AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_aquae_reg_300.orf -o00860_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.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 ctaA 300 heme O oxygenase #2 nirB 120 nitrite reductase (NAD(P)H) large subunit #3 hemC 300 porphobilinogen deaminase #4 aq_331 29 putative protein #5 dcuP 157 uroporphyrinogen decarboxylase #6 gsa 24 glutamate-1-semialdehyde aminotransferase #7 aq_943 300 putative protein #8 gcsH3 72 glycine cleavage system protein H #9 glyQ 290 glycyl-tRNA synthetase alpha subunit #10 proA 30 gamma-glutamyl phosphate reductase #11 gltX 279 glutamyl-tRNA synthetase #12 aq_1236 23 hypothetical protein #13 cysG 161 siroheme synthase #14 hemA 38 glutamyl tRNA reductase (delta-aminolevulinate synthase) #15 ssf 300 Na(+):solute symporter (Ssf family) Motif number 1 TGAGTATAGCCTTCCTTTCCGCATTCTTTAC 1 152 1 CTTCCTTCCG 0.966433 -149 CGAACAAGACCCGCTTTTTCCAGTTCTCTCA 3 78 0 CCGCTTTTCC 0.681622 -223 GTTTCCAGCGCCGCGCCTTCGACCGCTCGGC 3 277 0 CCGCGCTTCG 0.979235 -24 TCTGCCAGTTCCGCCACTCCGGCTTACCTAA 5 50 0 CCGCCCTCCG 0.996704 -108 GGGCGTGCGGGTTCGACTCCCGCCTCCGGCA 5 112 1 GTTCGCTCCC 0.722789 -46 TGACCCAGTACCTGCCCTCCGGAGTACCTAT 9 133 0 CCTGCCTCCG 0.947269 -158 GCTTTGCGTGCTTCCGCTTCGTTTGGCACCC 9 224 0 CTTCCCTTCG 0.980125 -67 ATGGGTTGAACCTCCACTCCCTGTTTTTGTA 11 32 1 CCTCCCTCCC 0.991802 -248 CTTTCTATTTCTTCCGCTTCACCGTCAATTT 11 77 1 CTTCCCTTCA 0.811621 -203 GTGAACTCCTCCGCGTTTTCCAGAGCCACTT 13 16 0 CCGCGTTTCC 0.894804 -146 AATCTCCAGAGCGCCTCTTCGTGAGGTAAAG 13 63 0 GCGCCCTTCG 0.967448 -99 GCGTCCACAATCGCCTTTCCCTTCTCACCCT 13 109 0 TCGCCTTCCC 0.782256 -53 ATGGCTTACTCCTCCACTCCGTATTTTTTAT 15 126 0 CCTCCCTCCG 0.995353 -175 ACGTAAAACTCTTCCGCTTCGGTCGCCCTGT 15 222 0 CTTCCCTTCG 0.980125 -79 TCAGCGGCTACTGCCATTCCGTTCCAGAAGG 15 272 0 CTGCCTTCCG 0.975987 -29 ***** ***** Masking position 8 Map Score: 23.7749 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 463 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 CAAAACTATAAGGGCTACTACAATTTTCTTCGCAGTACTG 1 114 0 AGCTAAATCT 0.706124 -187 TGAAAGTTATACGTATACGGGAGGTAACCT 2 1 0 AGCGGAGTCT 0.979055 -120 TATAGTTTAACAGAGCTCGGTAAAAGTCTTGAAGAAATAT 3 146 1 CGCGGAAACT 0.985707 -155 GCAGAACCTCGGGTTAGCGGAAATTAACATTCGTTTCATT 7 60 1 GGCGGAATCT 0.98272 -241 CCTCATGCGGATGCCCTCTGGAAAAAACTTCAGGAAGAAT 9 67 1 AGCTGAAACT 0.908099 -224 ACAGGTTTCACAGGACACGGGAATTCTCCTTGTTGAAATT 11 103 0 CGCGGAATCT 0.995986 -177 CCTCACGAAGAGGCGCTCTGGAGATTGCCTTTATAAGATT 13 68 1 AGCTGAGTCT 0.927902 -94 GATAAGTGCACAGCTTTCGGTAATTACCTTTGTTGTGGAG 15 52 1 CGCGGAATCT 0.995979 -249 CATTCCGTTCCAGAAGGCGGGAATTCTCATACCGGTACGT 15 249 0 CGCGGAATCT 0.995986 -52 TCATCCAGTCAGCGGCTACTGCCATTCCGTTCCAG 15 276 0 CGCGGTATCT 0.972128 -25 * * *** ** * * * Masking position 20 Map Score: 12.1974 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 60 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 AAAGGAGGAGAGCATGAACACC 1 3 1 AGGAGGAGAG 0.98149 -298 GTCAAGACAACCGAGGCGAGAACTAACGTC 1 56 0 CCGAGGCGAG 0.925317 -245 AAAGATTAAAAGGAGGAGAGC 1 290 1 AGGAGGAGAG 0.98149 -11 GAGTTTCCTCAGGAGGAGTGAAAG 2 107 1 AGGAGGAGTG 0.977293 -14 TTTATCTGGTAGGAAGGGTGGCCGAGCGGT 3 257 1 AGGAAGGGTG 0.875169 -44 GCCGAGCGGTCGAAGGCGCGGCGCTGGAAA 3 277 1 CGAAGGCGCG 0.854474 -24 TTTGTGGTGCCGGAGGCGGGAGTCGAACCC 5 120 0 CGGAGGCGGG 0.992026 -38 ATAGGTACTCCGGAGGGCAGGTACTGGGTC 9 133 1 CGGAGGGCAG 0.925317 -158 AAAGCAATAGAGGAGGGGGTTTAACTTTAT 9 250 1 AGGAGGGGGT 0.930177 -41 CTGGAAAACGCGGAGGAGTTCACGGGAAAG 13 24 1 CGGAGGAGTT 0.940934 -138 ATAAAAAATACGGAGTGGAGGAGTAAGCCA 15 126 1 CGGAGTGGAG 0.893157 -175 GCGACCGAAGCGGAAGAGTTTTACGTACCG 15 227 1 CGGAAGAGTT 0.668387 -74 ATTCCGTTCCAGAAGGCGGGAATTCTCATA 15 258 0 AGAAGGCGGG 0.894362 -43 ********** Masking position 4 Map Score: 15.2213 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 306 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 TATAATTTAAAAAGGTTATGAGCAGTACTGCG 1 92 1 AAAGGTAGAG 0.963162 -209 GAGTCCGTTGAAATGTTAAAAGAAAGATTAAA 1 268 1 AAATGTAAAG 0.844069 -33 ATGTTAAAAGAAAGATTAAAAGGAGGAGAGC 1 280 1 AAAGATAAAG 0.855997 -21 ATTGAAAATCAAGGGTAAAAATTTTATAAAGG 7 15 1 AAGGGTAAAT 0.912516 -286 TTCGTTTCATTAAGGTCAGAAGTCTAATAAGT 7 89 1 TAAGGTAAAG 0.944144 -212 CTTATCATTATAAGGATATAAGAATTTC 8 7 0 TAAGGAAAAG 0.661914 -66 TTACTTTGATAAAGGTCATAATATTAATATCA 8 50 1 AAAGGTAAAT 0.943355 -23 TCACAAAGCTAATGGTAAGGAGTGTTCCTTCC 9 161 1 AATGGTAGAG 0.804752 -130 AAGATTATAAAAAGGTATAAAGTTAAACCCCC 9 264 0 AAAGGTTAAG 0.897311 -27 ATTGTAATTCAAAGGTTAAAATAAACTCTC 11 260 1 AAAGGTAAAT 0.943355 -20 GTTCACGGGAAAGGTTTACAAGCTTTACCTCA 13 41 1 AAGGTTAAAG 0.788272 -121 TTATAAGATTAAGGGTGAGAAGGGAAAGGCGA 13 98 1 AAGGGTAAAG 0.979275 -64 ****** * *** Masking position 2 Map Score: 9.66557 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 363 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TTTTTTTTTGGGTGATTCCGGGTATAGCTC 3 32 0 GGTGATTCCG 0.838658 -269 TCTGGTAGGAAGGGTGGCCGAGCGGTCGAA 3 261 1 AGGGTGGCCG 0.822212 -40 GTGCCCTTTACGGGCGTGCGGGTTCGACTC 5 101 1 CGGGCGTGCG 0.984479 -57 TGCAGAACCTCGGGTTAGCGGAAATTAACA 7 59 1 CGGGTTAGCG 0.875213 -242 CCTAATAATGAGGGATTGCGACTATAATAA 7 165 1 AGGGATTGCG 0.936503 -136 TTTTTTCCAGAGGGCATCCGCATGAGGACA 9 64 0 AGGGCATCCG 0.955384 -227 TATTGCTTTGCGTGCTTCCGCTTCGTTTGG 9 229 0 CGTGCTTCCG 0.959158 -62 AAAGACGGGCTACCATATTCCTT 12 6 1 CGGGCTACCA 0.775795 -18 CAACTTTTCCCGTGAGTGCGTCCACAATCG 13 127 0 CGTGAGTGCG 0.902335 -35 AGTAGTGAGCGGGGAATCCGAATATAGTAG 15 21 0 GGGGAATCCG 0.90096 -280 TATTTACAACAGGGCGACCGAAGCGGAAGA 15 214 1 AGGGCGACCG 0.965033 -87 ********** Masking position 9 Map Score: 7.2579 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 148 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 AACGTCTTCAGGGGACTACTTTTGAGGTTG 1 32 0 GGGGACTACT 0.934883 -269 AGACAACCGAGGCGAGAACTAACGTCTTCA 1 52 0 GGCGAGAACT 0.907463 -249 TCAAAACTATAAGGGCTACTACAATTTTCT 1 125 0 AAGGGCTACT 0.890319 -176 TCCAGAAAACAGGGAGTACTTTTTAAAGAG 1 204 1 AGGGAGTACT 0.929833 -97 CTTTTCAGATAGGGGCTAGT 4 20 1 AGGGGCTAGT 0.872185 -10 TACTCCGGAGGGCAGGTACTGGGTCACAAA 9 138 1 GGCAGGTACT 0.81636 -153 AAAGCGGGAACTACTATATTCG 15 3 1 AGCGGGAACT 0.969769 -298 TCGCCATAAAAAGGGCAACTATTCCAAAGA 15 180 0 AAGGGCAACT 0.847222 -121 CGTTCCAGAAGGCGGGAATTCTCATACCGG 15 254 0 GGCGGGAATT 0.773101 -47 TCATCCAGTCAGCGGCTACTGCCATTCCGT 15 281 0 AGCGGCTACT 0.978935 -20 ********** Masking position 8 Map Score: 5.55813 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 169 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 GGGTGATTCCGGGTATAGCTCTTTGAAGTTGAGAGA 3 17 0 GGAAGTTTTA 0.946429 -284 GCACCGTTGGGGTGAAAGGTATATGAAGAGTATGAA 3 196 1 GGAAGTTATA 0.947064 -105 TGAAAATCAAGGGTAAAAATTTTATAAAGGCATACT 7 17 1 GGAAATTTAA 0.907318 -284 GTTTCATTAAGGTCAGAAGTCTAATAAGTTATTTAT 7 92 1 GGAAATTAAA 0.907329 -209 CTTTGATAAAGGTCATAATATTAATATCAA 8 53 1 GGAAAATAAA 0.554385 -20 AAATAGAAAGGGCTATAGATTTTATACAAAAACAGG 11 51 0 GGAAGTTTAA 0.975323 -229 AACATAAGGAGGGCACAGGTTTCACAGGACACGGGA 11 121 0 GGAAGTTCAA 0.935237 -159 TTTACTACAACGTCAAAGTTTTTACAAACCATACAA 11 155 1 CGAAGTTTAA 0.903706 -125 GAGGAGTTCACGGGAAAGGTTTACAAGCTTTACCTC 13 36 1 CGAAGTTACA 0.71444 -126 ACGCACTCACGGGAAAAGTTGTAAAATTCTTCAAGA 13 136 1 GGAAGTTAAA 0.975158 -26 CCCTTTTTATGGCGATAGCTATTTACAACAGGGCGA 15 195 1 GGAAGTTTTC 0.769695 -106 ** * ** * *** * Masking position 7 Map Score: 4.97925 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 134 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 8 CTCAAAAGTAGTCCCCTGAAGACGTTAGTT 1 36 1 GTCCCCTGAA 0.931015 -265 AGTACTCCCTGTTTTCTGGATGTTTTAAGT 1 194 0 GTTTTCTGGA 0.792423 -107 AGAGGTTCTCTCAACTTCAAAGAG 3 5 1 GTTCTCTCAA 0.876648 -296 TCCGGGTATAGCTCTTTGAAGTTGAGAGAA 3 16 0 GCTCTTTGAA 0.720829 -285 GCTTTTTCCAGTTCTCTCAATTGTTTGGTA 3 67 0 GTTCTCTCAA 0.876648 -234 AAAGGGCACCGTCCCCTCAAGACGGCGCGT 5 80 0 GTCCCCTCAA 0.824087 -78 TAATAATGTGGCTCTCTGCAATGATAACAA 7 189 1 GCTCTCTGCA 0.909773 -112 TCATGCGGATGCCCTCTGGAAAAAACTTCA 9 69 1 GCCCTCTGGA 0.988185 -222 CCCAGTACCTGCCCTCCGGAGTACCTATGT 9 131 0 GCCCTCCGGA 0.93489 -160 GAATTCCCGTGTCCTGTGAAACCTGTGCCC 11 117 1 GTCCTGTGAA 0.819741 -163 TCACGAAGAGGCGCTCTGGAGATTGCCTTT 13 70 1 GCGCTCTGGA 0.941451 -92 GAGAATTCCCGCCTTCTGGAACGGAATGGC 15 261 1 GCCTTCTGGA 0.920769 -40 ********** Masking position 10 Map Score: 9.89066 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 259 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 CGGGTAGTTATGTTTTGTAAGTCCTTACAGA 2 51 0 TTTTTGTAAG 0.927708 -70 TACCCGGAACTTTTTGGCACGTTTTTTGCAA 2 76 1 TTTTGGCACG 0.941176 -45 TTTTGGCACGTTTTTTGCAAGAGTTTCCTCA 2 87 1 TTTTTGCAAG 0.953172 -34 TTCTCTCAATTGTTTGGTAAGCATTTTTTTT 3 55 0 TTTTGGTAAG 0.974345 -246 AAAAGCCCTTTATTTGGCAAGTA 5 3 0 TTTTGGCAAG 0.983671 -155 AAAATAAAAATCTTAGGTAAGCCGGAGTGGC 5 38 1 TTTAGGTAAG 0.871892 -120 AGTGAGTGTTTATTTATTAAGTTTATGAAAT 7 263 0 TTTTATTAAG 0.745883 -38 CACTCCGTATTTTTTATCAAGGTTGTTCATA 15 112 0 TTTTATCAAG 0.823186 -189 * ********* Masking position 9 Map Score: 4.17893 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 69 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 10 AATTGTAGTAGCCCTTATAGTTTTGAGTATAG 1 129 1 GCCCTTTATT 0.945261 -172 TTATAAAAAAGCCCTTTATTTGGCAAGTA 5 8 0 GCCCTTATTG 0.98428 -150 AGGGGACGGTGCCCTTTACGGGCGTGCGGGTT 5 93 1 GCCCTTACGG 0.892284 -65 TAAAATTTTTACCCTTGATTTTCAATCACT 7 9 0 ACCCTTATTT 0.822035 -292 GCAGGGTTACGCCCTAATAATGAGGGATTGCG 7 153 1 GCCCTATATG 0.864478 -148 GTGAATATTTGCCCTTCTATGGGTTGAACCTC 11 14 1 GCCCTTTAGG 0.945649 -266 AAAATCTATAGCCCTTTCTATTTCTTCCGCTT 11 64 1 GCCCTTCTTT 0.923295 -216 TGAAACCTGTGCCCTCCTTATGTTTACTACAA 11 133 1 GCCCTCTTTG 0.947432 -147 TTCCCTTCTCACCCTTAATCTTATAAAGGCAA 13 92 0 ACCCTTATTT 0.822035 -70 TGGAATAGTTGCCCTTTTTATGGCGATAGCTA 15 184 1 GCCCTTTTTG 0.987202 -117 ****** ** ** Masking position 5 Map Score: 5.89331 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 165 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 AGAGGTTCTCTCAACTTCAAA 3 2 1 GAGGTTCTCT 0.886995 -299 TTTTTTTTGGGTGATTCCGGGTATAGCTCT 3 31 0 GTGATTCCGG 0.699312 -270 GGTCGAAGGCGCGGCGCTGGAAACGCC 3 284 1 GCGGCGCTGG 0.928377 -17 GGAACTGGCAGACGCGCCGTCTTGAGGGGA 5 69 1 GACGCGCCGT 0.696656 -89 AAGGGATTTTGTGGTGCCGGAGGCGGGAGT 5 127 0 GTGGTGCCGG 0.964989 -31 CCGCTAACCCGAGGTTCTGCAAAATTGAGT 7 50 0 GAGGTTCTGC 0.858493 -251 CTATAATAATGTGGCTCTCTGCAATGATAA 7 186 1 GTGGCTCTCT 0.913295 -115 CTTTAAGTATGAAGTTCTGGACATAGGTAC 9 111 1 GAAGTTCTGG 0.845107 -180 CGCTAAAGTGGCTCTGGAAAACGCGGA 13 8 1 GTGGCTCTGG 0.976928 -154 ACCTCACGAAGAGGCGCTCTGGAGATTGCC 13 67 1 GAGGCGCTCT 0.907813 -95 TCCGAATATAGTAGTTCCCGCTTT 15 5 0 GTAGTTCCCG 0.748334 -296 ********** Masking position 7 Map Score: 3.47435 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 330 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 CCTTACAGAGGTTGTAAAATGAAAGTTATA 2 30 0 GTTGTAAAAT 0.853869 -91 AGATTTTTATTTTATAAAAAAGCCCTTTAT 5 21 0 TTTATAAAAA 0.844984 -137 TGAGTATGCCTTTATAAAATTTTTACCCTT 7 25 0 TTTATAAAAT 0.803239 -276 AAAAAAACGCTTTATAAATAACTTATTAGA 7 111 0 TTTATAAATA 0.730154 -190 ACTTAAAGATTATAAAAAGGTATAAAGT 9 273 0 ATTATAAAAA 0.648483 -18 ACTCCCTGTTTTTGTATAAAATCTATAGCC 11 47 1 TTTGTATAAA 0.563071 -233 CTTTGTATGGTTTGTAAAAACTTTGACGTT 11 163 0 TTTGTAAAAA 0.922719 -117 CACGGGAAAAGTTGTAAAATTCTTCAAGA 13 143 1 GTTGTAAAAT 0.853869 -19 ATGAACAACCTTGATAAAAAATACGGAGTG 15 113 1 TTGATAAAAA 0.670328 -188 CGGTCGCCCTGTTGTAAATAGCTATCGCCA 15 204 0 GTTGTAAATA 0.782177 -97 ********** Masking position 5 Map Score: 2.48104 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 122 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 TTAAGTAGTTGTAAACGGTAAAGAATGCGGA 1 169 0 GAAACGGTAA 0.907795 -132 AGGCTTGAACGTGCAAGGGAAACAAATCCCA 1 232 1 GGCAAGGGAA 0.812758 -69 AAAGTTATACGTATACGGGAGGTAACCT 2 8 0 GATACGGGAG 0.879023 -113 TAGTTTAACAGAGCTCGGTAAAAGTCTTGAA 3 148 1 GGCTCGGTAA 0.877853 -153 GGGTCACAAAGCTAATGGTAAGGAGTGTTCC 9 158 1 GTAATGGTAA 0.69276 -133 AGGTTTCACAGGACACGGGAATTCTCCTTGT 11 110 0 GACACGGGAA 0.982983 -170 AACTTATCATGAACATGGTAAGGCTTCAATT 11 227 0 GACATGGTAA 0.923927 -53 AAGGAATATGGTAGCCCGTCTTT 12 10 0 GATATGGTAG 0.604385 -14 ACGCGGAGGAGTTCACGGGAAAGGTTTACAA 13 31 1 GTCACGGGAA 0.979117 -131 TTGTGGACGCACTCACGGGAAAAGTTGTAAA 13 130 1 ATCACGGGAA 0.786977 -32 TAAGTGCACAGCTTTCGGTAATTACCTTTGT 15 54 1 GTTTCGGTAA 0.739661 -247 * ********* Masking position 10 Map Score: 3.54924 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 455 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 AGCCCTTATAGTTTTGAGTATAGCCTTCCT 1 138 1 GTTTTGAGTA 0.936746 -163 TTTTCTGGATGTTTTAAGTAGTTGTAAACG 1 183 0 GTTTTAAGTA 0.946987 -118 TAAAATGAAAGTTATACGTATACGGGAGGT 2 16 0 GTTATACGTA 0.87389 -105 GAAGAATACGGCTTTAAGTATGAAGTTCTG 9 100 1 GCTTTAAGTA 0.936746 -191 CTCCTCTATTGCTTTGCGTGCTTCCGCTTC 9 235 0 GCTTTGCGTG 0.875914 -56 AAGCGGAAGAGTTTTACGTACCGGTATGAG 15 234 1 GTTTTACGTA 0.965622 -67 ********** Masking position 5 Map Score: 1.46088 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 57 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 ATCACCCAAAAAAAAAATGCTTACCAAACAA 3 46 1 AAAAAAATCT 0.843844 -255 TTTATTTTATAAAAAAGCCCTTTATTTGGCA 5 15 0 AAAAAAGCCT 0.92739 -143 GCCTGTGTCTAAAAAAACGCTTTATAAATAA 7 120 0 AAAAAAACCT 0.972169 -181 TAAACTTAATAAATAAACACTCACTTATAAT 7 269 1 AAATAAACCT 0.972169 -32 TTATCAAAGTAAATCAACACTTACTTATCAT 8 31 0 AAATCAACCT 0.927391 -42 TCAAAGGTTAAAATAAACTCTC 11 268 1 AAATAAACCT 0.972169 -12 ******** ** Masking position 6 Map Score: 2.44256 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 21 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467