AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_synecho_ctra_300.orf -o294_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 RCY09572 170 Synechocystis #2 RCY03028 235 Synechocystis #3 RCY51138 72 Synechocystis #4 RCY13969 300 Synechocystis #5 RCY02647 82 Synechocystis #6 RCY03061 131 Synechocystis #7 RCY19040 87 Synechocystis #8 RCY00322 209 Synechocystis #9 RCY31848 126 Synechocystis #10 RCY49375 196 Synechocystis #11 RCY28877 111 Synechocystis #12 RCY33348 233 Synechocystis #13 RCY24628 300 Synechocystis #14 RCY43106 241 Synechocystis #15 RCY31503 112 Synechocystis #16 RCY45353 165 Synechocystis #17 RCY05245 300 Synechocystis #18 RCY02313 283 Synechocystis #19 RCY32683 300 Synechocystis #20 RCY15084 118 Synechocystis #21 RCY34249 175 Synechocystis #22 RCY23408 94 Synechocystis #23 RCY05831 277 Synechocystis #24 RCY50309 68 Synechocystis #25 RCY54010 66 Synechocystis #26 RCY48465 153 Synechocystis #27 RCY04930 300 Synechocystis #28 RCY20723 104 Synechocystis #29 RCY11903 300 Synechocystis #30 RCY08996 83 Synechocystis #31 RCY40124 140 Synechocystis #32 RCY43085 300 Synechocystis #33 RCY00666 300 Synechocystis #34 RCY52274 113 Synechocystis #35 RCY04119 279 Synechocystis #36 RCY51088 297 Synechocystis #37 RCY15245 60 Synechocystis #38 RCY53600 132 Synechocystis #39 RCY33958 164 Synechocystis #40 RCY30371 298 Synechocystis #41 RCY39499 300 Synechocystis #42 RCY50255 220 Synechocystis #43 RCY52021 164 Synechocystis #44 RCY26608 38 Synechocystis #45 RCY00135 42 Synechocystis #46 RCY33655 258 Synechocystis #47 RCY27198 197 Synechocystis #48 RCY30985 201 Synechocystis #49 RCY43486 300 Synechocystis #50 RCT00066 300 Chlamydia_trachomatis #51 RCT00068 66 Chlamydia_trachomatis #52 RCT00070 26 Chlamydia_trachomatis #53 RCT00071 195 Chlamydia_trachomatis #54 RCT00225 300 Chlamydia_trachomatis #55 RCT00227 16 Chlamydia_trachomatis #56 RCT00228 119 Chlamydia_trachomatis #57 RCT00230 300 Chlamydia_trachomatis #58 RCT00231 68 Chlamydia_trachomatis #59 RCT00232 27 Chlamydia_trachomatis #60 RCT00253 132 Chlamydia_trachomatis #61 RCT00254 117 Chlamydia_trachomatis #62 RCT00255 219 Chlamydia_trachomatis #63 RCT00257 300 Chlamydia_trachomatis #64 RCT00281 167 Chlamydia_trachomatis #65 RCT00283 131 Chlamydia_trachomatis #66 RCT00284 300 Chlamydia_trachomatis #67 RCT00285 300 Chlamydia_trachomatis #68 RCT00404 300 Chlamydia_trachomatis #69 RCT00405 132 Chlamydia_trachomatis #70 RCT00430 300 Chlamydia_trachomatis #71 RCT00507 100 Chlamydia_trachomatis #72 RCT00508 63 Chlamydia_trachomatis #73 RCT00509 258 Chlamydia_trachomatis #74 RCT00511 62 Chlamydia_trachomatis #75 RCT00512 300 Chlamydia_trachomatis #76 RCT00649 300 Chlamydia_trachomatis #77 RCT00738 300 Chlamydia_trachomatis #78 RCT00775 300 Chlamydia_trachomatis #79 RCT00854 259 Chlamydia_trachomatis #80 RCT00776 22 Chlamydia_trachomatis Motif number 1 CCGTTTTGCTGGCGATCGGCCGTTGACCCA 8 153 1 GGCGATCGGC 0.538332 -57 AGAAGCGGCGATCGCCAGTGGTTATC 13 7 1 GGCGATCGCC 0.499998 -294 GGTTATAGAAGGCGATCGGGCTTCTGTACT 13 221 1 GGCGATCGGG 0.927004 -80 TTTGCGGAACTGCGATCGGGAAATGTCATT 16 24 1 TGCGATCGGG 0.918274 -142 GGTTTTCGGTGGCGATCGGGCCTAGAACCT 18 139 1 GGCGATCGGG 0.927004 -145 GGGTAATCGGGGCGATCGCCTGCTAAACTG 27 179 1 GGCGATCGCC 0.499998 -122 GTATTTTTAGGGCGATCGCCGCTAAATCCG 31 20 1 GGCGATCGCC 0.499998 -121 CTGACAACCCGGCGATCGCCAAAGCGGGGT 34 25 1 GGCGATCGCC 0.499998 -89 GGATTACCCCGGCGATCGCCACTGTCCCCG 34 87 1 GGCGATCGCC 0.499998 -27 TTCGGCCCCAGGCGATCGCCTAGGGATCGA 36 230 1 GGCGATCGCC 0.499998 -68 GGGAGATCGGCGGAGCTAAAC 38 122 0 GGAGATCGGC 0.905937 -11 CCCGGCAATAGGCGATCGGGGATCAAACAG 40 12 0 GGCGATCGGG 0.927004 -287 AGAAGGCGATCGCCGGTGGCCATT 42 5 1 GGCGATCGCC 0.499998 -216 ATAGACCACTGGCGATCGGCATGGTAACAG 48 84 1 GGCGATCGGC 0.538332 -118 GATCCCATGTGGCGATAGGCCGGGTCTAGC 50 118 1 GGCGATAGGC 0.905937 -183 ********** Masking position 5 Map Score: 54.3583 Number of sites scoring better than the average of aligned sites = 5863 Number in coding regions = 5323 Number in noncoding regions = 540 Number of orfs with sites within 600 bp upstream = 332 Fraction of orfs with sites within 600 bp upstream = 0.0533248 Motif number 2 CTAGGCCCTGGCCCCGTCGCTGTA 7 2 1 TAGCCCTCCC 0.676332 -86 GCACTAGATGCTTCCCCTGTCCCTTGGCCAGAA 8 32 0 CTTCCCTCCC 0.973648 -178 TGGCTCCTCTTTCTCCCTAGGCCAATGGGGTCA 11 16 1 TTCCCCTGCC 0.95861 -96 AACTGGTAGGTTGACCCAGACCCGTTGGAAAGG 12 32 0 TTGCCCACCC 0.63059 -202 AGAAAACTAATCTGCCCTTTGCCATCAATTTCT 13 64 0 TCTCCCTGCC 0.947285 -237 AGTTCCGCAAATTTCCCCAACCCT 16 2 0 ATTCCCCCCC 0.82021 -164 CGCCAGACCGTGTTCCCTGGCCCATGCAAACCC 17 203 0 TGTCCCTCCC 0.893731 -98 CCCATTGGGATCCCCCCTGGGCCATGAGCCCAG 18 97 0 TCCCCCTGCC 0.945235 -187 ACTCCGTTGGCCCATCCCGGCCCTGAATGGCAG 19 219 1 CCCTCCCCCC 0.46807 -82 AAACTCCCCCCGGCCATAGTGACTC 22 3 1 ACTCCCCGCC 0.609558 -92 TAGGGGTTCGATTCCCCTCACCCGCTTTGGGTA 23 121 1 ATTCCCTCCC 0.913945 -157 TGGGACTGGGTTTGCCCTGCCCCATCGGTGAGA 26 33 0 TTTCCCTCCC 0.981312 -121 ACCATCACTTTTTTCCCTTAGCCCAATAATTAC 26 94 1 TTTCCCTGCC 0.960181 -60 TGTGACAAGTTTGTTCCTAGCCCTCCAGTCTAG 28 33 1 TTGTCCTCCC 0.733802 -72 ACTCCAGTCGCTAACCCTTGGCCACGGTCCCAT 35 169 0 CTACCCTGCC 0.56218 -111 AGGTATCTCTCTCAGCCTCACCCAGGGGAACGC 38 16 0 CTCGCCTCCC 0.850242 -117 CCCATAAGGCTTTGACCTTTCCCGTCCCTTTTC 38 70 0 TTTACCTCCC 0.739494 -63 TTACCCAAAACCTTCCCCCATCCTGGACTTGGT 40 69 1 CCTCCCCTCC 0.519533 -230 GACCCGTATTTTTACCCCCACCCTAGTCTATGG 40 110 0 TTTCCCCCCC 0.957548 -189 AACGATCTTTTTTGTCCTGCCCCAAGGAATTTG 40 161 0 TTTTCCTCCC 0.802666 -138 CGTTTTAAACGCCCCCCTGACCCCCCAGATTTT 41 62 0 GCCCCCTCCC 0.773982 -239 TGGGAATTTATTGAACCTGTGCCCACATCAAAA 41 246 0 TTGACCTGCC 0.469055 -55 TTTGCACGACTGGGCCCTAACCCAGACCGGTGG 42 46 0 TGGCCCTCCC 0.850737 -175 AAACGATTGTTTTTGCCCTTGCCATAGATTTTT 42 198 1 TTTGCCCGCC 0.623656 -23 GGGGAAGTTATTTGCCCTTGTCCCTGCTCCGAT 43 117 1 TTTCCCTTCC 0.827609 -48 ACCTTTCCCTACCCCCACCCTAACG 45 3 1 CTTCCCTCCC 0.973648 -40 CTAACGACCATCTCCCCTTACCC 45 30 1 TCTCCCTCCC 0.975082 -13 AAACCCCGGCCTCCCCCTCCCCCAACCAAAATC 46 228 1 CTCCCCTCCC 0.972593 -31 GGCATTATTGTCCAGCCCAGCCCTTAGTTTTTG 47 139 1 TCCGCCCCCC 0.720898 -59 GGAAAAATCCTTCACCCTTAGCCCGGCTAATCC 49 268 1 TTCCCCTGCC 0.95861 -33 GTTTATGCTTCTCGCCCTAAGCCCTTCTGAGTT 54 13 1 CTCCCCTGCC 0.942184 -288 TCTTCTTCCCTTTTCCCGGCTTTGCT 61 4 1 TCTCCCTTCC 0.781546 -114 CTTGTTAAAGCCCTCCCTCCCCCGGA 62 4 0 CCCCCCTCCC 0.963565 -216 CTTTGGATTTTTGTGCCTATCCCACTTTCTAAG 66 162 1 TTGGCCTCCC 0.850598 -139 TCGATTCAGGATGCCCCTACCCCTAGAGCATGG 75 116 1 ATGCCCTCCC 0.878012 -185 *** **** *** Masking position 7 Map Score: 35.6531 Number of sites scoring better than the average of aligned sites = 1760 Number in coding regions = 1502 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 3 GCTAAGCCGGAAGGGGGATAATCCAACATCAAG 4 104 0 AGGGGGTAAC 0.741292 -197 AAGATACAGCGACGGGGCCAGGGCCTAG 7 6 0 GCGGGGCAGG 0.736176 -82 TAATACGGACACGGGGGGTATGGAAAAATACCC 12 160 0 AGGGGGTATG 0.680661 -74 TGCGGAAAAATGGGGGGACAATGGTGGCTTAAC 14 197 1 TGGGGGCAAG 0.924188 -45 ATTGTGAAATTACGGCGTAATGGCTGA 16 149 1 TCGGCGAATG 0.355556 -17 TGGTATTGGTTTCGGCGGTAACGC 33 2 0 TCGGCGTAAG 0.847633 -299 CGATCGCCAAAGCGGGGTCAACGATCTTGGTAG 34 37 1 ACGGGGCAAG 0.980715 -77 ATTTGTTCGGGGACAGTGGCGATCGCCG 34 96 0 TCGGGGCAGG 0.913088 -18 CTTGGAAGGAAACGGGGGCAGCGGTTGTAATTG 35 129 0 ACGGGGCAGG 0.961357 -151 GAATAATGGGACCGTGGCCAAGGGTTAGCGACT 35 164 1 ACGTGGCAAG 0.627969 -116 GAAAGCAACGATGGGGGACAAAGTAATTAAATT 36 200 0 AGGGGGCAAG 0.966518 -98 AAAGGAATTGATCGGGGACAATGTTCGATTCTA 36 272 0 ACGGGGCAAG 0.980715 -26 CAAAGTTAGCACCGGCGAAAAGGGACGGGAAAG 38 54 1 ACGGCGAAAG 0.872325 -79 TTCTTCTCAGATGGGCGGCAACCCCGTAAGATT 39 105 1 AGGGCGCAAC 0.832718 -60 TAGCTTAAGCAACGGCGGTAATG 39 152 1 ACGGCGTAAG 0.929445 -13 CCCCAAAATCTGGGGGGTCAGGGGGGCGTTTAA 41 58 1 TGGGGGCAGG 0.856393 -243 GGATAATCGGAGCAGGGACAAGGGCAAATAACT 43 122 0 ACAGGGCAAG 0.627969 -43 ATCTCTCGGAATGGGGGATAATCGGAGCAGGGA 43 137 0 AGGGGGTAAC 0.741292 -28 ATCCGGCGGTAATGTTTCTAAGAT 44 25 0 TCGGCGTAAG 0.847633 -14 AGCTACAACAACCGGGGGCAAAGCAAAACCCTA 46 93 0 ACGGGGCAAG 0.980715 -166 TCCATTGGGCAACGGCGTTAATGCACTGACTAA 48 155 1 ACGGCGTAAG 0.929445 -47 TATTTCTACTATCGGCGCTAGACCCGGCCTATC 50 131 0 ACGGCGTAGC 0.623572 -170 AGATAATCGATACGGGGACATACTTTGAAAAAG 50 196 0 TCGGGGCATC 0.513532 -105 GATGAGGGGCGAAAAAGCCAGCTCCTG 69 116 0 AGGGCGAAAG 0.79501 -17 GAACAGGGATATGGGCGGAAAGGCTTCCCTTTA 75 211 1 AGGGCGAAAG 0.79501 -90 * ***** *** * Masking position 10 Map Score: 24.106 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 918 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 GAGGTAAATATCCCCCTAACTTTAGAATCAGG 14 34 0 TCCCCCACTT 0.765401 -208 GCCACCATTGTCCCCCCATTTTTCCGCAGGGG 14 193 0 TCCCCCATTT 0.93992 -49 AACGTGTAATTCCCCCGATTTTAACCCAACGG 17 237 0 TCCCCCATTT 0.93992 -64 CGGGATTTCGTCCCCAGTTTTTTCCTATTTGA 17 272 1 TCCCCATTTT 0.79488 -29 GGTTGTTCATTCCCCAAACAATCCGCCAAATC 18 13 0 TCCCCAAAAT 0.684281 -271 AGCCCAAAGATCCCCTATGATTGGCGAAGAAA 20 31 1 TCCCCTTATT 0.49019 -88 GCAGAACTTTTCCCCATCCATCTAACTAACTT 21 105 0 TCCCCACATC 0.860599 -71 TCAGTTTGCATCCCCAAAAATTATCCC 25 6 0 TCCCCAAATT 0.95014 -61 GATTTATATTTCCCCCTCCATTTAACCATTCT 29 64 1 TCCCCCCATT 0.897393 -237 TCAATTGTATTCCCCAAAATTTTACCAGAGTC 32 37 0 TCCCCAATTT 0.935115 -264 AAGAAAAAACTCCCCCAGGATTGAACCAAGGA 39 78 0 TCCCCCGATT 0.919921 -87 TGAGTGACAGTCCCCCAGTATTGCGGTCGCTT 41 21 0 TCCCCCGATT 0.919921 -280 TCACTCAGTTTCCCCCAAAATCTGGGGGGTCA 41 46 1 TCCCCCAATC 0.940653 -255 GCAAATAACTTCCCCATAGATTAGCAGGCATT 43 100 0 TCCCCAAATT 0.95014 -65 AACGTTCACTTCCCCTAACATCATCGTCC 47 179 1 TCCCCTAATC 0.732619 -19 CTCATAGGCGTCCCCACATATTAGGAAGAGAC 57 182 0 TCCCCAAATT 0.95014 -119 GGGATCCATATCCCCCTCATTTCTAAGAAACC 70 224 0 TCCCCCCTTT 0.868672 -77 CCACCTCTACTCCCCAGTCATCTCTGTAATGG 73 56 0 TCCCCATATC 0.797001 -203 CAAAAGGTTTTCCCCATGCTTCCCCTAACAAA 78 84 0 TCCCCAGTTC 0.8598 -217 GTGGAACGACTCCCCAAAATATACCGCGACAG 79 151 0 TCCCCAATAT 0.621094 -109 AGTCTGGGGATCCCCAGGATTCAAAGAGCGAT 79 190 0 TCCCCAGTTC 0.8598 -70 ATCCTGGGGATCCCCAGACTTCCTTATTGGGG 79 202 1 TCCCCAATTC 0.916964 -58 ****** * *** Masking position 1 Map Score: 21.7387 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 312 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 CCTGGACCCTCCATGGCAAGCCCCGCTATGAATTGCTC 4 65 0 CCACACCCGA 0.951541 -236 GAGGGGACTCCCCTGGAGTTCTCCGCAAAGATACAGCG 7 28 0 CCCATCCCGA 0.920123 -60 TGCGACAGCCCCAAGCTGTCCCCCGTTTTGCTGGCGAT 8 131 1 CCATTCCCGT 0.739203 -79 GGAAAAATACCCAAAAACAACGCCGCGATGGCTAGAGA 12 134 0 CCAAACCCGA 0.909045 -100 AACAGATTGTCCATGATAACCACTGGCGATCGCCGCTT 13 13 0 CCATACCTGG 0.769353 -288 TCTATAACCACCATTAGTTACTCCGGCAATCCAGGCTC 13 192 0 CCAGTCCCGA 0.841232 -109 CCATTGTCCCCCCATTTTTCCGCAGGGGTAAATGATGG 14 183 0 CCCTTCCAGG 0.793581 -59 CTTTGGCAAACCAGGTTATTCCCAGCAACGCTTAGTTA 18 187 0 CCATTCCAGA 0.899514 -97 CCCCGATTACCCACGCTTACCACTGGGAAATAAACTCT 27 153 0 CCATACCTGA 0.883802 -148 CCCAATGCCTCCTCCGGCAAGATTTACCC 29 282 0 CCACTCCCGA 0.958521 -19 ATACCTTAGACCAAAGTTAGCACCGGCGAAAAGGGACG 38 43 1 CCATACCCGG 0.939645 -90 GTTTTAAACGCCCCCCTGACCCCCCAGATTTTGGGGGA 41 56 0 CCCTACCCCA 0.766551 -245 ATTCCCATAGCCAGTCTTTACACCCTAAGGAGACGCGA 41 272 1 CCATTCCCCA 0.797801 -29 TGGAATTTTACCCCAATGGCCACCGGCGATCGCCTTCT 42 11 0 CCCTGCCCGG 0.723544 -210 AATCCCCCTGCCATGCTCTCCACTGAAATGCCCCTTCC 46 167 1 CCATTCCTGA 0.899514 -92 ACTGAAATGCCCCTTCCAACCACCGGAAGCACCTTATT 46 188 1 CCCCACCCGA 0.950571 -71 ATTTTTATGGCCATTGATTACCCTGGAAGTTAGTGTTG 47 24 1 CCAATCCTGA 0.71591 -174 CAATAATGCCCCATGATAAGCCCCGATGTAACCAGTAT 47 111 0 CCATACCCGG 0.939645 -87 TGGCGATAGGCCGGGTCTAGCGCCGATAGTAGAAATAT 50 127 1 CCGCACCCGA 0.713485 -174 AAGCCCCCAACCAGCTTTTTCTCCGGAAAGGCAAAGCA 66 26 0 CCATTCCCGA 0.976625 -275 GCTTTTAAGGCCCACACTAACACAGCAAAAGGTGTTGG 68 58 1 CCCCACCAGA 0.804701 -243 GGATATGGATCCCTATAATTCTCAGAGAACAGCCAAAT 70 243 1 CCCATCCAGA 0.711652 -58 CACCTCTACTCCCCAGTCATCTCTGTAATGGATAGTAG 73 49 0 CCCTACCTGA 0.881651 -210 AAGGGGACACCCCCTCTCTTCGCAGTGAAAACGTATAC 79 111 0 CCCTTCCAGA 0.897609 -149 GAACGACTCCCCAAAATATACCGCGACAGACAAGGGGA 79 142 0 CCATTCGCGA 0.672704 -118 *** * * * *** * Masking position 11 Map Score: 17.5254 Number of sites scoring better than the average of aligned sites = 1071 Number in coding regions = 994 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 6 AGCAATTCATAGCGGGGCTTGCCATGGAGGG 4 66 1 AGCGGGCTTG 0.681622 -235 AAAAGTTTCAAGCTGGGATGGTTGGTAAGTT 4 181 1 AGCGGGATGG 0.985361 -120 ACGCCGAGTCAGTGGGGAAGGATGGCAAGGT 6 59 1 AGTGGGAAGG 0.821685 -73 TGATTTTAGCGGAGATGGGCATTAATCC 11 94 0 AGCGAGATGG 0.854784 -18 CGCTGTTGTGAGCCTGGATTGCCGGAGTAAC 13 183 1 AGCTGGATTG 0.819546 -118 AGCGTCGGCTAGCCTGGGTGATGTCACCCCG 13 258 1 AGCTGGGTGA 0.501844 -43 TGCCATTCAGGGCCGGGATGGGCCAACGGAG 19 220 0 GGCGGGATGG 0.936493 -81 CCCTATCATTAGCTTGGAAGGCTAAGGTTTT 23 95 0 AGCTGGAAGG 0.963795 -183 TTATCGAGGGAGCATGGATGACGGTCGAGGA 23 232 0 AGCTGGATGA 0.881304 -46 AACACCCGAAAGCTTGGATGTGCGAATTTTT 27 220 0 AGCTGGATGT 0.746099 -81 AAAAATTGCTAGTCTGGATGGTAAAAATTAT 29 149 1 AGTTGGATGG 0.873993 -152 CCCATTATTCAGCTTGGAAGGAAACGGGGGC 35 143 0 AGCTGGAAGG 0.963795 -137 TTCAGTGGAGAGCATGGCAGGGGGATTTTTA 46 163 0 AGCTGGCAGG 0.906388 -96 AAAAACTAAGGGCTGGGCTGGACAATAATGC 47 140 0 GGCGGGCTGG 0.842852 -58 GGATATTCGTAGTGGAGAAGGTTTCGGTTGA 62 55 1 AGTGAGAAGG 0.287227 -165 TATTTGGTAGAGCGTGGATGAGTGTTTCGTT 66 261 1 AGCTGGATGA 0.881304 -40 TAGAACTCAGAGCAGGGATGGTACCCATAGA 70 144 0 AGCGGGATGG 0.985361 -157 TGACACCGGTAGCTTGGAAGGCTACAGCTCT 76 178 0 AGCTGGAAGG 0.963795 -123 *** ******* Masking position 7 Map Score: 16.2471 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 288 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 AAAATTATTGAGAGGTTTGCCTTGCTAACA 1 151 1 AGAGGTTTGC 0.833243 -20 GGGAAGGCCTAGGGGTTTGCTTCTGTTCTA 15 25 1 AGGGGTTTGC 0.980758 -88 TTTTATTTTAAGGGCTTTGCGTATCCGTCG 16 109 0 AGGGCTTTGC 0.935383 -57 ACAGAAACTTAGGGGTTTGCATGGGCCAGG 17 191 1 AGGGGTTTGC 0.980758 -110 TTGTCGGCAAGGGGTTTTGCTCTGTGTTGC 19 149 1 GGGGTTTTGC 0.898575 -152 CCTGAATGGCAGGGTTTTCCCGTGTCATAC 19 240 1 AGGGTTTTCC 0.846012 -61 GCAGAGTGAAAGTGTTTTGCCAACTCCAGT 35 194 0 AGTGTTTTGC 0.890503 -86 TATGCATTGCAGTGTTTTGCAACATTTAAT 36 105 0 AGTGTTTTGC 0.890503 -193 TGATACTTTTAGGGTTTTGCTTTGCCCCCG 46 84 1 AGGGTTTTGC 0.979186 -175 ATCCTATTCGAGGGGTTGGCTCCTGTTTCT 67 119 0 AGGGGTTGGC 0.905647 -182 TCTCTTTGTCAGGGTTTTGC 71 91 1 AGGGTTTTGC 0.979186 -10 ********** Masking position 6 Map Score: 12.9828 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 74 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 CTCCCAAGAACTGGCCATGTACCGGGAATT 4 36 0 CTGGCCATGT 0.787081 -265 CATAGCGGGGCTTGCCATGGAGGGTCCAGG 4 73 1 CTTGCCATGG 0.969408 -228 ATTTGCCATGGTACTTAATAG 7 77 0 TTTGCCATGG 0.626161 -11 ACAAATGTTTCTGGCCAAGGGACAGGGGAA 8 24 1 CTGGCCAAGG 0.944784 -186 CCCCGTTTTGCTGGCGATCGGCCGTTGACC 8 151 1 CTGGCGATCG 0.902697 -59 AAGGCTGAAGCTGGCTATGGTCAAAATTGC 9 77 0 CTGGCTATGG 0.953525 -50 ATGATAACCACTGGCGATCGCCGCTTCT 13 9 0 CTGGCGATCG 0.902697 -292 GGCCTAGAACCTGGCCAAAGTGCTGGACCT 18 157 1 CTGGCCAAAG 0.80156 -127 CGGAGTTGACATTGCCATGGGAAAACTTTT 18 261 0 ATTGCCATGG 0.626161 -23 CTTTGGGCTTCTGGCGATGGCATTACTCC 20 10 0 CTGGCGATGG 0.970187 -109 AAACTCCCCCCGGCCATAGTGACTCAGGG 22 10 1 CCGGCCATAG 0.676963 -85 AACTTTTCTTGCTATGGTGCTCAATTT 25 50 0 CTTGCTATGG 0.891477 -17 TAATGGGACCGTGGCCAAGGGTTAGCGACT 35 167 1 GTGGCCAAGG 0.572736 -113 GCAAGCGCAACTTGCCATAGGCTAACTTCT 36 27 0 CTTGCCATAG 0.882083 -271 GGTGTAAAGACTGGCTATGGGAATTTATTG 41 266 0 CTGGCTATGG 0.953525 -35 TGTTTTTGCCCTTGCCATAGATTTTT 42 205 1 CTTGCCATAG 0.882083 -16 TTATAGACCACTGGCGATCGGCATGGTAAC 48 82 1 CTGGCGATCG 0.902697 -120 AAGTCCTAATCTTGCTCTGGCATGGAAGTT 77 101 1 CTTGCTCTGG 0.479545 -200 ********** Masking position 5 Map Score: 13.1394 Number of sites scoring better than the average of aligned sites = 1598 Number in coding regions = 1446 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 9 GGATACTATGCCGACACCCCTATTAAATCA 1 28 1 CCGACACCCC 0.919973 -143 AAAGGGGACAACTCAGGAAGGGTT 6 118 0 GGGACAACTC 0.754527 -14 AATCGGGGAGGGGACTCCCCTGGAGTTCTC 7 43 0 GGGACTCCCC 0.952458 -45 TATCGGTAGTGGGCCAACCCGGAAGAAGAA 18 54 1 GGGCCAACCC 0.945369 -230 AGTATGACACGGGAAAACCCTGCCATTCAG 19 241 0 GGGAAAACCC 0.753146 -60 GATGTCCGTTGCGACACCCCTCCTCGACCG 23 212 1 GCGACACCCC 0.885622 -66 AACGCAACGGCGGACTACCCATATTCTATT 24 40 0 CGGACTACCC 0.956316 -29 CTCAACCGCTCGGCCAACCCTGGTAA 27 7 0 CGGCCAACCC 0.962544 -294 TTTTGTAGCCCTGACAACCCGGCGATCGCC 34 15 1 CTGACAACCC 0.843239 -99 CTCAGATGGGCGGCAACCCCGTAAGATTGG 39 110 1 CGGCAACCCC 0.792141 -55 TAAGATCCGACGGACTACTCTTCAGCTTCC 42 169 0 CGGACTACTC 0.701525 -52 TTAAAAACCCCGGCCTCCCCCTCCCCCAAC 46 224 1 CGGCCTCCCC 0.948147 -35 ATCGAAAAAACTGACATCCCACGAACATAG 53 17 0 CTGACATCCC 0.629608 -179 TCTCCCTTGACGGACTTCCCGTAACTACGA 68 148 0 CGGACTTCCC 0.873409 -153 GACAGACAAGGGGACACCCCCTCTCTTCGC 79 126 0 GGGACACCCC 0.975243 -134 ********** Masking position 3 Map Score: 12.0474 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 270 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 GGCAATGAGTATATCCAAAAGAACGAAGTAC 2 56 1 ATACCAAAAG 0.693971 -180 AAATCGACAAATAAACAAAAATTGCTCTAAA 4 263 0 ATAACAAAAA 0.64209 -38 ACTCGGCGTTTTATCCAAAAAATAGACCATT 6 37 0 TTACCAAAAA 0.604745 -95 GTATGGAAAAATACCCAAAAACAACGCCGCG 12 145 0 ATACCAAAAA 0.943545 -89 ATCAGTTTGCATCCCCAAAAATTATCCC 25 8 0 ATCCCAAAAA 0.693971 -59 TTCAGTCAGAACAACCAAAAATTTGATTCGT 27 93 0 ACACCAAAAA 0.909929 -208 CTACAGCCGCATAGCTAAAAAGATACCCAAA 33 40 1 ATACTAAAAA 0.545292 -261 AGCTAAAAAGATACCCAAAAAATCAATATCA 33 52 1 ATACCAAAAA 0.943545 -249 CACTCTGCAAATAGCCAAAAACTGATCACCA 35 216 1 ATACCAAAAA 0.943545 -64 AATTTTCTTGATATACAAAAATTCGCTTTTG 36 173 0 ATAACAAAAA 0.64209 -125 ACCTGTGCCCACATCAAAAAAACAGACGGGG 41 234 0 ACACAAAAAA 0.646833 -67 CCATAGTTACAGCCAAAAAAGAAGGAAAA 46 9 1 ACACCAAAAA 0.909929 -250 CGCAGAGTCTATAGCAAAAAAAATCTAGCTT 54 187 0 ATACAAAAAA 0.751865 -114 ATAATCAAAAACAACCAAAAACCAACTATTT 60 65 0 ACACCAAAAA 0.909929 -68 CAAGCAAGCGATATCAAAAAATTACTACCTA 71 31 0 ATACAAAAAA 0.751865 -70 *** ******* Masking position 7 Map Score: 7.5667 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 11 TCCATAACCTCCACTAAGGCTGAAGCTGGCTA 9 90 0 CCACTAGCTG 0.817411 -37 GCCTAGGATGCCACTAGGATTGTATCGGCCAT 14 155 1 CCACTAGTTG 0.863819 -87 CACCATTGTCCCCCCATTTTTCCGCAGGGGTA 14 191 0 CCCCCATTTC 0.713993 -51 CAGAAGCAAACCCCTAGGCCTTCCCTTACATC 15 18 0 CCCCTAGCTT 0.808431 -95 CCCATGCAAACCCCTAAGTTTCTGTTAACCTG 17 184 0 CCCCTAGTTC 0.925092 -117 GCCCAAAGATCCCCTATGATTGGCGAAGAAAT 20 32 1 CCCCTAGTTG 0.974922 -87 GCTATATTTTCCCCTAGTACTGGGACTGGGTT 26 54 0 CCCCTATCTG 0.862879 -100 TGGCCAGGGCCCCCTAAGACTTCCTT 30 5 0 CCCCTAGCTT 0.808431 -79 AGCCATTAAGCCACTATGCCTGCATTTTTGTA 35 54 1 CCACTAGCTG 0.817411 -226 ATTACTTTGTCCCCCATCGTTGCTTTCGGCCC 36 206 1 CCCCCACTTG 0.741834 -92 AGAAAAAACTCCCCCAGGATTGAACCAAGGAG 39 77 0 CCCCCAGTTG 0.971643 -88 GGGCGGCAACCCCGTAAGATTGGGAAGATTAG 39 117 1 CCCGTAGTTG 0.706811 -48 GAGTGACAGTCCCCCAGTATTGCGGTCGCTTT 41 20 0 CCCCCATTTG 0.887116 -281 AAAACAATCATCCCTAAGATTGATAAACTGGG 46 36 1 TCCCTAGTTG 0.821047 -223 ATAGACTTAGCTACTAGGGTTGGTCGGGACCT 74 31 1 CTACTAGTTG 0.330529 -32 CCTAATATGACTCCCAAGTCTGAAATCTGAGC 76 236 1 CTCCCAGCTG 0.653047 -65 CTAGCGAGATCCCCTACTCTTTGAAGAGCTTT 77 160 0 CCCCTATTTT 0.578308 -141 ATTTTCATAACCCCTATTTTTGTCTAGAAGCA 78 47 1 CCCCTATTTG 0.899157 -254 CAAAAGGTTTTCCCCATGCTTCCCCTAACAAA 78 84 0 TCCCCAGTTC 0.56228 -217 AGTCTGGGGATCCCCAGGATTCAAAGAGCGAT 79 190 0 TCCCCAGTTC 0.56228 -70 ****** * *** Masking position 11 Map Score: 12.3421 Number of sites scoring better than the average of aligned sites = 864 Number in coding regions = 635 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 12 TGATAACTGTGTAATCTGGAATTTTTGTCAGATACCCTCA 17 137 1 GTGGTTTTCA 0.978872 -164 GCACATCCAAGCTTTCGGGTGTTTCTGCCACAGGCGGAAA 27 228 1 GTGGTTTTCA 0.978872 -73 GGCAAAAAAGAATTGCGGAATTTGTGACAAGTTTGTTCC 28 10 1 GTGGTTTTCA 0.978872 -95 TGAATCTAATGTTGTTAGGACTATTTTTCAGGAGCGCAAT 32 104 0 GTGGTATTCA 0.867003 -197 AATTTCCTGGGTAATTTGGCTTTTGTAACAAAATATTACA 35 82 0 GTGGTTTTCA 0.978872 -198 TGCTAACTTTGGTCTAAGGTATCTCTCTCAGCCTCACCCA 38 25 0 GTGGTCTTCA 0.906208 -108 AACTTAGGAGGATTTATGGCTCTTGTACCA 40 279 1 GTGGCTTTCA 0.89717 -20 TTATCTGGAGGCTCTTATGTCTTTTTTTCATACTAGAAAA 50 223 1 GTTGTTTTCA 0.784968 -78 TAGAGGGGTTGCTTTTCGGGCTTTTTTTCGTTGTTTTCAA 57 54 1 GTGGTTTTCG 0.89717 -247 GTCTTAAGAAGCCCTGTGGCTTTTTTAGCAGTAGCATCGT 68 243 0 GTGGTTTTCA 0.978872 -58 TTATTTCAAAGAGCTAAGGCTTTTCTCGCAACATTTTGCG 77 36 0 GTGGTTTTCA 0.978872 -265 * * ** *** * ** Masking position 14 Map Score: 10.8949 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 11 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 ATGCTTCCCCTGTCCCTTGGCCAGAAACATTT 8 26 0 TTCCCTGGCC 0.660944 -184 GGGTTTGATGACCCCATTGGCCTAGGGAGAAA 11 25 0 ACCCATGGCC 0.974039 -87 CTCTACACCTACCCCATCGGGCATTGTTAAGG 13 114 0 ACCCACGGGC 0.965252 -187 AACAGAAGCAAACCCCTAGGCCTTCCCTTACA 15 20 0 ACCCCAGGCC 0.742387 -93 GGTAACCCAAAGCCCCCTGGGCACCCAGGTAA 16 71 1 ACCCCTGGGC 0.944878 -95 CCCCGATTTTAACCCAACGGCCGCCAGACCGT 17 225 0 ACCCACGGCC 0.973514 -76 CCCAGGGGGGATCCCAATGGGCTTTAAACTGG 18 109 1 ACCCATGGGC 0.965939 -175 TCAGGATTAAACTCCGTTGGCCCATCCCGGCC 19 209 1 ATCCGTGGCC 0.803809 -92 AAACTCCCCCCGGCCATAGTGACTC 22 4 1 CCCCCCGGCC 0.764202 -91 CCCCGGTCTTTCTCCAACGGTCAGCCAGCTAT 31 78 0 TTCCACGGTC 0.439004 -63 TGTTGGGTTAACCCCACTGTGCCATTCGGTAA 33 131 0 ACCCATGTGC 0.584445 -170 GTGGAATTTTACCCCAATGGCCACCGGCGATC 42 18 0 ACCCATGGCC 0.974041 -203 TTGGGGTAAAATTCCACCGGTCTGGGTTAGGG 42 33 1 ATCCACGGTC 0.758846 -188 TATCCTACCATGCCCGCCGGGCAAGCTTGCAT 42 111 1 TCCCGCGGGC 0.685793 -110 CTCTGACTACAATCCAGTGGTCTGGTGATGGT 43 26 0 ATCCATGGTC 0.762601 -139 TAACTAGATCACTCCATTGGGCAACGGCGTTA 48 143 1 ATCCATGGGC 0.90742 -59 CTCTGCGAGAAACCCAATGGCCCATTTTAAAT 54 211 1 ACCCATGGCC 0.974041 -90 * **** ***** Masking position 9 Map Score: 15.7006 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 488 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 14 CCCAATCCACCAGAGTTCCATATTACTGGTAAAT 14 69 0 CGTTCCTATT 0.888938 -173 ACGAAGTTGACACTTTTCCTTATTT 15 98 1 CCTTCCTATT 0.87327 -15 TCCGGCTTCCCTATTCTGTTGAATA 21 2 1 CGTTCCTATT 0.888938 -174 GGCGGACTACCCATATTCTATTTTGCCCCGCCAT 24 28 0 CATTCTTTTT 0.648642 -41 TCACAAATTCCGCAATTCTTTTTTGCC 28 4 0 CCTTCTTTTT 0.849234 -101 TTTTTCAACCCAGAATTCTGTTTGCTTTCTTTGA 37 21 1 CGTTCTTTTG 0.718982 -40 TTGCGATAAGCGAGGTTCTTTTTTTGGAGGGGGA 50 38 1 CATTCTTTTT 0.648642 -263 TCAAAGTTCTCTCTGTTCTCTTTTCTTCCTATAT 57 90 1 CCTTCTTTTT 0.849234 -211 TCAAATTATCCTCGATTCTCTATTGTAATTGGAT 57 136 1 CCTTCTTATT 0.901995 -165 GTTTCCTCTCCCGCTTTCCTTATGCCAGGCTGCA 63 44 0 CGTTCCTATG 0.757862 -257 TATGAAATTGCTCTTTTCTTTATTATTAGTTTCC 63 72 0 CCTTCTTATT 0.901995 -229 ACTATCCTCGCCACCTTCTCTATTTTCTACAGGC 65 86 0 CATTCTTATT 0.751019 -46 GACTATACGTCAGGCTTCTGTTTTTGTAAAAAAC 66 203 0 CGTTCTTTTT 0.867423 -98 TTTAGAAGAACTGGTTTCTCTATTCAGAGGAGAC 70 94 1 CGTTCTTATT 0.91446 -207 TTCCTCACATCACCCTTCTATATGAGTCTAATAG 73 120 0 CCTTCTTATG 0.782559 -139 TGGGGATCCCCAGACTTCCTTATTGGGGAGGGTA 79 206 1 CGTTCCTATT 0.888938 -54 * * **** **** Masking position 7 Map Score: 9.35988 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 30 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 AGAAAATTCTCAAATAAACAGGATTT 5 67 0 TTCTCAAATA 0.924725 -16 CCAGAAACATTTGTCAAATAGGGGCTT 8 8 0 TTGTCAAATA 0.745381 -202 AAATTTCTCAAATAGGAAAAAACT 17 287 0 TTCTCAAATA 0.924725 -14 ACTGGAAAGGTTGTCAAAAATTCGCACATC 27 205 1 TTGTCAAAAA 0.633164 -96 CTTTGACCAATTCTCAAAAATT 37 49 1 TTCTCAAAAA 0.878683 -12 TCAAAAAGCTTTCTCAAATAGTTTACTATA 63 250 0 TTCTCAAATA 0.924725 -51 GACATGTTATTTCTCTAATAATTAACCAAT 68 112 0 TTCTCTAATA 0.830311 -189 AAAATAAAATTTCTCTAAAAGAAGATTGCA 76 88 1 TTCTCTAAAA 0.742598 -213 TTGAAGAGCTTTCTCAAAAACCTAGTCACC 77 142 0 TTCTCAAAAA 0.878683 -159 TTATCGTCTTTTCTCAATTAGCCTTCCGCG 78 181 0 TTCTCAATTA 0.609511 -120 AAAAACCTTTTTCTCTAATATACTTTCGTG 79 46 1 TTCTCTAATA 0.830311 -214 ********** Masking position 7 Map Score: 5.86259 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 19 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274