AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -intrC_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yckK 114 similar to glutamine ABC transporter (glutamine-binding protein) #2 yclA 89 similar to transcriptional regulator (LysR family) #3 yfjN 300 similar to hypothetical proteins #4 yfjM 195 yfjM #5 yfjL 29 alternate gene name: yztA #6 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #7 acoR 115 transcriptional regulator #8 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #9 ynbA 220 similar to GTP-binding protein protease modulator #10 ynbB 187 similar to hypothetical proteins #11 glnR 110 transcriptional regulator #12 glnA 60 glutamine synthetase #13 yqiY 80 similar to amino acid ABC transporter (permease) #14 yqiX 268 similar to amino acid ABC transporter (binding protein) #15 yqiW 162 similar to hypothetical proteins from B. subtilis #16 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #17 glnQ 155 glutamine ABC transporter (ATP-binding protein) #18 glnH 21 glutamine ABC transporter (glutamine-binding protein) #19 glnM 60 glutamine ABC transporter (integral membrane protein) #20 ytmM 29 similar to amino acid ABC transporter (permease) #21 ytmL 21 similar to amino acid ABC transporter (permease) #22 ytmI 152 similar to hypothetical proteins from B. subtilis #23 yxeN 22 similar to amino acid ABC transporter (permease) #24 yxeM 24 similar to amino acid ABC transporter (binding protein) #25 yxeK 185 similar to monooxygenase #26 yxeI 154 similar to penicillin amidase #27 yxeH 39 similar to hypothetical proteins #28 yxeF 87 yxeF #29 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 CTTATTCCCCACTTTTCTGGTTGATTT 1 98 0 CCCACTTTTC 0.900528 -17 AAGAAAGCGCCTCCTTATCATACCTTTTA 2 71 0 CCTCCTTATC 0.947198 -19 GATTATCTACCCTATTTTTTATATTCTGGT 3 139 0 CCTATTTTTT 0.390415 -162 TGTGTAAAAATCCCTTTATTTTGTTAGCCT 4 32 0 TCCCTTTATT 0.290492 -164 TTTCCTCTCCCCCTTTATATGATATCTC 4 178 0 CCCCCTTTAT 0.71025 -18 GTTCCCACTCTTTTCCTCATATG 5 17 0 CCCACTCTTT 0.604177 -13 TATCCATGCGCCTGCTTTTTCCTTTA 7 7 0 CCTGCTTTTT 0.899773 -109 ATATAAGGCGCCTGCTTTTTTATTGTTGAA 7 34 1 CCTGCTTTTT 0.899773 -82 AATAAGGAATCCTGCGCTTTCCCGAGAAAT 8 187 0 CCTGCGCTTT 0.446528 -114 GCTCGTATTTCCGCCTTTTCAAAGCAATCG 9 41 1 CCGCCTTTTC 0.969757 -180 CTCAATTTCCTCCTTTTCTTAACTTAGT 11 93 0 CCTCCTTTTC 0.982976 -18 AAAAGTTGAGCCGCTTTTTT 13 1 0 CCGCTTTTTT 0.770875 -80 AGCCTTTGTCTCCTTTTCTTACAGGAAA 13 63 0 TCTCCTTTTC 0.894385 -18 GATCCATTTCCCCCGTATTCATTACTTTT 14 250 0 CCCCCGTATT 0.824155 -19 GTTATATAATCCCCTTTTTCTGTAAGCAGT 15 39 1 CCCCTTTTTC 0.939865 -124 TGAAGACCTCTCCTTTTTCATCATCTGT 15 145 0 TCTCCTTTTT 0.829596 -18 CTTCAGAAAACCCCTTTATCTTTTCATTTC 16 11 1 CCCCTTTATC 0.829229 -142 ACAAGCTCCCCCATTTCTGTT 18 5 0 CCCCCATTTC 0.834116 -17 ATGAGCATCGCCTGCTCATCCCGGGATGGT 19 13 0 CCTGCTCATC 0.587264 -48 TCTTCTCCCCCCTCATCCGAAGAAATA 20 13 0 CCCCCTCATC 0.886399 -17 TGTGCTCCCTCCTGTTTTTCATCATTAAAA 22 11 1 CCTGTTTTTC 0.740263 -142 TGGTGAGTCACCGCCGTTTC 23 1 0 CCGCCGTTTC 0.907626 -22 TTGATTTTCCCGCCTTTTCTATTT 24 6 0 CCGCCTTTTC 0.969757 -19 TTGATCAGTCCCCTTTTCAATTCAGATT 26 137 0 TCCCCTTTTC 0.926252 -18 TCTTTCCTCCTTTTTTGGGCGAATG 28 73 0 CCTCCTTTTT 0.970755 -15 ATTTGAATTCCCCCTTGTTTTCTGTTTCA 29 10 1 CCCCCTTGTT 0.824756 -231 TTGCATATCCTCTCCGTTTTTTTATAAAAT 29 181 1 TCTCCGTTTT 0.598683 -60 ********** Masking position 2 Map Score: 33.0227 Number of sites scoring better than the average of aligned sites = 1810 Number in coding regions = 1237 Number in noncoding regions = 573 Number of orfs with sites within 600 bp upstream = 590 Fraction of orfs with sites within 600 bp upstream = 0.0947639 Motif number 2 CACTTATCGCATGCGAAAGCATTTCTTATCA 3 203 0 ATGGAAAGCA 0.933098 -98 CATGCGATAAGTGTAAAAGAAGCATGGTCAG 3 221 1 GTGAAAAGAA 0.832617 -80 AAAGATTTCCAAGGAAATAAATACGTCGATC 6 11 1 AAGAAATAAA 0.595226 -221 GTTTTACAGCATGCAAAAAAAAGACCGGATA 6 61 0 ATGAAAAAAA 0.878103 -171 TAAAGGAAAAAGCAGGCGCATGGA 7 4 1 AGGAAAAGCA 0.904796 -112 AGCCCGTTGTATGAAAAAGAAATAATGAGAA 8 64 1 ATGAAAAGAA 0.957816 -237 AAAAGAAATAATGAGAAAGAAGCTCACTATA 8 78 1 ATGGAAAGAA 0.949053 -223 ACTGCCCAATATGCAAAAGAAAGGAACATCC 9 111 1 ATGAAAAGAA 0.957816 -110 TATTTTAATGAAGAAAATGAACAGTATGACA 10 91 1 AAGAAATGAA 0.822538 -97 TATAACCAGAAGGAAAATAAAGGAGCAGTTG 15 14 0 AGGAAATAAA 0.548112 -149 AGAACAGATGATGAAAAAGGAGAGGTCTTCA 15 142 1 ATGAAAAGGA 0.877652 -21 CTGGACAATAAAGGAAATGAAAAGATAAAGG 16 23 0 AAGAAATGAA 0.822538 -130 GATATAGGTGAGGTGAAAGCAG 17 2 0 AGGGAAAGCA 0.886327 -154 TGAAAATTAAAAGTGAAAAAATGTCCATGAC 17 83 0 AAGGAAAAAA 0.800225 -73 TTTTCTATTCAAGCGAAAAGACCCTTGCGTG 25 33 0 AAGGAAAAGA 0.558596 -153 CATTTATATAAAGGGAAAGCAGGATAACATG 29 41 0 AAGGAAAGCA 0.904333 -200 CGAGGACAAGGTGCAAAAACATTCTGATATT 29 117 1 GTGAAAAACA 0.541617 -124 CGGAGAGGATATGCAAAAGAATTTTGCACTT 29 166 0 ATGAAAAGAA 0.957816 -75 *** ******* Masking position 6 Map Score: 14.5148 Number of sites scoring better than the average of aligned sites = 1368 Number in coding regions = 1163 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 3 TCATACTAAAAAAAAGTTATCCTTTAGATTTGTA 1 43 1 AAAATATCCT 0.812308 -72 TTACCAACGCAAAATAATTGCCCTGTTA 3 5 0 AAAATTGCCT 0.455213 -296 AATTTGGGATAAAGGTTCAGCCGTATCCCATAAT 3 257 1 AAAGCAGCCT 0.957139 -44 AACAAAAATCAAATCCTTTCATTATGGG 3 283 0 AAAAAATCCT 0.94578 -18 ATTGTAGGGGAAAAATAAAGCGCTTTCAACAATA 7 54 0 AAAAAAGCGT 0.90916 -62 TTGTTCCCGAAAAAAGCAATTGTTTCGACACATG 8 215 1 AAAAAATTGT 0.494987 -86 TATGCAAAAGAAAGGAACATCCATTTGAACGAAC 9 120 1 AAAGCATCCT 0.961552 -101 AGAATTTTCAAAATGCTCATCCGTGATATGCGGC 9 197 0 AAATCATCCT 0.736341 -24 TTGATTCTGGAAAGGAGCTTCCCTTCACTTGCCG 10 32 0 AAAGCTTCCT 0.84392 -156 TTTCTTCATTAAAATAGAAGCGGTCTACCATCGT 10 73 0 AAAAAAGCGT 0.909161 -115 CAAGAAGAGCAAAGTATCATCGGTGAATTAAAGA 10 136 1 AAAGCATCGT 0.941413 -52 TTACTAGATAAAAATTAAATCGCTGTACAATCCG 14 102 0 AAAAAATCGT 0.918087 -167 AAAGAAACATAAAGAATAATTCCTTGTAAACCTC 17 37 0 AAAGAATTCT 0.63445 -119 GACTAATCAAAAAAAGTAAACCTTCACTTCAGTA 22 42 0 AAAAAAACCT 0.668915 -111 TAAAAAATCCAGCCTTCTAAAGGCTG 26 3 1 AAAACAGCCT 0.951505 -152 AATAAAACGAAAAGATCCAGCCTTTAGAAGGCTG 26 20 0 AAAGCAGCCT 0.95696 -135 CAGCATAACGAAAGTCAAATCGATTCGTCAAAGA 26 69 0 AAAGAATCGT 0.927289 -86 TTATGCTGATAAAACCAATTCGTTCACAATATGT 26 95 1 AAAAATTCGT 0.707873 -60 **** ***** * Masking position 14 Map Score: 13.3955 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 578 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 AAGAAAGCGCCTCCTTATCATACCT 2 75 0 AGCGCCTCCT 0.899009 -15 TTTGTGCGCCTCCTTCTATTTAGG 6 218 0 TGCGCCTCCT 0.985927 -14 CTTATATCCATGCGCCTGCTTTTTCCTTTA 7 11 0 TGCGCCTGCT 0.881663 -105 TTCCTTGATCGCTCCTCCCTTACACGCCG 7 97 0 CGCTCCTCCC 0.929897 -19 ATTTTCAAAATGCTCATCCGTGATATGCGG 9 198 0 TGCTCATCCG 0.948901 -23 CGGGCTGCTTTGAGCATCCGGGTTGTTCGT 14 13 0 TGAGCATCCG 0.803632 -256 TGCAATAATTTGCACAACCCTATGTTACCA 16 86 0 TGCACAACCC 0.835994 -67 GAGCATCGCCTGCTCATCCCGGGATGGTTG 19 11 0 TGCTCATCCC 0.977782 -50 GAGCAGGCGATGCTCATCCCAATTTGATAA 19 26 1 TGCTCATCCC 0.977782 -35 CCTGCATCTCCTTCATGTCGTT 27 28 0 TGCATCTCCT 0.859878 -12 AAAATTCTTTTGCATATCCTCTCCGTTTTT 29 172 1 TGCATATCCT 0.793099 -69 TGTATGAACCTCCCTCAATTATTT 29 227 0 TGAACCTCCC 0.907293 -14 ********** Masking position 9 Map Score: 8.66477 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 331 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 TTCTTAGTGGCCTTGCTTTTGAACTTTTTGGA 3 85 0 CCTGTTTTGA 0.620719 -216 TGTAAAAATCCCTTTATTTTGTTAGCCTTTTT 4 28 0 CCTTTTTTGT 0.957087 -168 CTAAAATAAACCTGGATTTTCGGTAAATCCGG 4 70 1 CCGGTTTTCG 0.75702 -126 TCGGTAAATCCGGGTCTTTTTTGTACGCAGCT 4 89 1 CGGTTTTTTT 0.658837 -107 TTTTACTCAGCCTGTCTTTTCTCTAATTTATT 4 120 1 CCGTTTTTCT 0.980588 -76 ACTAAATATACCATTATTTTCTTACAATAAAT 4 145 0 CCTTTTTTCT 0.972372 -51 CGGGTGATATCCGGTCTTTTTTTTGCATGCTG 6 54 1 CCGTTTTTTT 0.925996 -178 AAGAAGTGTGCCAGTCTTTTGAGCCCGTAAAA 6 168 0 CCGTTTTTGA 0.857285 -64 AATGGATGTTCCTTTCTTTTGCATATTGGGCA 9 113 0 CCTTTTTTGC 0.866198 -108 CTCAAAGCAGCCCGGGTTTTTTTGTGCATAAA 14 29 1 CCGGTTTTTT 0.830307 -240 TACAACTGCTCCTTTATTTTCCTTCTGGTTAT 15 12 1 CCTTTTTTCC 0.91084 -151 TTATATAATCCCCTTTTTCTGTAAGCAGTAAA 15 40 1 CCTTTTCTGT 0.7264 -123 TTGATTTTCCCGCCTTTTCTATTT 24 5 0 CCGCTTTTCT 0.880508 -20 TTTGAATTCCCCCTTGTTTTCTGTTTCAACAT 29 12 1 CCTTTTTTCT 0.972372 -229 ATCAAGAATTCGTGTGTTTTCTACAATTTTCG 29 87 1 CGGTTTTTCT 0.886314 -154 CATATCCTCTCCGTTTTTTTATAAAATAGAAG 29 184 1 CCTTTTTTAT 0.775295 -57 GAACCTCCCTCAATTATTTTCTTAATATTGCT 29 214 0 CATTTTTTCT 0.665707 -27 ** ** ****** Masking position 7 Map Score: 12.3138 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 630 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 6 GTTGGAATCCTTTTTATCCAAAAAGTTCAAAA 3 69 1 TTTTTACAAA 0.913787 -232 AATAAAGGGATTTTTACACAATTCTTGACTAA 4 42 1 TTTTTACAAT 0.79034 -154 ATCCGGGTCTTTTTTGTACGCAGCTTTTACTC 4 96 1 TTTTTGCGCA 0.863884 -100 AACGGGCTGATTTTTGTACGAAACGTATTACC 8 40 0 TTTTTGCGAA 0.964393 -261 TGAGATTTTGTTTTTAATCATTTTGTCAGAGT 8 111 0 TTTTTACATT 0.600506 -190 AGAGGTCTGTTTTTTGCTCGTATTTCCGCCTT 9 26 1 TTTTTGCGTA 0.915398 -195 AGCCCGGGTTTTTTTGTGCATAAATTTCCAAG 14 37 1 TTTTTGCATA 0.90326 -232 CAGTTTCTCATTTTTATGCAATACTATTTTTA 14 179 0 TTTTTACAAT 0.790495 -90 TGTGCAAATTTTTTCATACAAAGGGGTATCGG 16 130 1 TTTTCACAAA 0.78302 -23 GATCATTTACTTTTTGGTCAAATTTTCTGATA 17 123 1 TTTTTGCAAA 0.959093 -33 CTTTCCTCCTTTTTTGGGCGAATGCGTGCCAC 28 65 0 TTTTTGCGAA 0.964492 -23 CTTGCTGAAATTTTCGCTCGAAATATCAGAAT 29 137 0 TTTTCGCGAA 0.903973 -104 ****** **** Masking position 4 Map Score: 7.33671 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 286 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 AAGATTTTGTCTTATGAAAACCAAA 1 4 1 ATTTGTCTAT 0.70655 -111 GCGGTCTACCATCGTTTCCGATTTGATTCTGG 10 56 0 ATCGTTCGAT 0.717249 -132 ATCCCTTAATATTTATTCATATATCCTTGGAA 14 62 0 ATTTTTCTAT 0.942875 -207 CTTTCCAGTGATCTCTTCTGATATTACTAGAT 14 127 0 ATCTTTCGAT 0.945622 -142 CTTTTTCATCATCTGTTCTTATGATAGCAAGG 15 129 0 ATCTTTCTAT 0.937542 -34 AAACCCCTTTATCTTTTCATTTCCTTTATTGT 16 18 1 ATCTTTCTTT 0.905597 -135 TTGACAAAATATTTTTTCCGCTGGACAATAAA 16 42 0 ATTTTTCGCT 0.817094 -111 TTGCACACCTATTTATTCCGTTGCAATAATTT 16 105 0 ATTTTTCGTT 0.924343 -48 AGGTGTGCAAATTTTTTCATACAAAGGGGTAT 16 127 1 ATTTTTCTAC 0.70655 -26 AGTCATGGACATTTTTTCACTTTTAATTTTCA 17 82 1 ATTTTTCCTT 0.736933 -74 TATATTTCTTCGGATGAGGGGGGAG 20 4 1 ATTTTTCGAT 0.950298 -26 GTTAAGATTAATTTTTTCTATTCAAGCGAAAA 25 45 0 ATTTTTCATT 0.653988 -141 GTACATTTTGATTTATTCATATTAAACGACTA 25 102 1 ATTTTTCTAT 0.942875 -84 TAAAGGCTGGATCTTTTCGTTTTATTTGATGT 26 28 1 ATCTTTCTTT 0.905597 -127 **** *** *** Masking position 1 Map Score: 8.2975 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 339 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 8 AATTTGGGATAAAGGTTCAGCCGTATCCCAT 3 257 1 AAAGGTCAGC 0.934039 -44 TATGCAAAAGAAAGGAACATCCATTTGAACG 9 120 1 AAAGGACATC 0.946374 -101 AGAATTTTCAAAATGCTCATCCGTGATATGC 9 200 0 AAATGTCATC 0.721826 -21 TTGATTCTGGAAAGGAGCTTCCCTTCACTTG 10 35 0 AAAGGGCTTC 0.941293 -153 CAAGAAGAGCAAAGTATCATCGGTGAATTAA 10 136 1 AAAGTTCATC 0.721815 -52 TATTCAATAAAAAGGCTCAACGAAAAAGTTG 13 23 0 AAAGGTCAAC 0.838489 -58 GAAGGAAAATAAAGGAGCAGTTGTAT 15 6 0 AAAGGGCAGT 0.873279 -157 ATGAAAAGATAAAGGGGTTTTCTGAAG 16 7 0 AAAGGGTTTT 0.496209 -146 TTTTTCATACAAAGGGGTATCGGG 16 139 1 AAAGGGTATC 0.941271 -14 CGTCCAAGACAAAGGTACATTTTGATTTATT 25 88 1 AAAGGACATT 0.8136 -98 AAACATGATAAAAGGAGTATCGCC 25 172 1 AAAGGGTATC 0.941271 -14 ***** ***** Masking position 3 Map Score: 3.73173 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 367 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 AAATACTTACTCATACTAAAAAAAAGTTATCC 1 33 1 TCAACTAAAA 0.554499 -82 TTCAATAAAATCAACCAGAAAAGTGGGGAATA 1 91 1 TCACCAAAAA 0.945494 -24 TATTTAGGGTTCACCATTATAAATGCAAGAAG 6 194 0 TCACATATAA 0.634298 -38 TAAAGCGCTTTCAACAATAAAAAAGCAGGCGC 7 41 0 TCACAAAAAA 0.937401 -75 CTGTTCATTTTCTTCATTAAAATAGAAGCGGT 10 83 0 TCTCATAAAA 0.787813 -105 AAAAGTTTCCTATTCAATAAAAAGGCTCAACG 13 32 0 TATCAAAAAA 0.545124 -49 TAATTCCTTGTAAACCTCAAAAGATATAGGTG 17 23 0 TAACCTAAAA 0.848371 -133 CTCCTGTTTTTCATCATTAAAATTACTGAAGT 22 19 1 TCACATAAAA 0.937384 -134 GATCTTTGACTAATCAAAAAAAGTAAACCTTC 22 51 0 TAACAAAAAA 0.828473 -102 CTTTATAGTATAAACAATAAAAGCTTAGTAAA 22 91 1 TAACAAAAAA 0.828473 -62 TTCGCATTATTCAGCCTAAAAACATGATAAAA 25 153 1 TCACCTAAAA 0.945494 -33 TGGCACGCATTCGCCCAAAAAAGGAGGAAAGA 28 66 1 TCGCCAAAAA 0.783439 -22 *** *** **** Masking position 9 Map Score: 5.59072 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 335 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 TATTGTAGGGGAAAAATAAAGCGCTTTCAAC 7 58 0 GAAAATAAAG 0.961383 -58 CCCGTTGTATGAAAAAGAAATAATGAGAAAG 8 66 1 GAAAAGAAAT 0.64185 -235 CTTTTTTCGGGAACAATAAGGAATCCTGCGC 8 200 0 GAACATAAGG 0.798813 -101 TGCCCAATATGCAAAAGAAAGGAACATCCAT 9 113 1 GCAAAGAAAG 0.774906 -108 CCATTTGAACGAACAAGAAACGATTCAGGAG 9 140 1 GAACAGAAAC 0.782348 -81 ATGTAGGAAGGAAATATAAAGAC 10 175 1 GAAAATAAAG 0.961383 -13 GAGATCACTGGAAAGATAAGCCTAAAGATAA 14 144 1 GAAAATAAGC 0.753905 -125 ATAACCAGAAGGAAAATAAAGGAGCAGTTGT 15 13 0 GGAAATAAAG 0.896136 -150 AAAGGAAATGAAAAGATAAAGGGGTTTTCTG 16 14 0 AAAAATAAAG 0.621175 -139 TTTTTCCGCTGGACAATAAAGGAAATGAAAA 16 31 0 GGACATAAAG 0.81328 -122 ACTGACTAAAGAAACATAAAGAATAATTCCT 17 47 0 GAAAATAAAG 0.961383 -109 TGAATAATGCGAAAAATAAACTCCTATATTC 25 135 0 GAAAATAAAC 0.906513 -51 ATAACATGTTGAAACAGAAAACAAGGGGGAA 29 18 0 GAAAAGAAAA 0.64185 -223 **** ****** Masking position 6 Map Score: 7.7351 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 337 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 AAGATTTTGTCTTATGAAAACCAAATACT 1 10 1 TCTTATGAAA 0.89896 -105 TATGGAGAACTCATATGATATTCTATTTAG 3 39 1 TCATATGATA 0.82713 -262 CTCTCCCCCTTTATATGATATCTCCACTAA 4 172 0 TTATATGATA 0.787969 -24 AATCAGCCCGTTGTATGAAAAAGAAATAAT 8 60 1 TTGTATGAAA 0.82338 -241 TCCAGTGATCTCTTCTGATATTACTAGATA 14 126 0 TCTTCTGATA 0.900715 -143 CATCATCTGTTCTTATGATAGCAAGGAAAC 15 125 0 TCTTATGATA 0.916639 -38 CGATACCCCTTTGTATGAAAAAATTTGCAC 16 131 0 TTGTATGAAA 0.82338 -22 ATGATCAAACTTTTCTGAAAATTAAAAGTG 17 99 0 TTTTCTGAAA 0.851046 -57 TTTGGTCAAATTTTCTGATAGGAGGATTGC 17 135 1 TTTTCTGATA 0.875716 -21 ********** Masking position 6 Map Score: 3.27529 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 239 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 12 TCAACCAGAAAAGTGGGGAATAAG 1 101 1 AAGTGGGGAA 0.229243 -14 CCTAAAAGGTATGATAAGGAGGCGCTTTCT 2 69 1 ATGATAAGGA 0.198441 -21 CGATAAGTGTAAAAGAAGCATGGTCAGTTT 3 225 1 AAAAGAAGCA 0.491203 -76 AGGCTAACAAAATAAAGGGATTTTTACACA 4 32 1 AATAAAGGGA 0.597427 -164 AATTTATTGTAAGAAAATAATGGTATATTT 4 144 1 AAGAAAATAA 0.374961 -52 ATATGAGGAAAAGAGTGGGAAC 5 18 1 AAGAGTGGGA 0.621985 -12 CTCCAAAGTGAAGATGAGAAGACTGATTTT 6 142 1 AAGATGAGAA 0.489017 -90 GTGAACCCTAAATAGAAGGAGGCGCACAAA 6 212 1 AATAGAAGGA 0.77203 -20 CAATATGCAAAAGAAAGGAACATCCATTTG 9 117 1 AAGAAAGGAA 0.782017 -104 TATTTTAATGAAGAAAATGAACAGTATGAC 10 91 1 AAGAAAATGA 0.63447 -97 GGCTATGTCCAAGAAGAGCAAAGTATCATC 10 127 1 AAGAAGAGCA 0.760849 -61 AAACTAAGTTAAGAAAAGGAGGAAATTGAG 11 91 1 AAGAAAAGGA 0.936337 -20 TTTACCTTTTAAGAGGAGGAATTTTACCAA 12 41 1 AAGAGGAGGA 0.947296 -20 TTTTTCCTGTAAGAAAAGGAGACAAAGGCT 13 61 1 AAGAAAAGGA 0.936337 -20 CTGCTTACAGAAAAAGGGGATTATATAACC 15 38 0 AAAAAGGGGA 0.529646 -125 ATATTTTGTCAAGAGAAGAAAACGTGGTAA 16 62 1 AAGAGAAGAA 0.891147 -91 GTAAAAAGAGAGGGAGCAGTG 21 6 1 AAGAGAGGGA 0.943559 -16 ATTCGCCCAAAAAAGGAGGAAAGA 28 74 1 AAAAGGAGGA 0.719861 -14 TTTTTTATAAAATAGAAGCAATATTAAGAA 29 198 1 AATAGAAGCA 0.491203 -43 AAGCAATATTAAGAAAATAATTGAGGGAGG 29 213 1 AAGAAAATAA 0.374961 -28 ********** Masking position 1 Map Score: 9.17005 Number of sites scoring better than the average of aligned sites = 1857 Number in coding regions = 1456 Number in noncoding regions = 401 Number of orfs with sites within 600 bp upstream = 423 Fraction of orfs with sites within 600 bp upstream = 0.0679409 Motif number 13 CGTATTTCCGCCTTTTCAAAGCAATCGATT 9 44 1 CCTTTTCAAA 0.948415 -177 AAAAAAGTTTCCTATTCAATAAAAAGGCTC 13 36 0 CCTATTCAAT 0.927699 -45 CCTATTCACTCCTTATCAAATTGGGATGAG 19 38 0 CCTTATCAAA 0.792401 -23 CTGCCTATTCACTCCTTATCAAA 19 48 0 CCTATTCACT 0.896202 -13 TTTTGTCACTCCTCTTCACAAAATATATAA 22 133 0 CCTCTTCACA 0.847869 -20 GATTTTCCCGCCTTTTCTATTT 24 3 0 CCTTTTCTAT 0.8325 -22 TGATCAGTCCCCTTTTCAATTCAGATTAAT 26 134 0 CCTTTTCAAT 0.959904 -21 ********** Masking position 6 Map Score: 1.57156 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 133 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 14 TGGTTTTCATAAGACAAAATCTT 1 3 0 AAACAAAATC 0.845896 -112 TTGTCTTATGAAAACCAAATACTTACTCATA 1 17 1 AAACCAAATA 0.708916 -98 AACAAAAATCAAATCCTTTCATTAT 3 286 0 AAATCAAATC 0.962588 -15 AAAATGATTAAAAACAAAATCTCATGGTTTG 8 119 1 AAACAAAATC 0.845896 -182 GCTCCTTTCCAGAATCAAATCGGAAACGATG 10 48 1 AGATCAAATC 0.842912 -140 AAGGATTCTTAACATCAAATCCAGGAGAAAT 11 22 0 AAATCAAATC 0.962588 -89 TTACTAGATAAAAATTAAATCGCTGTACAAT 14 105 0 AAATTAAATC 0.741816 -164 TATTTGATGTAATGTCAATTCTTTGACGAAT 26 50 1 AAGTCAATTC 0.754623 -105 CAGCATAACGAAAGTCAAATCGATTCGTCAA 26 72 0 AAGTCAAATC 0.917104 -83 TTATGCTGATAAAACCAATTCGTTCACAATA 26 95 1 AAACCAATTC 0.8857 -60 ** ******** Masking position 7 Map Score: 3.76501 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 217 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 ********** No masking Map Score: -1.08831e-11 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