AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_synecho_ctra_300.orf -o057_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 RCY32311 191 Synechocystis #2 RCY35515 195 Synechocystis #3 RCY47549 98 Synechocystis #4 RCY30106 164 Synechocystis #5 RCY08201 100 Synechocystis #6 RCY53401 171 Synechocystis #7 RCY46834 124 Synechocystis #8 RCY13164 111 Synechocystis #9 RCY00205 96 Synechocystis #10 RCY15170 266 Synechocystis #11 RCY16212 29 Synechocystis #12 RCY27781 300 Synechocystis #13 RCY37253 206 Synechocystis #14 RCY40141 87 Synechocystis #15 RCY11977 246 Synechocystis #16 RCY00456 110 Synechocystis #17 RCY08095 101 Synechocystis #18 RCY42619 279 Synechocystis #19 RCY23173 277 Synechocystis #20 RCY12795 137 Synechocystis #21 RCY26284 300 Synechocystis #22 RCY23327 241 Synechocystis #23 RCY31626 279 Synechocystis #24 RCT00348 169 Chlamydia_trachomatis #25 RCT00363 300 Chlamydia_trachomatis Motif number 1 GCCAATTTGCCCCCTAGGGTTCGGCAACGC 1 117 0 CCCCTAGGGT 0.818082 -75 TTTGCATTTTTCCCATGGCTGACCCCACCA 3 14 1 TCCCATGGCT 0.947265 -85 AAGTTTTTGTCCCCTGGGCTGACTCTGCCT 5 65 1 CCCCTGGGCT 0.994612 -36 GACAGTTTCCCCCCAGGGCTGAGGATTATC 7 104 0 CCCCAGGGCT 0.994359 -21 TACTCGCTCTCCCCTAGGGTACTCTGGCTT 10 110 1 CCCCTAGGGT 0.818082 -157 TATTTTAGCTTCCCATGGCTAGCCAATGGC 10 171 1 TCCCATGGCT 0.947265 -96 TTAGGCTGTTCCCATGGGCTAAAAATAAAT 12 99 1 CCCATGGGCT 0.908888 -202 AATAAAAATGCCCCTTGGCGATCGCCGGGG 15 181 0 CCCCTTGGCG 0.838388 -66 CGGGTTTCACCTCCTTGGGGTTGGGATAGC 15 226 0 CTCCTTGGGG 0.702784 -21 GATTTGGTAACTCCTTGGGTACTGGCGAAG 16 66 0 CTCCTTGGGT 0.934388 -45 AATTTACCGACCCCTTGGCTCCACTGAGTT 18 13 0 CCCCTTGGCT 0.988458 -267 AGAGTGCAGACTCCAGGGCTAACCTCAGCC 19 90 1 CTCCAGGGCT 0.982094 -188 GGTTCAAGTCCTCCAGGGCGCGTTGACCAC 19 179 1 CTCCAGGGCG 0.975322 -99 CCAGGCTTTTCCCCAGGGCTGACCGAATTC 21 75 0 CCCCAGGGCT 0.994359 -226 CAGAACTAATTTCCATGGGGAATAATGGTA 22 29 1 TTCCATGGGG 0.615204 -213 TGATCATCTCCCACAGGGCGGCATTGTACA 23 55 0 CCACAGGGCG 0.881653 -225 ********** Masking position 7 Map Score: 32.6732 Number of sites scoring better than the average of aligned sites = 1190 Number in coding regions = 1070 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 2 CCGAACCCTAGGGGGCAAATTGGCTTCGGA 1 123 1 GGGGGCAAAT 0.988292 -69 GGGTCAGCCATGGGAAAAATGCAAAAAC 3 9 0 TGGGAAAAAT 0.889389 -90 AAAGACGTTGGGGGGCAAATCATTCCAGAT 4 22 0 GGGGGCAAAT 0.988292 -143 AGTCAGCCCAGGGGACAAAAACTTCCTGAA 5 59 0 GGGGACAAAA 0.957802 -42 AGAAAAGGGGAAAATTCCCAATAAC 6 157 0 AGGGGAAAAT 0.874917 -15 CTCAGCCCTGGGGGGAAACTGTCC 7 111 1 GGGGGAAACT 0.905088 -14 TGGGGCAGTATGGGGCAACTCAGGCTAAAC 8 61 1 TGGGGCAACT 0.924177 -51 CACTTCCAGAAGGGAAAAATCGGTGCTTTA 12 20 1 AGGGAAAAAT 0.746423 -281 CCACAACCGTTGGGACAAACCCCCCGGCAG 12 187 0 TGGGACAAAC 0.81699 -114 GCAAGGCAAGTGGGAAAAAAGCAACTTTTG 20 72 1 TGGGAAAAAA 0.837078 -66 ACCAGTTCTTGGGGGCAAAAACTAGTCAAT 21 12 0 GGGGGCAAAA 0.981797 -289 CGGTCAGCCCTGGGGAAAAGCCTGGCAACC 21 80 1 TGGGGAAAAG 0.81699 -221 AAATTTGGCGGGGGGCAGAAATGCCAATAC 22 182 1 GGGGGCAGAA 0.87978 -60 GGAGGGGACAAATTAGGGGCAGG 22 229 0 GGGGACAAAT 0.972619 -13 TTCCAAGGAGTGGGGCAAAA 23 1 0 TGGGGCAAAA 0.96668 -279 ********** Masking position 7 Map Score: 20.9871 Number of sites scoring better than the average of aligned sites = 994 Number in coding regions = 881 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 3 CCAAAGAAGGCTCGCTTTCGGGAATCACCA 1 54 0 CTCGCTTTCG 0.631895 -138 GTCCCCTGGGCTGACTCTGCCTGGCTTTGC 5 73 1 CTGACTCTGC 0.880542 -28 CTGACTCTGCCTGGCTTTGCTTAAATCT 5 83 1 CTGGCTTTGC 0.960619 -18 TGCAGAAAGTCCGGCTCCCCCAGCTTAATT 6 122 1 CCGGCTCCCC 0.939723 -50 GTTTCTGTGGCCGACTATGCCTTCTTCGTT 7 48 1 CCGACTATGC 0.826516 -77 AGCGAAAATGCTGACTTTGCCATTTTACCG 10 53 1 CTGACTTTGC 0.789553 -214 CTGCAATTTACTCGCTCTCCCCTAGGGTAC 10 102 1 CTCGCTCTCC 0.907511 -165 CTAGGGTACTCTGGCTTTGGGAAAGGGTAA 10 123 1 CTGGCTTTGG 0.89344 -144 ATTTATTTAACTGGCTATGCCAAAGACCGC 15 44 1 CTGGCTATGC 0.976399 -203 GTGTTTAATGCTTGCTATCCCAACCCCAAG 15 213 1 CTTGCTATCC 0.68071 -34 GAAGTAAATTCTCGCTCCCCGCGGTGGGTT 17 30 1 CTCGCTCCCC 0.84494 -72 GCCTGGATTGCCGGCAATCCCCCCAGTCAA 18 240 1 CCGGCAATCC 0.919211 -40 GTGCCAAATTCCGGCAATGGTTTGAAGCAG 21 46 1 CCGGCAATGG 0.833297 -255 GGGGAAAAGCCTGGCAACCCAACCCAGACC 21 91 1 CTGGCAACCC 0.894061 -210 GTTCTGCTTGCCGGCACCGCTTTT 22 5 0 CCGGCACCGC 0.90341 -237 GGCCTCTGGTCTGGCAATGGTTGCTAGGCG 22 71 1 CTGGCAATGG 0.869731 -171 ********** Masking position 5 Map Score: 13.9832 Number of sites scoring better than the average of aligned sites = 1067 Number in coding regions = 984 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TCTGGAATGATTTGCCCCCCAACGTCTTTGGT 4 23 1 TTTCCCCCAA 0.808294 -142 TGCAACGAAATTTATCGCCCAATACTTTACAG 4 120 1 TTTCGCCCAA 0.943134 -45 CGGAGCTTTTATTTAGTGCCAAGTTTTGGCCG 6 40 1 ATTGTGCCAA 0.886821 -132 AAAGTTTTAGTTTCCCGGCCAAAACTTGGCAC 6 55 0 TTTCGGCCAA 0.982919 -117 TCTTCGTTAATCTTCGTGCCAAAACAAA 7 7 0 TCTGTGCCAA 0.817529 -118 AGATCCACCGATTTTGGGCCAATCCCAACGAT 12 49 0 ATTGGGCCAA 0.94316 -252 AGTTCAAACCTTATTCGGCCAAGGCTCAGAAT 12 148 0 TTACGGCCAA 0.935351 -153 AGTCTAATAATTTAGCTTCCAAAAAAAGTGAA 13 65 0 TTTCTTCCAA 0.776591 -142 TAGATAAAAATAAACGGGCCAAGGAAATATCC 13 127 0 TAAGGGCCAA 0.46382 -80 GTTTGAGGGCCTAGACCCAATAA 16 2 1 TTTGGGCCTA 0.751457 -109 GGGAGCGAGAATTTACTTCCAATCTCCCACTA 17 17 0 ATTCTTCCAA 0.620064 -85 TCATACCCTAATTTGCTGCCAATTCCCATCGA 19 51 0 ATTCTGCCAA 0.928052 -227 AAAACTGCATTCTAGCGGCCAACAGTCCGGGC 20 34 1 TCTCGGCCAA 0.939827 -104 ATTGACTAGTTTTTGCCCCCAAGAACTGGTTA 21 12 1 TTTCCCCCAA 0.815984 -289 CAAGAACTGGTTAAGGTGCCAAATTCCGGCAA 21 31 1 TTAGTGCCAA 0.805839 -270 CGTCCAGAGGATTTGCGGCCAACGGCGGGAAT 23 88 0 ATTCGGCCAA 0.964683 -192 *** ******* Masking position 12 Map Score: 12.1131 Number of sites scoring better than the average of aligned sites = 736 Number in coding regions = 673 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 AATGGCGATTAAACAAGTTC 1 1 1 AATGGCGATT 0.867639 -191 TAAGCTAGGGAACGCCGATGCGTTGCCGAA 1 98 1 AACGCCGATG 0.941753 -94 GCGGACTCGAAAAGCCGATGCTAATGCTAA 2 105 0 AAAGCCGATG 0.845279 -91 GATAATACCAAACTGCGATCTTT 5 4 0 AACTGCGATC 0.79944 -97 TCTGCAATCCAATGCCGATGATAACGCGAG 6 98 0 AATGCCGATG 0.937195 -74 ATGGCTAGCCAATGGCGATCGTAAAGATAT 10 185 1 AATGGCGATC 0.980819 -82 TATTTATTTAACTGGCTATGCCAAAGACCG 15 43 1 ACTGGCTATG 0.717328 -204 CTGCTTCAGCCCCGGCGATCGCCAAGGGGC 15 172 1 CCCGGCGATC 0.886949 -75 CTCCTTGGGTACTGGCGAAGTAGGGAACTT 16 56 0 ACTGGCGAAG 0.803791 -55 GATGTGAATTAACGGCGATCAAACCCACCG 17 51 0 AACGGCGATC 0.982316 -51 CTCCAACACCAATGGCGATCGCCATCGATG 19 27 1 AATGGCGATC 0.980819 -251 GTTAATTTCAACAGGCGATCGCCTAGCAAC 22 90 0 ACAGGCGATC 0.939182 -152 ********** Masking position 8 Map Score: 10.2089 Number of sites scoring better than the average of aligned sites = 2543 Number in coding regions = 2307 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 6 CCGAACCCTAGGGGGCAAATTGGCTTCGGAC 1 123 1 GGGGGAAATT 0.716647 -69 AAAGACGTTGGGGGGCAAATCATTCCAGATT 4 21 0 GGGGGAAATC 0.761158 -144 GCCAAAACTTGGCACTAAATAAAAGCTCCGA 6 39 0 GGCACAAATA 0.484778 -133 GGAACAAATTTTAGCCCTTTC 9 1 1 GGAACAATTT 0.602268 -96 GTAAATTGCAGGCCGAAAATCCGAGAGAATC 10 82 0 GGCCGAAATC 0.960199 -185 CGTTGGGATTGGCCCAAAATCGGTGGATCTC 12 51 1 GGCCCAAATC 0.884576 -250 CAAACCCCCCGGCAGTGATTCCAGTTCAAAC 12 171 0 GGCAGGATTC 0.691239 -130 AAGCTGTCAAGGAAGCAAATCCCCAACAAAC 15 133 0 GGAAGAAATC 0.89442 -114 GTGGGAGATTGGAAGTAAATTCTCGCTCCCC 17 19 1 GGAAGAAATT 0.870519 -83 AAGCTTATTGGGCAGTAATTTACCGACCCCT 18 28 0 GGCAGAATTT 0.937206 -252 GATGGGAATTGGCAGCAAATTAGGGTATGAT 19 53 1 GGCAGAAATT 0.954649 -225 TTCAAACCATTGCCGGAATTTGGCACCTTAA 21 41 0 TGCCGAATTT 0.402351 -260 ATCAAAGCGAGGAACAAAATTATGGCCGCTG 21 235 0 GGAACAAATT 0.681092 -66 TTTGGCGGGGGGCAGAAATGCCAATACAATT 22 185 1 GGCAGAATGC 0.691239 -57 TGCGGCCAACGGCGGGAATTTGTGATCATCT 23 76 0 GGCGGAATTT 0.892978 -204 TCCCGCCGTTGGCCGCAAATCCTCTGGACGA 23 90 1 GGCCGAAATC 0.960199 -190 CAAATCCTCTGGACGAAATTTTTCCTTTAAC 23 105 1 GGACGAATTT 0.812582 -175 ***** ***** Masking position 8 Map Score: 10.8905 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 843 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 CATTGGAGGGAAAGACGTTGAACTTGTTTAATCGCCAT 1 12 0 AAGTTCTTTT 0.820199 -180 TTATTATTGACCAATTGTTAACTTTGTTAACGAAAATT 2 30 0 CAGTTTTTTT 0.833452 -166 GGGCTTTTTTTCAACCTTTTTCTTTTTTGATTTCCGCT 3 65 0 TATTTTTTTT 0.780554 -34 GAAGCCTGAATCAAGATTTGAGTTTGTTGGGGATTTGC 15 112 1 TATTTTTTTT 0.780554 -135 CCTAGACCCAATAAGTTTTCCATTTATTTCGGGGAGAA 16 20 1 AATTTTTTTT 0.940742 -91 TTACTGCCCAATAAGCTTTGACTTTCTTTCGATAGCTG 18 41 1 AATTTTTTTT 0.940742 -239 TCTAAGTAAAATAAGATTTTTATTTCTCAGCTACGCCC 18 114 1 AATTTTTTTC 0.698413 -166 GCTACGCCCTCGATATTTTTTATTTTTTCGATCCTGTT 18 143 1 CATTTTTTTT 0.8462 -137 TCGCTTTGATAAAAACGTTGTAATTGTTTGCTATTGTA 21 256 1 AAGTTATTTT 0.625811 -45 AATCTTGTTGAAAGATTTTATGTTTTTTT 24 2 0 AATTTTTTTT 0.940715 -168 TTTGTTATGAAAAGGATTTTATTTTGTTGTTATAATTA 24 39 0 AATTTTTTTT 0.940742 -131 CATACGAGGGAAATAAGTTCTATTTTTTTGTTATGAAA 24 65 0 AAGTTTTTTT 0.93508 -105 TTTTCATTGAAAAATCTTTCTATTTCTTTTCTCTTCCC 25 217 1 AATTTTTTTT 0.940742 -84 TAGATTTGTTTTCCTTGTTTCTTCTCTTA 25 282 0 AAGTTCTTTT 0.820203 -19 * * *** *** ** Masking position 3 Map Score: 8.18251 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 50 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GAATGATTTGCCCCCCAACGTCTTTGGTTG 4 27 1 CCCCCCAACG 0.904612 -138 TGGAAAGGAGCCCTCCGGCAAACGTGATAT 4 80 1 CCCTCCGGCA 0.936717 -85 ACTAAATAAAAGCTCCGACAATATTAAAGG 6 27 0 AGCTCCGACA 0.817704 -145 GCCACAGAAACCCACCGCCATCTTCGTTAA 7 29 0 CCCACCGCCA 0.818149 -96 CATTCTATGGCCCCACACCATTGCGTTAAA 10 214 0 CCCCACACCA 0.554691 -53 TTGGGACAAACCCCCCGGCAGTGATTCCAG 12 178 0 CCCCCCGGCA 0.98095 -123 AAGGAAGCAAATCCCCAACAAACTCAAATC 15 126 0 ATCCCCAACA 0.902108 -121 CCTCTGCTTCAGCCCCGGCGATCGCCAAGG 15 169 1 AGCCCCGGCG 0.739323 -78 TAGGGAACTTCTCCCCGAAATAAATGGAAA 16 36 0 CTCCCCGAAA 0.69376 -75 GAAATTCTAAATCCCCAACATTCACTCTGC 18 190 1 ATCCCCAACA 0.902108 -90 CGAAACTGTGATCTCCAACACCAATGGCGA 19 15 1 ATCTCCAACA 0.725945 -263 GAGGACTTGAACCCCCGACATCAGGTTTTG 19 162 0 ACCCCCGACA 0.980855 -116 GGCATTTCTGCCCCCCGCCAAATTTTCCTC 22 177 0 CCCCCCGCCA 0.980951 -65 ATTTGTGATCATCTCCCACAGGGCGGCATT 23 60 0 ATCTCCCACA 0.492014 -220 ********** Masking position 6 Map Score: 9.32714 Number of sites scoring better than the average of aligned sites = 1610 Number in coding regions = 1499 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 9 GGGAAAGACGTTGAACTTGTTTAATCGCCATT 1 8 0 TTAATTTTTT 0.58831 -184 TTTTCAACCTTTTTCTTTTTTGATTTCCGCTCAAA 3 61 0 TTTCTTTTGT 0.840044 -38 CAGTTTGGTATTATCGTTTTTTGCTCCTCTCACCG 5 19 1 TTTCTTTTTT 0.931896 -82 CTTCTTCGTTTTCTCGTTTTTGGCTGTTTTGATCA 7 68 1 TTTCTTTTGT 0.840044 -57 ACAGATTCAGTTTTAGTTATTCCGTCCGGGTTCGG 12 245 1 TTTATTTTCT 0.837498 -56 CAGTCTCTTATTTTAAGTATTTTTTGGAACGAGGC 13 160 0 TTTAGTTTTT 0.809248 -47 CCTCGATATTTTTTATTTTTTCGATCCTGTTGAAG 18 150 1 TTTATTTTCT 0.837498 -130 TGATGAGAAATTGTCAGTTTTTACT 20 123 1 TTTCGTTTTT 0.812137 -15 GATAAAAACGTTGTAATTGTTTGCTATTGTACGAT 21 263 1 TTTATTTTTT 0.930692 -38 ATGAAAAGGATTTTATTTTGTTGTTATAATTAATC 24 36 0 TTTATTGTTT 0.679279 -134 GGGAAATAAGTTCTATTTTTTTGTTATGAAAAGGA 24 61 0 TTTATTTTTT 0.930692 -109 TGAAAAATCTTTCTATTTCTTTTCTCTTCCCTGTG 25 224 1 TTTATTTTTT 0.930692 -77 TAGATTTGTTTTCCTTGTTTCTTCTCTTAACTC 25 278 0 TTTCTTTTTT 0.931896 -23 ** ** ** *** * Masking position 8 Map Score: 6.39148 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 58 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 10 TGCCCCCCAACGTCTTTGGTTGTCGATAAC 4 35 1 CGTCTTTGGT 0.849179 -130 CAATACTTTACAGCCTAGGTTTTTTCCACA 4 139 1 CAGCCTAGGT 0.656357 -26 GCGTTATCATCGGCATTGGATTGCAGAAAG 6 101 1 CGGCATTGGA 0.881385 -71 TCTTTACGATCGCCATTGGCTAGCCATGGG 10 182 0 CGCCATTGGC 0.952981 -85 TCACAGGAGTCGTCCTTGGTA 12 290 1 CGTCCTTGGT 0.967086 -11 ACTGGTCAGTCAGCATTGGTTATTTT 13 191 1 CAGCATTGGT 0.92111 -16 CGATGGCGATCGCCATTGGTGTTGGAGATC 19 24 0 CGCCATTGGT 0.979226 -254 CCAGACTATGCGTCCTTAGTTCAGTTGGTA 19 119 1 CGTCCTTAGT 0.698354 -159 TGCCAAATTCCGGCAATGGTTTGAAGCAGA 21 47 1 CGGCAATGGT 0.856922 -254 TTACCGGGGTCACCCTTGGTCTGCTTTACG 21 172 0 CACCCTTGGT 0.937625 -129 CACAAATTCCCGCCGTTGGCCGCAAATCCT 23 83 1 CGCCGTTGGC 0.881106 -197 ********** Masking position 4 Map Score: 6.84588 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 611 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 ATGAGAGGGTATTTAGCCTGGGGCAGTATG 8 43 1 ATTTAGCCTG 0.957801 -69 TCATACTGTAGTTTAGCCTGAGTTGCCCCA 8 71 0 GTTTAGCCTG 0.887211 -41 TGAAATGTTAATTTAACTTAACAAGCTTTG 9 64 1 ATTTAACTTA 0.577159 -33 TTGCCTAATTATTTAGCCGGTCATTTACTT 13 31 1 ATTTAGCCGG 0.926947 -176 GAGTCTAATAATTTAGCTTCCAAAAAAAGT 13 68 0 ATTTAGCTTC 0.647421 -139 GTCTAATCAGATTTAACCTACTTACCTATA 14 56 1 ATTTAACCTA 0.685996 -32 GCCACTATTTATTTAACTGGCTATGCCAAA 15 38 1 ATTTAACTGG 0.832021 -209 AGGGTTGCTTAATTAACCTGCCGAGGTTGA 15 84 1 AATTAACCTG 0.778689 -163 ACCAGTTCTCAGTTAACCTGAAGATGGGTT 21 118 1 AGTTAACCTG 0.747306 -183 TGCCAATACAATTTAGCTTGGTCTTCCCTG 22 203 1 ATTTAGCTTG 0.934127 -39 CAGCTACGATAATTAGCTGGTAATTTTTCC 23 27 0 AATTAGCTGG 0.662962 -253 GGCGTTATGTGTTTAACTTGTAGTTTGCTT 25 19 1 GTTTAACTTG 0.754336 -282 ********** Masking position 5 Map Score: 4.78816 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 311 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 TTTCCGCTCAAAAGGAAGACGGTCTCGATT 3 43 0 AAAGGAAGAC 0.864229 -56 CCACTTCCAGAAGGGAAAAATCGGTGCTTT 12 19 1 AAGGGAAAAA 0.667675 -282 AAATTAGGGGCAGGGAAGACCAAGCTAAAT 22 213 0 CAGGGAAGAC 0.940331 -29 GAAACTACTCAAAGGAAGAGCTGAATATGC 25 60 1 AAAGGAAGAG 0.924119 -241 TCTTCTCTTGAAGAGAAGAGAACGTTTAAT 25 179 0 AAGAGAAGAG 0.954155 -122 TCTTCTCTTCAAGAGAAGAGGGCGTTTTTT 25 190 1 AAGAGAAGAG 0.954155 -111 ATCATACACACAGGGAAGAGAAAAGAAATA 25 237 0 CAGGGAAGAG 0.967898 -64 TTCATGAGTTAAGAGAAGAAACAAGGAAAA 25 273 1 AAGAGAAGAA 0.875509 -28 ********** Masking position 6 Map Score: 3.78565 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 109 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 GCGTTCCCTAGCTTAAATTATCTTGATGTCCAAAGA 1 77 0 GTAAAATCTA 0.598908 -115 AAATAATTTCGTTAAAATTAGCATTAGCATCGGCTT 2 88 1 GTAAAAGCTA 0.944724 -108 TGAAGCTCACGGTGAGAGGAGCAAAAAACGATAATA 5 27 0 GTAGAAGCAA 0.975091 -74 GGATTATCGTGATCAAAACAGCCAAAAACGAGAAAA 7 76 0 GTAAAAGCAA 0.934991 -49 ATTTTTAGCCCATGGGAACAGCCTAACACAATTTTT 12 89 0 CTGGAAGCTA 0.676127 -212 GGTTAAATCTGATTAGACAAACCAAAAACAAATGAC 14 38 0 GTAGAAACAA 0.773762 -50 CCTGAAGATGGGTTAGATCAGCTTGACAAACCGCAG 21 134 1 GTAGAAGCTA 0.978956 -167 GGGTGACCCCGGTAAAAACAGCAATATAACCAATAA 21 187 1 GTAAAAGCAA 0.934991 -114 CTATCAGCGTCGTAAGAAAAGCTTGAAATAGCGCCT 25 95 0 CTAGAAGCTA 0.917257 -206 TTGCCTAACGGATCAGAATAGCATCATTAAACGTTC 25 154 1 GTAGAAGCTA 0.978956 -147 CTGTTCATGAGTTAAGAGAAGAAACAAGGAAAACAA 25 270 1 GTAGAAGAAA 0.755171 -31 * * *** *** * * Masking position 7 Map Score: 5.5548 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 46 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 CGCCGATGCGTTGCCGAACCCTAGGGGGCAA 1 110 1 TTGCCGACCC 0.94771 -82 ATTTTAGCCCTTTCCGTTCCCGTACCAGGGA 9 18 1 TTTCCGTCCC 0.918773 -79 TAACCCCATTTACCCTTTCCCAAAGCCAGAG 10 131 0 TACCCTTCCC 0.901006 -136 AAAAATAAATTTCCCTAGCCCCCTCATACAT 12 119 1 TTCCCTACCC 0.968385 -182 TGATGATGTCTAACCGAACCCGGACGGAATA 12 262 0 TAACCGACCC 0.945953 -39 GCCAAGGAAATATCCTAGCCCGAAAAAGAAA 13 111 0 TATCCTACCC 0.940516 -96 TAATGCTTGCTATCCCAACCCCAAGGAGGTG 15 218 1 TATCCCACCC 0.876888 -29 GGGCAGTAATTTACCGACCCCTTGGCTCCAC 18 19 0 TTACCGACCC 0.95568 -261 TAGCTTGGTCTTCCCTGCCCCTAATTTGTCC 22 216 1 TTCCCTGCCC 0.904076 -26 ******* *** Masking position 1 Map Score: 5.7559 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 213 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 15 TCAATAATAATTGCCCAGTCCTGTTGGTCA 2 58 1 TTGCCCAGTC 0.849566 -138 CAGGCAGAGTCAGCCCAGGGGACAAAAACT 5 66 0 CAGCCCAGGG 0.958909 -35 CCAATGCTGACTGACCAGTCTCTTATTTTA 13 180 0 CTGACCAGTC 0.918986 -27 TCCTCTGCTTCAGCCCCGGCGATCGCCAAG 15 168 1 CAGCCCCGGC 0.947092 -79 AACATTCACTCTGCCCAGTCTTGCTCAAAC 18 206 1 CTGCCCAGTC 0.982937 -74 TGCCGGCAATCCCCCCAGTCAATATTCCTC 18 248 1 CCCCCCAGTC 0.848316 -32 GGGCTAACCTCAGCCCAGACTATGCGTCCT 19 105 1 CAGCCCAGAC 0.986106 -173 CCTGGCAACCCAACCCAGACCAGTTCTCAG 21 100 1 CAACCCAGAC 0.887961 -201 CAACCATTGCCAGACCAGAGGCCAAACCAA 22 64 0 CAGACCAGAG 0.809769 -178 ********** Masking position 5 Map Score: 4.61105 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 421 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405