AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_synecho_ctra_100.orf -o294_synecho_ctra_100.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 RCY03061 131 Synechocystis #4 RCY19040 87 Synechocystis #5 RCY00322 209 Synechocystis #6 RCY33348 233 Synechocystis #7 RCY31503 112 Synechocystis #8 RCY45353 165 Synechocystis #9 RCY05245 300 Synechocystis #10 RCY02313 283 Synechocystis #11 RCY34249 175 Synechocystis #12 RCY23408 94 Synechocystis #13 RCY05831 277 Synechocystis #14 RCY50309 68 Synechocystis #15 RCY54010 66 Synechocystis #16 RCY48465 153 Synechocystis #17 RCY04930 300 Synechocystis #18 RCY20723 104 Synechocystis #19 RCY11903 300 Synechocystis #20 RCY08996 83 Synechocystis #21 RCY40124 140 Synechocystis #22 RCY00666 300 Synechocystis #23 RCY52274 113 Synechocystis #24 RCY53600 132 Synechocystis #25 RCY33958 164 Synechocystis #26 RCY50255 220 Synechocystis #27 RCY52021 164 Synechocystis #28 RCY26608 38 Synechocystis #29 RCY00135 42 Synechocystis #30 RCY33655 258 Synechocystis #31 RCY43486 300 Synechocystis #32 RCT00066 300 Chlamydia_trachomatis #33 RCT00068 66 Chlamydia_trachomatis #34 RCT00070 26 Chlamydia_trachomatis #35 RCT00071 195 Chlamydia_trachomatis #36 RCT00225 300 Chlamydia_trachomatis #37 RCT00227 16 Chlamydia_trachomatis #38 RCT00228 119 Chlamydia_trachomatis #39 RCT00230 300 Chlamydia_trachomatis #40 RCT00231 68 Chlamydia_trachomatis #41 RCT00232 27 Chlamydia_trachomatis #42 RCT00253 132 Chlamydia_trachomatis #43 RCT00281 167 Chlamydia_trachomatis #44 RCT00285 300 Chlamydia_trachomatis #45 RCT00405 132 Chlamydia_trachomatis #46 RCT00430 300 Chlamydia_trachomatis #47 RCT00507 100 Chlamydia_trachomatis #48 RCT00649 300 Chlamydia_trachomatis #49 RCT00738 300 Chlamydia_trachomatis #50 RCT00854 259 Chlamydia_trachomatis #51 RCT00776 22 Chlamydia_trachomatis Motif number 1 GGAGGGGACTCCCCTGGAGTTCTCCGCAAAGATAC 4 32 0 CCCCGATCCC 0.958658 -56 TAGATGCTTCCCCTGTCCCTTGGCCAGAAACATTT 5 26 0 CCCTCCTGCC 0.625171 -184 AACCAGGCGGCCCTGCGACAGCCCCAAGCTGTCCC 5 118 1 CCCTGAACCC 0.854556 -92 AGAAGCAAACCCCTAGGCCTTCCCTTACATCTCCC 7 14 0 CCCTGCTCCT 0.805695 -99 GTGTTCCCTGGCCCATGCAAACCCCTAAGTTTCTG 9 192 0 GCCCGCACCC 0.895465 -109 TTGTTCATTCCCCAAACAATCCGCCAAATCCT 10 8 0 CCCACATCCC 0.719701 -276 TGGGATCCCCCCTGGGCCATGAGCCCAGAAAAATT 10 90 0 CCTGCCTACC 0.424552 -194 CGACACCCCTCCTCGACCGTCATCCATGCTCCCTC 13 223 1 CCTCCCTACC 0.852747 -55 TTTATATTTCCCCCTCCATTTAACCATTCTGAGAA 19 66 1 CCCCCATACC 0.82694 -235 CAGTTAATAACCCTGACAGATCACTCCACCAGTTC 19 199 0 CCCTCAACCT 0.39753 -102 CCCAATGCCTCCTCCGGCAAGATTT 19 286 0 CCCAGCTCCC 0.917505 -15 TTTTAAACACCCCCGGTCTTTCTCCAACGGTCAGC 21 85 0 CCCCTCTCCC 0.823745 -56 CGTTGACCCCGCTTTGGCGATCGCCGGGTTGTCAG 23 25 0 GCTTGCACCC 0.484278 -89 ATTCTGGATTACCCCGGCGATCGCCACTGTCCCCG 23 82 1 ACCCGCACCC 0.897324 -32 TTAGCGTTTAGCTCCGCCGATCTCCC 24 117 1 GCTCCCACCC 0.705597 -16 GAAAAAACTCCCCCAGGATTGAACCAAGGAGGAGC 25 73 0 CCCCGATACC 0.835875 -92 ACCCCAATGGCCACCGGCGATCGCCTTCT 26 5 0 CCACGCACCC 0.71109 -216 AGGCATTGTACCCCTGGAGTGACCCCCGGTGGCTT 27 72 0 CCCCGATACC 0.835875 -93 AGTTATTTGCCCTTGTCCCTGCTCCGATTATCCCC 27 122 1 CCTTCCTCCC 0.906477 -43 ACCTTTCCCTACCCCCACCCTAACG 29 1 1 ACCTCCTCCC 0.813881 -42 ATTAAAAATCCCCCTGCCATGCTCTCCACTGAAAT 30 161 1 CCCCCCTCCT 0.913669 -98 CACTGAAATGCCCCTTCCAACCACCGGAAGCACCT 30 187 1 CCCCCCACCC 0.983857 -72 CTTATTAAAAACCCCGGCCTCCCCCTCCCCCAACC 30 220 1 ACCCGCTCCC 0.926895 -39 CCTCCCCCTCCCCCAACCAAAATCTTTTACCG 30 237 1 CCCCCCAACT 0.615706 -22 TTGTGCATACCCTGCAGCGTGCTCCGATTGGGTCT 31 81 1 CCTGGCTCCC 0.781675 -220 CTGGAAAAATCCTTCACCCTTAGCCCGGCTAATCC 31 266 1 CCTTCCTACC 0.680387 -35 TCGGCGCTAGACCCGGCCTATCGCCACATGGGATC 32 118 0 ACCCCCACCC 0.891299 -183 GACCAGCACCCCCTCTGAGTTCTCCCCCGAACCTG 39 18 1 CCCTGATCCC 0.895003 -283 AGGAGAGCATCCTTCTCCTTTCACCTATTGGTTAT 40 25 1 CCTTCCTCCC 0.906477 -44 TCGATCCTTTACCACGGCAACCTCCTTTAGAAATA 44 53 1 ACCAGCACCC 0.507727 -248 TCTTCGCTTCCCTCTAGAAATCTCTATATCGATAA 45 14 1 CCTCGAACCT 0.363267 -119 TAGCCTCTTTCCTCTAGCGAGATCCCCTACTCTTT 49 170 0 CCTCGCAACC 0.809685 -131 **** ** * * ** Masking position 2 Map Score: 36.325 Number of sites scoring better than the average of aligned sites = 3007 Number in coding regions = 2740 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 2 CCGTTTTGCTGGCGATCGGCCGTTGACCCA 5 153 1 GGCGATCGGC 0.53327 -57 TTTGCGGAACTGCGATCGGGAAATGTCATT 8 24 1 TGCGATCGGG 0.892377 -142 GGTTTTCGGTGGCGATCGGGCCTAGAACCT 10 139 1 GGCGATCGGG 0.881086 -145 GGGTAATCGGGGCGATCGCCTGCTAAACTG 17 179 1 GGCGATCGCC 0.499996 -122 GTATTTTTAGGGCGATCGCCGCTAAATCCG 21 20 1 GGCGATCGCC 0.499996 -121 CTGACAACCCGGCGATCGCCAAAGCGGGGT 23 25 1 GGCGATCGCC 0.499996 -89 GGATTACCCCGGCGATCGCCACTGTCCCCG 23 87 1 GGCGATCGCC 0.499996 -27 GGGAGATCGGCGGAGCTAAAC 24 122 0 GGAGATCGGC 0.871634 -11 AGAAGGCGATCGCCGGTGGCCATT 26 5 1 GGCGATCGCC 0.499996 -216 GATCCCATGTGGCGATAGGCCGGGTCTAGC 32 118 1 GGCGATAGGC 0.871634 -183 ********** Masking position 5 Map Score: 29.5403 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 3 TGATTTAATAGGGGTGTCGGCATAGTATCCC 1 27 0 GGGGTGCGGC 0.926084 -144 AACCCTTCCTGAGTTGTCCCCTTT 3 118 1 GAGTTGCCCC 0.960994 -14 GACTCCCCTGGAGTTCTCCGCAAAGATACAG 4 30 0 GAGTTCCCGC 0.868876 -58 GAGAACTCCAGGGGAGTCCCCTCCCCGATTC 4 43 1 GGGGAGCCCC 0.506863 -45 TTCTTCTTCCGGGTTGGCCCACTACCGATAA 10 53 0 GGGTTGCCCA 0.948036 -231 AAAGCCCATTGGGATCCCCCCTGGGCCATGA 10 103 0 GGGATCCCCC 0.881573 -181 CGGTCGAGGAGGGGTGTCGCAACGGACATCA 13 211 0 GGGGTGCGCA 0.810025 -67 AATAGAATATGGGTAGTCCGCCGTTGCGTTT 14 40 1 GGGTAGCCGC 0.890301 -29 TTACCAGGGTTGGCCGAGCGGTTGAGG 17 7 1 GGGTTGCCGA 0.886222 -294 GGCGAATTATGAGTTCGCTGCCTCAACCGCT 17 27 0 GAGTTCCTGC 0.632117 -274 TGAGGGTTCCCTCCCTGGATTGTT 20 70 0 GGGTTCCTCC 0.952496 -14 AAAATATGTTGGGTTAACCCCACTGTGCCAT 22 138 0 GGGTTACCCC 0.892521 -163 CAATCTTACGGGGTTGCCGCCCATCTGAGAA 25 108 0 GGGTTGCGCC 0.975505 -57 CAAGCCACCGGGGGTCACTCCAGGGGTACAA 27 71 1 GGGGTCCTCC 0.626327 -94 CACCCCCTCTGAGTTCTCCCCCGAACCTGCT 39 24 1 GAGTTCCCCC 0.937314 -277 CCTATTCGAGGGGTTGGCTCCTGTTTCTGAC 44 116 0 GGGTTGCTCC 0.970597 -185 GCGAAGAGAGGGGGTGTCCCCTTGTCTGTCG 50 126 1 GGGGTGCCCC 0.523793 -134 ****** **** Masking position 3 Map Score: 24.1546 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 408 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 CTAGGCCCTGGCCCCGTCGCTGTA 4 2 1 TGGCCCTCCC 0.978345 -86 ATGCTTCCCCTGTCCCTTGGCCAGAAACATTTG 5 25 0 TTCCCTTCCA 0.802699 -185 AACTGGTAGGTTGACCCAGACCCGTTGGAAAGG 6 32 0 TGACCCACCC 0.810408 -202 TTTGGGTATTTTTCCATACCCCCCGTGTCCGTA 6 157 1 TTCCATACCC 0.655684 -77 GTTCCGCAAATTTCCCCAACCCT 8 1 0 TTCCCCACCT 0.771545 -165 CGCCAGACCGTGTTCCCTGGCCCATGCAAACCC 9 203 0 TTTCCCTCCC 0.88001 -98 TAGGGGTTCGATTCCCCTCACCCGCTTTGGGTA 13 121 1 ATCCCCTCCC 0.883095 -157 TGGGACTGGGTTTGCCCTGCCCCATCGGTGAGA 16 33 0 TTGCCCTCCC 0.979342 -121 CCATCACTTTTTTCCCTTAGCCCAATAATTACC 16 95 1 TTCCCTTCCC 0.978958 -59 ACCCCGGCGATCGCCACTGTCCCCGAACAAAT 23 92 1 TGCCACTCCC 0.926052 -22 CCCATAAGGCTTTGACCTTTCCCGTCCCTTTTC 24 70 0 TTGACCTCCC 0.664826 -63 CGCTAAATTGTGGCCATTTTCCCATAAGGCTTT 24 90 0 TGCCATTCCC 0.839546 -43 TTTGCACGACTGGGCCCTAACCCAGACCGGTGG 26 46 0 TGGCCCTCCC 0.978345 -175 AACGATTGTTTTTGCCCTTGCCATAGATTTTT 26 199 1 TTGCCCTCCA 0.805666 -22 GGGAAGTTATTTGCCCTTGTCCCTGCTCCGATT 27 118 1 TGCCCTTCCC 0.977942 -47 ACCTTTCCCTACCCCCACCCTAACGA 29 4 1 TTCCCTACCC 0.941643 -39 CTAACGACCATCTCCCCTTACCC 29 30 1 TTCCCCTCCC 0.991099 -13 GAAAAATCCTTCACCCTTAGCCCGGCTAATCCA 31 269 1 TACCCTTCCC 0.831959 -32 TTTATGCTTCTCGCCCTAAGCCCTTCTGAGTTT 36 14 1 TGCCCTACCC 0.938939 -287 TAGGGAGGTTTATACCCTAACCTTTATTTTGCA 38 64 0 TTACCCTCCT 0.530725 -56 * ****** *** Masking position 11 Map Score: 24.0241 Number of sites scoring better than the average of aligned sites = 1238 Number in coding regions = 1076 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 5 TGAGAGGTTTGCCTTGCTAACA 1 159 1 GCCTTGCTAC 0.903806 -12 TCGCAGGGCCGCCTGGTTAGCAATGCGCTCA 5 105 0 GCCTGGTTAC 0.918065 -105 TAAAACCTTAGCCTTCCAAGCTAATGATAGG 13 94 1 GCCTTCCAAC 0.957915 -184 CGGGGCGATCGCCTGCTAAACTGGAAAGGTT 17 186 1 GCCTGCTAAC 0.965651 -115 TAAACTATCCGCCTGGAAAACGGCTTGCCAG 22 178 0 GCCTGGAAAC 0.812567 -123 TACCATGCCCGCCGGGCAAGCTTGCATTTTG 26 116 1 GCCGGGCAAC 0.815291 -105 GGGGTACAATGCCTGCTAATCTATGGGGAAG 27 93 1 GCCTGCTAAC 0.965651 -72 ACTGAAATGCCCCTTCCAACCACCGGAAGCA 30 188 1 CCCTTCCAAC 0.697093 -71 GCTTTGAGATGCCTTGTTAATCTAGAAATGG 31 49 1 GCCTTGTTAT 0.506472 -252 TAAGAAACAGCCTGCTAAACACAAGAGTCC 32 281 0 GCCTGCTAAC 0.965651 -20 CCAACGAAATGCCTTCTAAATCAAAAACTCA 36 40 0 GCCTTCTAAT 0.720269 -261 TAGAGCTGTAGCCTTCCAAGCTACCGGTGTC 48 177 1 GCCTTCCAAC 0.957915 -124 TCACTCAGATGCCTTGTTAACACATAAAAAG 48 269 1 GCCTTGTTAC 0.890242 -32 ********* * Masking position 9 Map Score: 10.2507 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 114 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 TCGGCATAGTATCCCCCTTGCAGAGATTGG 1 12 0 ATCCCCCTTG 0.558427 -159 CGGGGAGGGGACTCCCCTGGAGTTCTCCGC 4 40 0 ACTCCCCTGG 0.57815 -48 ATTTGCCATGGTACTTAATAG 4 77 0 TTTGCCATGG 0.648247 -11 ATGCTTCCCCTGTCCCTTGGCCAGAAACAT 5 28 0 TGTCCCTTGG 0.872993 -182 GGTAACCCAAAGCCCCCTGGGCACCCAGGT 8 71 1 AGCCCCCTGG 0.718203 -95 CGCCAGACCGTGTTCCCTGGCCCATGCAAA 9 206 0 TGTTCCCTGG 0.464923 -95 CCCATTGGGATCCCCCCTGGGCCATGAGCC 10 100 0 TCCCCCCTGG 0.835687 -184 TAGCAAAAGTTTTCCCATGGCAATGTCAAC 10 257 1 TTTCCCATGG 0.877589 -27 TAGGCTTGTTTTTCCCTGAGGGGCCTACTG 11 64 0 TTTCCCTGAG 0.650624 -112 CCAGCTATATTTTCCCCTAGTACTGGGACT 16 59 0 TTTCCCCTAG 0.954649 -95 CCATCACTTTTTTCCCTTAGCCCAATAATT 16 95 1 TTTCCCTTAG 0.868804 -59 GAACTCATAATTCGCCCTAGACAGGTTCAA 17 42 1 TTCGCCCTAG 0.780709 -259 GTTCAACTCCTGTACCCTGGACTTAAAACG 17 66 1 TGTACCCTGG 0.605081 -235 ACAGAGTTTATTTCCCAGTGGTAAGCGTGG 17 151 1 TTTCCCAGTG 0.332198 -150 ACAGGCGGAAATTCCCTTGGATGAAGGATA 17 257 1 ATTCCCTTGG 0.710202 -44 CCATGGCTATTTTCCCCTAGACTGGAGGGC 18 52 0 TTTCCCCTAG 0.954649 -53 TCCGGCAAGATTTACCCTAGCTTAAAGCAA 19 269 0 TTTACCCTAG 0.596142 -32 TCGTTGCAGGTTCCCCTTGGGTGCTATGGT 21 121 1 TTCCCCTTGG 0.900936 -20 TCCTTGACTTTTTCCTCTGGTTGATTAACT 22 211 1 TTTCCTCTGG 0.779671 -90 TTTTTGCGTTCCCCTGGGTGAGGCTGAG 24 9 1 TTCCCCTGGG 0.718903 -124 GTTTCTAAGTTTTGCCTTAGTAAAAACAAG 25 28 1 TTTGCCTTAG 0.629942 -137 AACGATTGTTTTTGCCCTTGCCATAGATTT 26 199 1 TTTGCCCTTG 0.735932 -22 GGCAAATAACTTCCCCATAGATTAGCAGGC 27 103 0 TTCCCCATAG 0.693227 -62 GGGGAAGTTATTTGCCCTTGTCCCTGCTCC 27 117 1 TTTGCCCTTG 0.735932 -48 GTCTTTCATTTGTCCCTGGGTGGTGCTAGA 31 112 1 TGTCCCTGGG 0.659046 -189 AAGTCTTCGCTTCCCTCTAGAAATCTCTAT 45 11 1 TTCCCTCTAG 0.527275 -122 AAATAGCCTCTTTCCTCTAGCGAGATCCCC 49 178 0 TTTCCTCTAG 0.628984 -123 AGAGAGGGGGTGTCCCCTTGTCTGTCGCGG 50 130 1 TGTCCCCTTG 0.843533 -130 ********** Masking position 5 Map Score: 19.5713 Number of sites scoring better than the average of aligned sites = 2745 Number in coding regions = 2401 Number in noncoding regions = 344 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 7 GTCCATGGCATCGGTGGAAATGTTTGATTTAA 1 50 0 TCGGTGGAAG 0.851835 -121 TGACCCAGACCCGTTGGAAAGGTTCCACACCA 6 22 0 CCGTTGGAAG 0.710814 -212 TAATACGGACACGGGGGGTATGGAAAAATACC 6 161 0 ACGGGGGTAG 0.740715 -73 CTTCTAGGGTCGGGCGGCTATGCTGGAAAAGC 19 117 1 CGGGCGGTAG 0.803152 -184 GGTATTGGTTTCGGCGGTAACGC 22 2 0 TCGGCGGAAG 0.953218 -299 AAAGTTAGCACCGGCGAAAAGGGACGGGAAAG 24 55 1 CCGGCGAAAG 0.943611 -78 AGCTTAAGCAACGGCGGTAATG 25 153 1 ACGGCGGAAG 0.953218 -12 AAGGCGATCGCCGGTGGCCATTGGGGTAAAAT 26 13 1 CCGGTGGCAT 0.815351 -208 GCAAGCTTGCCCGGCGGGCATGGTAGGATATA 26 109 0 CCGGCGGCAG 0.99198 -112 GATCAAGCCACCGGGGGTCACTCCAGGGGTAC 27 68 1 CCGGGGGCAT 0.874109 -97 ATCCGGCGGTAATGTTTCTAAGAT 28 25 0 CCGGCGGAAG 0.992496 -14 GCTACAACAACCGGGGGCAAAGCAAAACCCTA 30 93 0 CCGGGGGAAG 0.983244 -166 TATTCTTCTCCCGGCGAACACGAAAGTATATT 50 62 0 CCGGCGACAG 0.939939 -198 ******* ** * Masking position 10 Map Score: 12.9311 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 478 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 AGGGGAAGCATCTAGTGCAAGGGATACCTTTCC 5 47 1 TTATGAAGGG 0.653383 -163 CAAACCGAGTTTTATTTTAAGGGCTTTGCGTAT 8 115 0 TTATTAAGGG 0.788764 -51 AGCCTTCCAAGCTAATGATAGGGGTTCGATTCC 13 103 1 GTATGTAGGG 0.927279 -175 GGGATAATTTTTGGGGATGCAAACT 15 3 1 GTATTTTGGG 0.890221 -64 ATGATTGCACGGTAATTATTGGGCTAAGGGAAA 16 105 0 GTATTTTGGG 0.890221 -49 GCGCTTAACATGGACTTCTAGGGTCGGGCGGCT 19 103 1 TGATTTAGGG 0.930674 -198 GGTACATGGGTATTTTTAGGGCGATCGCCGC 21 9 1 GTATTTAGGG 0.961917 -132 CATGGTGATATTGATTTTTTGGGTATCTTTTTA 22 55 0 TGATTTTGGG 0.811674 -246 AAGAGTTATTGATACTTTTAGGGTTTTGCTTTG 30 75 1 GTATTTAGGG 0.961917 -184 TGCGAAAGAGTAGACTTGTAGGGATTGGTTACT 36 141 1 TGATTTAGGG 0.930674 -160 AAAAACCGAGTATACTGCTAGGGAGGTTTATAC 38 82 0 TTATGTAGGG 0.902242 -38 CTTTTCTTCCTATATTTGTAGGGCTAGTCAAAT 39 109 1 TTATTTAGGG 0.948139 -192 GCTGTTCTCTGAGAATTATAGGGATCCATATCC 46 243 0 GGATTTAGGG 0.948842 -58 * ** ** ***** Masking position 4 Map Score: 13.1009 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 33 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 CAAGGTAATAGCAAAACTGGAAACTTCAAA 9 38 0 GCAAAACTGG 0.91862 -263 CTCAAATAGGAAAAAACTGGGGACGAAATC 9 275 0 AAAAAACTGG 0.934202 -26 CAACCCGGAAGAAGAATTGGCCAATTTTTC 10 68 1 GAAGAATTGG 0.764411 -216 CATGAGCCCAGAAAAATTGGCCAATTCTTC 10 78 0 GAAAAATTGG 0.911271 -206 ATTGACTAAAGAAAAATTGAGCACCATAGC 15 37 1 GAAAAATTGA 0.746972 -30 TGCAATCATAGAAAAACTGATTAGGAACGA 16 129 1 GAAAAACTGA 0.911271 -25 GCGATCGCCTGCTAAACTGGAAAGGTTGTC 17 190 1 GCTAAACTGG 0.697475 -111 CCCTAAGATTGATAAACTGGGATATTACAA 30 47 1 GATAAACTGG 0.879483 -212 CGAAACTGCCAAAAAACTGGATAGAAAGAT 33 38 0 AAAAAACTGG 0.934202 -29 ACCACTATCGAAAAAACTGACATCCCACGA 35 23 0 AAAAAACTGA 0.803195 -173 TCCTCTTTACAAAAAATTGAGCAATAATTT 43 45 0 AAAAAATTGA 0.539829 -123 TAGATTTTTAGAAGAACTGGTTTCTCTATT 46 88 1 GAAGAACTGG 0.91862 -213 AAAGTTTATAAAAAAACTGGACCCGACCGA 48 22 0 AAAAAACTGG 0.934202 -279 ********** Masking position 5 Map Score: 8.70357 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 435 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 10 GCCGAGTCAGTGGGGAAGGATGGCAAGGTCC 3 61 1 TGGGGAGGAT 0.913621 -71 GCCAAGGGACAGGGGAAGCATCTAGTGCAAG 5 37 1 AGGGGAGCAT 0.540631 -173 AGGAAAAAACTGGGGACGAAATCCCGCCGAA 9 267 0 TGGGGAGAAA 0.713651 -34 TTCAACAGAATAGGGAAGCCGGA 11 3 0 TAGGGAGCCG 0.897113 -173 GGATAATTTTTGGGGATGCAAACTGATTGAC 15 12 1 TGGGGAGCAA 0.871522 -55 CCCCGTAAGATTGGGAAGATTAGTTTTAGCT 25 126 1 TTGGGAGATT 0.490007 -39 TCACTAGAGTTAGGGAAGCTGAAGAGTAGTC 26 156 1 TAGGGAGCTG 0.882727 -65 TGCTAATCTATGGGGAAGTTATTTGCCCTTG 27 106 1 TGGGGAGTTA 0.607448 -59 TTATCAATCTTAGGGATGATTGTTTTCCTTC 30 31 0 TAGGGAGATT 0.752505 -228 GGTTGGGGGAGGGGGAGGCCGGGGTTTTTAA 30 224 0 GGGGGAGCCG 0.680419 -35 AACTAGGGATGGATTAGCCGGGCT 31 287 0 TAGGGAGGAT 0.83757 -14 TCGTGTAGTATAGGGACGGCTCTTTGTTTTG 35 68 1 TAGGGAGGCT 0.873736 -128 AGTATACTGCTAGGGAGGTTTATACCCTAAC 38 76 0 TAGGGAGTTT 0.619713 -44 TCCTAATATGTGGGGACGCCTATGAGATTGG 39 188 1 TGGGGAGCCT 0.951605 -113 AAGTCTGCGCTAGGGATGAAGTTTTATTCTT 39 259 0 TAGGGAGAAG 0.704767 -42 ACTAGCGATATGGGGATGGTTTCTTAGAAAT 46 207 1 TGGGGAGGTT 0.924546 -94 AAAAAGGTTTTTGGGAAGCCGAAGGTTTTTT 50 27 0 TTGGGAGCCG 0.733716 -233 ACTTCCTTATTGGGGAGGGTAGCTATCTGCA 50 219 1 TGGGGAGGTA 0.850132 -41 ****** **** Masking position 6 Map Score: 9.57633 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 561 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 11 CGTGCTGGGTCAACGGCCGATCGCCAGCAA 5 158 0 CAACGGCCGA 0.822388 -52 AATGGGCAAGCAATCGCGGCGAATCTCTAG 6 111 1 CAATCGCGGC 0.943213 -123 GAATCTCTAGCCATCGCGGCGTTGTTTTTG 6 131 1 CCATCGCGGC 0.864402 -103 ATCCGTTAGTCAATGGCGGCTCTCAGAATT 9 96 0 CAATGGCGGC 0.949078 -205 GATTTTAACCCAACGGCCGCCAGACCGTGT 9 223 0 CAACGGCCGC 0.967799 -78 CCCTGAGTCACTATGGCCGGGGGGAGTTT 12 10 0 CTATGGCCGG 0.878505 -85 AATCTCGCAACAATGGCGGGGCAAAATAGA 14 16 1 CAATGGCGGG 0.926219 -53 GACTGAAACGCAACGGCGGACTACCCATAT 14 46 0 CAACGGCGGA 0.788201 -23 ATTTTTAGGGCGATCGCCGCTAAATCCGAT 21 22 1 CGATCGCCGC 0.920339 -119 TACCACGCTCCTACAGCCGCATAGCTAAAA 22 30 1 CTACAGCCGC 0.548655 -271 CCCGCTTTGGCGATCGCCGGGTTGTCAGGG 23 23 0 CGATCGCCGG 0.886127 -91 GGGACAGTGGCGATCGCCGGGGTAATCCAG 23 85 0 CGATCGCCGG 0.886127 -29 TTAGCTTAAGCAACGGCGGTAATG 25 151 1 CAACGGCGGT 0.678502 -14 AATTTTACCCCAATGGCCACCGGCGATCGC 26 16 0 CAATGGCCAC 0.519947 -205 GAAGATCAAGCCACCGGGGGTCACTCCAGG 27 65 1 CCACCGGGGG 0.621277 -100 GGAGCTACAACAACCGGGGGCAAAGCAAAA 30 98 0 CAACCGGGGG 0.810656 -161 GATATTTCTACTATCGGCGCTAGACCCGGC 32 136 0 CTATCGGCGC 0.738558 -165 TACCATTGAGCTACGGGCGCGCTCAAGTAG 48 149 0 CTACGGGCGC 0.804245 -152 ********** Masking position 3 Map Score: 13.7281 Number of sites scoring better than the average of aligned sites = 1971 Number in coding regions = 1859 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 12 AACCCAACGGCCGCCAGACCGTGTTCCCTGG 9 216 0 CCGCCGACCG 0.968413 -85 CCCAAACAATCCGCCAAATCCT 10 2 0 CCGCCAATCC 0.942269 -282 GGGAAAAGTTCTGCTTAACCGGGCGGTCTGC 11 123 1 CTGCTAACCG 0.813191 -53 GTTTCGGAGACCGCTGTACCCATTACCCAAA 13 146 0 CCGCTTACCC 0.873893 -132 CCTCAACCGCTCGGCCAACCCTGGTAA 17 7 0 TCGGCAACCC 0.672345 -294 TCCAGCATAGCCGCCCGACCCTAGAAGTCCA 19 113 0 CCGCCGACCC 0.987935 -188 AGGGCGATCGCCGCTAAATCCGATTGCAGGA 21 28 1 CCGCTAATCC 0.899282 -113 AATGAAATAGCTGGCTGACCGTTGGAGAAAG 21 72 1 CTGGCGACCG 0.730461 -69 GCGTTACCGCCGAAACCAATACCACGC 22 7 1 CCGCCAAACC 0.865945 -294 TAACGTTTTTCCGCTTGACCCTCCATAAACT 22 253 1 CCGCTGACCC 0.978163 -48 CACCCTTAGCCCGGCTAATCCATCCCTAGTT 31 280 1 CCGGCAATCC 0.859382 -21 TCTACTATCGGCGCTAGACCCGGCCTATCGC 32 129 0 GCGCTGACCC 0.80164 -172 AAGAAACAGCCTGCTAAACACAAGAGTCCTC 32 279 0 CTGCTAACAC 0.555142 -22 CCAAACTAAGCTGCTAAACCGCAACCATCAA 46 11 1 CTGCTAACCG 0.813191 -290 TATTCTTCTCCCGGCGAACACGAAAGTATAT 50 63 0 CCGGCAACAC 0.783473 -197 ***** ***** Masking position 8 Map Score: 9.22169 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 692 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 13 GGCAATGAGTATATCCAAAAGAACGAAGTAC 2 56 1 ATACCAAAAG 0.767737 -180 ACTCGGCGTTTTATCCAAAAAATAGACCATT 3 37 0 TTACCAAAAA 0.690424 -95 GTATGGAAAAATACCCAAAAACAACGCCGCG 6 145 0 ATACCAAAAA 0.954457 -89 ATCAGTTTGCATCCCCAAAAATTATCCC 15 8 0 ATCCCAAAAA 0.782501 -59 TTCAGTCAGAACAACCAAAAATTTGATTCGT 17 93 0 ACACCAAAAA 0.955268 -208 CTACAGCCGCATAGCTAAAAAGATACCCAAA 22 40 1 ATACTAAAAA 0.646765 -261 AGCTAAAAAGATACCCAAAAAATCAATATCA 22 52 1 ATACCAAAAA 0.954457 -249 CCATAGTTACAGCCAAAAAAGAAGGAAAA 30 9 1 ACACCAAAAA 0.955268 -250 AATCAGCGAAACTGCCAAAAAACTGGATAGA 33 43 0 ACTCCAAAAA 0.712109 -24 CGCAGAGTCTATAGCAAAAAAAATCTAGCTT 36 187 0 ATACAAAAAA 0.763519 -114 AACTTTGAAAACAACGAAAAAAAGCCCGAAA 39 67 0 ACACGAAAAA 0.734416 -234 ATAATCAAAAACAACCAAAAACCAACTATTT 42 65 0 ACACCAAAAA 0.955268 -68 CAAGCAAGCGATATCAAAAAATTACTACCTA 47 31 0 ATACAAAAAA 0.763519 -70 *** ******* Masking position 7 Map Score: 7.62092 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 14 AAAATTATTGAGAGGTTTGCCTTGCTAACA 1 151 1 AGGGTGCTTG 0.975728 -20 CCAGCAAAACGGGGGACAGCTTGGGGCTGTCGCA 5 131 0 GGGGAGCTGG 0.97941 -79 ACAGAAACTTAGGGGTTTGCATGGGCCAGGGAAC 9 191 1 AGGGTGCTGG 0.987498 -110 AGGATTTGGCGGATTGTTTGGGGAATGAACA 10 8 1 GGGGTGTTGG 0.791012 -276 ATAGTGACTCAGGGGCCAGCTTTGTCCTATGCTT 12 26 1 AGGGAGCTTG 0.98021 -69 TTTATTTCCCAGTGGTAAGCGTGGGTAATCGGGG 17 157 1 AGGGAGCTGG 0.989828 -144 TGATACTTTTAGGGTTTTGCTTTGCCCCCGGTTG 30 84 1 AGGTTGCTTG 0.79762 -175 GGGGCATTTCAGTGGAGAGCATGGCAGGGGGATT 30 167 0 AGGGAGCTGG 0.989828 -92 CAATGAATTTATTGGGCAGCTTTGAGATGCCTTG 31 31 1 ATGGAGCTTG 0.829225 -270 ** ** *** *** Masking position 12 Map Score: 6.427 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 103 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 CTTACTATTTTAAGGGAATTGATGACCAATCC 1 97 0 TAGGGATTGA 0.691772 -74 CCAAAATTATTGAGAGGTTTGCCTTGCTAACA 1 149 1 TAGAGTTTGC 0.851983 -22 ACATGAAGTCTAAGGATTTTGATCGCAAATTT 2 187 1 TAGGATTTGA 0.416132 -49 GCTGAACAATTGAGCGCATTGCTAACCAGGCG 5 95 1 TAGCGATTGC 0.79573 -115 AAGGGAAGGCCTAGGGGTTTGCTTCTGTTCTA 7 23 1 CAGGGTTTGC 0.957509 -90 AGTTTTATTTTAAGGGCTTTGCGTATCCGTCG 8 109 0 TAGGGTTTGC 0.983253 -57 TAACAGAAACTTAGGGGTTTGCATGGGCCAGG 9 189 1 TAGGGTTTGC 0.983253 -112 TGGCCACAATTTAGCGTTTAGCTCCGCCGATC 24 107 1 TAGCGTTAGC 0.688389 -26 ATTGATACTTTTAGGGTTTTGCTTTGCCCCCG 30 82 1 TAGGGTTTGC 0.983253 -177 ACATCCTATTCGAGGGGTTGGCTCCTGTTTCT 44 119 0 CAGGGTTGGC 0.824545 -182 GGTCTCTTTGTCAGGGTTTTGC 47 89 1 TAGGGTTTGC 0.983253 -12 * **** ***** Masking position 3 Map Score: 7.95765 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 129 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604