AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_synecho_reg_100.orf -o00051_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 slr1118 38 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #2 sll1063 224 hypothetical protein. #3 sll1196 112 pfkA; phosphofructokinase. [EC:2.7.1.11] #4 sll0648 127 lim; lipophilic protein. [EC:2.4.1.-] #5 slr2074 300 manA; mannose-6-phosphate isomerase. [EC:5.3.1.8] #6 slr1448 300 cscK; fructokinase. [EC:2.7.1.4] #7 sll1757 144 hypothetical protein. [EC:2.7.1.69] #8 sll1605 262 fabZ; (3R)-hydroxymyristol acyl carrier protein dehydrase. #9 sll1370 50 rfbM; GDP-mannose pyrophosphorylase. [EC:2.7.7.22] #10 sll1369 59 hypothetical protein. #11 sll1182 96 petC; cytochrome b6/f complex iron-sulfur subunit. #12 sll1181 156 hlyD; HlyD family of secretion proteins. #13 slr1271 251 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #14 slr0943 121 fda; fructose-bisphosphate aldolase. [EC:4.1.2.13] #15 slr0952 206 fbp; fructose-1,6-bisphosphatase (D-fructose-1,6-bisphosphate 1- #16 sll0325 222 hypothetical protein. #17 sll0018 283 fda; fructose-bisphosphate aldolase. [EC:4.1.2.13] [SP:ALF_SYNY3] #18 sll0456 93 hypothetical protein. #19 sll0455 127 hom; homoserine dehydrogenase (HDH). [EC:1.1.1.3] [SP:DHOM_SYNY3] #20 sll0593 206 glk; glucokinase. [EC:2.7.1.2] #21 sll0745 111 pfkA; phosphofructokinase. [EC:2.7.1.11] #22 slr1556 152 ddh; 2-hydroxyaciddehydrogenase. [EC:1.1.1.-] #23 slr1656 300 murG; UDP-N-acetylglucosamine-N-acetylmuramyl-(pentape ptide) Motif number 1 TTTGGCGATCGCCGGGGGGCAAATGTGTATA 2 107 0 GCCGGGGGCA 0.993769 -118 ATCGGGGATAGGATGGGGCAAATGCGCCGCA 2 160 0 GGAGGGGCAA 0.866525 -65 GGAGCCAAATTCTAGGGGCCATACCAAAGTC 4 22 1 TCTGGGGCCA 0.915472 -106 CAGAGGCTGAGGCAAGGGGCATGGGCTATCA 5 68 1 GGCAGGGGCA 0.899937 -233 TTTCTGAATTGCTGTGGGCCAAGACTTCTAA 6 224 1 GCTTGGGCCA 0.944049 -77 CGCAATTTCAGCTTTGGGGGTGCCTCCTATC 7 120 0 GCTTGGGGGT 0.698412 -25 TTTGGCGGATTGTTTGGGGAATGAACAACCC 8 15 1 TGTTGGGGAA 0.801915 -248 GGGCTCATGGCCCAGGGGGGATCCCAATGGG 8 99 1 CCCGGGGGGA 0.902572 -164 TTGGATAATTGGTGGGAGGAAAAAGCTAAGT 10 38 1 GGTGGAGGAA 0.715102 -22 GTTTTAAAACCCATGGGGGCACACTGTCTGG 12 49 0 CCAGGGGGCA 0.834248 -108 AATTCTGGGGGCGATCGCCAAAGA 12 143 0 TCTGGGGCGA 0.831591 -14 CGTAACCGGAGGTGTGGGCGATCGCCTGCCA 13 91 1 GGTTGGGCGA 0.823139 -161 TAAAGGTTACGGCTGGGGGAAATTGGGTTAC 13 157 0 GGCGGGGGAA 0.986447 -95 ACAAGAGGATGGCAGGGGCAAGTTTCACCGT 14 43 1 GGCGGGGCAA 0.963247 -79 CCTTTAAGGAGCTAAGGGGCACCCGAATCAC 14 77 0 GCTAGGGGCA 0.936737 -45 GCCCCCCAATTCTGGGGGGAATAGTGTTCAA 15 129 0 TCTGGGGGAA 0.957782 -78 GAATTGGGGGGCTAGGGGGCTTTTAAAAGAC 15 148 1 GCTGGGGGCT 0.945117 -59 ACAGCTTCAAGCCCTGGGGAAAGGGAAGTCC 16 166 1 GCCTGGGGAA 0.97259 -57 ATCGCCTATTGCCGGGGGGAAGAGATATAGA 17 26 1 GCCGGGGGAA 0.991756 -258 ACCAAGTCCAGGATGGGGGAAGGTTTTGGGT 17 71 0 GGAGGGGGAA 0.947448 -213 CATAGACTAGGGTGGGGGTAAAAATACGGGT 17 111 1 GGTGGGGTAA 0.772008 -173 TAGCACAAATTCCTTGGGGCAGGACAAAAAA 17 156 1 TCCTGGGGCA 0.899054 -128 TTTTTCAATGGCTTTGGGGCC 20 196 1 GCTTGGGGCC 0.810216 -11 TTTTCCCCAAGCTTGGGGGAAACTCGGGAAA 23 212 0 GCTGGGGGAA 0.991724 -89 *** ******* Masking position 6 Map Score: 39.2733 Number of sites scoring better than the average of aligned sites = 2781 Number in coding regions = 2472 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 2 TTGCCCCAATTTGGCGATCGCCGGGGGGCA 2 117 0 TTGGCGATCG 0.997439 -108 CTGGTTTTCGGTGGCGATCGGGCCTAGAAC 8 137 1 GTGGCGATCG 0.991726 -126 TCCATCATCTTTGGCGATCGCCCCCAGAAT 12 136 1 TTGGCGATCG 0.997439 -21 TGTTGATTGGCAGGCGATCGCCCACACCTC 13 99 0 CAGGCGATCG 0.985857 -153 CCCCCGGCAATAGGCGATCGGGGATCAAAC 17 14 0 TAGGCGATCG 0.991942 -270 TGGCAAGGATTTGGCGATCGCCTTTTTTGG 18 37 1 TTGGCGATCG 0.997439 -57 CTTTAGGTTACTGGCGATCGGCTCCCCATT 19 82 0 CTGGCGATCG 0.995487 -46 GGATTAGGGATTGGCGATAGATTGGGGTTC 21 20 1 TTGGCGATAG 0.974482 -92 CGGCACTACCTTGGTGATCGATAGTACGAT 22 36 0 TTGGTGATCG 0.974482 -117 ********** Masking position 7 Map Score: 26.6755 Number of sites scoring better than the average of aligned sites = 2133 Number in coding regions = 1924 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 3 TAATTTTTTGCCCCAATTTGGCGATCGCCGGG 2 122 0 CCCAATTTGC 0.984404 -103 TCGACCATAACCCTGATTTTGCCCGACGGGTT 6 123 0 CCCGATTTGC 0.977045 -178 GCTGGGAATAACCTGGTTTGCCAAAGTTTTTC 8 199 1 ACCGGTTTCC 0.846523 -64 AAAGAACTGCCCCCAGTTTAGCCAAAGTTTCG 11 63 0 CCCAGTTTGC 0.977026 -34 AATAAATGTAACCCAATTTCCCCCAGCCGTAA 13 150 1 ACCAATTTCC 0.955836 -102 TAACCTTTATCCACAATTTCCCCCGATTATTA 13 179 1 CCAAATTTCC 0.865911 -73 TTCAAAGTCCCCCAAATTTGCCGGAGCTTTAG 15 102 0 CCCAATTTCC 0.987669 -105 TGGAAAAGCTCCCAAACTTGGCAAAAATGAGA 16 112 1 CCCAACTTGC 0.916706 -111 CAGAATCACAGCCGGACTTCCCTTTCCCCAGG 16 178 0 GCCGACTTCC 0.824751 -45 CGTTTCCCTGCCCCAACTAAGCAGAGGATAAT 23 62 0 CCCAACTAGC 0.868322 -239 TAAGGGCAAACCCGAACTTTGCCAACACCTCC 23 160 0 CCCAACTTGC 0.983992 -141 GGAAACCTTTCCCGAGTTTCCCCCAAGCTTGG 23 205 1 CCCAGTTTCC 0.980196 -96 GTAAAATCCAACCTAATTTTCCCCAAGCTTGG 23 227 0 ACCAATTTCC 0.955822 -74 *** ***** ** Masking position 8 Map Score: 19.2598 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 293 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 CAGCATCGGAGCCAAATTCTAGGGGCCATA 4 15 1 GCCAAATTCT 0.916617 -113 TCTCATTTCTGACAATTCTTCTCGCAGAAT 5 178 0 GACAATTCTT 0.854526 -123 GGTAGTCGGAGCCATTTCTTCTGCTCTTTT 6 278 1 GCCATTTCTT 0.694926 -23 GGCGAATTAAGCCAACGTCTGTCAAATTAT 7 39 0 GCCAACGTCT 0.754694 -106 CAAACAATCCGCCAAATCCT 8 1 0 GCCAAATCCT 0.939461 -262 AGAAAAATTGGCCAATTCTTCTTCCGGGTT 8 69 0 GCCAATTCTT 0.961364 -194 AACCTGGTTTGCCAAAGTTTTTCAAAAATT 8 208 1 GCCAAAGTTT 0.924091 -55 CCCCAGTTTAGCCAAAGTTTCGATGCGGTG 11 55 0 GCCAAAGTTT 0.924091 -42 TAATGGTATAGACAAAGTTTTAAAACCCAT 12 66 0 GACAAAGTTT 0.741856 -91 TGCATAAAGGGCCAATTTTGTTTGAAGAAT 13 230 1 GCCAATTTTG 0.825539 -22 TCTGCGCCTTGACAATTTTTAACGATCTTT 17 184 0 GACAATTTTT 0.806241 -100 TGGGTCGCAAGACAATTCTTTATATGGGTC 17 230 0 GACAATTCTT 0.854526 -54 AGCCAATGTTGATTGCAAAAC 18 2 1 GCCAATGTTG 0.811461 -92 AAAGGCGATCGCCAAATCCTTGCCATTATT 18 32 0 GCCAAATCCT 0.939461 -62 CCAATCTATCGCCAATCCCTAATCCGGCGG 21 15 0 GCCAATCCCT 0.809962 -97 ********** Masking position 4 Map Score: 13.8451 Number of sites scoring better than the average of aligned sites = 841 Number in coding regions = 765 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 CATTTGCCCCATCCTATCCCCGATAAACTA 2 167 1 ATCCTATCCC 0.823181 -58 GGTTTTCCTTGCCGATATAGTTCT 3 99 0 TTCCTTGCCG 0.834336 -14 CTTTATCCTAAACCCTTCCCAATCCCATCT 4 102 1 AACCCTTCCC 0.94222 -26 TCCCAATCCCATCTTTGCCC 4 118 1 ATCTTTGCCC 0.943409 -10 CTTATGGACCATCCTTTCCCAAAACCATGG 5 240 0 ATCCTTTCCC 0.979297 -61 CCTAAATAATTTCCTCGCCCAATCAACTCT 12 103 1 TTCCTCGCCC 0.882708 -54 CAACACGGTGAAACTTGCCCCTGCCATCCT 14 48 0 AAACTTGCCC 0.763742 -74 CAGCCGGACTTCCCTTTCCCCAGGGCTTGA 16 172 0 TCCCTTTCCC 0.835542 -51 GGGGTTCTATATCTCTTCCCCCCGGCAATA 17 32 0 ATCTCTTCCC 0.826336 -252 GATTACCCAAAACCTTCCCCCATCCTGGAC 17 67 1 AACCTTCCCC 0.892487 -217 CGATCGCCAAATCCTTGCCATTATTGTTTT 18 27 0 ATCCTTGCCA 0.920849 -67 CAGTATTCTTTTCCCTGCCCAAGTCCAGAT 19 50 1 TTCCCTGCCC 0.968929 -78 CCAGCTCCGTTTCCCTGCCCCAACTAAGCA 23 71 0 TTCCCTGCCC 0.968929 -230 GGCAAACCCGAACTTTGCCAACACCTCCCA 23 158 0 AACTTTGCCA 0.524788 -143 CTGACTAGGAAACCTTTCCCGAGTTTCCCC 23 198 1 AACCTTTCCC 0.964258 -103 ********** Masking position 8 Map Score: 14.947 Number of sites scoring better than the average of aligned sites = 1162 Number in coding regions = 1007 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 6 TTACTGCTAAAACATTAGGGATAAAATAGT 1 19 1 ATAGGGAAAA 0.881501 -20 CCGGCGATCGCCAAATTGGGGCAAAAAATTAGATA 2 123 1 CATGGGGAAA 0.757692 -102 TTTATCGGGGATAGGATGGGGCAAATGCGCCGCAA 2 159 0 AGTGGGGAAA 0.719773 -66 AAGCACCGTACAAATATGGGGTAAACTTTATCCTA 4 77 1 CTTGGGGAAA 0.971557 -51 GGGATTGGGAAGGGTTTAGGATAAAGTTTACCCCA 4 93 0 ATTAGGAAAA 0.892778 -35 ACTTTTGCTAAAAATCTAGGACAAACGAAAATTTT 8 232 0 ATTAGGAAAA 0.892778 -31 GCGATCGCCAAAGATGATGGACAAAGAGTTGATTG 12 122 0 ATATGGAAAA 0.453759 -35 TTTTTGAATGATATTAAAGGGTAAAGTCAGACAAG 14 13 1 ATAAGGGAAA 0.91418 -109 TCCATGTTAAGTAAAAATCCCATACCT 14 105 0 CTAAGTAAAA 0.345667 -17 CCTAGCCCCCCAATTCTGGGGGGAATAGTGTTCAA 15 129 0 CTTGGGGGAA 0.802615 -78 GGACGAAACCTAAAGGGAAAACAGCTTTGAT 20 7 1 ATAAGGGAAA 0.91418 -200 TAGAAAGACTCAAATTAAGGATAAATTAAGGGGGT 21 82 1 CTAAGGAAAA 0.91418 -30 ATCGTTGCTTCATTTTTAGGAAAAATATCTGGTAA 22 74 1 CTTAGGAAAA 0.937593 -79 TAATTAAACACCAATCTAGGGAAAATAGTCCTGGG 23 31 0 CTTAGGGAAA 0.964424 -270 TTAGTTTGTGAATCTATGGGAAAAACAATGCCAGC 23 96 0 ATTGGGAAAA 0.912981 -205 CCTAGTCAGTCGATTTAAGGGCAAACCCGAACTTT 23 172 0 CTAAGGGAAA 0.950545 -129 TAATTTTCCCCAAGCTTGGGGGAAACTCGGGAAAG 23 211 0 CCTGGGGAAA 0.822524 -90 * * ***** *** Masking position 14 Map Score: 13.9795 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 566 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 7 AAAGTAGGTTAAGGATTGAGGACAATTTTAA 3 17 1 AAGGATTGGG 0.808794 -96 TGGGATTGGGAAGGGTTTAGGATAAAGTTTA 4 98 0 AAGGGTTTGG 0.977128 -30 CTGGCCCTCCCATGGTTTTGGGAAAGGATGG 5 231 1 CATGGTTTGG 0.753237 -70 GATGGTCCATAAGGGTTTCGGAGTTAACCAT 5 257 1 AAGGGTTTGG 0.977128 -44 ATTTTGCCCGACGGGTTTTGGAATTAGAACG 6 109 0 ACGGGTTTGG 0.951597 -192 CGGGCAAAATCAGGGTTATGGTCGAGAAAAT 6 130 1 CAGGGTTAGG 0.950917 -171 GGGCTTTAAACTGGTTTTCGGTGGCGATCGG 8 127 1 CTGGTTTTGG 0.696119 -136 GCACTTTGGCCAGGTTCTAGGCCCGATCGCC 8 149 0 CAGGTTCTGG 0.841506 -114 AAAAATTCACACAGTTTTAGGTGAGGGCA 12 9 0 ACAGTTTTGG 0.493529 -148 AATTGTGGATAAAGGTTACGGCTGGGGGAAA 13 166 0 AAAGGTTAGG 0.674718 -86 GACTTCTCTTAAGGATCAGGGATGGAGGGGG 16 19 1 AAGGATCAGG 0.71597 -204 AGGATGGGGGAAGGTTTTGGGTAATCAAGTT 17 62 0 AAGGTTTTGG 0.948002 -222 CAATAATGGCAAGGATTTGGCGATCGCCTTT 18 31 1 AAGGATTTGC 0.669582 -63 TGCTAAAAGACAGGATTTTGTGTAGTTTTTC 20 171 1 CAGGATTTGT 0.597297 -36 TAAACCGCCGGATTAGGGATTGGCGATA 21 8 1 CCGGATTAGG 0.824175 -104 ******** ** Masking position 6 Map Score: 8.65722 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 776 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 8 TTGATTTTACCCGCCCGACCCTAGGACATCATC 2 13 0 CCCCCACCTA 0.982446 -212 GAGCTAAGGGGCACCCGAATCACAACACGGTGA 14 67 0 GCCCCATCAC 0.938166 -55 AGCCCCCTAGCCCCCCAATTCTGGGGGGAATAG 15 136 0 CCCCCATCTG 0.968165 -71 TTTTACGGCTCCGCCGGAGTCAACCCCCTCCAT 16 40 0 CCCCGATCAA 0.931053 -183 ATTTTTACCCCCACCCTAGTCTATGGCTGAGTT 17 103 0 CCCCCATCTA 0.991342 -181 TTAATTTTGCTCACCCTAACCAAAAAAGGCGAT 18 53 0 TCCCCACCAA 0.875434 -41 CTGGCGATCGGCTCCCCATTCTATCTGGACTTG 19 69 0 GCCCCATCTA 0.98599 -59 GGTCAAAATCGAACCCCAATCTATCGCCAATCC 21 27 0 GACCCATCTA 0.873408 -85 TTTGCCAACACCTCCCAAATCAAGATAAAACTT 23 142 0 CCCCCATCAA 0.989355 -159 ** *** * **** Masking position 8 Map Score: 6.91574 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 109 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 ACAATCCATCCCATTGGTTTTGATTTTACCC 2 34 0 CCTTGGTTTT 0.887579 -191 CTTACTGCAACCTTTAGTTTATCGGGGATAG 2 180 0 CCTTAGTTTA 0.788502 -45 TACCAATAGGTTTAAGTATCGTT 2 212 0 CCATAGGTTT 0.798111 -13 ATCTGGCCCTCCCATGGTTTTGGGAAAGGAT 5 229 1 CCATGGTTTT 0.818282 -72 CAATACAGCCCCTTTAGGCTAATCGATTGAA 6 52 0 CCTTAGGCTA 0.936217 -249 ATTCCAAAACCCGTCGGGCAAAATCAGGGTT 6 116 1 CCTCGGGCAA 0.721149 -185 AGGGGGGATCCCAATGGGCTTTAAACTGGTT 8 112 1 CCATGGGCTT 0.946606 -151 ACAGTGTGCCCCCATGGGTTTTAAAACTTTG 12 53 1 CCATGGGTTT 0.893296 -104 TATACCATTACCATTAGCCTAAATAATTTCC 12 86 1 CCTTAGCCTA 0.708398 -71 ATTTTCCAGTCCGTTGGTCATTTTGGTTGAG 13 23 0 CCTTGGTCAT 0.905088 -229 AGCTTTTCCACCCTTGGTCAAACCGTCATAG 16 91 0 CCTTGGTCAA 0.905088 -132 ACCCAAATACCCATTAGGCAATAGAACTTAG 17 255 1 CCTTAGGCAA 0.893296 -29 AGCTGTTTTCCCTTTAGGTTTCGTCC 20 6 0 CCTTAGGTTT 0.873915 -201 CAATAGCTGACCCATGGTCAAAATCGAACCC 21 44 0 CCATGGTCAA 0.844694 -68 ** ******** Masking position 2 Map Score: 10.2353 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 789 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 10 AGGGAAAAACCCGCATTACGATTTA 5 4 1 GAAAACCCCA 0.889358 -297 CTAATCGATTGAACACTCCACCCCCATAACGC 6 33 0 GAACATCCCC 0.973305 -268 TTCATTCCCCAAACAATCCGCCAAATCCT 8 8 0 AAACATCCCC 0.761073 -255 TTTGGGGAATGAACAACCCTCCCATCTTATCG 8 27 1 GAACACCCCC 0.990023 -236 TAGATAAAAAGAACTGCCCCCAGTTTAGCCAA 11 70 0 GAACTCCCCA 0.954091 -27 TACAGAACACTCCTCAACCAAAATGA 13 5 1 GAACATCCCA 0.95042 -247 TTAACCCCTGGAACATTTCCACTGCATAAAGG 13 208 1 GAACATTCAC 0.626137 -44 ACCAAGGGTGGAAAAGCTCCCAAACTTGGCAA 16 104 1 GAAAACTCCA 0.808657 -119 GCAAAAATGAGAACTACTCATCACAAAATGTA 16 132 1 GAACTCTCTC 0.644847 -91 CCAGGTGGAGGAACTGCTCTCCTAAAGTTGCT 20 74 1 GAACTCTCCC 0.954089 -133 CGAACTTTGCCAACACCTCCCAAATCAAGATA 23 148 0 CAACACTCCA 0.780325 -153 ***** *** ** Masking position 3 Map Score: 4.7681 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 320 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 TACTTTTTACTGCTAAAACATTAGGGATAAA 1 13 1 TGCTAAAAAT 0.901742 -26 GGACTGAGATGGCTAAAATGCGTGTTTTTTA 6 173 1 GGCTAAAAGC 0.816054 -128 CGTTGCGGCCAGCTAAAAAACACGCATTTTA 6 186 0 AGCTAAAAAC 0.901213 -115 GGAAAACTTTTGCTAAAAATCTAGGACAAAC 8 241 0 TGCTAAAATC 0.947453 -22 TCTGGCTAGTTGATAAAAATTCACACAGTTT 12 23 0 TGATAAAATT 0.661541 -134 CTCCTAAAGTTGCTAAAACTTGCTGAAACGG 20 92 1 TGCTAAAATT 0.918743 -115 CCAAGCAAAAAGCTAAAATTCTCCCGTTTCA 20 115 0 AGCTAAAATC 0.918297 -92 TGACCTAAACTGCTAAAAGACAGGATTTTGT 20 161 1 TGCTAAAAAC 0.936041 -46 GGTAATAAAAGGCTAAAAAATTTAACGTTAT 22 104 1 GGCTAAAAAT 0.860637 -49 TCCCAAATCAAGATAAAACTTGATCACTATT 23 132 0 AGATAAAATT 0.549221 -169 ******** ** Masking position 6 Map Score: 4.17667 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 244 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 GTTAAGGATTGAGGACAATTTTAAGAATTC 3 24 1 GAGGACAATT 0.903261 -89 CCCAGCATCGGAGCCAAATTCTAGGGGCCA 4 13 1 GAGCCAAATT 0.808898 -115 TTGATTGGGCGAGGAAATTATTTAGGCTAA 12 99 0 GAGGAAATTA 0.778293 -58 GGATAGAGGAGCAAAATTTAGAACAGAA 16 205 0 GAGCAAAATT 0.947689 -18 TGGTTAGGGTGAGCAAAATTAATTTATTTC 18 64 1 GAGCAAAATT 0.947689 -30 AAGGCAACGGGAGGAAAATT 19 118 1 GAGGAAAATT 0.972341 -10 ACCTGGGCCAGAGGAAATTAACCGTTAAAT 20 50 0 GAGGAAATTA 0.778293 -157 CAACTAAGCAGAGGATAATTAAACACCAAT 23 51 0 GAGGATAATT 0.863011 -250 CCCCAAGCTTGGGGAAAATTAGGTTGGATT 23 225 1 GGGGAAAATT 0.891464 -76 ********** Masking position 7 Map Score: 6.30896 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 236 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 13 AGGTTTAAGTATCGTTGCTTACTGCAACCT 2 198 0 ATCGTTGCTT 0.968395 -27 AGAAAATACTATCGTTGCGGCCAGCTAAAA 6 199 0 ATCGTTGCGG 0.968847 -102 ACCTTAACTAAGCGTTGCTGGGAATAACCT 8 183 1 AGCGTTGCTG 0.968847 -80 AGTACGATAAATCGTAGCTGTTACTAGGTT 22 14 0 ATCGTAGCTG 0.954511 -139 CGTTAATACTATCGTTGCTTCATTTTTAGG 22 64 1 ATCGTTGCTT 0.968395 -89 ********** Masking position 5 Map Score: 2.49773 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 28 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 TAAAGTTTACCCCATATTTGTACGGTGCTTAG 4 75 0 CCCATTTTGA 0.722665 -53 CCTTCCCAATCCCATCTTTGCCC 4 115 1 CCCATTTTGC 0.944177 -13 TCCCCATCATCTCATTTCTGACAATTCTTCTC 5 185 0 CTCATTCTGC 0.960994 -116 GGACAAGATCATCCTATCTGGCCCTCCCATGG 5 214 1 ATCCTTCTGC 0.706244 -87 CTAAAAAACACGCATTTTAGCCATCTCAGTCC 6 173 0 CGCATTTAGC 0.695158 -128 TTGATCTTGGATCTTGTTTGCACTTTCGATAG 7 93 1 ATCTTTTTGA 0.502033 -52 CTCTTTGTCCATCATCTTTGGCGATCGCCCCC 12 129 1 ATCATTTTGC 0.935284 -28 CCCTGCCATCCTCTTGTCTGACTTTACCCTTT 14 28 0 CTCTTTCTGC 0.917735 -94 ATGAGTAGTTCTCATTTTTGCCAAGTTTGGGA 16 121 0 CTCATTTTGC 0.975208 -102 ATTTTTAACGATCTTTTTTGTCCTGCCCCAAG 17 168 0 ATCTTTTTGC 0.867445 -116 TTATATGGGTCTCATCTTAGGCTAGTTTCTGC 17 209 0 CTCATTTAGC 0.907064 -75 ***** **** * Masking position 7 Map Score: 4.42233 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 167 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 15 ACGTTCTAATTCCAAAACCCGTCGGGCAAA 6 108 1 TCCAAAACCC 0.884415 -193 CGAAAACCAGTTTAAAGCCCATTGGGATCC 8 117 0 TTTAAAGCCC 0.952617 -146 CCCAAGGTTTTTCAAAGCCGCTTGGATAAT 10 17 1 TTCAAAGCCG 0.92423 -43 TAGACAAAGTTTTAAAACCCATGGGGGCAC 12 58 0 TTTAAAACCC 0.887117 -99 GGGAATAGTGTTCAAAGTCCCCCAAATTTG 15 114 0 TTCAAAGTCC 0.891657 -93 GGAACGTCTTTTAAAAGCCCCCTAGCCCCC 15 154 0 TTAAAAGCCC 0.919364 -53 ACGGGTCGAATTCAATGCCCTAGCACAAAT 17 136 1 TTCAATGCCC 0.929614 -148 TCTTTGATTGTTCAAAACGCTGTTTAAACT 19 16 0 TTCAAAACGC 0.826629 -112 ********** Masking position 5 Map Score: 2.70175 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 330 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282