AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_bsub_reg_300.orf -o00910_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yccC 216 similar to asparaginase #2 nasE 31 assimilatory nitrite reductase (subunit) #3 nasD 121 assimilatory nitrite reductase (subunit) #4 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #5 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #6 ynbA 220 similar to GTP-binding protein protease modulator #7 ynbB 187 similar to hypothetical proteins #8 glnR 110 transcriptional regulator #9 glnA 60 glutamine synthetase #10 gltA 146 glutamate synthase (large subunit) #11 ypcA 155 similar to glutamate dehydrogenase #12 ypbH 158 similar to negative regulation of competence MecA homolog #13 ypbG 85 similar to hypothetical proteins #14 ypbF 62 ypbF #15 ypbD 59 ypbD #16 ypbB 265 ypbB #17 ansB 44 L-aspartase #18 ansA 181 L-asparaginase #19 yqhI 300 similar to aminomethyltransferase #20 asnB 149 asparagine synthetase #21 metK 300 S-adenosylmethionine synthetase #22 yurR 300 similar to opine catabolism #23 narJ 25 nitrate reductase (protein J) #24 narG 195 nitrate reductase (alpha subunit) #25 ywiD 143 ywiD #26 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #27 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #28 hutP 300 transcriptional regulator #29 hutH 112 histidase #30 yxbB 300 alternate gene name: yxaP; similar to hypothetical proteins Motif number 1 TTGTCATATCCTTCTTTTTTTGTCTTTTCA 1 103 0 CTTCTTTTTT 0.883946 -114 ATCTTAAATATTCCTTTTTGCTGTGCTACG 3 67 1 TTCCTTTTTG 0.864663 -55 TTTCTCATTATTTCTTTTTCATACAACGGG 5 66 0 TTTCTTTTTC 0.825382 -235 TTATAGTGAGCTTCTTTCTCATTATTTCTT 5 80 0 CTTCTTTCTC 0.840799 -221 GTCGAAACAATTGCTTTTTTCGGGAACAAT 5 214 0 TTGCTTTTTT 0.784163 -87 CAAATGGATGTTCCTTTCTTTTGCATATTG 6 117 0 TTCCTTTCTT 0.816952 -104 CCGACTAAAATGGCTTTCTCCTGAATCGTT 6 158 0 TGGCTTTCTC 0.513597 -63 ACGATAGAAACGTCTTTTTTTATTGTCCGT 13 29 1 CGTCTTTTTT 0.761481 -57 AATCTTTAACCTTCTTTCTCTTTGCTGGTT 17 25 0 CTTCTTTCTC 0.840799 -20 GAACTTCCGCTCCTTTTTCACCTTGAGCT 18 10 1 CTCCTTTTTC 0.960267 -172 GTGTTTCTCTGTCCTTTTTTGTATGTTTTT 19 249 1 GTCCTTTTTT 0.862372 -52 TAAGCGGCTTTCCCTTTTTTATCGTTGTAT 20 31 1 TCCCTTTTTT 0.81585 -119 GTCACACACTCTGCTTTTTTCACAAAATGT 24 101 0 CTGCTTTTTT 0.885863 -95 CGAAATCCTCCTTTTTTCTTTCATTAT 25 8 1 CTCCTTTTTT 0.947997 -136 ATGTTTTCAGTCTCTTTTTTTGTGGATTCA 26 38 1 TCTCTTTTTT 0.649257 -139 AGCCCGCCAATTCCTTTCTTCATTGGATTC 26 102 0 TTCCTTTCTT 0.816952 -75 GACTTTTTTTGCCCTTTTTTAAAATAGGAT 27 27 1 GCCCTTTTTT 0.764883 -274 ACGATTTCCCTCTCTTTTTCTAGTAACATC 27 79 0 TCTCTTTTTC 0.710487 -222 CGAATTACCAGTTCTTTTTCTTAAAAATTA 27 207 0 GTTCTTTTTC 0.77633 -94 TTATGAAAAAGCGCTTTTTCTGCAGAGGAC 27 241 1 GCGCTTTTTC 0.647423 -60 AAAACCTGTTCTGCTTTCTGCGTCACGCTA 28 170 1 CTGCTTTCTG 0.752431 -131 CACAGCATAGCTCCTTTTTGTATGGGCGCT 29 62 1 CTCCTTTTTG 0.931735 -51 AAGCCCAACTCCTTTTTCTTTACTTTGG 29 95 0 CTCCTTTTTC 0.960267 -18 TAAGAAACCTCGCCTTTTTGAACTGCGCCG 30 76 1 CGCCTTTTTG 0.851209 -225 TAAGAAACCTCGCCTTTTTGAATTGCGCCG 30 194 1 CGCCTTTTTG 0.851209 -107 ********** Masking position 5 Map Score: 23.2676 Number of sites scoring better than the average of aligned sites = 2338 Number in coding regions = 1880 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 465 Fraction of orfs with sites within 600 bp upstream = 0.0746868 Motif number 2 AACATTCCCACCTTACTGAATTG 1 3 1 CTTCCCACCT 0.899503 -214 CTATTTCTCTCCTTACATCCATA 1 204 0 ATTCTCTCCT 0.924165 -13 GTCCATTCCTCCTCAATGATAGT 2 19 0 CATTCCTCCT 0.937519 -13 GAAGCTCGTAAGTTTTCTCCTATTAAAAATT 4 140 0 ATTTTCTCCT 0.90387 -40 GTCTTTATATTTCCTTCCTACATATACTT 7 169 0 ATTCCTTCCT 0.889608 -19 ATTTTTTAAAAATTTCTCCTGGATTTGATG 8 10 1 AATTTCTCCT 0.805677 -101 CTCAATTTCCTCCTTTTCTTAACT 8 97 0 ATTTCCTCCT 0.974429 -14 TTGGTAAAATTCCTCCTCTTAAAAGGT 9 44 0 AATTCCTCCT 0.943831 -17 AACGTTCCCTCCTGCCTCTACTT 12 146 0 CTTCCCTCCT 0.977829 -13 CTATCCACCTACATTCTTCCTGACAAAAATC 16 244 0 AATTCTTCCT 0.732741 -22 ACTTCCGCTCCTTTTTCACCTTGAGCTGATT 18 13 1 CTTTTCACCT 0.630171 -169 TTCACTCCGCAGTTTGCTCCTTCGGCGCCTG 19 79 0 ATTTGCTCCT 0.774674 -222 GATTTGCTTCCTCCTGCACAAG 21 289 0 ATTGCTTCCT 0.68303 -12 GAGAGTTCACTCCTTCCGAGTCAG 24 182 0 ATTCACTCCT 0.750404 -14 CTTTTTCACCTCATTGTTTTT 26 166 0 CTTTTCACCT 0.630171 -11 ATTCAATGAGAATTCCTTCCTGTTTATACAA 27 120 0 ATTCCTTCCT 0.889608 -181 GACATTTCCCCCTAATTGATTGT 27 288 0 CTTTCCCCCT 0.802012 -13 AGACAGCGGCGCTTGCCTCCTTGTCTGGATA 28 121 1 GTTGCCTCCT 0.85871 -180 TTTTCATTGAGCATCCCTCCTAAAATAGAGT 30 38 0 GATCCCTCCT 0.909274 -263 TTTTCATTGAGCATCCCTCCTAAAATAGAGT 30 156 0 GATCCCTCCT 0.909274 -145 * ********* Masking position 4 Map Score: 18.7592 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 283 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 3 GGAAAAAACATTTGATAAGGAGCGGATCATCTG 3 99 1 TTTGTAGAGC 0.91483 -23 TTTGTCAGAGTATTATAGTGAGCTTCTTTCTCA 5 89 0 TATTTAGAGC 0.676125 -212 AATCGATTGCTTTGAAAAGGCGGAAATACGAGC 6 41 0 TTTGAAGCGG 0.836413 -180 CCGATTTGATTCTGGAAAGGAGCTTCCCTTCAC 7 38 0 TCTGAAGAGC 0.791558 -150 CATTTTTACCTTTTAAGAGGAGGAATTTTACCA 9 37 1 TTTTAGGAGG 0.646677 -24 TATACTATTCTCTGAAAGGGAGCATGTGAGAAA 11 107 1 TCTGAAGAGC 0.791558 -49 TTTTGTATGTTTTTTAGCTGCGCCGTTGATAAA 19 265 1 TTTTAGGCGC 0.867651 -36 TAAAAAAACCTTTTCCATCGAGGAAAGGGTTTG 21 160 0 TTTTCAGAGG 0.759139 -141 GGCGGGCTGATTTTTTAAAGCGCTTACATTACA 26 124 1 TTTTTAGCGC 0.93191 -53 ATTCGCGAATTATGAAAAAGCGCTTTTTCTGCA 27 232 1 TATGAAGCGC 0.736385 -69 AAAAAGCGCTTTTTCTGCAGAGGACGCTCTGGC 27 246 1 TTTTTGGAGG 0.58155 -55 TCGCAAGGCGTTTTATAAAGAGCCAGCCGAATG 28 55 0 TTTTTAGAGC 0.923246 -246 TTTTCTTTACTTTGGTAAAGCGCCCATACAAAA 29 77 0 TTTGTAGCGC 0.924366 -36 CTTATAAGCTTTTTTCATTGAGCATCCCTCCTA 30 47 0 TTTTCAGAGC 0.908439 -254 AACCTCGCCTTTTTGAACTGCGCCGTGCTGTAG 30 81 1 TTTTAAGCGC 0.947436 -220 CTTATAAGCTTTTTTCATTGAGCATCCCTCCTA 30 165 0 TTTTCAGAGC 0.908439 -136 AACCTCGCCTTTTTGAATTGCGCCGCGCTGTAG 30 199 1 TTTTAAGCGC 0.947436 -102 **** ** **** Masking position 3 Map Score: 14.6836 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 310 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 AAAAACATTTGATAAGGAGCGGATCATCTG 3 102 1 GATAAGGAGC 0.903944 -20 AGTATTTCTCGGGAAAGCGCAGGATTCCTT 5 184 1 GGGAAAGCGC 0.72694 -117 CGATTGCTTTGAAAAGGCGGAAATACGAGC 6 41 0 GAAAAGGCGG 0.932233 -180 ATTTGATTCTGGAAAGGAGCTTCCCTTCAC 7 38 0 GGAAAGGAGC 0.939339 -150 CGGAAACGATGGTAGACCGCTTCTATTTTA 7 68 1 GGTAGACCGC 0.332116 -120 ACTAAGTTAAGAAAAGGAGGAAATTGAG 8 93 1 GAAAAGGAGG 0.905521 -18 ACTATTCTCTGAAAGGGAGCATGTGAGAAA 11 110 1 GAAAGGGAGC 0.891158 -46 GCTCAAGGTGAAAAAGGAGCGGAAGTTC 18 9 0 AAAAAGGAGC 0.67723 -173 GATAAAAAAGGGAAAGCCGCTTAACCAGTA 20 24 0 GGAAAGCCGC 0.904423 -126 ATAAATAACAGAGAAACCGGTTGCTGGGCT 21 42 0 GAGAAACCGG 0.412297 -259 CCCTAATGTGGAAAAACCGCGAAGTTCGTC 22 212 0 GAAAAACCGC 0.826219 -89 ATCTTTGAATGAAAGGCAGCTAATGACCCA 24 30 1 GAAAGGCAGC 0.777081 -166 CGCGAATTATGAAAAAGCGCTTTTTCTGCA 27 235 1 GAAAAAGCGC 0.917809 -66 ACGATATCCAGACAAGGAGGCAAGCGCCGC 28 126 0 GACAAGGAGG 0.643483 -175 GCGCCCATACAAAAAGGAGCTATGCTGTGA 29 61 0 AAAAAGGAGC 0.67723 -52 TCTTTACTTTGGTAAAGCGCCCATACAAAA 29 77 0 GGTAAAGCGC 0.762538 -36 ACGCCAACTTGATAAGGAGGATGCTGAAG 30 282 1 GATAAGGAGG 0.800265 -19 ********** Masking position 4 Map Score: 11.7538 Number of sites scoring better than the average of aligned sites = 1271 Number in coding regions = 1093 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 5 GCTACGCTGGAAAAAACATTTGATAAGGAG 3 91 1 AAAAAACATT 0.878716 -31 TATTTTCTGGAAAAGACATGTGTAAGTTTT 4 72 1 AAAAGACATG 0.757359 -108 TTTTTAACGAAAAAAAACTGCTGAAATCAG 11 29 0 AAAAAAACTG 0.728934 -127 TTTTTTCGTTAAAAAACATGGAAAAACATA 11 44 1 AAAAAACATG 0.920804 -112 CGGCGCAGCTAAAAAACATACAAAAAAGGA 19 260 0 AAAAAACATA 0.564909 -41 TATGTAAAAAAATAAACATGAATACAACGA 20 52 0 AATAAACATG 0.515592 -98 TTATGAAATAAAAAAACCTTTTCCATCGAG 21 171 0 AAAAAACCTT 0.929795 -130 CAAAGATCAAAAAAAACCGGCTCTAT 24 7 0 AAAAAACCGG 0.75612 -189 CAGCCGGCCAAAAAAACAATGAGGTGAAAA 26 155 1 AAAAAACAAT 0.416256 -22 AATATTCCTTAAAAAACATTTACTTCCATG 27 161 1 AAAAAACATT 0.878716 -140 ATTTTTAAGAAAAAGAACTGGTAATTCGCG 27 209 1 AAAAGAACTG 0.419251 -92 GCAATCGCTGAAAAAACCTGTTCTGCTTTC 28 158 1 AAAAAACCTG 0.955064 -143 AAAGACTATAAAAAAACCTTTTGACTTCTG 28 223 1 AAAAAACCTT 0.929795 -78 ATGCTCAATGAAAAAAGCTTATAAGAAACC 30 55 1 AAAAAAGCTT 0.721603 -246 ATGCTCAATGAAAAAAGCTTATAAGAAACC 30 173 1 AAAAAAGCTT 0.721603 -128 ********** Masking position 6 Map Score: 9.35866 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 393 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 6 GCTCATCCGTGATATGCGGCAGCTGACATCCGACTAA 6 180 0 GATGGCAGGC 0.976802 -41 TGACCATGATATGCTGAAGCAGTTATAT 15 42 1 ACTGGCAGAA 0.839937 -18 TTTTTCTGTTGAAATGTGGCAGCAACATCATTACAAT 16 95 0 GATGGCAGAA 0.942847 -171 CGGGATACAGGCGCCGAAGGAGCAAACTGCGGAGTGA 19 72 1 GCCGGGAGAC 0.832669 -229 TCCCGAGCTGGCGGAGGGACAGGCCCTATGA 21 5 1 GCTGGGAGAA 0.940726 -296 TCTTTCGGGAGGCCTTGTGCAGGAGGAAGCAAATC 21 276 1 GCTTGCAGGA 0.908931 -25 TCAGGATCAGGCACAGGCGCAGTCACAAGACGGAGAA 22 12 0 GCAGGCAGAA 0.948752 -289 GAAAACAGACGCGATGCGGCAGTGGCAAAAGTCCAAA 22 89 0 GATGGCAGGA 0.969114 -212 ATATTAATTGGTTCAGCAGCAGAAGTCAAAAGGTTTT 28 235 0 GCAGGCAGGC 0.979276 -66 GAACTGCGCCGTGCTGTAGCAGCTGGCGGCCATTAAT 30 95 1 GCTGGCAGGC 0.994152 -206 GAATTGCGCCGCGCTGTAGCAGCTGGCGGTCATTAAT 30 213 1 GCTGGCAGGC 0.994152 -88 * *** **** * * Masking position 11 Map Score: 8.65583 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 210 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 7 CTGTTCTCTCTATATGATATTCAAGCGGAT 5 271 0 TATATGATAT 0.94738 -30 TATAACACATTATATGAGATGATGAGTCAT 12 104 0 TATATGAGAT 0.956028 -55 TATAATGTGTTATATGATTTGTGTGCAAGT 12 120 1 TATATGATTT 0.788931 -39 TCCTAATACCTATATGATATAATCAGCTCA 18 34 0 TATATGATAT 0.94738 -148 AGACCTTGTATATATGATACGGAACTCGCT 21 249 0 TATATGATAC 0.847091 -52 TGTCAAATGCTATATGAGATT 30 2 0 TATATGAGAT 0.956028 -299 TGTCAAATGCTATATGAGATTAATGGCCGC 30 120 0 TATATGAGAT 0.956028 -181 ********** Masking position 4 Map Score: 5.81089 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 8 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ATGATTAATCATTGTACATTTTATCTATTCAG 1 170 0 ATTACATTTT 0.77861 -47 TTCGTATATTTTGTTACATTTTATAACATGTA 3 36 1 TGTACATTTT 0.633402 -86 GACCCTCATTATTTTACATTTTCTGAATCAAG 4 27 1 ATTACATTTT 0.77861 -153 AGATTTTGTTTTTAATCATTTTGTCAGAGTAT 5 109 0 TTATCATTTT 0.846245 -192 GATATGTCATACTGTTCATTTTCTTCATTAAA 7 94 0 ATTTCATTTT 0.846245 -94 ACTGTTTTGCTATATACATTTTTACCTTTTAA 9 21 1 TTTACATTTT 0.916349 -40 GGTATTATTTTTATTTTACGTTCATAT 14 6 1 TTTTTATTTT 0.684449 -57 GTTGATTTGCTCTTTTTATTTTAACAGATTTC 16 212 0 TTTTTATTTT 0.684449 -54 TTTTTATCGTTGTATTCATGTTTATTTTTTTA 20 46 1 TTTTCATGTT 0.730016 -104 TCGCGTCTGTTTTCTTCATTTTCATGACGATT 22 112 1 TTTTCATTTT 0.944884 -189 TATTATAATGTCTATTCATTTTACCAAATCAA 22 263 0 TTTTCATTTT 0.944884 -38 TTCTCCTTTGTGTGAACATTTTGTGAAAAAAG 24 86 1 TTAACATTTT 0.77861 -110 AAAATTAATCTATCATCATTTTCCATGGAAGT 27 182 0 TTATCATTTT 0.846245 -119 * * ******** Masking position 8 Map Score: 6.25193 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 318 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 9 GATTGCAATTCAGTAAGGTGGGAATGTT 1 7 0 CAGAAGGGGG 0.929557 -210 CAAAAACTATCATTGAGGAGGAATGGAC 2 14 1 CATGAGGGGA 0.647071 -18 AATGAGGGTCTAGAAAGGGGAATCTT 4 5 0 TAGAAGGGAA 0.750839 -175 ATAGAGAGAACAGAGAGGTGAAG 5 288 1 CAGGAGGGAA 0.968954 -13 TTAAAGTCATCATTAAGGGGGATGTTATGTAG 16 164 0 CATAAGGGGA 0.781163 -102 AAACGATAACCAGCAAAGAGAAAGAAGGTTAA 17 18 1 CAGAAAGGAA 0.849932 -27 GAGCGAATGACAGCAAGGGGAGAGACCTGACC 19 32 1 CAGAAGGGAG 0.968954 -269 TTTCAGGTGCCAGGACAGAGAACCTTCATTTT 19 210 1 CAGACAGGAA 0.758763 -91 GGCGCAGTCACAAGACGGAGAAG 22 2 0 CAAACGGGAA 0.897415 -299 AAAATGTTCACACAAAGGAGAAGGAAGGCTGC 24 76 0 CACAAGGGAA 0.876485 -120 TGTCACTTATCAGGAGGGTGAATGCATTTATA 25 35 0 CAGAGGGGAA 0.905518 -109 GCCAAAAAAACAATGAGGTGAAAAAG 26 161 1 CAAGAGGGAA 0.889998 -16 TAGCGTGACGCAGAAAGCAGAACAGGTTTTTT 28 168 0 CAGAAGCGAA 0.817062 -133 CGGCGCAGTTCAAAAAGGCGAGGTTTCTTATA 30 74 0 CAAAAGGGAG 0.889998 -227 CCAGCTGCTACAGCACGGCGCAGTTCAAAAAG 30 89 0 CAGACGGGCA 0.907365 -212 CGGCGCAATTCAAAAAGGCGAGGTTTCTTATA 30 192 0 CAAAAGGGAG 0.889998 -109 CCAGCTGCTACAGCGCGGCGCAATTCAAAAAG 30 207 0 CAGGCGGGCA 0.83419 -94 *** **** *** Masking position 2 Map Score: 16.1455 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 299 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 10 TTTAATAGGAGAAAACTTACGAGCTTCGCC 4 144 1 GAAAACTTAC 0.722257 -36 ATATCGTTTTGAAAACCTACAATGATTATA 10 72 1 GAAAACCTAC 0.943852 -75 TATCGTTTGAGAAAACGCCCCATT 13 5 0 GAAAACGCCC 0.891741 -81 GAATAAAACCTCCCAGATTGTTC 16 4 1 TAAAACCTCC 0.89139 -262 AGACCTGACCGAAAACCTCGGGATACAGGC 19 54 1 GAAAACCTCG 0.924036 -247 CGAAATCCTCCTTTTTTCTTT 25 2 1 GAAATCCTCC 0.964165 -142 AGGAAAACCTCCTGTGCTAAGG 25 132 0 GAAAACCTCC 0.986576 -12 AAAAGAGAGGGAAATCGTCCATTTGAACCT 27 91 1 GAAATCGTCC 0.919049 -210 ********** Masking position 4 Map Score: 4.26013 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 158 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 11 ATTATCTTGATTCAATCATCAATTGTCAAGA 1 59 1 TTCAATCATA 0.726239 -158 AGATAAAATGTACAATGATTAATCATCATAT 1 176 1 TACAATGATA 0.897193 -41 ATACGTTTCGTACAAAAATCAGCCCGTTGTA 5 44 1 TACAAAAATA 0.616188 -257 TGTCCGTGAATACAATAAGAAATAAAGTATT 5 159 1 TACAATAAGA 0.830372 -142 TTTGAAAACCTACAATGATTATAGAGTTGTT 10 79 1 TACAATGATA 0.897193 -68 GCAACATCATTACAATAAGTAAGAGGAATAG 16 80 0 TACAATAAGA 0.830373 -186 TTTAACAGATTTCAAACAGAAATCGACGTTT 16 194 0 TTCAAACAGA 0.634192 -72 TAAACATGAATACAACGATAAAAAAGGGAAA 20 39 0 TACAACGATA 0.770083 -111 TAAATAGGGGTTCAATGATGACAATTTTAAT 20 114 1 TTCAATGATA 0.908432 -36 CTGCCTTTCATTCAAAGATCAAAAAAAACCG 24 18 0 TTCAAAGATA 0.821198 -178 ACACTTGGAATTCAATGAGAATTCCTTCCTG 27 129 0 TTCAATGAGA 0.933354 -172 CTGGCCAAATTTCAACAATCAATTAGGGGGA 27 274 1 TTCAACAATA 0.602077 -27 AAAGCGCCCATACAAAAAGGAGCTATGCTGT 29 63 0 TACAAAAAGA 0.693849 -50 ATAAGCTTTTTTCATTGAGCATCCCTCCTAA 30 46 0 TTCATTGAGA 0.708507 -255 ATAAGCTTTTTTCATTGAGCATCCCTCCTAA 30 164 0 TTCATTGAGA 0.708507 -137 ********* * Masking position 4 Map Score: 6.0538 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 213 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 12 TTTTTAATAGGAGAAAACTTACGAGCTTCGCC 4 142 1 GAGAAACTAC 0.691293 -38 AAATAATGAGAAAGAAGCTCACTATAATACTC 5 83 1 AAAGAACCAC 0.694619 -218 CGGGAACAATAAGGAATCCTGCGCTTTCCCGA 5 192 0 AAGGAACTGC 0.970916 -109 ATTTGATGTTAAGAATCCTTACATCGTATTGA 8 33 1 AAGAATCTAC 0.623698 -78 TCTCAGGCAAAAGAACTCTTGCTCGACGCAAC 19 112 1 AAGAACCTGC 0.844407 -189 CTTATCGCTCAAGGAATCATACAACCTTGCAA 21 110 0 AAGGAACTAC 0.937929 -191 CATGAAAATGAAGAAAACAGACGCGATGCGGC 22 106 0 AAGAAACGAC 0.880763 -195 TCAAAGATCAAAAAAAACCGGCTCTAT 24 6 0 AAAAAACGGC 0.693942 -190 CACAAAGGAGAAGGAAGGCTGCGTTCAGGCAG 24 66 0 AAGGAAGTGC 0.780225 -130 CATAGTTCACAAGGAAACACGCTGTCTCTGTT 24 130 1 AAGGAACCGC 0.973095 -66 AAAAGCTTATAAGAAACCTCGCCTTTTTGAAC 30 67 1 AAGAAACCGC 0.968965 -234 AAAAGCTTATAAGAAACCTCGCCTTTTTGAAT 30 185 1 AAGAAACCGC 0.968965 -116 ****** * *** Masking position 5 Map Score: 3.71873 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 286 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 13 CAAAAAAAGAAGGATATGACAACAAAAAAT 1 111 1 AGGATATGAC 0.880569 -106 TGTCAGCTGCCGCATATCACGGATGAGCAT 6 189 1 CGCATATCAC 0.833036 -32 GATTATATTCAGCATATGACTGACCATGAT 15 22 1 AGCATATGAC 0.974077 -38 TAACTGCTTCAGCATATCATGGTCAGTCAT 15 37 0 AGCATATCAT 0.813793 -23 GTCGAAGGAAAGCATTTGATTTGGTAAAAT 22 248 1 AGCATTTGAT 0.889076 -53 AATCTCATATAGCATTTGACATCTAGTACT 30 11 1 AGCATTTGAC 0.967205 -290 AATCTCATATAGCATTTGACATCTAGTACT 30 129 1 AGCATTTGAC 0.967205 -172 ********** Masking position 4 Map Score: 2.24644 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 79 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ATGAGGGTCTAGAAAGGGGAATCTT 4 6 0 AGAAAGGGGA 0.593634 -174 GATTGCTTTGAAAAGGCGGAAATACGAGCA 6 40 0 AAAAGGCGGA 0.750071 -181 GAACTTATCAATAAGACGGACAATAAAAAA 13 44 0 ATAAGACGGA 0.89301 -42 AAAGTCATCATTAAGGGGGATGTTATGTAG 16 164 0 TTAAGGGGGA 0.926047 -102 TGCGCCGTTGATAAAGGGGAGGAATTAG 19 283 1 ATAAAGGGGA 0.885808 -18 ATACAACGATAAAAAAGGGAAAGCCGCTTA 20 31 0 AAAAAAGGGA 0.519929 -119 TCCTTGAGCGATAAGAGTGAAAGGCACAAA 21 127 1 ATAAGAGTGA 0.7559 -174 TGTACATTGTATAAGAGGGAGCGAGTTCCG 21 230 1 ATAAGAGGGA 0.96385 -71 AGGCGCAGTCACAAGACGGAGAAG 22 5 0 ACAAGACGGA 0.611173 -296 TTGCATGATGATAAGGGTGAATCCAATGAA 26 84 1 ATAAGGGTGA 0.832483 -93 TCAACAATCAATTAGGGGGAAATGTC 27 285 1 ATTAGGGGGA 0.808106 -16 GTACTCTATTTTAGGAGGGATGCTCAATGA 30 36 1 TTAGGAGGGA 0.693715 -265 GTACTCTATTTTAGGAGGGATGCTCAATGA 30 154 1 TTAGGAGGGA 0.693715 -147 CGCCAACTTGATAAGGAGGATGCTGAAG 30 283 1 ATAAGGAGGA 0.771238 -18 ********** Masking position 10 Map Score: 5.73188 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 230 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 15 TCAATCATCAATTGTCAAGAAAAATTCATTGTA 1 70 1 ATTGTAGAAA 0.839653 -147 AAGTTCTAAAAATTTTATGAAAAAT 3 3 0 AATTTAGAAA 0.638158 -119 TAGGACCATTATTTTCTGGAAAAGACATGTGTA 4 63 1 ATTTTTGAAA 0.657245 -117 AACAATTGCTTTTTTCGGGAACAATAAGGAATC 5 206 0 TTTTTGGAAA 0.64516 -95 AGGAACATCCATTTGAACGAACAAGAAACGATT 6 132 1 ATTTGAGAAA 0.723317 -89 GACCGCTTCTATTTTAATGAAGAAAATGAACAG 7 82 1 ATTTTAGAAA 0.9431 -106 TTTTCCATGTTTTTTAACGAAAAAAAACTGCTG 11 36 0 TTTTTAGAAA 0.913321 -120 ATCAACGATTTTTGTCAGGAAGAATGTAGGTGG 16 238 1 TTTGTAGAAA 0.769907 -28 TGTTTTCTTCATTTTCATGACGATTTTCGCTCA 22 119 1 ATTTTAGACA 0.73995 -182 AAGTAAATGTTTTTTAAGGAATATTAACACTTG 27 153 0 TTTTTAGAAA 0.913684 -148 TGATAGATTAATTTTTAAGAAAAAGAACTGGTA 27 199 1 ATTTTAGAAA 0.943056 -102 GGCGTTTTTTAAGATGATGCCTGATTG 28 5 1 TTTTTAGATA 0.550914 -296 AGTTATCAGAATTTTTAGGAATTGA 28 286 1 ATTTTAGAAT 0.638183 -15 ***** * *** * Masking position 10 Map Score: 2.81331 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 169 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281