AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_ecoli_mtub_300.orf -o190_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #2 nrdB 21 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #3 ygaM 139 orf, hypothetical protein #4 nrdH 247 glutaredoxin-like protein; hydrogen donor #5 Rv0567 281 hypothetical protein Rv0567 #6 Rv0568 109 hypothetical protein Rv0568 #7 Rv0569 134 hypothetical protein Rv0569 #8 nrdZ 25 nrdZ #9 nrdF 224 nrdF #10 Rv1982c 300 hypothetical protein Rv1982c #11 nrdG 130 nrdG #12 Rv3049c 133 hypothetical protein Rv3049c #13 Rv3050c 127 hypothetical protein Rv3050c #14 nrdE 65 nrdE #15 nrdI 34 nrdI #16 nrdH 300 nrdH Motif number 1 AACTCCCAACAGGACACACTC 2 4 1 TCCCAACAGG 0.6995 -18 CTGGATATGAGCGTGACGGGGTAGGGGGAT 4 90 0 GCGTGACGGG 0.585244 -158 TGCGTAGCTTTCGCGACGGATTTACAGTCC 5 109 0 TCGCGACGGA 0.733343 -173 ATCCTGCACCTGCCACCACGGTCAAGCTGG 5 146 1 TGCCACCACG 0.705807 -136 ATCCGGGCATGGGCGCCGGGCATGGCCACG 5 177 1 GGGCGCCGGG 0.990924 -105 GCGCCGGGCATGGCCACGCCCGCGCGTTGG 5 189 1 TGGCCACGCC 0.866922 -93 GGCGACGTTGGGGCACCAACGCGCGGGCGT 5 204 0 GGGCACCAAC 0.852882 -78 GTAGACAGCGGCGCGACACCCGCACTCCAA 5 242 1 GCGCGACACC 0.960511 -40 CACGTTGGTCGGCCACCCACCATGTCATTG 6 15 0 GGCCACCCAC 0.759069 -95 CAACGTGAACTGAGGACGGCAAATCGGCCT 6 38 1 TGAGGACGGC 0.656399 -72 GGGACCCGCTGGGCGACCCCATGCGGATAC 7 20 0 GGGCGACCCC 0.972264 -115 AAAAGTCCCCTCGGGACCCGCTGGGCGACC 7 32 0 TCGGGACCCG 0.533751 -103 GGGGACTTTTGGCCACCGGCGCTGGTGGCC 7 52 1 GGCCACCGGC 0.971421 -83 GAGGGCAGTAGGCCACCAGCGCCGGTGGCC 7 62 0 GGCCACCAGC 0.932678 -73 CACGCACCCGGCGCAACGGCGGGAGGGCAG 7 84 0 GCGCAACGGC 0.97618 -51 CTTTCATGGCGTGCACCAGCACTGTAGCTT 9 85 0 GTGCACCAGC 0.724139 -140 TCAATGACAAGGAGGACGGCCGAAATGCCC 9 119 1 GGAGGACGGC 0.80427 -106 CTGCCGGACTTGACGCCCACAGGAGCGTAC 9 158 1 TGACGCCCAC 0.621857 -67 CGTACGCACCGGCCAACAGCGGCATGACCA 9 183 1 GGCCAACAGC 0.91162 -42 CCATGGCAAGGCAGGACGGCCCTCG 9 210 1 GCAGGACGGC 0.760797 -15 TTGATATTCAGCGCCACAGGTAGATGGTAC 10 29 0 GCGCCACAGG 0.822796 -272 CTGACCGGCTGCACACCAGCAAGACTGCCG 10 94 1 GCACACCAGC 0.830082 -207 TTTTGGAGTCGCGCGCCGGCGACCGTGAGG 10 157 1 GCGCGCCGGC 0.97426 -144 GGCCCCTGCTTGCCGACCGCTCCCCCATCA 10 220 1 TGCCGACCGC 0.930156 -81 GCGAGCGGATTCGCGACACGCAAACACAAC 11 23 1 TCGCGACACG 0.876338 -108 GTACCTTGTCGGACCCCAGGGGTAGTGTTT 11 66 1 GGACCCCAGG 0.638755 -65 CACTTCACCAGGACAACAAGCTGCCTTGCT 11 103 0 GGACAACAAG 0.373137 -28 CGATGTCAACGGCCGCCGCGC 12 2 0 GGCCGCCGCG 0.969107 -132 TACTGGGTATTTGCGCCGGCGAGGGTGACT 12 73 1 TTGCGCCGGC 0.881437 -61 TTTCACTCTGGCGCGCCGGTG 13 2 0 GCGCGCCGGT 0.818572 -126 AGAGTGAAAGTGGCGACGGCTTCGCGGCGT 13 23 1 TGGCGACGGC 0.983776 -105 AATGTGAGGTTCACGACGCGACACGCCGCG 13 45 0 TCACGACGCG 0.793903 -83 CTGGGCAGACTGGCCACGCCAGGCTTGGTT 13 76 0 TGGCCACGCC 0.866922 -52 AGGTCAGCGCTTGCAACGCGGTAAGGTGCT 13 104 1 TTGCAACGCG 0.455798 -24 TAAGAGGCGTGCGCGCCGGAGG 14 3 0 GCGCGCCGGA 0.88062 -63 TCTTACTCTGGGGGGCCGGGCGAAACGGAC 14 28 1 GGGGGCCGGG 0.922458 -38 CTCTTCTCCGTGCCACCCCCTAGGTGCCAC 16 49 1 TGCCACCCCC 0.811433 -252 ACCCCCTAGGTGCCACCCCCTAGGTGTAGT 16 63 1 TGCCACCCCC 0.811433 -238 GGGAAGTTCATCGCGCCCCGTGGATCTGGT 16 132 0 TCGCGCCCCG 0.914677 -169 TCCCGTCATAGCGCGACCACGTCCGTCGAC 16 179 0 GCGCGACCAC 0.902958 -122 ATGTTGAGCGGCCCGACAAGGCTCCAGATT 16 208 0 GCCCGACAAG 0.714589 -93 TGACAGGATCTGGCAACGACTCAAGTAGTG 16 248 0 TGGCAACGAC 0.83209 -53 ********** Masking position 7 Map Score: 50.7373 Number of sites scoring better than the average of aligned sites = 14940 Number in coding regions = 14337 Number in noncoding regions = 603 Number of orfs with sites within 600 bp upstream = 487 Fraction of orfs with sites within 600 bp upstream = 0.0782204 Motif number 2 GTTAAAAATAACTGTTCGGCGATTTCTTGAA 1 39 0 ACTGTCGGCG 0.811445 -262 AGTGTTCTAAGCAGCTTCCCGTACTACAGGT 1 229 1 GCAGTTCCCG 0.940563 -72 CCCTCCTTCGCGAGATAGCCGTGTGTGCTCT 5 20 1 CGAGTAGCCG 0.838147 -262 GTCGTTGTACCCTGCTAGGCGGCAGGTTGCC 5 60 1 CCTGTAGGCG 0.894662 -222 CTGCTAGGCGGCAGGTTGCCCGAGCGGCCAA 5 71 1 GCAGTTGCCC 0.801657 -211 TGCCCGGATACCAGCTTGACCGTGGTGGCAG 5 155 0 CCAGTTGACC 0.904332 -127 CTGTTTGTAATGAGTTCAGCGACACGAAGAA 9 29 1 TGAGTCAGCG 0.575072 -196 AGCCGGTCAGCGAGTTCGGCGGCTAGTCGGT 10 73 0 CGAGTCGGCG 0.979401 -228 AAATCTGGCCCCTGCTTGCCGACCGCTCCCC 10 214 1 CCTGTTGCCG 0.964376 -87 TGTTCGCGCTCGAGCTTGGTGATGGGGGAGC 10 238 0 CGAGTTGGTG 0.671493 -63 AATCCGCTCGCCTGTTTCGCCGG 11 3 0 CCTGTTCGCC 0.910444 -128 AAACAGGCGAGCGGATTCGCGACACGCAAAC 11 17 1 GCGGTTCGCG 0.869719 -114 TGTTCAGCGGCGAGTTTGGCGCTTCAGTCAC 12 97 0 CGAGTTGGCG 0.9818 -37 GATCGGTCTTCCTGTTCAGCGGCGAGTTTGG 12 109 0 CCTGTCAGCG 0.895693 -25 GAAAGTGGCGACGGCTTCGCGGCGTGTCGCG 13 28 1 ACGGTTCGCG 0.747679 -100 TGGTTGAATGTGAGGTTCACGACGCGACACG 13 50 0 TGAGTTCACG 0.669181 -78 GCCAGTCTGCCCAGGTCAGCGCTTGCAACGC 13 92 1 CCAGTCAGCG 0.961178 -36 CCGGCAGATCCCAGGTTCACCAGGTCTCACC 16 104 1 CCAGTTCACC 0.895008 -197 CCAGGTCTCACCAGATCCACGGGGCGCGATG 16 123 1 CCAGTCCACG 0.970221 -178 ATCGGCATCGCCAGGTCGACGGACGTGGTCG 16 165 1 CCAGTCGACG 0.973096 -136 CGACAAGGCTCCAGATTCCCGTCATAGCGCG 16 194 0 CCAGTTCCCG 0.985969 -107 CCAGATCCTGTCAGATTCCCGATTTCCGCAA 16 265 1 TCAGTTCCCG 0.909615 -36 **** ****** Masking position 6 Map Score: 27.4733 Number of sites scoring better than the average of aligned sites = 3722 Number in coding regions = 3583 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 3 CATTGACTTTCCCGGACACCTTGTCTGACC 1 85 1 CCCGGACACC 0.925156 -216 ACCTAAGGTGCGCGAAAGCCACTTTTTCCT 1 112 1 CGCGAAAGCC 0.779491 -189 GCGTCTTTGACCCCGAAGCCTGTCTTCGGG 4 32 1 CCCCGAAGCC 0.980093 -216 CAAAAAGAAACCCCGAAGACAGGCTTCGGG 4 43 0 CCCCGAAGAC 0.872459 -205 ACAGAGCACACACGGCTATCTCGCGAAGGA 5 23 0 CACGGCTATC 0.645802 -259 GGCGCCCATGCCCGGATACCAGCTTGACCG 5 164 0 CCCGGATACC 0.905672 -118 CGCGTTGGTGCCCCAACGTCGCCTACGGTC 5 211 1 CCCCAACGTC 0.526323 -71 GCGGGTGTCGCGCCGCTGTCTACCGACCGT 5 235 0 CGCCGCTGTC 0.954223 -47 GGCGACCCCATGCGGATACCCCAGCTGG 7 9 0 TGCGGATACC 0.778974 -126 TTCGCTCAAGCGACGAAGTCG 8 15 1 CGACGAAGTC 0.636309 -11 AAATATGGGTAGCCGAAATCACTAAGCTAC 9 62 1 AGCCGAAATC 0.597665 -163 GGGCGTCAAGTCCGGCAGTCGGTCCTTGGG 9 146 0 TCCGGCAGTC 0.90862 -79 ACCGACTAGCCGCCGAACTCGCTGACCGGC 10 73 1 CGCCGAACTC 0.904428 -228 CCAGCAAGACTGCCGCCATCCGGCATGCCC 10 109 1 TGCCGCCATC 0.821456 -192 ACATCTTGCGTACCGAAATCTGGCCCCTGC 10 199 1 TACCGAAATC 0.57975 -102 TCGGCTACGACCCCGCAACCGGAGTCTGAG 10 274 1 CCCCGCAACC 0.972554 -27 GCGCGGCGGCCGTTGACATCG 12 2 1 CGCGGCGGCC 0.894287 -132 TTGACATCGCTGCGGCAATCAACAACACTC 12 23 1 TGCGGCAATC 0.890954 -111 ACGCGACACGCCGCGAAGCCGTCGCCACTT 13 30 0 CCGCGAAGCC 0.725298 -98 GTCCGTTTCGCCCGGCCCCCCAGAGTAAGA 14 28 0 CCCGGCCCCC 0.819402 -38 CGCGGCAGACATAGATAAGG 15 1 1 CGCGGCAGAC 0.899432 -34 GGCACCGCAATCTTCCTTATCT 15 23 0 CACCGCAATC 0.852763 -12 GACCTGGCGATGCCGATGCCGGGAAGTTCA 16 152 0 TGCCGATGCC 0.870233 -149 ACCGCTCCTTTGCGGAAATCGGGAATCTGA 16 275 0 TGCGGAAATC 0.875504 -26 ********** Masking position 10 Map Score: 23.2251 Number of sites scoring better than the average of aligned sites = 6163 Number in coding regions = 5712 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 4 GTAGACAGAGCACACACGGCTATCTCGCGA 5 27 0 CACACACGGC 0.906626 -255 GTTCGAATCCTGCACCTGCCACCACGGTCA 5 140 1 TGCACCTGCC 0.62797 -142 CCATGCCCGGCGCCCATGCCCGGATACCAG 5 172 0 CGCCCATGCC 0.788741 -110 CGGGCATGGCCACGCCCGCGCGTTGGTGCC 5 193 1 CACGCCCGCG 0.933099 -89 CGGCGCGACACCCGCACTCCAACAATTTCG 5 250 1 CCCGCACTCC 0.826152 -32 GGCCTCAGTTCACGCTCGGCGCTTTGAGCA 6 63 1 CACGCTCGGC 0.973994 -47 CCCCTCGGGACCCGCTGGGCGACCCCATGC 7 26 0 CCCGCTGGGC 0.944713 -109 TGGCCTACTGCCCTCCCGCCGTTGCGCCGG 7 77 1 CCCTCCCGCC 0.963268 -58 CAATCGTGCACGCACCCGGCGCAACGGCGG 7 92 0 CGCACCCGGC 0.981546 -43 CAGGAGCGTACGCACCGGCCAACAGCGGCA 9 177 1 CGCACCGGCC 0.968042 -48 GCCCTGTCTGCCCAGCTGGCGTTTTTGGAG 10 135 1 CCCAGCTGGC 0.741475 -166 AGTTGTGCCTCACGGTCGCCGGCGCGCGAC 10 164 0 CACGGTCGCC 0.956047 -137 GTGTCGCGAATCCGCTCGCCTGTTTCGCCG 11 12 0 TCCGCTCGCC 0.911687 -119 GCGCGGCGGCCGTTGACATCG 12 2 1 CGCGGCGGCC 0.949556 -132 GCGCTTCAGTCACCCTCGCCGGCGCAAATA 12 80 0 CACCCTCGCC 0.940661 -54 GCAGACTGGCCACGCCAGGCTTGGTTGAAT 13 72 0 CACGCCAGGC 0.883567 -56 CCTCCGGCGCGCACGCCTCTTACTCTG 14 8 1 CGCGCACGCC 0.989598 -58 GTCCGTTTCGCCCGGCCCCCCAGAGTAAGA 14 28 0 CCCGGCCCCC 0.878198 -38 ********** Masking position 3 Map Score: 22.222 Number of sites scoring better than the average of aligned sites = 3446 Number in coding regions = 3295 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 TCCATAAAGCCGCGATGAACCTCAGTTAAG 3 82 1 CGCGATGAAC 0.839806 -58 CATGCCCGGCGCCCATGCCCGGATACCAGC 5 171 0 GCCCATGCCC 0.733809 -111 GCGCGGGCGTGGCCATGCCCGGCGCCCATG 5 184 0 GGCCATGCCC 0.800748 -98 TAGACAGCGGCGCGACACCCGCACTCCAAC 5 243 1 CGCGACACCC 0.631426 -39 TGGGCAATGACATGGTGGGTGG 6 3 1 GGCAATGACA 0.530861 -107 ATGAGTTCAGCGACACGAAGAATAAAATAT 9 38 1 CGACACGAAG 0.648989 -187 TGCTGGTGCACGCCATGAAAGACCGTCAAT 9 94 1 CGCCATGAAA 0.785975 -131 GGAGGACGGCCGAAATGCCCAAGGACCGAC 9 129 1 CGAAATGCCC 0.786418 -96 CGGCCAACAGCGGCATGACCATGGCAAGGC 9 192 1 CGGCATGACC 0.737222 -33 TGCCGCCATCCGGCATGCCCTGTCTGCCCA 10 119 1 CGGCATGCCC 0.517853 -182 GGCCAGATTTCGGTACGCAAGATGTCGAGA 10 194 0 CGGTACGCAA 0.508993 -107 ACAAATCCTCGGCTACGACCCCGCAACCGG 10 266 1 GGCTACGACC 0.898374 -35 AGCGGATTCGCGACACGCAAACACAACTTC 11 26 1 CGACACGCAA 0.694532 -105 CCAGGGTATCGGATATGACGAGTGTTGTTG 12 42 0 GGATATGACG 0.546235 -92 GTTCACGACGCGACACGCCGCGAAGCCGTC 13 37 0 CGACACGCCG 0.926316 -91 TGGGCAGACTGGCCACGCCAGGCTTGGTTG 13 75 0 GGCCACGCCA 0.939779 -53 ATCCACGGGGCGCGATGAACTTCCCGGCAT 16 137 1 CGCGATGAAC 0.839806 -164 CCGTCGACCTGGCGATGCCGATGCCGGGAA 16 157 0 GGCGATGCCG 0.908134 -144 GACGTGGTCGCGCTATGACGGGAATCTGGA 16 186 1 CGCTATGACG 0.883402 -115 CGCAAAGGAGCGGTACGCCC 16 291 1 CGGTACGCCC 0.917525 -10 ********** Masking position 5 Map Score: 17.462 Number of sites scoring better than the average of aligned sites = 5212 Number in coding regions = 5008 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 6 TTTCCCGGACACCTTGTCTGACCTAAGGTGCG 1 92 1 ACCTGTCTGC 0.784654 -209 TGTGTGCTCTGTCTACCCGGTCGTTGTACCCT 5 41 1 GTCACCCGGC 0.767302 -241 CGCTCCCATTGGCCGCTCGGGCAACCTGCCGC 5 78 0 GGCGCTCGGC 0.827845 -204 TCCTGCACCTGCCACCACGGTCAAGCTGGTAT 5 147 1 GCCCCACGGC 0.66232 -135 CGCGGGCGTGGCCATGCCCGGCGCCCATGCCC 5 181 0 GCCTGCCCGC 0.789679 -101 AACTGAGGACGGCAAATCGGCCTCAGTTCACG 6 45 1 GGCAATCGGC 0.872423 -65 GCATGGGGTCGCCCAGCGGGTCCCGAGGGGAC 7 26 1 GCCAGCGGGC 0.876224 -109 AACGGCGGGAGGGCAGTAGGCCACCAGCGCCG 7 68 0 GGGAGTAGGC 0.392751 -67 TCGGTCCTTGGGCATTTCGGCCGTCCTCCTTG 9 126 0 GGCTTTCGGC 0.780319 -99 TCCTGTGGGCGTCAAGTCCGGCAGTCGGTCCT 9 150 0 GTCAGTCCGC 0.872528 -75 ACCATGGCAAGGCAGGACGGCCCTCG 9 209 1 GGCGGACGGC 0.736402 -16 CGAGTTCGGCGGCTAGTCGGTCTACCTCAGGG 10 62 0 GGCAGTCGGC 0.994053 -239 GCAGCCGGTCAGCGAGTTCGGCGGCTAGTCGG 10 74 0 AGCAGTTCGC 0.489726 -227 TCTTGCTGGTGTGCAGCCGGTCAGCGAGTTCG 10 86 0 GTGAGCCGGC 0.639634 -215 GCTGCACACCAGCAAGACTGCCGCCATCCGGC 10 101 1 AGCAGACTGC 0.791457 -200 CATCCGGCATGCCCTGTCTGCCCAGCTGGCGT 10 125 1 GCCTGTCTGC 0.847209 -176 CCGGCGAAACAGGCGAGCGGATTC 11 3 1 GGCAAACAGC 0.294211 -128 GTGTTGCAGTACCTTGTCGGACCCCAGGGGTA 11 58 1 ACCTGTCGGC 0.925517 -73 CCTGTTCAGCGGCGAGTTTGGCGCTTCAGTCA 12 98 0 GGCAGTTTGC 0.652705 -36 CTCACATTCAACCAAGCCTGGCGTGGCCAGTC 13 67 1 ACCAGCCTGC 0.831549 -61 AGCCTGGCGTGGCCAGTCTGCCCAGGTCAGCG 13 81 1 GGCAGTCTGC 0.822709 -47 CAGAGTAAGAGGCGTGCGCGCCGGAGG 14 6 0 GGCTGCGCGC 0.564466 -60 TGGGGGGCCGGGCGAAACGGACTATCACGCGC 14 36 1 GGCAAACGGC 0.870613 -30 TCATAGCGCGACCACGTCCGTCGACCTGGCGA 16 172 0 ACCCGTCCGC 0.705028 -129 GGAATCTGGAGCCTTGTCGGGCCGCTCAACAT 16 206 1 GCCTGTCGGC 0.978455 -95 *** ****** * Masking position 10 Map Score: 28.9674 Number of sites scoring better than the average of aligned sites = 2124 Number in coding regions = 1991 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 CTTGTCTGACCTAAGGTGCGCGAAAGCCAC 1 104 1 CTAAGGTGCG 0.442686 -197 GCTTCGGGGTCAAAGACGCGTATTTATTAT 4 21 0 CAAAGACGCG 0.842309 -227 TAAAATGAAGATACGGCGCGATGATACGCG 4 212 0 ATACGGCGCG 0.90443 -36 CGGACTGTAAATCCGTCGCGAAAGCTACGC 5 108 1 ATCCGTCGCG 0.56994 -174 GACGTTGGGGCACCAACGCGCGGGCGTGGC 5 201 0 CACCAACGCG 0.682772 -81 GGTCGGTAGACAGCGGCGCGACACCCGCAC 5 237 1 CAGCGGCGCG 0.996397 -45 GACTTTTGGCCACCGGCGCTGGTGGCCTAC 7 55 1 CACCGGCGCT 0.969654 -80 GCACCCGGCGCAACGGCGGGAGGGCAGTAG 7 81 0 CAACGGCGGG 0.924197 -54 GTAATGAGTTCAGCGACACGAAGAATAAAA 9 35 1 CAGCGACACG 0.729503 -190 ACTTGACGCCCACAGGAGCGTACGCACCGG 9 165 1 CACAGGAGCG 0.908371 -60 CACCGGCCAACAGCGGCATGACCATGGCAA 9 189 1 CAGCGGCATG 0.682277 -36 TACCATCTACCTGTGGCGCTGAATATCAAA 10 30 1 CTGTGGCGCT 0.343258 -271 GCCTCACGGTCGCCGGCGCGCGACTCCAAA 10 158 0 CGCCGGCGCG 0.991006 -143 CCGGCGAAACAGGCGAGCGGATTCGCG 11 8 1 AACAGGCGAG 0.737388 -123 TGGGTATTTGCGCCGGCGAGGGTGACTGAA 12 76 1 CGCCGGCGAG 0.940318 -58 TCTTCCTGTTCAGCGGCGAGTTTGGCGCTT 12 104 0 CAGCGGCGAG 0.975329 -30 CACCGGCGCGCCAGAGTGAA 13 1 1 CACCGGCGCG 0.99757 -127 CCTCCGGCGCGCACGCCTCTT 14 2 1 CTCCGGCGCG 0.993931 -64 CCCCCAGAGTAAGAGGCGTGCGCGCCGGAG 14 12 0 AAGAGGCGTG 0.568947 -54 CCGATTTCCGCAAAGGAGCGGTACGCCC 16 283 1 CAAAGGAGCG 0.778315 -18 ********** Masking position 5 Map Score: 29.4414 Number of sites scoring better than the average of aligned sites = 3996 Number in coding regions = 3801 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 8 ATTGACTTTCCCGGACACCTTGTCTGACCTAA 1 86 1 CCGACACCTG 0.780089 -215 GGGTCATTTTCACACTATCTTGCAGTGAATCC 1 177 1 CACCTATCTG 0.841675 -124 CTGCTTAGAACACTATATATAGGGGGTATGTT 1 211 0 CACATATATG 0.874405 -90 GATTCAACCACACAATATATAGCAAATAGTGG 4 131 0 CACATATATG 0.874847 -117 ATCTTTTTTCAACTACATCTAGTATCTCTGTA 4 160 1 AACACATCTG 0.899802 -88 GACCGTGAGGCACAACTTCTCGACATCTTGCG 10 177 1 CACACTTCTG 0.969402 -124 GACACGCAAACACAACTTCTTGTGTTGCAGTA 11 37 1 CACACTTCTG 0.969401 -94 AGGCCTCAAACACTACCCCTGGGGTCCGACAA 11 71 0 CACACCCCTG 0.943433 -60 AAATGTTATTCAGAACATCTTGTATCTCTTCT 16 24 1 CAGACATCTG 0.964475 -277 TACTCGAAAACACTACACCTAGGGGGTGGCAC 16 72 0 CACACACCTG 0.986184 -229 TGTCGGGCCGCTCAACATATCGAAGATGCACT 16 220 1 CTCACATATG 0.798891 -81 *** ****** * Masking position 10 Map Score: 7.84385 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 214 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TATATATAGGGGGTATGTTTGGGATTCACTG 1 199 0 GGGTAGTTTG 0.941475 -102 GACGGGGTAGGGGGATTTTTGTGATTCACCA 4 75 0 GGGGATTTTG 0.985751 -173 CTCATATCCAGGGTAATTTCGACCACTATTT 4 109 1 GGGTATTTCG 0.98575 -139 CGGGTCCCGAGGGGACTTTTGGCCACCGGCG 7 42 1 GGGGATTTTG 0.985751 -93 CCTGGGTACTGGGTATTTGCGCCGGCGAGGG 12 67 1 GGGTATTGCG 0.96197 -67 CAGGGAATTTCGAAAATGTTAT 16 2 1 AGGGATTTCG 0.943909 -299 ***** ***** Masking position 5 Map Score: 3.78115 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 60 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 GGAAAAAGTGGCTTTCGCGCACCTTAGGTC 1 111 0 GCTTTCGCGC 0.921385 -190 AAAATGAAGATACGGCGCGATGATACGCGT 4 211 0 TACGGCGCGA 0.675696 -37 GGTTCGTCCCTCCTTCGCGAGATAGCCGTG 5 13 1 TCCTTCGCGA 0.790096 -269 GCGGCAGGTTGCCCGAGCGGCCAATGGGAG 5 78 1 GCCCGAGCGG 0.787295 -204 AACCTGCGTAGCTTTCGCGACGGATTTACA 5 113 0 GCTTTCGCGA 0.865132 -169 GCATGGCCACGCCCGCGCGTTGGTGCCCCA 5 196 1 GCCCGCGCGT 0.952875 -86 TTGGAGTGCGGGTGTCGCGCCGCTGTCTAC 5 242 0 GGTGTCGCGC 0.784999 -40 CTGCCCTCCCGCCGTTGCGCCGGGTGCGTG 7 84 1 GCCGTTGCGC 0.947876 -51 CGACTTCGTCGCTTGAGCGAATCGC 8 6 0 GCTTGAGCGA 0.785527 -20 GCCGCTGTTGGCCGGTGCGTACGCTCCTGT 9 176 0 GCCGGTGCGT 0.892277 -49 CCTCACGGTCGCCGGCGCGCGACTCCAAAA 10 157 0 GCCGGCGCGC 0.997382 -144 CCATCACCAAGCTCGAGCGCGAACAAATCC 10 244 1 GCTCGAGCGC 0.883567 -57 GATGTCAACGGCCGCCGCGC 12 1 0 GCCGCCGCGC 0.988844 -133 GTTGTTGATTGCCGCAGCGATGTCAACGGC 12 19 0 GCCGCAGCGA 0.913124 -115 AGTCACCCTCGCCGGCGCAAATACCCAGTA 12 73 0 GCCGGCGCAA 0.917979 -61 CCACTTTCACTCTGGCGCGCCGGTG 13 6 0 TCTGGCGCGC 0.960471 -122 ACGCCGCGAAGCCGTCGCCACTTTCACTCT 13 23 0 GCCGTCGCCA 0.862932 -105 CCTCCGGCGCGCACGCCTCTTA 14 3 1 TCCGGCGCGC 0.987038 -63 ********** Masking position 7 Map Score: 30.0008 Number of sites scoring better than the average of aligned sites = 3475 Number in coding regions = 3330 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 11 ACACCTTGTCTGACCTAAGGTGCGCGAAAG 1 100 1 TGACCTAAGG 0.906886 -201 CATAATTTTCTTAACTGAGGTTCATCGCGG 3 91 0 TTAACTGAGG 0.955792 -49 CCGACCAACGTGAACTGAGGACGGCAAATC 6 33 1 TGAACTGAGG 0.991215 -77 GCGCCGAGCGTGAACTGAGGCCGATTTGCC 6 55 0 TGAACTGAGG 0.991215 -55 GTTGTCCTGGTGAAGTGGGGTTCTG 11 116 1 TGAAGTGGGG 0.935213 -15 ********** Masking position 6 Map Score: 2.48567 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 57 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 CTGACCTAAGGTGCGCGAAAGCCACTTTTT 1 109 1 GTGCGCGAAA 0.920293 -192 ATAGCAAATAGTGGTCGAAATTACCCTGGA 4 115 0 GTGGTCGAAA 0.983809 -133 TATATATTGTGTGGTTGAATCTTTTTTCAA 4 142 1 GTGGTTGAAT 0.774837 -106 GATACTAGATGTAGTTGAAAAAAGATTCAA 4 156 0 GTAGTTGAAA 0.889204 -92 ACCAGCGCCGGTGGCCAAAAGTCCCCTCGG 7 48 0 GTGGCCAAAA 0.867269 -87 TAAAATATGGGTAGCCGAAATCACTAAGCT 9 60 1 GTAGCCGAAA 0.960615 -165 GGATCTGCCGGTACTCGAAAACACTACACC 16 85 0 GTACTCGAAA 0.925451 -216 ********** Masking position 8 Map Score: 1.82676 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 284 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TTCCTGAGTTATCCACAAAGTTATGCACTT 1 141 1 ATCCACAAAG 0.765492 -160 TTTCAGAAAAGTCCATAAAGCCGCGATGAA 3 71 1 GTCCATAAAG 0.683366 -69 ACGCGTCTTTGACCCCGAAGCCTGTCTTCG 4 30 1 GACCCCGAAG 0.973834 -218 GGCAAAAAGAAACCCCGAAGACAGGCTTCG 4 45 0 AACCCCGAAG 0.940769 -203 CACGATTGAAGTCCCCAAGGAAGGGACGCT 7 114 1 GTCCCCAAGG 0.982043 -21 GACGGCCGAAATGCCCAAGGACCGACTGCC 9 133 1 ATGCCCAAGG 0.751373 -92 GAATATCAAAGACCCTGAGGTAGACCGACT 10 50 1 GACCCTGAGG 0.960949 -251 GCGCGCCGGCGACCGTGAGGCACAACTTCT 10 167 1 GACCGTGAGG 0.825501 -134 TACCTTGTCGGACCCCAGGGGTAGTGTTTG 11 67 1 GACCCCAGGG 0.959209 -64 GTCTCACCAGATCCACGGGGCGCGATGAAC 16 127 1 ATCCACGGGG 0.839845 -174 ********** Masking position 4 Map Score: 4.66463 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 276 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 14 ********** No masking Map Score: -5.58897e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: -5.58897e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0