AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_synecho_ctra_300.orf -o064_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY07838 269 Synechocystis #2 RCY50648 180 Synechocystis #3 RCY10954 211 Synechocystis #4 RCY26047 35 Synechocystis #5 RCY44892 192 Synechocystis #6 RCY43438 300 Synechocystis #7 RCY33884 213 Synechocystis #8 RCY28358 232 Synechocystis #9 RCY44461 245 Synechocystis #10 RCY22265 286 Synechocystis #11 RCY39566 239 Synechocystis #12 RCY11341 81 Synechocystis #13 RCY10798 68 Synechocystis #14 RCY31626 279 Synechocystis #15 RCY15876 126 Synechocystis #16 RCY14629 300 Synechocystis #17 RCY18065 158 Synechocystis #18 RCY45983 163 Synechocystis Motif number 1 TTAAATCGCTTGCCGTGGGGGGTGGTCTCTGTTTT 1 73 1 TGCTGGGGGG 0.98141 -197 ATTAACTACTCTGGTTTGGGGACGAGCCATGGGAC 1 116 1 CTGTGGGGGA 0.936927 -154 ATTCCCTCCGCTATGTTGGGGGCTGAGCCTTTCAG 1 176 1 CTTTGGGGTG 0.911844 -94 AGCCAATTTTCGATGTAGGGGAAAAAT 2 3 0 CGTTGGGGAA 0.897155 -178 TGGCTTTAGCCGTTTTGGGGGATGTCAAAGAGCCA 2 33 0 CGTTGGGGGT 0.746966 -148 CAGATAAATTTGAGTTGGGGGGTAAAATGGCAATA 2 89 1 TGGTGGGGAA 0.934833 -92 AAGGACAAATTGGGATGTGGGCGAGTTTAACAACT 2 139 0 TGGTTGGGAG 0.92091 -42 CGCTGGCGATCGCCGTGGGGGGAAGCTCTCATCTG 3 32 1 CGCTGGGGAG 0.981851 -180 GTTTGGGCTATTTTTTAGGGATGGATTGGGACGAC 5 40 0 TTTTGGGAGA 0.443451 -153 ACAGCGGCAACGGTGTCGGGGTATGGTCTGTAATG 5 117 1 CGTTGGGGTG 0.950641 -76 GAAAATTTTACTTTTTGGGGGCAAGAATTTGGCTA 6 76 1 CTTTGGGGAG 0.96963 -225 AATGTCGTAGCTAGATGGGGGGTGAATGGGATCAA 6 183 1 CTGTGGGGGA 0.936927 -118 TCCCAGCAACTTAGTTGAGGGGAAGGTTTTCTGTT 7 21 0 TTGTAGGGAG 0.655247 -193 GCCAAGGGACTTGGATGGGGAAATGGAACTTCACC 7 70 1 TTGTGGGATG 0.747763 -144 GAAAGTCGTTTTTCTTTGGGGCTAGACGACACAGG 8 64 0 TTCTGGGGAG 0.953849 -169 GAACGTAAAATTGGTTAGGGGGGGGGAAAGTCGTT 8 89 0 TTGTGGGGGG 0.986311 -144 AATCATGGCATGGCACCGGGAAAGGATCTGTAGGG 8 124 0 TGCCGGGAGG 0.806393 -109 TTTAAGAAATTTGGCTTTGGGTGAGCTGGGTGGGG 8 160 0 TTGTTGGGAG 0.86213 -73 TGCGCCCTTACTCGCCCTGGGATGGGCC 8 215 1 CTGCTGGGGG 0.835124 -18 ATTGCTAGTCCGTCCTGGGGAGCGGTCAACTTTGC 9 148 1 CGCTGGGAGG 0.928229 -98 CGTACAATGGCTAGACGGGGGTTAGGTCCGATCAT 9 182 1 CTGCGGGGAG 0.970945 -64 CCCCTTTGTTTGTATTTGGGGTTAGGTTATAGTTG 11 27 0 TGATGGGGAG 0.856195 -213 TTGAGTATATCGTGATTGGGGCAAGGCAAATTCAG 11 188 0 CGGTGGGGAG 0.992779 -52 ACCGGAGAAATGTTCCTTGGGGTTGCGGGAAAACA 15 56 1 TGTCTGGGTG 0.424756 -71 ACGGCTTTGTTTCGGCAGGGGCAAGTTTAAACATT 15 101 0 TTGCGGGGAG 0.959629 -26 AAGGTGAGATTGGTCTAGGGACAAGGATAATCGAA 16 18 0 TGTTGGGAAG 0.880592 -283 AGGATATTGCTGAGGCGGGGATTGGCGAAAAAGTT 16 223 1 TGGCGGGAGG 0.913684 -78 AATGTCAAGCCGTTCTGCGGGGCGGAATTCCCCCA 18 113 1 CGTTCGGGGG 0.813963 -51 ** * * **** ** Masking position 9 Map Score: 37.5056 Number of sites scoring better than the average of aligned sites = 3148 Number in coding regions = 2872 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 2 CCCAACATAGCGGAGGGAATTTGGCCGTTCAACTGT 1 160 0 CGGGGAAGCC 0.996273 -110 AAAGTCGCTGAGGTGCAAACAACGCCCTAGCGAAAG 3 136 0 AGGCAAAGCC 0.925646 -76 TGGAGATATGCCATGGCCAAACTGCCAA 5 3 0 CAGGCCAGCC 0.953368 -190 TAGGAAAAAACAGGGGAAAGAATGCCCTTTGTTTGG 5 69 0 CGGGAAAGCC 0.996514 -124 GTCGCCTTTACAGCGGCAACGGTGTCGGGGTATGGT 5 108 1 CGGGCAAGTC 0.937988 -85 ATTACGATCAAAGGGGCAATAAATCCCTTTGTTTAA 5 161 0 AGGGCAATCC 0.745568 -32 GGGTTAGATGCTGGGGAAATGTAGCCAAATTCTTGC 6 96 0 CGGGAAAGCC 0.996514 -205 TGAACGGAATCTTTGCCCAATCAGCCTGCACAGTGG 6 144 1 CTGCCCAGCC 0.842522 -157 CTTTGGGATACTACGGACAAATTGCCGGGTTCGGAT 7 123 1 CAGGACAGCC 0.956257 -91 AGTAAACAACCTGGGCACATTATGCCCCTTTCTCGG 10 28 1 CGGCACAGCC 0.978362 -259 AAGGCAAATTCAGGGGGAAAACTACCAGCCAGTCAC 11 165 0 CGGGGAAACC 0.968797 -75 TTGCCCCACTCCTTGGAAAAATTACCAGCTAATTAT 14 13 1 CTGGAAAACC 0.807714 -267 AAACTTGCCCCTGCCGAAACAAAGCCGTC 15 108 1 CGCGAAAGCC 0.959955 -19 GCTCAACTTCCTGCGGGAATACGGCCAGTGATAGGC 18 67 1 CGGGGAAGCC 0.996273 -97 CAAAGGAAGGATGGGGGAATTCCGCCCCGCAGAACG 18 123 0 AGGGGAAGCC 0.978017 -41 * * ***** *** Masking position 9 Map Score: 22.5509 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 753 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 3 TAGGAATCCCCTGGCTTTAGCCGTTTTGGGGG 2 47 0 CTGGCTTGCC 0.903983 -134 GCTTCCCCCCACGGCGATCGCCAGCGTTATGC 3 26 0 ACGGCATGCC 0.925222 -186 TCTTTCACTCCCGCCGTTCGCCAATAAGATGG 3 76 1 CCGCCTTGCC 0.994367 -136 TATAATCGGACAGGCTTTCGCTAGGGCGTTGT 3 122 1 CAGGCTTGCT 0.826751 -90 GTTCGCCGCCCTTGCCCCCAATCGGAG 4 6 1 CCGCCTTCCC 0.993463 -30 TCTCCCATTACAGACCATACCCCGACACCGTT 5 125 0 CAGACATCCC 0.689606 -68 CCATCTAGCTACGACATTACCCCACTGTGCAG 6 169 0 ACGACTTCCC 0.9414 -132 CCAAAGAAAAACGACTTTCCCCCCCCCTAACC 8 80 1 ACGACTTCCC 0.941399 -153 AATAAGCAGACCGGCCTTTGCT 12 1 0 CCGGCTTGCT 0.971708 -81 TCACAAATTCCCGCCGTTGGCCGCAAATCCTC 14 82 1 CCGCCTTGCC 0.994367 -198 AGCAACTTTTTCGCCAATCCCCGCCTCAGCAA 16 229 0 TCGCCATCCC 0.827082 -72 TCTGATTAAAACGCCCTTTGCTGCTGTTTCAG 16 269 1 ACGCCTTGCT 0.942415 -32 TGCATTCTCCCCGCCCTGTCCTCTGGCTTTCA 18 32 0 CCGCCTGCCT 0.873254 -132 ***** ** *** Masking position 5 Map Score: 15.0591 Number of sites scoring better than the average of aligned sites = 1318 Number in coding regions = 1218 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 4 TGTTGGGGGCTGAGCCTTTCAGCTACAGTG 1 189 1 TGAGCCTTTC 0.597622 -81 AGGGATTTATTGCCCCTTTGATCGTAATTG 5 169 1 TGCCCCTTTG 0.903837 -24 CCCCAGCATCTAACCCACTCCCTAGTTTTG 6 116 1 TAACCCACTC 0.783829 -185 GCTACGACATTACCCCACTGTGCAGGCTGA 6 164 0 TACCCCACTG 0.734231 -137 GAAGTTCCATTTCCCCATCCAAGTCCCTTG 7 72 0 TTCCCCATCC 0.752711 -142 GGAACTTCACCGCCCCATTCGAGCTTAATC 7 94 1 CGCCCCATTC 0.932553 -120 AAAACGACTTTCCCCCCCCCTAACCAATTT 8 87 1 TCCCCCCCCC 0.774705 -146 ATGCCATGATTACCCCACCCAGCTCACCCA 8 148 1 TACCCCACCC 0.88282 -85 GGGCACATTATGCCCCTTTCTCGGCCGGCC 10 40 1 TGCCCCTTTC 0.973203 -247 CTATTCTGAGTGACTCATCCGTTTGAGCGG 10 68 0 TGACTCATCC 0.569342 -219 CCCTGTAAACTGACCCAATCAAGCGACCGC 10 148 1 TGACCCAATC 0.885406 -139 TACAGCAAAGCCCCCCTTTGTTTGTATTTG 11 44 0 CCCCCCTTTG 0.307288 -196 GAATTTGCCTTGCCCCAATCACGATATACT 11 190 1 TGCCCCAATC 0.957889 -50 TTTTGCCCCACTCCTTGGAAAAA 14 4 1 TGCCCCACTC 0.985796 -276 TTCGAACCAGTGACCCCATCGATGTCAACG 14 179 1 TGACCCCATC 0.691616 -101 TGACCCATTGGTAAGGGTTT 15 1 1 TGACCCATTG 0.861657 -126 TGTTTAAACTTGCCCCTGCCGAAACAAAGC 15 103 1 TGCCCCTGCC 0.828383 -24 AGGCTATCATTGCCTCTTTCACTGATAGGA 17 57 1 TGCCTCTTTC 0.738682 -102 GGGGCGGAATTCCCCCATCCTTCCTTTGAT 18 131 1 TCCCCCATCC 0.923626 -33 CTTCCTTTGATGAGCCACTCTGAT 18 150 1 TGAGCCACTC 0.739469 -14 ********** Masking position 6 Map Score: 16.6882 Number of sites scoring better than the average of aligned sites = 2229 Number in coding regions = 1998 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 260 Fraction of orfs with sites within 600 bp upstream = 0.0417604 Motif number 5 CGTTCAACTGTTGTTTAACTGTCCCATGGC 1 141 0 TTGTTTAACT 0.965892 -129 CCCAGGGTAATTATTTAACCACTGTAGCTG 1 208 0 TTATTTAACC 0.732899 -62 AACTTTAATGTTGTTTAAATATTGCCATTT 2 113 0 TTGTTTAAAT 0.69053 -68 AACATTAAAGTTGTTAAACTCGCCCACATC 2 131 1 TTGTTAAACT 0.918565 -50 TGTGGAGGGCTTCTTTCACTCCCGCCGTTC 3 65 1 TTCTTTCACT 0.842097 -147 ACTTTGCTGCTTGTTTAACTCTAATTATTG 3 167 1 TTGTTTAACT 0.965892 -45 ACTCTAATTATTGTTTAACTACTTAGAAAT 3 184 1 TTGTTTAACT 0.965892 -28 AAAGCCAAATTTCTTAAACTAAGTGCCATC 8 177 1 TTCTTAAACT 0.918565 -56 ACGAAATTTTTCCTTTAACCACAAAGGGAT 14 117 1 TCCTTTAACC 0.769594 -163 CTCTATAGTTTTCTTAAACTGTGCCGAAAC 17 18 0 TTCTTAAACT 0.918565 -141 AGAGTCAATCTTCTTTAACCTTCTCTTAAC 17 122 1 TTCTTTAACC 0.946629 -37 ********** Masking position 8 Map Score: 9.90801 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 83 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 CACCCCCCACGGCAAGCGATTTAATTAATACT 1 65 0 GGCAGCATTT 0.592876 -205 TTGGGGACGAGCCATGGGACAGTTAAACAACA 1 131 1 GCCAGGACAG 0.984668 -139 ATAGCAATAGGCCAAGGAATAGGGCCGATATA 1 240 0 GCCAGGATAG 0.971236 -30 TGGCAGTTTGGCCATGGCATATCTCCATGTCG 5 12 1 GCCAGGATAT 0.95987 -181 GTATTTGTCGGCCAAGGGACTTGGATGGGGAA 7 60 1 GCCAGGACTT 0.902835 -154 GGGTAATCATGGCATGGCACCGGGAAAGGATC 8 131 0 GGCAGGACCG 0.926245 -102 GGCAGGGGAAATTAGTGAGTAA 10 1 1 GGCAGGAAAT 0.956738 -286 TCGTGATTGGGGCAAGGCAAATTCAGGGGGAA 11 182 0 GGCAGGAAAT 0.956738 -58 TTTTGTCAGCGGCAATCAATAGCAACAAATCT 13 34 1 GGCATCATAG 0.538964 -35 CCCACAGGGCGGCATTGTACAGCTACGATAAT 14 44 0 GGCATGACAG 0.894698 -236 TTTAAATGGAGCCATGCTATATTACTAAATTG 14 242 0 GCCAGCATAT 0.862248 -38 TTCCCGCAACCCCAAGGAACATTTCTCCGGTT 15 55 0 CCCAGGACAT 0.792324 -72 GCTTTGTTTCGGCAGGGGCAAGTTTAAACATT 15 101 0 GGCAGGCAAG 0.809007 -26 TCCAAACCAGGGCAGGGTAAGTATGGGATCAT 16 129 1 GGCAGGAAGT 0.791512 -172 GTTTATGAAAGCCAGAGGACAGGGCGGGGAGA 18 27 1 GCCAAGACAG 0.808797 -137 **** ** **** Masking position 4 Map Score: 11.1696 Number of sites scoring better than the average of aligned sites = 1106 Number in coding regions = 1003 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 7 GTCAAAGAGCCAATTTTCGATGTAGGGGAAAA 2 13 0 CAATTTTGTG 0.829515 -168 GTTTTCAGATAAATTTGAGTTGGGGGGTAAAA 2 84 1 AAATTTGGTG 0.849654 -97 GCCCACATCCCAATTTGTCCTTGAAGAGGAGT 2 152 1 CAATTTGCTT 0.965843 -29 AAATCAACGAAAATTTTACTTTTTGGGGGCAA 6 68 1 AAATTTTCTT 0.904781 -233 CCGAACCCGGCAATTTGTCCGTAGTATCCCAA 7 125 0 CAATTTGCGT 0.816844 -89 ACATTGACCACAATTTTTGTTTGAAATATTTG 7 182 1 CAATTTTGTT 0.905999 -32 CGACACAGGAAAATTTTCGCTTCCATCTTAGC 8 41 0 AAATTTTGTT 0.857587 -192 CCCCCCTAACCAATTTTACGTTCCCCTACAGA 8 101 1 CAATTTTCTT 0.938308 -132 TTAGTTTAAGAAATTTGGCTTTGGGTGAGCTG 8 167 0 AAATTTGCTT 0.946428 -66 TTTTCCCCCTGAATTTGCCTTGCCCCAATCAC 11 180 1 GAATTTGCTG 0.732921 -60 CCTCTGGACGAAATTTTTCCTTTAACCACAAA 14 110 1 AAATTTTCTT 0.904786 -170 CCAGTGTCCTAAATTTGGCATTAGTCGTAAGC 16 91 1 AAATTTGCTT 0.946428 -210 AACCAAGTCGATTTGGGTTTATGAAAGCCA 18 9 1 CGATTTGGTT 0.738644 -155 ******* * ** Masking position 3 Map Score: 8.46342 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 274 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 ACAGTGGTTAAATAATTACCCTGGGATTATA 1 213 1 AATATTACCC 0.811059 -57 ACTACTTAGAAATCAATTCCC 3 201 1 AATAATTCCC 0.648023 -11 AATGTAGCCAAATTCTTGCCCCCAAAAAGTA 6 84 0 AATCTTGCCC 0.749448 -217 TTTTGAACGGAATCTTTGCCCAATCAGCCTG 6 141 1 AATTTTGCCC 0.927549 -160 GGCCGACAAATACATTTTCCCAGCAACTTAG 7 42 0 TACTTTTCCC 0.647694 -172 CTACTTTGCGTCTTTTTTCCC 9 235 1 TCTTTTTCCC 0.843903 -11 TTGTTTACTCACTAATTTCCCCTGCC 10 6 0 ACTATTTCCC 0.897265 -281 AAAGTTAGAGTCTGTTTTCCCAAAACTCCAG 10 182 0 TCTTTTTCCC 0.843903 -105 CAATTTCACCAATCTTTTCCCC 10 275 1 AATTTTTCCC 0.970894 -12 ACTTTTTGTTAAGGTTTTGCCAACGGTGACT 11 140 1 AAGTTTTGCC 0.641918 -100 TTCTCAATATAATGTTTTCCCGCAACCCCAA 15 72 0 AATTTTTCCC 0.970894 -55 GAGCGTCAGGAATTATTAGCCAAGGTGAGAT 16 43 0 AATATTAGCC 0.573347 -258 CCATAGCGATAATTTTTTGCCAATGATCCCA 16 152 0 AATTTTTGCC 0.912606 -149 *** ******* Masking position 7 Map Score: 6.12951 Number of sites scoring better than the average of aligned sites = 976 Number in coding regions = 826 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 9 CGGATAACCACCGAAAAGCTCTGGATGTATTA 6 227 0 CCGAAAACCT 0.944984 -74 CAATAGTCAACAGAAAACCTTCCCCTCAACTA 7 13 1 CAGAAAACTC 0.969492 -201 ATGAGTCACTCAGAATAGCTTCTAGATTTGCT 10 80 1 CAGAATACTC 0.850633 -207 TGGCTTTTTTCAGAACAGCCTTAATCCATTTT 10 235 0 CAGAACACTT 0.811182 -52 ATCGATAATACAGCAAAGCCCCCCTTTGTTTG 11 50 0 CAGCAAACCC 0.955793 -190 ACGATCAGGACAGAAAACCATT 11 228 1 CAGAAAACTT 0.941775 -12 CCGCCGTTGGCCGCAAATCCTCTGGACGAAAT 14 92 1 CCGCAAACTC 0.97122 -188 AACTTGTTCCCCGAAAATCCCTTTGTGGTTAA 14 131 0 CCGAAAACCT 0.944984 -149 CTCTCCTTCACCGCAAAACTTCCATAGCGATA 16 172 0 CCGCAAACTC 0.97122 -129 ******* * ** Masking position 7 Map Score: 6.28467 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 115 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 GGGGGGTGGTCTCTGTTTTTAAGTTAGATT 1 89 1 CTCTGTTTTT 0.87538 -181 AGATTAACTACTCTGGTTTGGGGACGAGCC 1 114 1 CTCTGGTTTG 0.968477 -156 TCTAGGAATCCCCTGGCTTTAGCCGTTTTG 2 51 0 CCCTGGCTTT 0.955324 -130 GCATTCTTTCCCCTGTTTTTTCCTAGACGT 5 80 1 CCCTGTTTTT 0.932436 -113 CGAAAGGTAGCACTGTTTTGTCAAATTTTG 6 34 1 CACTGTTTTG 0.803104 -267 CTAACCCACTCCCTAGTTTTGAACGGAATC 6 125 1 CCCTAGTTTT 0.814469 -176 CGAACTTGATCCCCGGTTTAGCAAAGATTT 9 92 1 CCCCGGTTTA 0.816153 -154 TCGATGGGGTCACTGGTTCGAATCCAGTTA 14 171 0 CACTGGTTCG 0.756154 -109 AGGAACATTTCTCCGGTTTTCCTTGGTGGG 15 43 0 CTCCGGTTTT 0.915851 -84 ACTTACCCTGCCCTGGTTTGGACTCGGAGC 16 121 0 CCCTGGTTTG 0.983703 -180 CCGCCCTGTCCTCTGGCTTTCATAAACCCA 18 24 0 CTCTGGCTTT 0.915851 -140 ********** Masking position 8 Map Score: 9.30079 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 627 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 11 CGATCGCCGTGGGGGGAAGCTCTCATCTGT 3 38 1 GGGGGGAAGC 0.875488 -174 CAATAAGATGGCGGAGACGGTGGGATATAA 3 97 1 GCGGAGACGG 0.8928 -115 AGCAGCAAAGTCGCTGAGGTGCAAACAACG 3 148 0 TCGCTGAGGT 0.463941 -64 TTGCCCCCAATCGGAGAGGGATCT 4 22 1 TCGGAGAGGG 0.815009 -14 TGGTCTGTAATGGGAGAAGCTTTAAACAAA 5 140 1 TGGGAGAAGC 0.883849 -53 AGCTAGATGGGGGGTGAATGGGATCAATTC 6 191 1 GGGGTGAATG 0.914718 -110 CTCGAATGGGGCGGTGAAGTTCCATTTCCC 7 87 0 GCGGTGAAGT 0.932016 -127 GCGAGTAAGGGCGCAGAAGCACCGATGGCA 8 200 0 GCGCAGAAGC 0.935244 -33 ATTGGTGTGTTGGCTGAATTCTAATATCAA 9 49 1 TGGCTGAATT 0.454676 -197 CAATATCTCTGGGCAGAAGGATCCCGGAAA 9 122 0 GGGCAGAAGG 0.970196 -124 TTTCCTTGGTGGGCAGAATTATCCAAAACC 15 26 0 GGGCAGAATT 0.799726 -101 TGGAAGTTTTGCGGTGAAGGAGAGTCCTCC 16 180 1 GCGGTGAAGG 0.969811 -121 AGGACAGGGCGGGGAGAATGCAGTTGCTCA 18 42 1 GGGGAGAATG 0.936571 -122 ********** Masking position 7 Map Score: 7.48915 Number of sites scoring better than the average of aligned sites = 1228 Number in coding regions = 1081 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 12 ATCCCTAAAAAATAGCCCAAACAAAGGGCA 5 53 1 AATAGCCCAA 0.865222 -140 ATTTGTCCGTAGTATCCCAAAGATTAAGCT 7 115 0 AGTATCCCAA 0.865223 -99 CTAATATCAAAATTGCCCAATGGCGAACTT 9 69 1 AATTGCCCAA 0.901948 -177 AAAAGTTTAGAGTTGCCCAAAGTCTAGAAA 11 116 0 AGTTGCCCAA 0.975738 -124 TGGGGCCTCCAGTGTCCTAAATTTGGCATT 16 83 1 AGTGTCCTAA 0.767892 -218 TGAAAAACTTAGTGGCCTAATTTCTTGGGC 17 91 1 AGTGGCCTAA 0.935334 -68 GGGAGAATGCAGTTGCTCAACTTCCTGCGG 18 53 1 AGTTGCTCAA 0.901948 -111 ATCAGAGTGGCTCATCAAAGGAAGG 18 149 0 AGTGGCTCAT 0.721606 -15 ********** Masking position 9 Map Score: 2.437 Number of sites scoring better than the average of aligned sites = 829 Number in coding regions = 746 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 13 TTAAGTTAGATTAACTACTCTGGTTTGGGGA 1 107 1 TTAACACTCT 0.948058 -163 GGGTAATTATTTAACCACTGTAGCTGAAAGG 1 203 0 TTAACACTGT 0.778218 -67 GTGGGCGAGTTTAACAACTTTAATGTTGTTT 2 127 0 TTAACACTTT 0.703044 -54 GGTTCTCAAATCTCAAATAATGC 9 3 1 TTCTCAATCT 0.841097 -243 ACACACCAATTTCACTAATCTGTTGGCATTA 9 28 0 TTCACAATCT 0.967252 -218 TGCTCATTTTTTCAATAATCTGTTAGCCAGA 10 108 1 TTCAAAATCT 0.767351 -179 GCCACTCAATTTCACCAATCTTTTCCCC 10 269 1 TTCACAATCT 0.967252 -18 ATGATAGCCTTTAACAAATCTCTATAGTTTT 17 36 0 TTAACAATCT 0.949035 -123 ***** ***** Masking position 7 Map Score: 1.78671 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 36 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 AATGTAGCCAAATTCTTGCCCCCAAAAAGTA 6 84 0 AATTCTGCCC 0.817887 -217 TTATGGTGTGAATTGATCCCATTCACCCCCC 6 199 0 AATTGTCCCA 0.852887 -102 AAGAAAAACGACTTTCCCCCCCCCTAACCAA 8 83 1 ACTTTCCCCC 0.895417 -150 CCAATGGCGAACTTGATCCCCGGTTTAGCAA 9 85 1 ACTTGTCCCC 0.988002 -161 ACGTCCATAAACTTGTTCCCCGAAAATCCCT 14 141 0 ACTTGTCCCC 0.988002 -139 TTAAATTAACAATTGCTCCCC 14 269 1 AATTGTCCCC 0.981102 -11 CACTATAGCAACTTTTTCGCCAATCCCCGCC 16 236 0 ACTTTTCGCC 0.821597 -65 AGGATGGGGGAATTCCGCCCCGCAGAACGGC 18 121 0 AATTCGCCCC 0.893042 -43 ***** ***** Masking position 1 Map Score: 2.57767 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 412 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 TTTCGATGTAGGGGAAAAAT 2 1 0 GGGGAAAAAT 0.518549 -180 GCGATCGCCGTGGGGGGAAGCTCTCATCTG 3 37 1 TGGGGGGAAG 0.889795 -175 CCTCTCCGATTGGGGGCAAGGGCGGCGAAC 4 11 0 TGGGGGCAAG 0.984215 -25 TTTTACTTTTTGGGGGCAAGAATTTGGCTA 6 81 1 TGGGGGCAAG 0.984215 -220 GGGGGGTGAATGGGATCAATTCACACCATA 6 199 1 TGGGATCAAT 0.86823 -102 TTGGTTAGGGGGGGGGAAAGTCGTTTTTCT 8 84 0 GGGGGGAAAG 0.950042 -149 TTGCTAAACCGGGGATCAAGTTCGCCATTG 9 86 0 GGGGATCAAG 0.958174 -160 TATATCGTGATTGGGGCAAGGCAAATTCAG 11 188 0 TTGGGGCAAG 0.804187 -52 AGGGATTTTCGGGGAACAAGTTTATGGACG 14 141 1 GGGGAACAAG 0.924688 -139 TTGACATCGATGGGGTCACTGGTTCGAATC 14 177 0 TGGGGTCACT 0.631585 -103 GGGGAGCAATTGTTAATTTA 14 270 0 GGGGAGCAAT 0.961207 -10 AGGGTAAGTATGGGATCATTGGCAAAAAAT 16 142 1 TGGGATCATT 0.596169 -159 AGGACAGGGCGGGGAGAATGCAGTTGCTCA 18 42 1 GGGGAGAATG 0.755141 -122 ********** Masking position 8 Map Score: 12.1189 Number of sites scoring better than the average of aligned sites = 1322 Number in coding regions = 1132 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196