AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_synecho_ctra_300.orf -o110_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 RCY37834 300 Synechocystis #2 RCY04306 300 Synechocystis #3 RCY15530 257 Synechocystis #4 RCY50074 106 Synechocystis #5 RCY22351 217 Synechocystis #6 RCY16359 57 Synechocystis #7 RCY37028 61 Synechocystis #8 RCY30977 165 Synechocystis #9 RCY07893 147 Synechocystis #10 RCY44389 59 Synechocystis #11 RCY35764 206 Synechocystis #12 RCY36190 150 Synechocystis #13 RCY49047 96 Synechocystis #14 RCY44729 201 Synechocystis #15 RCY10129 213 Synechocystis #16 RCY17386 35 Synechocystis #17 RCT00127 206 Chlamydia_trachomatis #18 RCT00187 300 Chlamydia_trachomatis #19 RCT00189 215 Chlamydia_trachomatis #20 RCT00190 82 Chlamydia_trachomatis #21 RCT00362 68 Chlamydia_trachomatis #22 RCT00363 300 Chlamydia_trachomatis Motif number 1 CAGTGCCACAGAAAAATACCGCCCTTTTTAGAAA 1 52 0 GAAACCGCCC 0.962578 -249 ATTTTTCTGTGGCACTGTCCTCACGCTCGCGCGC 1 69 1 GCATCCTCAC 0.470236 -232 ACAGGAATCCGCAACTCCCTCCCTAACTCTCTTT 1 165 1 GAATCTCCCT 0.785556 -136 GGTCTCCGCCGCAATAATCCCCCTTGGGGGAAAA 2 239 1 GAAACCCCCT 0.980477 -62 GTAGTTCCTTGGCATTTTCCCCCAAGGGGGATTA 2 253 0 GCATCCCCCA 0.948191 -48 AAAATGCCAAGGAACTACCGCCAACGATGAGGAG 2 269 1 GAATCGCCAA 0.74862 -32 GAAATTTCAGGTAAATCACGCCCCACTGGATTGC 3 149 1 GAATCGCCCC 0.983555 -109 GTGACGATTTGTAAAAATCCGCCCAATTTTTAAA 3 216 1 GAAACCGCCC 0.962578 -42 GTCGAGGGCAGTTAGACCCCTCCCAACC 4 5 0 GTAACCTCCC 0.802684 -102 ATAATTGTCAGTAAGTGTCGCCCCCGTAATCCGT 5 38 0 GAATCGCCCC 0.983555 -180 AAAATCCGGGGCCAAACCCCGCCAGTGTTGATAA 5 102 0 GCAACCGCCA 0.799877 -116 CAATGACGCTGATACTTTCCCCCCATGGTAGTGG 5 166 0 GTATCCCCCC 0.966986 -52 GCAGAATGGAGCAACAAGCGCCCTTTGCTTAATC 6 13 1 GAAACGCCCT 0.962268 -45 TAAAAAAGCAGAAAAATTTCCCCATAGGTAGAAA 7 21 0 GAAATCCCCA 0.663753 -41 ACCTAGACCAGCAAGTTTCGCCATTAAACAAATA 8 72 0 GAATCGCCAT 0.779681 -94 AGGCGTGGGGGCAACTCAACCCCAAACCTGTATC 11 31 0 GAATACCCCA 0.68613 -176 TTAGTTTTCAGGAAAATTCCCCCTAGATTTAGTT 11 72 1 GAAACCCCCT 0.980477 -135 GTATAGAATTGTTAATGGCCTCCCGTTTTCCCTT 11 132 1 GTATCCTCCC 0.818346 -75 ATTTTTCAATGAAAAAAACGCCCTCTTCTCTTGA 22 198 0 GAAACGCCCT 0.962268 -103 * ** * ****** Masking position 4 Map Score: 21.9256 Number of sites scoring better than the average of aligned sites = 1366 Number in coding regions = 1215 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 2 CCAAGACTACGGAGGGGGCAATGAAGTTTC 1 257 0 GGAGGGGGCA 0.982741 -44 AATAATCCCCCTTGGGGGAAAATGCCAAGG 2 251 1 CTTGGGGGAA 0.919135 -50 TGGCGATCGGGGCAAGCTCAAGCC 3 5 1 GATCGGGGCA 0.980274 -253 TGCCGTCAACGATGGGAGAATTCGGCTTGA 3 28 0 GATGGGAGAA 0.722003 -230 CACGACTGTGGATGGGGGAAGCAACCATCT 3 73 1 GATGGGGGAA 0.973116 -185 CTGCCACTACCATGGGGGGAAAGTATCAGC 5 163 1 CATGGGGGGA 0.905245 -55 CAATGGAATCGGACTGGGCAATGACGCTGA 5 188 0 GGACTGGGCA 0.850986 -30 CCCAGGGAGGCGTGGGGGCAACTCAACCCC 11 42 0 CGTGGGGGCA 0.987539 -165 GCAACTAAATCTAGGGGGAATTTTCCTGAA 11 78 0 CTAGGGGGAA 0.854971 -129 GATCTAGAAAGGTCGGGGAAAACGTATAGA 11 109 1 GGTCGGGGAA 0.976562 -98 AAGGTGTAATGAACTGGGCAGACTTTCTAG 15 187 1 GAACTGGGCA 0.781711 -27 CTTTGGTTATCGTCGGGGCAGGTTTATGCG 18 132 1 CGTCGGGGCA 0.982819 -169 ********** Masking position 10 Map Score: 14.0629 Number of sites scoring better than the average of aligned sites = 1354 Number in coding regions = 1245 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 3 CCCGGACTTTCCTCAGATTCCCTGTGACAGGAAT 1 139 1 CCAATCCCTG 0.666562 -162 GCCCTTCACTCCTCATCGTTGGCGGT 2 285 0 CTCCTCTCAT 0.635758 -16 AGGGGTTGAACGTCCGCTACCCTTAGAACTGTGA 3 186 1 CCCCTCCCTT 0.988826 -72 AATTTAGAATCTGCCACTACCATGGGGGGAAAGT 5 153 1 CCCCTCCATG 0.975793 -65 TTGAGTTGCCCCCACGCCTCCCTGGGTTAGTTTT 11 46 1 CACCCCCCTG 0.769 -161 ATTAGCCTAGCCGCCCCTGTCCAGTGAAGGTGTA 12 26 1 CCCCTTCCAG 0.903137 -125 GTAGCTGGCTTTACCACTCCCCTTACTTTCGGCA 12 57 1 TCCCTCCCTT 0.92675 -94 ATGTTCCCGTCCACCGCTACCAATAACTGCCACT 14 62 1 CCCCTCCAAT 0.803903 -140 CTACCAATAACTGCCACTTTCATGGACTGTAACC 14 78 1 CCCCTTCATG 0.889782 -124 GTTCATCGGACTAAATCTACCCTTTTTGAGGATA 15 18 0 CAACTCCCTT 0.71119 -196 TTCATTACACCTTTAACTACCATGGTCTTAATTA 15 166 0 CTACTCCATG 0.720543 -48 TATCCCCTATCCTGTCATTAGTAT 17 193 0 TCCCTTCCTG 0.852136 -14 CCTTTAAACGCCCTCTCTTCTCTGTCACTCAATC 18 165 1 CTCCTCTCTG 0.944941 -136 CAATCTAAAGCCTCAACTCTTCTGCATATCTCTT 18 194 1 CCACTTTCTG 0.683077 -107 CATCATTAAACGTTCTCTTCTCTTCAAGAGAAGA 22 175 1 CTCCTCTCTT 0.882986 -126 ATGAAAAAAACGCCCTCTTCTCTTGAAGAGAAGA 22 190 0 CCCCTCTCTT 0.959394 -111 TTTCTATTTCTTTTCTCTTCCCTGTGTGTATGAT 22 233 1 TTCCTCCCTG 0.901868 -68 * ** ** ***** Masking position 8 Map Score: 13.1832 Number of sites scoring better than the average of aligned sites = 1884 Number in coding regions = 1745 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 4 CACGCTCGCGCGCACTGGGCGTTACCCAGC 1 90 1 CGCACTGGGC 0.968153 -211 AAAGGCCAAACTTGCTGGGTAACGCCCAGT 1 103 0 CTTGCTGGGT 0.711492 -198 CCCAAGACTACGGAGGGGGCAATGAAGTTT 1 258 0 CGGAGGGGGC 0.964975 -43 TTTTAGGATTCTGTGGGGGTTTGCTTTTGT 2 81 1 CTGTGGGGGT 0.797618 -220 TGGCGATCGGGGCAAGCTCAAGC 3 4 1 CGATCGGGGC 0.764416 -254 ATTATCAACACTGGCGGGGTTTGGCCCCGG 5 101 1 CTGGCGGGGT 0.962381 -117 CCAATGGAATCGGACTGGGCAATGACGCTG 5 189 0 CGGACTGGGC 0.985615 -29 TAAGTTTTTTCTGACTGGGCCAGCCCCACT 9 58 1 CTGACTGGGC 0.968764 -90 GCCCCCACGCCTCCCTGGGTTAGTTTTCAG 11 53 1 CTCCCTGGGT 0.78518 -154 CCAAACGTTTCGGGCTGGGTTGCCGAAAGT 12 81 0 CGGGCTGGGT 0.979915 -70 ATCTTTTCTACGCACGGAGTAAAAACATCT 19 12 0 CGCACGGAGT 0.808567 -204 ACCATTGAGTCGGAGTGAGT 21 59 1 CGGAGTGAGT 0.740441 -10 ********** Masking position 1 Map Score: 8.57395 Number of sites scoring better than the average of aligned sites = 863 Number in coding regions = 802 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 TAATTGAAACTTCATTGCCCCCTCCGTAGTCTTG 1 252 1 TTCTCCCCTC 0.774282 -49 CTCGAAACTATGCGTTTCCCCCGGAGAATTTTAG 2 53 1 TGCTCCCCGG 0.962841 -248 ATTAAGTTTGTTGATGGTCTCCGCCGCAATAATC 2 224 1 TTGTTCCCGC 0.972101 -77 TTTCAGATGGTTGCTTCCCCCATCCACAGTCGTG 3 73 0 TTGTCCCATC 0.727107 -185 CCTCACACAATTCTTCCTCTCAGGATAACTGCTC 3 112 1 TTCTTCCAGG 0.881569 -146 CACGCCCCACTGGATTGCCTCAGGGGTTGAACGT 3 165 1 TGGTCCCAGG 0.952665 -93 GTGGAAAAGTTTGATCGACCCAGGCCACGGAACT 4 74 0 TTGTACCAGG 0.772183 -33 CCCGCCAGTGTTGATAATCCCCGGGGATGGGTAA 5 85 0 TTGTTCCCGG 0.978769 -133 CCCCGGATTTTTGGCGATCGCCGGTTGTAATTTA 5 125 1 TTGCTCCCGG 0.954982 -93 TAATTACTGGCCTCCCTCAGCCAAAGAACTT 8 145 0 TGGCCCCAGC 0.875002 -21 GCAATAGCAATGGCTCACCTCCGGCGATCGAACT 14 11 1 TGGTCCCCGG 0.982708 -191 CCAAAGTATGTTCCCGTCCACCGCTACCAATAAC 14 55 1 TTCCCCCCGC 0.931467 -147 TTGACTGGAGTTATTTATCTCCGCCCCCCCACTT 14 175 1 TTATTCCCGC 0.752733 -27 GGGAGTTACTTTGGTTATCGTCGGGGCAGGTTTA 18 124 1 TTGTTCTCGG 0.73728 -177 *** * ** **** Masking position 1 Map Score: 10.5821 Number of sites scoring better than the average of aligned sites = 1155 Number in coding regions = 1078 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 CTTTGGGAAGCCCGGACTTTCCTCAGATTCC 1 129 1 CCCGACTTTC 0.989863 -172 GCAACTCCCTCCCTAACTCTCTTTTTCTAGT 1 175 1 CCCTACTCTC 0.930239 -126 ATACGTTTTCCCCGACCTTTCTAGATCTGCA 11 105 0 CCCGCCTTTC 0.985009 -102 CTTTCCCAACTTTCCATTAGCCTA 12 4 1 TCCCACTTTC 0.948151 -147 TTTACCACTCCCCTTACTTTCGGCAACCCAG 12 66 1 CCCTACTTTC 0.977445 -85 TCCAGTCAACTCCGGCCATTCTGTTAATCTT 14 153 0 TCCGCCATTC 0.788189 -49 TATCTCCGCCCCCCCACTTTCC 14 190 1 CCCCACTTTC 0.985302 -12 **** ****** Masking position 10 Map Score: 4.75628 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 50 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 CCACACTGCCCAACCTAGAAAAACTGTATTC 2 136 1 CAACCTAGAA 0.72874 -165 AAAGTTTGATCGACCCAGGCCACGGAACTTA 4 72 0 CGACCCAGCC 0.984775 -35 GTTCAGACTACAACCTAGACCAGCAAGTTTC 8 87 0 CAACCTAGCC 0.961214 -79 TTACCGTAACCAACCCAACACCAACTACATC 9 30 0 CAACCCAAAC 0.941431 -118 GGGGGCAACTCAACCCCAAACCTGTATCAAT 11 28 0 CAACCCCAAC 0.873602 -179 ACCGGGGGTTCGACCAAAAACAAGCTCTCTC 11 172 0 CGACCAAAAC 0.817304 -35 TTACTTTCGGCAACCCAGCCCGAAACGTTTG 12 79 1 CAACCCAGCC 0.989112 -72 ATCGAACTAACGACCAAGCCAAAGTATGTTC 14 37 1 CGACCAAGCA 0.813809 -165 TAACTCCAGTCAACTCCGGCCATTCTGTTAA 14 157 0 CAACTCCGCC 0.773386 -45 AAGCAAATTACAACCAAGTACAGTCGTAGTT 15 49 0 CAACCAAGAC 0.957023 -165 ******** ** Masking position 3 Map Score: 6.12094 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 447 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 TTTTGGCACAAAAGCAAACCCCCACAGAAT 2 88 0 AAAGCAAACC 0.923295 -213 GCAGTGTGGGAAGGCAAATTGAGGCAATTT 2 115 0 AAGGCAAATT 0.860415 -186 TATTGTCGCAAAAGCAGACTAAAACAGCAT 2 171 0 AAAGCAGACT 0.891066 -130 GTTGACGGCAAAGGCAGATCTAAACCACGA 3 48 1 AAGGCAGATC 0.739237 -210 ACTAAGGTTAAGAACAGATTAAGCAAAGGG 6 33 0 AGAACAGATT 0.457237 -25 CCATAAAAATAGAGCAAATTCTAGATGTTC 8 114 0 AGAGCAAATT 0.872224 -52 GGCCGATAGTTAAGCAAATTACAACCAAGT 15 61 0 TAAGCAAATT 0.673211 -153 ACCCATAAAGAAAGCAAATTAAACAACAGC 19 192 0 AAAGCAAATT 0.946768 -24 AAGGATTTCTAAAACAAACTCATGTTTCGA 20 21 1 AAAACAAACT 0.763593 -62 CTACAATAACAAAGCAAACTACAAGTTAAA 22 30 0 AAAGCAAACT 0.936028 -271 TAACTCATGAACAGCAAATCATACACACAG 22 254 0 ACAGCAAATC 0.753173 -47 AGAAACAAGGAAAACAAATCTA 22 289 1 AAAACAAATC 0.763593 -12 ********** Masking position 6 Map Score: 5.6127 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 306 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 TGGGCGTTACCCAGCAAGTTTGGCCTTTGGGAAG 1 105 1 CCACAATGGC 0.87517 -196 AAGGCAAATTGAGGCAATTTTGGCACAAAAGCAA 2 101 0 GAGCAATGGC 0.875166 -200 GTCTGCTTTTGCGACAATACTGACCAAGGTTATG 2 182 1 GCGCAATGAC 0.970468 -119 CAAGGAACTACCGCCAACGATGAGGAGTGAAGGG 2 276 1 CCGCAATGAG 0.986679 -25 TCTGCCTTTGCCGTCAACGATGGGAGAATTCGGC 3 32 0 CCGCAATGGG 0.987692 -226 CCCCCGTAATCCGTCAACAGTGACCGTCACCCCA 5 18 0 CCGCAATGAC 0.986679 -200 ATTAAACAGTCCGCTAATTCTGAGTTAAATTTCC 9 115 1 CCGTAATGAG 0.927557 -33 TCCGGCCATTCTGTTAATCTTGAGAACGGCTAAT 14 140 0 CTGTAATGAG 0.588453 -62 TAAATAACTCCAGTCAACTCCGGCCATTCTGTTA 14 158 0 CAGCAACGGC 0.767194 -44 TACGAATGTAGCGCCAAGTATGAGACGAACTAGA 20 51 0 GCGCAATGAG 0.970468 -32 *** *** **** Masking position 7 Map Score: 5.37427 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 378 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 GTCCGGGCTTCCCAAAGGCCAAACTTGCTGGG 1 114 0 CCCAAAGGAA 0.896948 -187 TCCTAAAATTCTCCGGGGGAAACGCATAGTTT 2 57 0 CTCCGGGGAA 0.929842 -244 TGGCATTTTCCCCCAAGGGGGATTATTGCGGC 2 246 0 CCCCAAGGGA 0.957117 -55 AGCAGTTATCCTGAGAGGAAGAATTGTGTGAG 3 113 0 CTGAGAGGGA 0.69813 -145 ACTGGATTGCCTCAGGGGTTGAACGTCCGCTA 3 173 1 CTCAGGGGGA 0.970353 -85 TGTTGATAATCCCCGGGGATGGGTAAACCATG 5 79 0 CCCCGGGGGG 0.929765 -139 ATCGCCAAAAATCCGGGGCCAAACCCCGCCAG 5 111 0 ATCCGGGGAA 0.626432 -107 ATCTGCCACTACCATGGGGGGAAAGTATCAGC 5 161 1 ACCATGGGGA 0.672357 -57 GAAAAATTTCCCCATAGGTAGAAAATTAATTA 7 13 0 CCCATAGGGA 0.921503 -49 CTCTCTCTTTCCCAAGGGAAAACGGGAGGCCA 11 147 0 CCCAAGGGAA 0.923226 -60 CAAAGTAACTCCCAGAGAAAGAAAGTAGCTTG 18 105 0 CCCAGAGAGA 0.797025 -196 CATAAACCTGCCCCGACGATAACCAAAGTAAC 18 128 0 CCCCGACGAA 0.702081 -173 TAGGAAACTACTCAAAGGAAGAGCTGAATATG 22 57 1 CTCAAAGGGA 0.896948 -244 ******** ** Masking position 12 Map Score: 5.16811 Number of sites scoring better than the average of aligned sites = 2071 Number in coding regions = 1841 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 11 GTCACAAACCACAGCGGCCTATGGCTCTAA 1 216 0 ACAGCGGCCT 0.979925 -85 TTCACTAAGTTCCGTGGCCTGGGTCGATCA 4 67 1 TCCGTGGCCT 0.966576 -40 GGATGGGTAAACCATGGCCTAGAATAATTG 5 65 0 ACCATGGCCT 0.96863 -153 TTTTCATCATACCGCTGCCTATTTAGCGCT 13 17 0 ACCGCTGCCT 0.954796 -80 ACCTTTAACTACCATGGTCTTAATTACCCT 15 162 0 ACCATGGTCT 0.87597 -52 AAATTAAACAACAGCCGCCTCTTTATGTAG 19 177 0 ACAGCCGCCT 0.917984 -39 TCACTCCGACTCAATGGTCTAACGGCAGGG 21 47 0 TCAATGGTCT 0.619778 -22 CTGATATTAAACAGTTGCCTAACGGATCAG 22 140 1 ACAGTTGCCT 0.931441 -161 ********** Masking position 10 Map Score: 3.80525 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 362 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 ACTATGCGTTTCCCCCGGAGAATTTTAGGA 2 59 1 TCCCCCGGAG 0.945432 -242 TTACCTGAAATTTCCCGGAGCAGTTATCCT 3 133 0 TTTCCCGGAG 0.798719 -125 ATTTCGCCGGAATCAGAATTTA 3 246 0 TTCGCCGGAA 0.850917 -12 AGTGTTGATAATCCCCGGGGATGGGTAAAC 5 83 0 ATCCCCGGGG 0.978359 -135 ATTTTTGGCGATCGCCGGTTGTAATTTAGA 5 131 1 ATCGCCGGTT 0.893034 -87 TTTTGGTCGAACCCCCGGTTAGGAGTAAAC 11 184 1 ACCCCCGGTT 0.766999 -23 CGTTAGTTCGATCGCCGGAGGTGAGCCATT 14 19 0 ATCGCCGGAG 0.988216 -183 GATTAACAGAATGGCCGGAGTTGACTGGAG 14 155 1 ATGGCCGGAG 0.932831 -47 TACTTTGGTTATCGTCGGGGCAGGTTTATG 18 130 1 ATCGTCGGGG 0.846986 -171 ********** Masking position 6 Map Score: 3.59558 Number of sites scoring better than the average of aligned sites = 940 Number in coding regions = 866 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 13 ACTTGCTGGGTAACGCCCAGTGCGCGCGAG 1 94 0 TAACGCCCAG 0.964702 -207 CAGGAATCCGCAACTCCCTCCCTAACTCTC 1 166 1 CAACTCCCTC 0.843457 -135 GCACAAAAGCAAACCCCCACAGAATCCTAA 2 83 0 AAACCCCCAC 0.82796 -218 ATAACCAAAGTAACTCCCAGAGAAAGAAAG 18 112 0 TAACTCCCAG 0.881736 -189 CGCAGCCTTTAAACGCCCTCTCTTCTCTGT 18 160 1 AAACGCCCTC 0.971157 -141 CTCTTGCGATTAACGCCTTGCTTGATTAAC 18 223 1 TAACGCCTTG 0.909224 -78 GTTAAACACATAACGCCTTGTATAA 22 6 0 TAACGCCTTG 0.909224 -295 TCAATGAAAAAAACGCCCTCTTCTCTTGAA 22 197 0 AAACGCCCTC 0.971157 -104 ********** Masking position 3 Map Score: 4.61468 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 105 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 GAAAGTCCGGGCTTCCCAAAGGCCAAACTT 1 120 0 GCTTCCCAAA 0.958078 -181 ATCCGCAACTCCCTCCCTAACTCTCTTTTT 1 171 1 CCCTCCCTAA 0.957838 -130 CCTCAATTTGCCTTCCCACACTGCCCAACC 2 121 1 CCTTCCCACA 0.958931 -180 TCAGATGGTTGCTTCCCCCATCCACAGTCG 3 75 0 GCTTCCCCCA 0.873299 -183 GCAGTTAGACCCCTCCCAACC 4 2 0 CCCTCCCAAC 0.894904 -105 TAATTACTGGCCTCCCTCAGCCAAAGAAC 8 147 0 GCCTCCCTCA 0.937997 -19 ATTTTATATGGCCTCCAAAAGTATTGTCGG 17 37 0 GCCTCCAAAA 0.852805 -170 ATAAAAAAAGCCTTTCCTAATTAAAATCTT 17 123 0 CCTTTCCTAA 0.633686 -84 ACGATCCTCTCCTTCCAAAATGTTTCCCTC 18 264 1 CCTTCCAAAA 0.84789 -37 ********** Masking position 4 Map Score: 4.34509 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 311 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 15 CCTAGCACCAATTTCCCAAGACTACGGAGG 1 272 0 ATTTCCCAAG 0.954055 -29 CAAGCTCTCTCTTTCCCAAGGGAAAACGGG 11 153 0 CTTTCCCAAG 0.983611 -54 CTTTCCCAACTTTCCATTAG 12 1 1 CTTTCCCAAC 0.968447 -150 CATAAAAGGCCTTTGCCAAGAGTGATAATT 19 84 0 CTTTGCCAAG 0.887549 -132 ********** Masking position 4 Map Score: 0.128672 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 23 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234