1627 Number in coding regions = 1541 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 TATTGAGAGGTTTGCCTTGCTAACA 1 156 1 TTTGCCTTGC 0.675756 -15 CCTAAAGTAGTTTGCTCAGGAACAGTTCTA 2 96 0 TTTGCTCAGG 0.471762 -140 ATTTGCCATGGTACTTAATAG 4 77 0 TTTGCCATGG 0.878684 -11 GTTCCGCAAATTTCCCCAACCCT 8 4 0 TTTCCCCAAC 0.799416 -162 AATAACCTGGTTTGCCAAAGTTTTTCAAAA 10 205 1 TTTGCCAAAG 0.613059 -79 AAAATTTTCGTTTGTCCTAGATTTTTAGCA 10 232 1 TTTGTCCTAG 0.5585 -52 TAGCAAAAGTTTTCCCATGGCAATGTCAAC 10 257 1 TTTCCCATGG 0.870025 -27 AAGCAGAACTTTTCCCCATCCATCTAACTA 11 109 0 TTTCCCCATC 0.689781 -67 CATATTCTATTTTGCCCCGCCATTGTTGCG 14 21 0 TTTGCCCCGC 0.848572 -48 TGGGACTGGGTTTGCCCTGCCCCATCGGTG 16 36 0 TTTGCCCTGC 0.951723 -118 CCAGCTATATTTTCCCCTAGTACTGGGACT 16 59 0 TTTCCCCTAG 0.97346 -95 CCATCACTTTTTTCCCTTAGCCCAATAATT 16 95 1 TTTCCCTTAG 0.794981 -59 GAACTCATAATTCGCCCTAGACAGGTTCAA 17 42 1 TTCGCCCTAG 0.864064 -259 CCATGGCTATTTTCCCCTAGACTGGAGGGC 18 52 0 TTTCCCCTAG 0.97346 -53 TAACAGAATTTTTGCCCAACT 19 2 0 TTTGCCCAAC 0.81176 -299 ATGATTTATATTTCCCCCTCCATTTAACCA 19 62 1 TTTCCCCCTC 0.685481 -239 TCCGGCAAGATTTACCCTAGCTTAAAGCAA 19 269 0 TTTACCCTAG 0.70725 -32 GTCGTTGCAGGTTCCCCTTGGGTGCTATGG 21 120 1 GTTCCCCTTG 0.750487 -21 ATCCTTCATCTTGGCCCTTGTGGAATCCCT 22 102 0 TTGGCCCTTG 0.780042 -199 TCCTTGACTTTTTCCTCTGGTTGATTAACT 22 211 1 TTTCCTCTGG 0.739994 -90 TTTTTGCGTTCCCCTGGGTGAGGCTGA 24 8 1 GTTCCCCTGG 0.877261 -125 GTTTCTAAGTTTTGCCTTAGTAAAAACAAG 25 28 1 TTTGCCTTAG 0.807533 -137 AACGATTGTTTTTGCCCTTGCCATAGATTT 26 199 1 TTTGCCCTTG 0.956789 -22 GGCAAATAACTTCCCCATAGATTAGCAGGC 27 103 0 TTCCCCATAG 0.447103 -62 GGGGAAGTTATTTGCCCTTGTCCCTGCTCC 27 117 1 TTTGCCCTTG 0.956789 -48 GGGTTTTGCTTTGCCCCCGGTTGTTGTAGC 30 95 1 TTGCCCCCGG 0.688843 -164 ********** Masking position 2 Map Score: 25.3685 Number of sites scoring better than the average of aligned sites = 3225 Number in coding regions = 2878 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 4 CTGGGTCAACGGCCGATCGCCAGCAAAACG 5 154 0 GGCCGATCGC 0.985037 -56 TAGAGATTCGCCGCGATTGCTTGCCCATTA 6 110 0 CCGCGATTGC 0.943082 -124 AAAAACAACGCCGCGATGGCTAGAGATTCG 6 130 0 CCGCGATGGC 0.985037 -104 CAATGACATTTCCCGATCGCAGTTCCGCAA 8 25 0 TCCCGATCGC 0.934489 -141 CAGGTTCTAGGCCCGATCGCCACCGAAAAC 10 140 0 GCCCGATCGC 0.982658 -144 TGGGTAATCGGGGCGATCGCCTGCTAAACT 17 178 1 GGGCGATCGC 0.987091 -123 TCGGATTTAGCGGCGATCGCCCTAAAAATA 21 21 0 CGGCGATCGC 0.995481 -120 CCTGACAACCCGGCGATCGCCAAAGCGGGG 23 24 1 CGGCGATCGC 0.995481 -90 TGGATTACCCCGGCGATCGCCACTGTCCCC 23 86 1 CGGCGATCGC 0.995481 -28 CGTTTAGCTCCGCCGATCTCCC 24 121 1 CGCCGATCTC 0.925878 -12 CAATGGCCACCGGCGATCGCCTTCT 26 6 0 CGGCGATCGC 0.995481 -215 TGGAATTTTACCCCAATGGCCACCGGCGAT 26 19 0 CCCCAATGGC 0.788713 -202 CTGGAGTGACCCCCGGTGGCTTGATCTTCT 27 64 0 CCCCGGTGGC 0.899385 -101 ********** Masking position 7 Map Score: 30.3179 Number of sites scoring better than the average of aligned sites = 2926 Number in coding regions = 2717 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 5 CTTTGCGGAGAACTCCAGGGGAGTCCCCTCC 4 36 1 AATCCAGGGG 0.910104 -52 TCTGGGCTCATGGCCCAGGGGGGATCCCAAT 10 96 1 TGCCCAGGGG 0.837232 -188 TGTCAGTAGGCCCCTCAGGGAAAAACAAGCC 11 61 1 CCCTCAGGGA 0.759331 -115 GTTTATCCTTCATCCAAGGGAATTTCCGCCT 17 259 0 CACCAAGGGA 0.876385 -42 CCTAGCCCTCCAGTCTAGGGGAAAATAGCCA 18 48 1 CATCTAGGGG 0.910104 -57 AATTTAGTAACAATCCAGGGAGGGAACCCTC 20 62 1 CATCCAGGGA 0.973638 -22 ACCATAGCACCCAAGGGGAACCTGCAAC 21 123 0 CACCAAGGGG 0.960691 -18 TCTCTCAGCCTCACCCAGGGGAACGCAAAAA 24 11 0 TCCCCAGGGG 0.932181 -122 CTCCTTGGTTCAATCCTGGGGGAGTTTTTTC 25 77 1 CATCCTGGGG 0.931849 -88 ACTCTGACTACAATCCAGTGGTCTGGTGATG 27 28 0 CATCCAGTGG 0.942052 -137 CACCGGGGGTCACTCCAGGGGTACAATGCCT 27 76 1 CATCCAGGGG 0.992276 -89 TTGGAAGGGGCATTTCAGTGGAGAGCATGGC 30 176 0 CATTCAGTGG 0.672869 -83 CTATCTAGCACCACCCAGGGACAAATGAAAG 31 114 0 CCCCCAGGGA 0.966032 -187 ** ******** Masking position 8 Map Score: 12.1394 Number of sites scoring better than the average of aligned sites = 1119 Number in coding regions = 1010 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 6 TATTAAATCAAACATTTCCACCGATGCCAT 1 48 1 AACATTTCCA 0.636179 -123 CTAGGTGACGGACCTTGCCATCCTTCCCCA 3 71 0 GACCTTGCCA 0.972316 -61 CTAGGCCCTGGCCCCGTCGCTGTA 4 5 1 GCCCTGGCCC 0.924438 -83 CGACAGCCCCAAGCTGTCCCCCGTTTTGCT 5 133 1 AAGCTGTCCC 0.738035 -77 CTTGGTGTGGAACCTTTCCAACGGGTCTGG 6 20 1 AACCTTTCCA 0.924419 -214 ACCAGTTTAAAACCTTGCACAAACGGCTTG 6 58 1 AACCTTGCAC 0.647982 -176 ATCAAGCAATGACATTTCCCGATCGCAGTT 8 31 0 GACATTTCCC 0.80167 -135 GTTTTGCTATTACCTTGCCAATATCTTGGT 9 51 1 TACCTTGCCA 0.774935 -250 TCGGGCCTAGAACCTGGCCAAAGTGCTGGA 10 154 1 AACCTGGCCA 0.939643 -130 CTCCGGAGTTGACATTGCCATGGGAAAACT 10 264 0 GACATTGCCA 0.833923 -20 GGTTAAGCAGAACTTTTCCCCATCCATCTA 11 113 0 AACTTTTCCC 0.527092 -63 GCATAGGACAAAGCTGGCCCCTGAGTCACT 12 28 0 AAGCTGGCCC 0.84932 -67 TTTGTCAGGAGAACTTTCCCG 13 2 0 GAACTTTCCC 0.615347 -276 AATTTTTGACAACCTTTCCAGTTTAGCAGG 17 197 0 AACCTTTCCA 0.924419 -104 GTCTTAGGGGGCCCTGGCCAACTGGTAGGA 20 17 1 GCCCTGGCCA 0.88367 -67 ATAAGGCTTTGACCTTTCCCGTCCCTTTTC 24 70 0 GACCTTTCCC 0.965839 -63 TGCAAAATGCAAGCTTGCCCGGCGGGCATG 26 119 0 AAGCTTGCCC 0.898577 -102 GATTGTTTTTGCCCTTGCCATAGATTTTT 26 202 1 GCCCTTGCCA 0.92272 -19 ********** Masking position 5 Map Score: 19.0586 Number of sites scoring better than the average of aligned sites = 1050 Number in coding regions = 947 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 7 TGATTTAATAGGGGTGTCGGCATAGTATCC 1 28 0 GGGGTGTCGG 0.863109 -143 AACCCTTCCTGAGTTGTCCCCTTT 3 118 1 GAGTTGTCCC 0.759504 -14 GACTCCCCTGGAGTTCTCCGCAAAGATACA 4 31 0 GAGTTCTCCG 0.829801 -57 GAGAACTCCAGGGGAGTCCCCTCCCCGATT 4 43 1 GGGGAGTCCC 0.847379 -45 TTCTTCTTCCGGGTTGGCCCACTACCGATA 10 54 0 GGGTTGGCCC 0.95361 -230 AATGGGTACAGCGGTCTCCGAAACTCGATA 13 153 1 GCGGTCTCCG 0.931179 -125 CGGTCGAGGAGGGGTGTCGCAACGGACATC 13 212 0 GGGGTGTCGC 0.712694 -66 AATAGAATATGGGTAGTCCGCCGTTGCGTT 14 40 1 GGGTAGTCCG 0.928842 -29 TACTGGGACTGGGTTTGCCCTGCCCCATCG 16 39 0 GGGTTTGCCC 0.74063 -115 TTACCAGGGTTGGCCGAGCGGTTGAG 17 7 1 GGGTTGGCCG 0.981221 -294 TATTTTTAGGGCGATCGCCGCTAAATCCGA 21 21 1 GCGATCGCCG 0.851795 -120 GGCGATCGCCGGGTTGTCAGGGCTACAAAA 23 15 0 GGGTTGTCAG 0.680602 -99 GGGGACAGTGGCGATCGCCGGGGTAATCCA 23 86 0 GCGATCGCCG 0.851795 -28 CCAATCTTACGGGGTTGCCGCCCATCTGAG 25 110 0 GGGGTTGCCG 0.887327 -55 AGAAGGCGATCGCCGGTGGCCATTG 26 6 1 GCGATCGCCG 0.851795 -215 GGAAGCTGAAGAGTAGTCCGTCGGATCTTA 26 169 1 GAGTAGTCCG 0.722143 -52 GTTGGGGGAGGGGGAGGCCGGGGTTTTTAA 30 224 0 GGGGAGGCCG 0.948331 -35 ATACCCTGCAGCGTGCTCCGATTGGGTCTT 31 87 1 GCGTGCTCCG 0.645308 -214 ********** Masking position 3 Map Score: 20.0534 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 779 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 GATGCCATGGACTAGAACCCCAACTATGGAT 1 70 1 ATAGAACCCC 0.653883 -101 TGTTAGCAAGGCAAACCTCTCAATAATTT 1 152 0 AGCAAACCTC 0.781462 -19 TTTAGAACAGAAGCAAACCCCTAGGCCTTCC 7 26 0 AGCAAACCCC 0.983262 -87 TTTTAGGGTAACCCAAAGCCCCCTGGGCACC 8 65 1 ACCAAAGCCC 0.762456 -101 CTCGACGGATACGCAAAGCCCTTAAAATAAA 8 107 1 AGCAAAGCCC 0.961222 -59 TCCCTGGCCCATGCAAACCCCTAAGTTTCTG 9 192 0 AGCAAACCCC 0.983262 -109 TGTTTGGGGAATGAACAACCCTCCCATCTTA 10 25 1 AGAACAACCC 0.839042 -259 TGATCAAAACCCATTGAATCTC 11 164 0 GTCAAAACCC 0.680139 -12 GGGTGAGGGGAATCGAACCCCTATCATTAGC 13 113 0 ATCGAACCCC 0.842138 -165 CCTTGGATGAAGGATAAACCCGAATAGGAGA 17 271 1 AGATAAACCC 0.675336 -30 ACCGGGGGCAAAGCAAAACCCTAAAAGTATC 30 85 0 AGCAAAACCC 0.980662 -174 GAAGCACCTTATTAAAAACCCCGGCCTCCCC 30 213 1 ATAAAAACCC 0.837719 -46 GCTGCAGGGTATGCACAACCCATTTCTAGAT 31 68 0 AGCACAACCC 0.936386 -233 CCAGGGACAAATGAAAGACCCAATCGGAGCA 31 100 0 AGAAAGACCC 0.723735 -201 * ********* Masking position 9 Map Score: 9.29411 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 503 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 9 GCTCAATTGTTCAGCGTTAACCATCTTAACGG 5 78 0 TCAGCTAACC 0.837163 -132 GAGTTTTCGTGCTGGGTCAACGGCCGATCGCC 5 163 0 GCTGGTAACG 0.931315 -47 TTCCAACGGGTCTGGGTCAACCTACCAGTTTA 6 35 1 TCTGGTAACC 0.966871 -199 CCCAGGGGGCTTTGGGTTACCCTAAAAAATAA 8 60 0 TTTGGTACCC 0.855287 -106 GGGGAAAAGTTCTGCTTAACCGGGCGGTCTGC 11 122 1 TCTGCTACCG 0.931017 -54 TTATGAGTTCGCTGCCTCAACCGCTCGGCCAA 17 20 0 GCTGCTAACC 0.949612 -281 TTTCTCCTATTCGGGTTTATCCTTCATCCAAG 17 272 0 TCGGGTATCC 0.72263 -29 AAATGAAATAGCTGGCTGACCGTTGGAGAAAG 21 71 1 GCTGGTACCG 0.955952 -70 AAAAAAATATGTTGGGTTAACCCCACTGTGCC 22 140 0 GTTGGTAACC 0.790039 -161 TTAACGTTTTTCCGCTTGACCCTCCATAAACT 22 252 1 TCCGCTACCC 0.873677 -49 GATCGCCAAAGCGGGGTCAACGATCTTGGTAG 23 38 1 GCGGGTAACG 0.853592 -76 GCGAATGTATTCTGGATTACCCCGGCGATCGC 23 74 1 TCTGGTACCC 0.979041 -40 GGTATCTCTCTCAGCCTCACCCAGGGGAACGC 24 16 0 TCAGCTACCC 0.891641 -117 ***** * **** Masking position 9 Map Score: 8.58794 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 291 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 10 TGTAATCTGGAATTTTTGTCAGATACCCTCACCT 9 146 1 AATTTTTGAT 0.8389 -155 AGAATTGGCCAATTTTTCTGGGCTCATGGCCCAG 10 80 1 AATTTTTCGT 0.597834 -204 GACAAACGAAAATTTTTGAAAAACTTTGGCAAAC 10 214 0 AATTTTTGAC 0.87796 -70 GGTCTGCTACAATTTTTGAGATTCAATGGGTTTT 11 147 1 AATTTTTGAC 0.877966 -29 TATGGTGCTCAATTTTTCTTTAGTCAATCAGTTT 15 31 0 AATTTTTCTT 0.848411 -36 AAACGAATCAAATTTTTGGTTGTTCTGACTGAAG 17 91 1 AATTTTTGTT 0.89829 -210 TGGATGTGCGAATTTTTGACAACCTTTCCAGTTT 17 203 0 AATTTTTGAC 0.877966 -98 TTTCTAACAGAATTTTTGCCCAACT 19 2 0 AATTTTTGCC 0.764204 -299 CCAGACTAGCAATTTTTGCTTTTCCAGCATAGCC 19 132 0 AATTTTTGTC 0.924255 -169 TTTAGACTTAAATTTTTCAATCATTGCTTTAAGC 19 246 1 AATTTTTCTT 0.848411 -55 AAATTTTGTTAATTTTTCTATCCTACCAGTTGGC 20 33 0 AATTTTTCTT 0.848411 -51 GGTGATATTGATTTTTTGGGTATCTTTTTAGCTA 22 51 0 ATTTTTTGTC 0.564938 -250 ATTGAAGTTAATTTTTCGTTTCTAAGTTTTGCC 25 10 1 AATTTTTCTT 0.848411 -155 ******** * * Masking position 1 Map Score: 5.97062 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 285 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 11 GTACTTCGTTCTTTTGGATATACTCATTGCC 2 56 0 CTTTTGGTAT 0.896603 -180 AATGGTCTATTTTTTGGATAAAACGCCGAGT 3 37 1 TTTTTGGTAA 0.85403 -95 CGCGGCGTTGTTTTTGGGTATTTTTCCATAC 6 145 1 TTTTTGGTAT 0.970281 -89 GGGATAATTTTTGGGGATGCAAACTGAT 15 8 1 TTTTTGGGAT 0.896603 -59 ACGAATCAAATTTTTGGTTGTTCTGACTGAA 17 93 1 TTTTTGGTGT 0.948685 -208 TTTGGGTATCTTTTTAGCTATGCGGCTGTAG 22 40 0 TTTTTAGTAT 0.784751 -261 TGATATTGATTTTTTGGGTATCTTTTTAGCT 22 52 0 TTTTTGGTAT 0.970281 -249 TTTTCCTTCTTTTTTGGCTGTAACTATGG 30 9 0 TTTTTGGTGT 0.948685 -250 ******* *** Masking position 5 Map Score: 4.25844 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 34 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 ACTACTTTAGGTAAAACTGACAATGGACAGTAC 2 115 1 GTACTGACAA 0.95601 -121 GAGTCCTGTCGGTTTCCTGACAAGCCGTTTGTG 6 75 0 GGTCTGACAA 0.971808 -159 AAATAAGGAAAAGTGTCAACTTCGTACTA 7 94 0 GGAGTGTCAA 0.796863 -19 AAGAAGGTGAGGGTATCTGACAAAAATTCCAGA 9 151 0 GGACTGACAA 0.965493 -150 TTCCCTGAGGGGCCTACTGACAAAATGGGCTAC 11 50 0 GGTCTGACAA 0.971808 -126 CGGGAAAGTTCTCCTGACAAAAGTCTAGGC 13 8 1 GTTCTGACAA 0.963996 -270 AAGAATTGCGGAATTTGTGACAAGTTTGTTCCT 18 18 1 GATGTGACAA 0.74559 -87 ATATTTTTTTGTCAAGCTGGCAAGCCGTTTTCC 22 162 1 GTACTGGCAA 0.852339 -139 TGGCTTTTGTAGCCCTGACAACCCGGCGATC 23 9 1 GTCCTGACAA 0.907322 -105 CAGTGGTCTGGTGATGGTGTCAATTTCGTCTTG 27 11 0 GTTGTGTCAA 0.789646 -154 ** * ******* Masking position 8 Map Score: 4.52244 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 63 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 CAACTATGGATTGGTCATCAATTCCCTTAA 1 90 1 TTGGTCATCA 0.665487 -81 GGATTCATTCTCCTTCATCAAATTTGCGAT 2 208 0 TCCTTCATCA 0.946581 -28 GACCTTGCCATCCTTCCCCACTGACTCGGC 3 61 0 TCCTTCCCCA 0.864133 -71 GATGGCAAGGTCCGTCACCTAGGCCATATA 3 79 1 TCCGTCACCT 0.920246 -53 TCGGCGGGATTTCGTCCCCAGTTTTTTCCT 9 268 1 TTCGTCCCCA 0.749777 -33 CCCCTCCTCGACCGTCATCCATGCTCCCTC 13 228 1 ACCGTCATCC 0.779356 -50 TTCGGGTTTATCCTTCATCCAAGGGAATTT 17 265 0 TCCTTCATCC 0.935963 -36 CCCTTAATGATTCGTCATCATGGTGATATT 22 76 0 TTCGTCATCA 0.893029 -225 CATTCGGTAATCCTTCATCTTGGCCCTTGT 22 111 0 TCCTTCATCT 0.866434 -190 AAAGACTACTTCGGTCATCACCGTGGTAGT 31 174 0 TCGGTCATCA 0.889275 -127 GCTGGAAAAATCCTTCACCCTTAGCCCGGC 31 265 1 TCCTTCACCC 0.931828 -36 ********** Masking position 5 Map Score: 4.69061 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 340 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 CCGATCGCCAGCAAAACGGGGGACAGCTTGG 5 141 0 GCAAACGGGG 0.973499 -69 CAAGGTAATAGCAAAACTGGAAACTTCAAAG 9 37 0 GCAAACTGGA 0.957749 -264 CTCAAATAGGAAAAAACTGGGGACGAAATCC 9 274 0 AAAAACTGGG 0.772275 -27 GCCCACTACCGATAAGATGGGAGGGTTGTTC 10 37 0 GAAAGATGGG 0.804449 -247 GGGGCCTACTGACAAAATGGGCTACCTTGAT 11 44 0 GAAAAATGGG 0.946257 -132 TGAGAAAAAGGAAAAAAGGGACAAAAT 16 7 0 GAAAAAGGGA 0.880837 -147 GCGATCGCCTGCTAAACTGGAAAGGTTGTCA 17 190 1 GCAAACTGGA 0.957749 -111 GTTAGCACCGGCGAAAAGGGACGGGAAAGGT 24 58 1 GCAAAAGGGA 0.904913 -75 CCCTAAGATTGATAAACTGGGATATTACAAG 30 47 1 GAAAACTGGG 0.971904 -212 ** ******** Masking position 5 Map Score: 4.00853 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 269 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 15 TCATCGTTGCTTGGTGTGGAAC 6 3 1 ATCGTTGCTT 0.840775 -231 GAGATTCGCCGCGATTGCTTGCCCATTATC 6 108 0 GCGATTGCTT 0.686077 -126 ATCGGGAAATGTCATTGCTTGATTATTTTT 8 38 1 GTCATTGCTT 0.873027 -128 TTCAAAGGAAGTCGTTGCTAACCTAAAACT 9 14 0 GTCGTTGCTA 0.916903 -287 CGGTCTGGCGGCCGTTGGGTTAAAATCGGG 9 226 1 GCCGTTGGGT 0.788391 -75 GTCCCTGATGTCCGTTGCGACACCCCTCCT 13 206 1 TCCGTTGCGA 0.677474 -72 TGGGTAGTCCGCCGTTGCGTTTCAGTCTAA 14 49 1 GCCGTTGCGT 0.969608 -20 AAATTTTTCAATCATTGCTTTAAGCTAGGG 19 255 1 ATCATTGCTT 0.659867 -46 GTCCCTTTTCGCCGGTGCTAACTTTGGTCT 24 50 0 GCCGGTGCTA 0.849755 -83 CATTACCGCCGTTGCTTAAGCTAAAAC 25 148 0 GCCGTTGCTT 0.980746 -17 AGCCAAATTAACCATTGCTAAATGCGACGA 31 145 1 ACCATTGCTA 0.756889 -156 ********** Masking position 6 Map Score: 3.63566 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 475 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795